Bio-Protocols have been written in Korean or English, or both mixed languages, originally by me, while I was studying, usually at Academia. Here, I started translating them into English, and I am still studying some subjects, so I hope to share there whenever I have time.
I began my laboratory work in 2000 or before when I helped post-graduates’ projects while I was a psychology BA student. My academic journey and curiosity had traveled with biological psychology (physiology and behavior), and then immunology, neurobiology, ophthalmology, and nanomedicine. Nanomedicine opened my industry career, where I researched exosomes and viral gene delivery.
While studying and researching, I learned computer languages such as Command Line, C, and HTML. Command Line, C, and HTML were just part of my college curriculum back then, in the late 90s, maybe, and then to handle big datasets such as NGS, I learned more computer languages such as Python, R, and SQL.
My bio-protocols have been made since 2001. I start to post them one by one.
If anybody wants to share your old and current bio-protocols (simple or manual-like or whatever), you could send them here as well. Also, any comments and questions would be welcome. I just noticed that visitors are downloading the PDF files of the protocols, even though I just started sharing the protocols that were mostly originally generated around 20 years ago. I know the bio-manual protocols are basic and mostly were not changed, except we are using mostly commercial kits, like cooking.
Please feel free to subscribe or send thank-you notes that will drive me to share more.
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Com-related
Clustalo
I am one of old users who have used since 2000, but they do not provide any more distance matrix – pair to pair comparison and % identity matrix. If you want to check that. Instead of using at Web App Clustalo or Jalview, Install the program in your local computer.
Installation on MAC: conda install -c bioconda clustalo
Please check the version: clusalo –version
Run:
clustalo -i input.fa -o aligned.fasta –distmat-out=dist.txt –percent-id –full –force
Featurecount install and more
Click hereHISAT2 install and more
Click hereMac screen recording
Command + Shift + 5
PDB RCSB API Python Query
If you want to try date range attribute and some more, like getting the update PDBs, click here
- original 2025 paper
- simple guide manual
PyMol (free version) general
Click herePymol align
alignto PDBID (eg 9DW7), object=all_to_PDBID (eg 9DW7)
UniProt_seqs download in terminal
time for acc in ‘cat filename.txt’; do curl “https//rest.uniprot.org/uniprotkb/$acc.fasta”; done>filename.fasta
or visit here:id_mapping
UniProt info or seq (simple, one item) download in terminal
curl “https://rest.uniprot.org/uniprotkb/P12345.txt” -o uniprot_P12345.txt
curl “https://rest.uniprot.org/uniprotkb/P12345.fasta” -o P12345.fasta
curl “https://rest.uniprot.org/uniprotkb/accessions?accessions=P02708,P16473,P07202,P01266,P54298,Q05586,P55087,P32926,Q02413,Q13018&format=fasta” -o autoimmune_targets.fasta
for id in P02708 P16473 P07202 P01266 P54298 Q05586 P55087 P32926 Q02413 Q13018; do
curl “https://rest.uniprot.org/uniprotkb/$id.txt” -o “uniprot_$id.txt”
done
YouTube transcript extract
Molecular work
Antibiotics preparation
Cloning general
Click herePlasmid extraction: general and traditional method
Click here- plasmid miniprep (Alkaline manual), June 04 2021
- CsCl-EtBr plasmid DNA prep, Nov 11 2001
ChIP
In 2008 t0 2013, I performed ChIP-PCR and/or ChIP-seq using brain and retina tissues, and cells. This is general simple protocols
Cellular work
Cytotoxicity assay—tritiated thymidine
FACS-cell preparation general
T cell enrichment—nylon wool column
- Manual
- Commercial
Animal work
Adoptive cell transfer (ACT)
Mice brain Abbreviations
A
A1 = A1 noradrenergic cell field
A5 = A5 noradrenergic cell field
A7 = A7 noradrenergic cell field
A8 = A8 dopaminergic cell field
A11 = A11 dopaminergic cell field
A12 = A12 dopaminergic cell field
A13 = A13 dopaminergic cell field
A14 = A14 dopaminergic cell field
AAD = anterior amygdaloid area, dorsal
AAV = anterior amydgaloid area, ventral
AC = anterior commissural nucleus
aca = anterior commissure, anterior part
Acb = accumbens nucleus
AcbC = accumbens nucleus, core
AcbSh = accumbens nucleus, shell
aci = anterior commissure, intrabulbar part
ACo = anterior cortical amygdaloid nucleus
acp = anterior commissure, posterior part
Acs5 = accessory trigeminal nucleus
Acs6/7 = accessory nucleus 6/7
Ac7 = accessory facial nucleus
AD = anterodorsal thalamic nucleus
ADP = anterodorsal preoptic nucleus
AHA = anterior hypothalamic area, anterior part
AHC = anterior hypothalamic area, central part
AHiAL = amygdalohippocampal area, anterolateral part
AHiPM = amygdalohippocampal area, posteromedial part
AHP = anterior hypothalamic area, posterior part
AI = agranular insular cortex
AInt = anterior interposed nucleus
AIP = agranular insular cortex, posterior part
al = ansa lenticularis
AL = nucleus of the ansa lenticularis
alv = alveus
AM = anteromedial thalamic nucleus
Amb = ambiguus nucleus
AMV = anteromedial thalamic nucleus, ventral part
Ang = angular thalamic nucleus
Ant = anterior lobe, cerebellum
AOB = accessory olfactory bulb
AOD = anterior olfactory nucleus, dorsal part
AOE = anterior olfactory nucleus, external part
AOL = anterior olfactory nucleus, lateral part
AOM = anterior olfactory nucleus, medial part
AOP = anterior olfactory nucleus, posterior part
aot = accessory optic tract
AOV = anterior olfactory nucleus, ventral part
AP = area postrema
APir = amygdalopiriform transistion area
apmf = ansoparamedian fissure
APO = anterior preoptic nucleus
APT = anterior pretectal nucleus
APTD = anterior pretectal nucleus, dorsal part
APTV = anterior pretectal nucleus, ventral part
Aq = aqueduct of Sylvius
Arc = arcuate hypothalamic nucleus
ArcD = arcuate hypothalamic nucleus, dorsal part
ArcL = arcuate hypothalamic nucleus, lateral part
ArcLP = arcuate hypothalamic nucleus, lateroposteror part
ArcMP = arcuate hypothalamic nucleus, medioposteror part
AStr = amygdalostriatal transition area
ATg = anterior tegmental nucleus
Au1 = primary auditory cortex
AuD = auditory cortex, dorsal part
AuV = auditory cortex, ventral part
AV = anteroventral thalamic nucleus
AVC = anteroventral cochlear nucleus
AVPe = anteroventral periventricular nucleus
AVPO = anteroventral preoptic nucleus
AV = anteroventral thalamic nucleus
AVDM = anteroventral thalamic nucleus, dorsomedial part
AVPe = anterventral periventricular nucleus
AVPO = anterventral preoptic nucleus
AVVL = anteroventral thalamic nucleus, ventrolateral part
B
B = basal nucleus of Meynert
B4 = B4 serotonergic cell group
B9 = B9 serotonergic cell group
BAC = bed nucleus of the anterior commissure
BAOT = bed nucleus of the accessory olfactory tract
Bar = Barrington’s nucleus
bas = basilar artery
bic = brachium of the inferior colliculus
BIC = nucleus of the brachium of the inferior colliculus
BLA = basolateral amygdaloid nucleus, anterior part
BLP = basolateral amygdaloid nucleus, lateral part
BLV = basolateral amygdaloid nucleus, ventral part
BMA = basomedial amygdaloid nucleus, anterior part
BMP = basomedial amygdaloid nucleus, posterior part
Bo = Botzinger complex
bp = brachium pontis
bsc = brachium of the superior colliculus
BST = bed nucleus of the stria terminalis
BSTIA = bed nucleus of the stria terminalis, intraamygdaloid division
BSTLD = bed nucleus of the stria terminalis, lateral division, dorsal part
BSTLI = bed nucleus of the stria terminalis, lateral division, intermediate part
BSTLJ = bed nucleus of the stria terminalis, lateral division, juxtacap
BSTLP = bed nucleus of the stria terminalis, lateral division, posterior part
BSTLV = bed nucleus of the stria terminalis, lateral division, ventral part
BSTMA = bed nucleus of the stria terminalis, medial division, anterior part
BSTMPI = bed nucleus of the stria terminalis, medial posterointermediate part
BSTMPL = bed nucleus of the stria terminalis, medial posterolateral part
BSTMPM = bed nucleus of the stria terminalis, medial posteromedial part
BSTMV = bed nucleus of the stria terminalis, medial division, ventral part
BSTS = bed nucleus of the stria terminalis, supracap division
C
C1 = C1 adrenergic cell field
C2 = C2 adrenergic cell field
C3 = C3 adrenergic cell field
CA1 = CA1 field of the hippocampus
CA2 = CA2 field of the hippocampus
CA3 = CA3 field of the hippocampus
CB = cell bridges of the ventral striatum
cbc = cerebellar commissure
cc = corpus callosum
CC = central canal
CeC = central amygdaloid nucleus, capsular divison
CeL = central amygdaloid nucleus, lateral division
CeM = central amygdaloid nucleus, medial divison
CeMAD = central amygdaloid nucleus, medial anterodorsal part
CeMAV = central amygdaloid nucleus, medial anteroventral part
CeMPV = central amygdaloid nucleus, medial posteroventral part
cg = cingulum
Cg1 = cingulate cortex, area 1
Cg2 = cingulate cortex, area 2
CGA = central gray, alpha part
CGPn = central gray of the pons
CI = compact interfascicular nucleus
cic = commissure of the inferior colliculus
CIC = central nucleus of the inferior colliculus
Circ = circular nucleus
CL = central lateral thalamic nucleus
Cl = claustrum
CLi = caudal linear nucleus of the raphe
CM = central medial thalamic nucleus
Cnf = cuneiform nucleus Cop = copula pyramis
cp = cerebral peduncle, basal
CPO = caudal periolivary nucleus
CPu = caudate putamen (striatum)
Crus1 = crus 1 of the ansiform lobule
Crus2 = crus 2 of the ansiform lobule
csc = commissure of the superior colliculus
cst = commissure stria terminalis
Cu = cuneate nucleus
CxA = cortex-amygdala transition zone
D
D3V = dorsal part of the third ventricle
das = dorsal acoustic stria
DC = dorsal cochlear nucleus
DCIC = dorsal cortex of the inferior colliculus
DEn = dorsal endopiriform nucleus
df = dorsal fornix
DG = dentate gyrus
dhc = dorsal hippocampal commissure
Dk = nucleus of Darkschewitsch
DLG = dorsal lateral geniculate nucleus
DLL = dorsal nucleus of the lateral lemniscus
dlo = dorsolateral olfactory tract
DLO = dorsolateral orbital cortex
DLPAG = dorsal lateral periaqueductal gray
DM = dorsomedial hypothalamic nucleus
DMC = dorsomedial hypothalamic nucleus, compact part
DMD = dorsomedial hypothalamic nucleus, diffuse part
DMPAG = dorsomedial periaqueductal gray
DMPn = dorsomedial pontine nucleus
DMSp5 = dorsomedial spinal trigeminal nucleus
DMTg = dorsomedial tegmental area
DMV = dorsomedial hypothalamic nucleus, ventral part
DP = dorsal peduncular nucleus
DpG = deep gray layer of the superior colliculus
DPGi = dorsal paragigantocellular nucleus
DpMe = deep mesencephalic nucleus
DPO = dorsal periolivary area
DpWh = deep whitelayer of the superior colliculus
DR = dorsal raphe nucleus
DRC = dorsal raphe nucleus, caudal part
DRD = dorsal raphe nucleus, dorsal part
DRI = dorsal raphe nucleus, inferior part
DRV = dorsal raphe nucleus, ventral part
DRVL = dorsal raphe, ventrolateral part
Dsc = lamina dissecans, entorhinal cortex
DT = dorsal terminal nucleus of the accessory optic tract
DTgC = dorsal tegmental nucleus, central part
DTgP = dorsal tegmental nucleus, pericentral part
dtgx = dorsal tegemetnal decussation
DTM = dorsal tuberomammillary nucleus
DTr = dorsal transition zone
DTT = dorsal tenia tecta
E
E/OV = ependyma and olfactory ventricle
ec = external capsule
ECIC = external cortex of the inferior colliculus
Ect = entorhinal cortex
ECu = external cuneate nucleus
EF = epifornical nucleus
EMi = epimicrocellular nucleus
eml = external medullary lamina
EPI = external plexiform layer of the olfactory bulb
EPIA = external plexiform layer of the accessory olfactory bulb
ERS = epirubrospinal nucleus
Eth = ethmoid thalamic nucleus
EVe = nucleus of origin of the vestibular efferent fibers
EW = Edinger-Westphal nucleus
exc = extreme capsule
F
f = fornix
F = nucleus of the fields of Forel
FC = fasciola cinereum
FF = fields of Forel
fi = fimbria hippocampus
Fl = flocculus
fmi = forceps minor of the corpus callosum
fmj = forceps major of the corpus callosum
fr = fasciculus retroflexus
FrA = frontal association cortex
Fu = fusiform nucleus
FVe = F cell group of the vestibular complex
G
g7 = genu of the facial nerve
gcc = genu of the corpus callosum
Gem = gemini hypothalamic nucleus
Gi = gigantocellular reticular nucleus
GI = granular insular cortex
GiA = gigantocellular reticular nucleus, alpha part
GiV = gigantocellular reticular nucleus, ventral part
Gl = glomerular layer of olfactory bulb
GlA = glomerular layer of the accessory olfactory bulb
GrA = granule cell layer of accessory olfactory bulb
GrC = granulce cell later of the cochlear nucleus
GrDG = granule cell layer of the dentate gyrus
GrO = granule cell layer of olfactory bulb
H
hbc = habenular commissure
HDB = nucleus of the horizontal limb of the diagonal band
hif = hippcampal fissure
I, J, K
I = intercalated nuclei amygdala
I3 = interoculomotor nucleus
I5 = intertrigenimal nucleus
IAD = interanterior dorsal thalamic nucleus
IAM = interanteromedial thalamic nucleus
ias = intermediate acoutstic stria
ic = internal capsule
icf = intercrural fissure
ICj = islands of Calleja
ICjM = islanads of Calleja, major island
icp = inferior cerebellar peduncle
IF = interfascicular nucleus
IG = indusium griseum
IGL = intergeniculate leaflet
IL = infralimbic cortex
ILL = intermediate nucleus of the lateral lemniscus
IM = intercalated amygdaloid nucleus, main
IMA = intramedullary thalamic area
IMD = intermediodorsal thalamic area
IMLF = interstitial nucleus of the medial longitudinal fasciculus
IMLFG = interstitial nucleus of the medial lonitudinal fasciculus, greater part
In = intercalated nucleus of the medulla
InCo = intercollicular nucleus
Inf = intracerebellar nucleus
InG = intermediate grey layer of the superior colliculus
IntDL = interposed cerebellar nucleus, dorsolateral hump
InWh = intermediate white layer of the superior colliculus
IO = inferior olive
IOB = inferior olive, subnucleus B of the medial nucleus
IOBe = inferior olive, beta subnucleus
IOC = inferior olive, subnucleus C of the medial nucleus
IOD = inferior olive, dorsal accessory nucleus
IODM = inferior olive, dorsomedial cell group
IODMC = inferior olive, dorsomedial cell column
IOK = inferior olive, cap of Kooy medial nucleus
IOM = inferior olive, medial nucleus
IOPr = inferior olive, principal nucleus
IOVL = inferior olive, ventrolateral protrusion
IP = interpeduncular nucleus
IPAC = interstitial nucleus of the posterior limb of the anterior commissure
IPACL = interstitial nucleus of the posterior limb of the anterior commissure, lateral part
IPACM = interstitial nucleus of the posterior limb of the anterior commissure, medial part
IPC = interpeduncular nucleus, caudal subnucleus
IPDL = interpeduncular nucleus, dorsolateral subnucleus
IPDM = interpeduncular nucleus, dorsomedial subnucleus
ipf = interpenduncular fossa
IPI = interpeduncular nucleus, intermediate subnucleus
IPl = internal plexiform layer of the olfactory bulb
IPR = interpeduncular nucleus, rostral subnucleus
IRt = intermediate reticular nucleus
IS = inferior salivatory nucleus
K = Koelliker-Fuse nucleus
L
L4V = lateral recess of the fourth ventricle
La = lateral amygdaloid nucleus
LA = lateraanterior hypothalamic nucleus
LAcbSh = lateral part of accumbens shell
LaDL = lateral amygdaloid nucleus, dorsolateral part
Lat = lateral cerebellar nuclues (dentate)
LatPC = lateral cerebellar nucleus, parvicellular part
LaVL = lateral amygdaloid nucleus, ventralateral part
LaVM = lateral amygdaloid nucleus, ventromedial part
LC = locus coeruleus
Ld = lambdoid septal zone
LDDM = laterodorsal thalamic nucleus, dorsomedial part
LDTg = laterodorsal tegmental nucleus
LDTgV = laterodorsal tegmental nucleus, ventral part
LDVL = laterodorsal thalamic nucleus, ventrolateral part
LEnt = lateral entorhinal cortex
lfp = longitudinal fasciculus of the pons
LGP = lateral globus pallidus
LH = lateral hypothalamic area
LHb = lateral habenular nucleus
LHbL = lateral habenular nucleus, lateral part
LHbM = lateral habenular nucleus, medial part
Li = linear nucleus of the medulla
ll = lateral leminiscus
LM = lateral mammillary nucleus
LMol = lacunosum molecular layer of the hippocampus
lo = lateral olfactory tract
LO = lateral orbital cortex
LOT = nucleus of the lateral olfactory tract
LPAG = lateral periaqueductal gray
LPB = lateal parabrachial nucleus
LPBC = lateral parabrachial nucleus, central part
LPBD = lateral parabrachial nucleus, dorsal part
LPBE = lateral parabrachial nucleus, external part
LPBI = lateral parabrachial nucleus, internal part
LPBS = lateral parabrachial nucleus, superior part
LPBV = lateral parabrachial nucleus, ventral part
LPBX = lateral parabrachial nuclues, external lateral part
LPGi = lateral paragigantocellular nucleus
LPLC = lateral posterior thalamic nucleus, laterocaudal part
L = basal
LPLR = lateral posterior thalamic nucleus, laterorostral part
LPMC = lateral posterior thalamic nucleus, mediocaudal part
L = basal
LPMR = lateral posterior thalamic nucleus, mediorostral part
L = basal
LPO = lateral preoptic area
LR4V = lateral recess of the fourth ventricle
LTr = lateral reticular nucleus
LRtPC = lateral reticular nucleus, parvicellular part
LSD = lateral septal nucleus, dorsal part
LSI = lateral septal nucleus, intermediate part
LSV = lateral septal nucleus, ventral part
LRt = lateral reticular nucleus
LSO = lateral superior olive
LSt = lateral striatal stripe
LT = lateral terminal nucleus of the accessory optic tract
LV = lateral ventricle
LVe = lateral vestibular nucleus
LVPO = lateral ventral periolivary nucleus
M
M1 = primary motor cortex
M2 = secondary motor cortex
m5 = motor root tirgeminal nerve
MA3 = medial accessory oculomotor nucleus
maot = medial accessory optic tract
MCLH = magnocellular nucleus of the lateral hypothalamic area
mcp = middle cerebellar peduncle
MCPC = magnocellular nucleus of the posterior commisssure
MCPO = magnocellular preoptic nucleus
MD = mediodorsal thalamic nucleus
MDC = mediodorsal thalamic nucleus, central part
MdD = medullary reticular nucleus, dorsal part
MDL = mediodorsal thalamic nucleus, lateral part
MDM = mediodorsal thalamic nucleus, medial part
MdV = medullary reticular nucleus, ventral part
Me = medial amygdaloid nucleus
ME = median eminence
Me5 = mesencephalic trigeminal nucleus
me5 = mesencephalic trigeminal tract
MeA = medial amygdaloid nucleus, anterior part
MeAD = medial amygdaloid nucleus, anterodorsal part
MeAV = medial amygdaloid nucleus, anteroventral part
Med = medial (fastigial) cerebellar nucleus
MedDL = medial cerebellar nucleus, dorsolateral protuberance
MEnt = medial entorinal cortex
MePD = medial amygdaloid nucleus, posterdorsal part
MePV = medial anygdaloid nucleus, posteroventral part
mfb = medial forebrain bundle
MG = medial geniculate nucleus
MGD = medial geniculate nucleus, dorsal part
MGM = medial geniculate nucleus, medial part
MGP = medial globus pallidus
MGV = medial geniculate nucleus, ventral part
MHb = medial habenular nucleus
Mi = mitral cell layer of the olfactory bulb
MiA = mitral cell layer of the accessory olfactory bulb
Min = minimus nucleus
MiTg = microcellular tegmental nucleus
ml = medial lemniscus
ML = medial mammillary nucleus, lateral part
mlf = medial longitudinal fasciculus
MM = medial mammillary nucleus, medial part
MMn = medial mammillary nucleus, median part
MnPO = median preoptic nucleus
MnR = median raphe nucleus
MO = medial orbital cortex
Mo5 = motor trigeminal nucleus
MoDC = molecular layer of the dorsal cochlear nucleus
Mol = molecular layer of the denate gyrus
mp = mammillary peduncle
MP = medial mammillary nucleus, posterior part
MPA = medial preoptic area
MPB = medial parabrachial nucleus
MPBE = medial parabrachial nucleus, external part
MPOC = medial preoptic nucleus, central part
MPOL = medial preoptic nucleus, lateral part
MPOM = medial preoptic nucleus, medial part
MPT = medial pretectal nucleus
MRe = mammillary recess of the third ventricle
MS = medial septal nucleus
MSO = medial superior olive
mt = mammillothalamic tract
MT = medial terminal nucleus of the accessory optic tract
mtg = mammillotegmental tract
MTu = medial tuberal nucleus
MVe = medial vestibular nucleus
MVeMC = medial vestibular nucleus, medial caudal part
MVePC = medial vestibular nucleus, parvicellular part
MVPO = medioventral periolivary nucleus
MZMG = marginal zone of the medial geniculate
N, O
ns = nigrostriatal bundle
O = nucleus O
ocb = olivocochlear bundle
ON = olfactory nerve layer
Op = optic nerve layer of the superior colliculus
OPC = oval paracentral nucleus
OPT = olivary pretectal nucleus
opt = optic tract
Or = oriens layer, hippocampus
OT = nucleus of the optic tract
OV = olfactory part of lateral ventricle
ox = optic chasm
P, Q
P5 = peritrigeminal zone
P7 = perifacial zone
Pa4 = paratrochlear nucleus
Pa5 = paratrigeminal nucleus
Pa6 = paraabducens nucleus
PaAP = paraventricular hypothalamic anterior, parvicellular
PaDC = paraventricular hypothalamic dorsal cap
PAG = peraaqueductal gray
PaLM = paraventricular hypothalamic area, lateral magnocellular part
PaMM = paraventricular hypothalamic area, medial, magnocellular part
PaMP = paraventricular hypothalamic area, medial, parvicellular part
PaPo = paraventricular hypothalamic nucleus, posterior
PaS = parasubiculum
PaV = paraventricular hypothalamic nucleus, ventral part
PBG = parabigeminal nucleus
PBP = parabrachial pigmented nucleus
PBW = parabrachial waist
PC = paracentral thalamic nucleus
pc = posterior commissure
PC3 = parvicellular trigeminal nucleus
PC5 = parvicellular nucleus of the trigeminal valve
pcuf = preculminate fissure, cerebellum
PCGl = paracochlear glial substance
pcn = precentral fissure, cerebellum
PCom = nucleus posterior commissure
PCRt = parvicellular reticular nucleus
PCRtA = parvicellular reticular nucleus, alpha part
PDTg = posterodorsal tegmental nucleus
Pe = periventricular hypothalamic nucleus
PeF = perifornical nucleus
PF = parafascicular thalamic nucleus
PFl = paraflocculus
pfs = parafloccular sulcus
PH = posterior hypothalamic area
PIL = posterior intralaminar thalamic nucleus
PInt = posterior interposed nucleus
Pir = piriform cortex
PL = paralemniscal nucleus
PLCo = posterolateral cortical amygdaloid nucleus
plf = posterolateral fissure
PLi = posterior limitans thalamic nucleus
PM = paramedian lobule
pm = principal mammillary tract
PMCo = posteromedial cortical amygdaloid nucleus
PMD = premammillary nucleus dorsal
PMn = paramedian reticular nucleus
PMR = paramedian raphe nucleus
PMV = premammillary nucleus, ventral part
PN = paranigral nucleus
Pn = pontine nulei
PnC = pontine reticular nucleus, caudal
PnO = pontine reticular nucleus, oral
PnR = pontine raphe nucleus
PnV = pontine reticular nucleus, ventral
Po = posterior thalamic nuclear group
PoDG = polymorph layer, dentate gyrus
PoMn = poteromedian thalamic nucleus
PoT = postthalamic nuclear group, triangular part
PP = peripenduncular nucleus
ppf = prepyramidal fissure
PPT = posterior pretectal nucleus
PPtA = posterior parietal association area
PPTg = pedunculopontine tegmental nucleus
PPy = peripyramidal nucleus
Pr = prepositus hypoglossal nucleus
PR = prerubral field
Pr5 = principal sensory trigeminal nucleus
Pr5DM = principal sensory trigeminal nucleus, dorsomedial part
Pr5VL = principal sensory trigeminal nucleus, ventrolateral part
prb = Probst’s bundle
PrC = precommissural nucleus
prf = primary fissure
PRh = perirhinal cortex
PrL = prelimbic cortex
PrS = presubiculum
PS = parastrial nucleus
psf = postsuperior fissure, cerebellum
PSol = parasolitary nucleus
PSTh = parasubthalamic nucleus
PT = parataenial thalamic nucleus
PV = paraventricular thalamic nucleus
pv = periventricular fiber system
PVA = paraventricular thalamic nucleus, anterior part
PVP = paraventricular thalamic nucleus, posterior part
Py = pyramidal cell layer of the hippocampus
py = pyramidal tract
R
R = red nucleus
Rad = stratum radiatum of the hippocampus
Rbd = rhabdoid nucleus
RC = raphe cap
RCe = solitary tract nucleus, rostral central subnucleus
RCh = retrochiasmatic area
Re = reuniens thalamic nucleus
REth = retroethmoid nucleus
rf = rhinal fissure
Rh = rhomboid thalamic nucleus
RI = rostral interstitial nucleus of the medial longitudinal fasciculus
Rli = rostral linear nucleus raphe
RMC = red nucleus, magnocellular part
RMg = raphe magnus nucleus
Ro = nucleus of Roller
ROb = raphe obscurus nucleus
RPa = raphe pallidus nucleus
RPC = red nucleus, parvocellular part
RPF = retroparafascicular
RPO = rostral periolivary region
RR = retrorubral nucleus
RRF = retrorubral field
rs = rubrospinal tract
RSA = retrosplenial agranular cortex
RSG = retrosplenial glanular cortex
Rt = reticular thalamic nucleus
RtTg = reticulotegmental nucleus of pons
RtTgP = reticulotegmental nucleus of the pons, pericentral part
RVL = rostroventrolateral reticular nucleus
S
S = subiculum
S1 = primary somatosensory cortex
S1BF = somatosensory 1, barrel field
S1DZ = somatosensory 1, dysgranular zone
S1FL = somatosensory 1, forelimb region
S1HL = somatosensory 1, hindlimb region
S1J = somatosensory 1, jaw region
S1Tr = somatosensory 1, trunk region
S2 = second somatosensory cortex
s5 = sensory root of trigeminal nerve
Sag = sagulum nucleus
Sc = scaphoid thalamic nucleus
SC = superior colliculus
scc = splenium corpus callosum
SCh = suprachiasmatic nucleus
SChDM = suprachiasmatic nucleus, dorsomedial part
SChVL = suprachiasmatic nucleus, ventrolateral part
SCO = subcommissural organ
SCom = subcommissural nucleus
scp = superior cerebellar peduncle
sf = secondary fissure
SFi = septofimbrial nucleus
SFO = subfornical organ
SG = suprageniculate thalamic nucleus
SHi = septohippocampal nucleus
SHy = septohypothalamic nucleus
SI = substantia innominata
Sim = simple lobule
SLEA = sublentic extended amygdala
SLEAC = sublentic extended amygdala, central division
SLEAM = sublentic extended amygdala, medial division
SLu = stratum lucidem of the hippocampus
SM = nucleus stria medullaris
sm = stria medullaris, thalamus
SMT = submammillothalamic nucleus
SMV = superior medullary velum
SNC = substantia nigra, pars compacta (compact part)
SNL = substantia nigra, lateral part
SNR = substantia nigra, pars reticularis (reticular part)
SO = supraoptic nucleus
sol = solitary tract
Sol = solitary tract nucleus
SolC = solitary tract nucleus, commissural subnucleus
SolCe = solitary tract nucleus, central subnucleus
SolDL = solitary tract nucleus, dorsolateral subnucleus
SolDM = solitary tract nucleus, dorsomedial subnucleus
SolG = solitary tract nucleus, gelatinous subnucleus
SolI = solitary tract nucleus, interstitial subnucleus
SolIM = solitary tract nucleus, intermediate tract nucleus
SolM = solitary tract nucleus, medial subnucleus
SolV = solitary tract nucleus, central subnucleus
SolVL = solitary tract nucleus, ventrolateral subnucleus
SOR = supraoptic nucleus
sox = supraoptic decussation
sp5 = spinal trigeminal tract
Sp5I = spinal trigeminal nucleus, interpolar part
Sp5O = spinal trigeminal nucleus, oral part
Sp5ODM = spinal trigeminal nucleus, dorsomedial part
Sp5OVL = spinal trigeminal nucleus, ventrolateral part
SPa = subparaventricular zone
SPF = subparafascicular thalamic nucleus
SPFPC = subparafascicular thalamic, parvicellular part
Sph = sphenoid nucleus
SPO = superior paraolivary nucleus
SPTg = subpedencular tegmental nucleus
SpVe = spinal vestibular nucleus
st = stria terminalis
StA = strial part preoptic area
Stg = stigmoid hypothalamic nucleus
STh = subthalamic nucleus
str = superior thalamic radiation
Su3 = supraoculomotor central gray
Su3C = supraoculomotor cap
Su5 = supratrigeminal nucleus
Sub = submedius thalamic nucleus
SubB = subbrachial nucleus
SubCD = subcoeruleus nucleus, dorsal part
SubCV = subcoeruleus nucleus, ventral part
SubG = subgeniculate nucleus
SuM = supramammillary nucleus
SuML = supramammillary nucleus, lateral part
SuMM = supramammillary nucleus, medial part
sumx = supramammillary decussation
SuVe = superior vestibular nucleus
T, U
TC = tuber cinereum area
Te = terete hypothalamic nucleus
Te2C = temporal cortex, area 2, central part
TeA = temporal cortex, association area
tfp = transverse fibers of the pons
ts = tectospinal tract
TS = triangular septal nucleus
Tu = olfactory tubercle
Tz = nucleus trapezoid body
tz = trapezoid body
unc = uncinate fasciculus
V, W
V1 = primary visual cortex
V1B = primary visual cortex, binocular region
V1M = primary visual cortex, monocular region
V2L = secondary visual cortex, lateral part
V2ML = visual cortex 2, mediolateral part
V2MM = visual cortex 2, mediomedial part
VA = ventral anterior thalamic nucleus
VCP = ventral cochlear nucleus, posterior part
VDB = nucleus of the verticle limb of the diagonal band
VeCb = vestibulocerebellar nucleus
vhc = ventral hippocampal commissure
VL = ventrolateral thalamic nucleus
VLG = ventrolateral geniculate nucleus
VLGMC = ventrolateral geniculate nucleus, magnocellular part
VLGPC = ventrolateral geniculate nucleus, parvicellular part
VLL = ventral nucleus of the lateral lemniscus
VLPAG = ventrolateral periaqueductal gray
VLPO = ventrolateral preoptic nu
VMPO = ventromedial preoptic nu
VLTg = ventrolateral tegmental area
VM = ventromedial thalamic nucleus
VMH = ventromedial hypothalamic nucleus
VMHC = ventromedial hypothalamic nucleus, central part
VMHDM = ventromedial hypothalamic nucleus, dorsomedial part
VMHVL = ventromedial hypothalamic nucleus, ventrolateral part
vn = vomerolnasal nerve
VO = ventro orbital cortex
VOLT = vascular organ of the lamina terminalis
VP = ventral pallidum
VPL = ventral posterolateral thalamic nucleus
VPM = ventral posteromedial thalamic nucleus
VPPC = ventral posterior nucleus, parvicellular part
VRe = ventral reuniens thalamic nucleus
vsc = ventral spinocerebellar tract
VTA = ventral tegmental area
VTg = ventral tegmental nucleus (Gudden)
vtgx = ventral tegmental decussation
VTM = ventral tuberomammillary nucleus
VTRZ = visual tegmental relay zone
VTT = ventral tenia tecta
X, Y, Z
X = nucleus X
Xi = xiphoid thalamic nucleus
xscp = decussation of the superior cerebellar peduncle
Y = nucleus Y
ZI = zona incerta
ZID = zona incerta, dorsal part
ZIV = zona incerta, ventral part
ZL = zona limitans
Zo = zonal layer of superior colliculus (stratum zonale)
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3v = third ventricle
4 = trochlear nucleus
4n = trochlear nerve
6 = abducens nucleus
7n = root of the facial nerve
7 = facial nucleus
7DI = facial nucleus, dorsal intermediate subnucleus
7DL = facial nucleus, dorsolateral subnucleus
7DM = facial nucleus, dorsomedial subnucleus
7L = facial nucleus, lateral subnucleus
7VM = facial nucleus, ventromedial subnucleus
7VI = facial nucleus, ventral intermediate subnucleus
7L = facial nucleus, lateral subnucleus
10 = doral motor nucleus of the vagus
12 = hypoglossal nucleus
Conventions
This list of abbreviations is taken with minor modification from The Mouse Brain in Stereotaxic Coordinates by Keith Franklin and George Paxinos (Academic Press, 1997). Upper case letters are generally used to designate nuclei and cortical regions; for example, SC for the superior colliculus. However, only first letters are capitalized, thus CPu, for caudate putamen. Lower case letters are generally used for fiber tracts, e.g., mlf for the medial longitudinal fasciculus.
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