title: hapo_newborn_cordblood_K0767


title: hapo_newborn_cordblood_K0738

status: Public on Feb 16 2026

type: genomic

city: Chicago

first: Jami

middle: L

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

country: USA

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

tag: Sex

value: Male

tag: tissue

value: cord clood

tag: developmental stage

value: newborn

tag: cell type

value: whole blood cells


title: hapo_newborn_cordblood_K0739

value: Female


title: hapo_newborn_cordblood_K0742


title: hapo_newborn_cordblood_K0762


title: hapo_newborn_cordblood_K0754


title: hapo_newborn_cordblood_K0755


title: hapo_newborn_cordblood_K0712


title: hapo_newborn_cordblood_K0789


title: hapo_newborn_cordblood_K0710


title: hapo_newborn_cordblood_K0735


title: hapo_newborn_cordblood_K0746


title: hapo_newborn_cordblood_K0705


title: hapo_newborn_cordblood_K0730


title: hapo_newborn_cordblood_K0696


title: hapo_newborn_cordblood_K0690


title: hapo_newborn_cordblood_K0683


title: hapo_newborn_cordblood_K0691


title: hapo_newborn_cordblood_K0693


title: hapo_newborn_cordblood_K0733


title: hapo_newborn_cordblood_K0680


title: hapo_newborn_cordblood_K0669


title: hapo_newborn_cordblood_K0635


title: hapo_newborn_cordblood_K0641


title: hapo_newborn_cordblood_K0647


title: hapo_newborn_cordblood_K0666


title: hapo_newborn_cordblood_K0698


title: hapo_newborn_cordblood_K0677


title: hapo_newborn_cordblood_K0615


title: hapo_newborn_cordblood_K0612


title: hapo_newborn_cordblood_K0614


title: hapo_newborn_cordblood_K0609


title: hapo_newborn_cordblood_K0596


title: hapo_newborn_cordblood_K0600


title: hapo_newborn_cordblood_K0601


title: hapo_newborn_cordblood_K0592


title: hapo_newborn_cordblood_K0603


title: hapo_newborn_cordblood_K0591


title: hapo_newborn_cordblood_K0580


title: hapo_newborn_cordblood_K0623


title: hapo_newborn_cordblood_K0589


title: hapo_newborn_cordblood_K0588


title: hapo_newborn_cordblood_K0574


title: hapo_newborn_cordblood_K0555


title: hapo_newborn_cordblood_K0570


title: hapo_newborn_cordblood_K0550


title: hapo_newborn_cordblood_K0529


title: hapo_newborn_cordblood_K0552


title: hapo_newborn_cordblood_K0508


title: hapo_newborn_cordblood_K0514


title: hapo_newborn_cordblood_K0544


title: hapo_newborn_cordblood_K0483


title: hapo_newborn_cordblood_K0498


title: hapo_newborn_cordblood_K0485


title: hapo_newborn_cordblood_K0484


title: hapo_newborn_cordblood_K0458


title: hapo_newborn_cordblood_K0509


title: hapo_newborn_cordblood_K0455


title: hapo_newborn_cordblood_K0420


title: hapo_newborn_cordblood_K0482


title: hapo_newborn_cordblood_K0444


title: hapo_newborn_cordblood_K0486


title: hapo_newborn_cordblood_K0426


title: hapo_newborn_cordblood_K0411


title: hapo_newborn_cordblood_K0408


title: hapo_newborn_cordblood_K0479


title: hapo_newborn_cordblood_K0430


title: hapo_newborn_cordblood_K0390


title: hapo_newborn_cordblood_K0383


title: hapo_newborn_cordblood_K0389


title: hapo_newborn_cordblood_K0433


title: hapo_newborn_cordblood_K0402


title: hapo_newborn_cordblood_K0370


title: hapo_newborn_cordblood_K0361


title: hapo_newborn_cordblood_K0359


title: hapo_newborn_cordblood_K0349


title: hapo_newborn_cordblood_K0377


title: hapo_newborn_cordblood_K0341


title: hapo_newborn_cordblood_K0327


title: hapo_newborn_cordblood_K0336


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title: hapo_newborn_cordblood_K0351


title: hapo_newborn_cordblood_K0320


title: hapo_newborn_cordblood_K0266


title: hapo_newborn_cordblood_K0324


title: hapo_newborn_cordblood_K0318


title: hapo_newborn_cordblood_K0262


title: hapo_newborn_cordblood_K0258


title: hapo_newborn_cordblood_K0367


title: hapo_newborn_cordblood_K0238


title: hapo_newborn_cordblood_K0261


title: hapo_newborn_cordblood_K0235


title: hapo_newborn_cordblood_K0254


title: hapo_newborn_cordblood_K0243


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title: hapo_newborn_cordblood_K0231


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title: hapo_newborn_cordblood_K0212


title: hapo_newborn_cordblood_K0211


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title: hapo_newborn_cordblood_K0223


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title: hapo_newborn_cordblood_K0178


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title: hapo_newborn_cordblood_K0177


title: hapo_newborn_cordblood_K0130


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title: hapo_newborn_cordblood_K0173


title: hapo_newborn_cordblood_K0114


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title: hapo_newborn_cordblood_K0162


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title: hapo_newborn_cordblood_K0073


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title: hapo_newborn_cordblood_K0062


title: hapo_newborn_cordblood_K0069


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title: hapo_newborn_cordblood_K0052


title: hapo_newborn_cordblood_K0031


title: hapo_newborn_cordblood_K0029


title: hapo_newborn_cordblood_K0015


title: hapo_newborn_cordblood_K0030


title: hapo_newborn_cordblood_K0279


title: hapo_newborn_cordblood_G3256


title: hapo_newborn_cordblood_G3302


title: hapo_newborn_cordblood_G3427


title: hapo_newborn_cordblood_K0061


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title: hapo_newborn_cordblood_G3223


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title: hapo_newborn_cordblood_G3222


title: hapo_newborn_cordblood_G3135


title: hapo_newborn_cordblood_G3119


title: hapo_newborn_cordblood_K0011


title: hapo_newborn_cordblood_G3247


title: hapo_newborn_cordblood_G3134


title: hapo_newborn_cordblood_K0010


title: hapo_newborn_cordblood_G3092


title: hapo_newborn_cordblood_G3062


title: hapo_newborn_cordblood_G3028


title: hapo_newborn_cordblood_G3022


title: hapo_newborn_cordblood_G3242


title: hapo_newborn_cordblood_G3003


title: hapo_newborn_cordblood_G2933


title: hapo_newborn_cordblood_G2955


title: hapo_newborn_cordblood_G2850


title: hapo_newborn_cordblood_G2901


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title: hapo_newborn_cordblood_G2826


title: hapo_newborn_cordblood_G2759


title: hapo_newborn_cordblood_G2840


title: hapo_newborn_cordblood_G2811


title: hapo_newborn_cordblood_G2758


title: hapo_newborn_cordblood_G2663


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title: hapo_newborn_cordblood_G2634


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title: hapo_newborn_cordblood_G2652


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title: hapo_newborn_cordblood_G2556


title: hapo_newborn_cordblood_G2702


title: hapo_newborn_cordblood_G2539


title: hapo_newborn_cordblood_G2472


title: hapo_newborn_cordblood_G2458


title: hapo_newborn_cordblood_G2474


title: hapo_newborn_cordblood_G2488


title: hapo_newborn_cordblood_G2615


title: hapo_newborn_cordblood_G2394


title: hapo_newborn_cordblood_G2416


title: hapo_newborn_cordblood_G2375


title: hapo_newborn_cordblood_G2341


title: hapo_newborn_cordblood_G2338


title: hapo_newborn_cordblood_G2366


title: hapo_newborn_cordblood_G2302


title: hapo_newborn_cordblood_G2291


title: hapo_newborn_cordblood_G2327


title: hapo_newborn_cordblood_G2289


title: hapo_newborn_cordblood_G2287


title: hapo_newborn_cordblood_G2264


title: hapo_newborn_cordblood_G2262


title: hapo_newborn_cordblood_G2268


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title: hapo_newborn_cordblood_G2234


title: hapo_newborn_cordblood_G2239


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title: hapo_newborn_cordblood_G2183


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title: hapo_newborn_cordblood_G2179


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title: hapo_newborn_cordblood_G2140


title: hapo_newborn_cordblood_G2108


title: hapo_newborn_cordblood_G2118


title: hapo_newborn_cordblood_G2107


title: hapo_newborn_cordblood_G2110


title: hapo_newborn_cordblood_G2142


title: hapo_newborn_cordblood_G2055


title: hapo_newborn_cordblood_G2053


title: hapo_newborn_cordblood_G2106


title: hapo_newborn_cordblood_G2039


title: hapo_newborn_cordblood_G2027


title: hapo_newborn_cordblood_G2005


title: hapo_newborn_cordblood_G1989


title: hapo_newborn_cordblood_G1985


title: hapo_newborn_cordblood_G2021


title: hapo_newborn_cordblood_G1966


title: hapo_newborn_cordblood_G1940


title: hapo_newborn_cordblood_G1978


title: hapo_newborn_cordblood_G1898


title: hapo_newborn_cordblood_G1941


title: hapo_newborn_cordblood_G1826


title: hapo_newborn_cordblood_G1897


title: hapo_newborn_cordblood_G1859


title: hapo_newborn_cordblood_G1872


title: hapo_newborn_cordblood_G1843


title: hapo_newborn_cordblood_G1813


title: hapo_newborn_cordblood_G1810


title: hapo_newborn_cordblood_G1785


title: hapo_newborn_cordblood_G1806


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title: hapo_newborn_cordblood_G1782


title: hapo_newborn_cordblood_G1770


title: hapo_newborn_cordblood_G1766


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title: hapo_newborn_cordblood_G1702


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title: hapo_newborn_cordblood_G1667


title: hapo_newborn_cordblood_G1688


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title: hapo_newborn_cordblood_G1642


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title: hapo_newborn_cordblood_G1917


title: hapo_newborn_cordblood_G1523


title: hapo_newborn_cordblood_G1524


title: hapo_newborn_cordblood_G1419


title: hapo_newborn_cordblood_G1465


title: hapo_newborn_cordblood_G1410


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title: hapo_newborn_cordblood_G1391


title: hapo_newborn_cordblood_G1349


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title: hapo_newborn_cordblood_G1332


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title: hapo_newborn_cordblood_G1038


title: hapo_newborn_cordblood_G1127


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title: hapo_newborn_cordblood_G0639


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title: hapo_newborn_cordblood_F1850


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title: hapo_newborn_cordblood_F1803


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title: hapo_newborn_cordblood_F1801


title: hapo_newborn_cordblood_F1800


title: hapo_newborn_cordblood_F1795


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title: hapo_newborn_cordblood_F1788


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title: hapo_newborn_cordblood_F1759


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title: hapo_newborn_cordblood_F1700


title: hapo_newborn_cordblood_F1687


title: hapo_newborn_cordblood_F1722


title: hapo_newborn_cordblood_F1677


title: hapo_newborn_cordblood_F1676


title: hapo_newborn_cordblood_F1688


title: hapo_newborn_cordblood_F1685


title: hapo_newborn_cordblood_F1686


title: hapo_newborn_cordblood_F1696


title: hapo_newborn_cordblood_F1675


title: hapo_newborn_cordblood_F1674


title: hapo_newborn_cordblood_F1695


title: hapo_newborn_cordblood_F1668


title: hapo_newborn_cordblood_F1656


title: hapo_newborn_cordblood_F1665


title: hapo_newborn_cordblood_F1663


title: hapo_newborn_cordblood_F1645


title: hapo_newborn_cordblood_F1641


title: hapo_newborn_cordblood_F1635


title: hapo_newborn_cordblood_F1646


title: hapo_newborn_cordblood_F1633


title: hapo_newborn_cordblood_F1614


title: hapo_newborn_cordblood_F1612


title: hapo_newborn_cordblood_F1606


title: hapo_newborn_cordblood_F1616


title: hapo_newborn_cordblood_F1605


title: hapo_newborn_cordblood_F1628


title: hapo_newborn_cordblood_F1594


title: hapo_newborn_cordblood_F1593


title: hapo_newborn_cordblood_F1579


title: hapo_newborn_cordblood_F1584


title: hapo_newborn_cordblood_F1588


title: hapo_newborn_cordblood_F1603


title: hapo_newborn_cordblood_F1578


title: hapo_newborn_cordblood_F1572


title: hapo_newborn_cordblood_F1566


title: hapo_newborn_cordblood_F1555


title: hapo_newborn_cordblood_F1545


title: hapo_newborn_cordblood_F1565


title: hapo_newborn_cordblood_F1556


title: hapo_newborn_cordblood_F1542


title: hapo_newborn_cordblood_F1559


title: hapo_newborn_cordblood_F1530


title: hapo_newborn_cordblood_F1520


title: hapo_newborn_cordblood_F1516


title: hapo_newborn_cordblood_F1501


title: hapo_newborn_cordblood_F1510


title: hapo_newborn_cordblood_F1502


title: hapo_newborn_cordblood_F1509


title: hapo_newborn_cordblood_F1537


title: hapo_newborn_cordblood_F1492


title: hapo_newborn_cordblood_F1483


title: hapo_newborn_cordblood_F1473


title: hapo_newborn_cordblood_F1477


title: hapo_newborn_cordblood_F1467


title: hapo_newborn_cordblood_F1438


title: hapo_newborn_cordblood_F1412


title: hapo_newborn_cordblood_F1423


title: hapo_newborn_cordblood_F1403


title: hapo_newborn_cordblood_F1397


title: hapo_newborn_cordblood_F1387


title: hapo_newborn_cordblood_F1386


title: hapo_newborn_cordblood_F1381


title: hapo_newborn_cordblood_F1366


title: hapo_newborn_cordblood_F1377


title: hapo_newborn_cordblood_F1365


title: hapo_newborn_cordblood_F1357


title: hapo_newborn_cordblood_F1348


title: hapo_newborn_cordblood_F1329


title: hapo_newborn_cordblood_F1326


title: hapo_newborn_cordblood_F1317


title: hapo_newborn_cordblood_F1313


title: hapo_newborn_cordblood_F1294


title: hapo_newborn_cordblood_F1291


title: hapo_newborn_cordblood_F1287


title: hapo_newborn_cordblood_F1281


title: hapo_newborn_cordblood_F1279


title: hapo_newborn_cordblood_F1309


title: hapo_newborn_cordblood_F1278


title: hapo_newborn_cordblood_F1277


title: hapo_newborn_cordblood_F1273


title: hapo_newborn_cordblood_F1261


title: hapo_newborn_cordblood_F1257


title: hapo_newborn_cordblood_F1205


title: hapo_newborn_cordblood_F1221


title: hapo_newborn_cordblood_F1214


title: hapo_newborn_cordblood_F1203


title: hapo_newborn_cordblood_F1202


title: hapo_newborn_cordblood_F1196


title: hapo_newborn_cordblood_F1194


title: hapo_newborn_cordblood_F1193


title: hapo_newborn_cordblood_F1191


title: hapo_newborn_cordblood_F1190


title: hapo_newborn_cordblood_F1186


title: hapo_newborn_cordblood_F1182


title: hapo_newborn_cordblood_F1173


title: hapo_newborn_cordblood_F1162


title: hapo_newborn_cordblood_F1155


title: hapo_newborn_cordblood_F1151


title: hapo_newborn_cordblood_F1150


title: hapo_newborn_cordblood_F1147


title: hapo_newborn_cordblood_F1140


title: hapo_newborn_cordblood_F1139


title: hapo_newborn_cordblood_F1137


title: hapo_newborn_cordblood_F1136


title: hapo_newborn_cordblood_F1130


title: hapo_newborn_cordblood_F1135


title: hapo_newborn_cordblood_F1128


title: hapo_newborn_cordblood_F1118


title: hapo_newborn_cordblood_F1109


title: hapo_newborn_cordblood_F1114


title: hapo_newborn_cordblood_F1085


title: hapo_newborn_cordblood_F1107


title: hapo_newborn_cordblood_F1076


title: hapo_newborn_cordblood_F1072


title: hapo_newborn_cordblood_F1061


title: hapo_newborn_cordblood_G0441


title: hapo_newborn_cordblood_F1056


title: hapo_newborn_cordblood_F1037


title: hapo_newborn_cordblood_F1033


title: hapo_newborn_cordblood_F1027


title: hapo_newborn_cordblood_F1405


title: hapo_newborn_cordblood_F1023


title: hapo_newborn_cordblood_F1026


title: hapo_newborn_cordblood_F1404


title: hapo_newborn_cordblood_F1016


title: hapo_newborn_cordblood_F1014


title: hapo_newborn_cordblood_F1316


title: hapo_newborn_cordblood_F1362


title: hapo_newborn_cordblood_F1310


title: hapo_newborn_cordblood_F1325


title: hapo_newborn_cordblood_F1005


title: hapo_newborn_cordblood_F1004


title: hapo_newborn_cordblood_F0992


title: hapo_newborn_cordblood_F0985


title: hapo_newborn_cordblood_F0983


title: hapo_newborn_cordblood_F0984


title: hapo_newborn_cordblood_F0962


title: hapo_newborn_cordblood_F0952


title: hapo_newborn_cordblood_F0941


title: hapo_newborn_cordblood_F0929


title: hapo_newborn_cordblood_F0928


title: hapo_newborn_cordblood_F0927


title: hapo_newborn_cordblood_F0925


title: hapo_newborn_cordblood_F0921


title: hapo_newborn_cordblood_F0915


title: hapo_newborn_cordblood_F1010


title: hapo_newborn_cordblood_F0910


title: hapo_newborn_cordblood_F0905


title: hapo_newborn_cordblood_F0901


title: hapo_newborn_cordblood_F0889


title: hapo_newborn_cordblood_F0881


title: hapo_newborn_cordblood_F0870


title: hapo_newborn_cordblood_F0899


title: hapo_newborn_cordblood_F0868


title: hapo_newborn_cordblood_F0863


title: hapo_newborn_cordblood_F0860


title: hapo_newborn_cordblood_F0858


title: hapo_newborn_cordblood_F0856


title: hapo_newborn_cordblood_F0853


title: hapo_newborn_cordblood_F0885


title: hapo_newborn_cordblood_F0851


title: hapo_newborn_cordblood_F0850


title: hapo_newborn_cordblood_F0847


title: hapo_newborn_cordblood_F0846


title: hapo_newborn_cordblood_F0842


title: hapo_newborn_cordblood_F0845


title: hapo_newborn_cordblood_F0835


title: hapo_newborn_cordblood_F0833


title: hapo_newborn_cordblood_F0832


title: hapo_newborn_cordblood_F0822


title: hapo_newborn_cordblood_F0831


title: hapo_newborn_cordblood_F0817


title: hapo_newborn_cordblood_F0814


title: hapo_newborn_cordblood_F0813


title: hapo_newborn_cordblood_F0804


title: hapo_newborn_cordblood_F0793


title: hapo_newborn_cordblood_F0797


title: hapo_newborn_cordblood_F0782


title: hapo_newborn_cordblood_F0777


title: hapo_newborn_cordblood_F0765


title: hapo_newborn_cordblood_F0772


title: hapo_newborn_cordblood_F0759


title: hapo_newborn_cordblood_F0752


title: hapo_newborn_cordblood_F0748


title: hapo_newborn_cordblood_F0741


title: hapo_newborn_cordblood_F0740


title: hapo_newborn_cordblood_F0737


title: hapo_newborn_cordblood_F0729


title: hapo_newborn_cordblood_F0724


title: hapo_newborn_cordblood_F0719


title: hapo_newborn_cordblood_F0717


title: hapo_newborn_cordblood_F0714


title: hapo_newborn_cordblood_F0713


title: hapo_newborn_cordblood_F0709


title: hapo_newborn_cordblood_F0708


title: hapo_newborn_cordblood_F0707


title: hapo_newborn_cordblood_F0700


title: hapo_newborn_cordblood_F0699


title: hapo_newborn_cordblood_F0695


title: hapo_newborn_cordblood_F0685


title: hapo_newborn_cordblood_F0696


title: hapo_newborn_cordblood_F0673


title: hapo_newborn_cordblood_F0667


title: hapo_newborn_cordblood_F0662


title: hapo_newborn_cordblood_F0674


title: hapo_newborn_cordblood_F0656


title: hapo_newborn_cordblood_F0649


title: hapo_newborn_cordblood_F0661


title: hapo_newborn_cordblood_F0631


title: hapo_newborn_cordblood_F0659


title: hapo_newborn_cordblood_F0634


title: hapo_newborn_cordblood_F0638


title: hapo_newborn_cordblood_F0630


title: hapo_newborn_cordblood_F0624


title: hapo_newborn_cordblood_F0610


title: hapo_newborn_cordblood_F0607


title: hapo_newborn_cordblood_F0628


title: hapo_newborn_cordblood_F0602


title: hapo_newborn_cordblood_F0599


title: hapo_newborn_cordblood_F0606


title: hapo_newborn_cordblood_F0596


title: hapo_newborn_cordblood_F0595


title: hapo_newborn_cordblood_F1318


title: hapo_newborn_cordblood_F0583


title: hapo_newborn_cordblood_F0581


title: hapo_newborn_cordblood_F0598


title: hapo_newborn_cordblood_F0576


title: hapo_newborn_cordblood_F0575


title: hapo_newborn_cordblood_F1290


title: hapo_newborn_cordblood_F0573


title: hapo_newborn_cordblood_F0564


title: hapo_newborn_cordblood_F0555


title: hapo_newborn_cordblood_F0554


title: hapo_newborn_cordblood_F0549


title: hapo_newborn_cordblood_F0544


title: hapo_newborn_cordblood_F0535


title: hapo_newborn_cordblood_F1228


title: hapo_newborn_cordblood_F0534


title: hapo_newborn_cordblood_F1230


title: hapo_newborn_cordblood_F0533


title: hapo_newborn_cordblood_F0529


title: hapo_newborn_cordblood_F0520


title: hapo_newborn_cordblood_F0515


title: hapo_newborn_cordblood_F0512


title: hapo_newborn_cordblood_F0510


title: hapo_newborn_cordblood_F0505


title: hapo_newborn_cordblood_F0501


title: hapo_newborn_cordblood_F0482


title: hapo_newborn_cordblood_F0479


title: hapo_newborn_cordblood_F0478


title: hapo_newborn_cordblood_F0475


title: hapo_newborn_cordblood_F0464


title: hapo_newborn_cordblood_F0446


title: hapo_newborn_cordblood_F0457


title: hapo_newborn_cordblood_F0455


title: hapo_newborn_cordblood_F0445


title: hapo_newborn_cordblood_F2113


title: hapo_newborn_cordblood_F1170


title: hapo_newborn_cordblood_F0444


title: hapo_newborn_cordblood_F0437


title: hapo_newborn_cordblood_F0429


title: hapo_newborn_cordblood_F0427


title: hapo_newborn_cordblood_F0413


title: hapo_newborn_cordblood_F0419


title: hapo_newborn_cordblood_F0411


title: hapo_newborn_cordblood_F0407


title: ss3_23_058s_P20_accepted_hits_sorted_deduplicated.bam

type: SRA

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

description:
Library name: Single cell sample 524
Smart-seq3

library_source: transcriptomic single cell

data_processing:
Samples were de-multiplexed yielding single-cell fastq files that were quality-trimmed using Trim Galore and UMI were extracted using the UMI-tools package.
Reads were then mapped to the danio rerio reference genome GRCz11 using STAR and duplicates were removed using UMI-tools dedup based on identified UMI’s
Per cell and gene raw-count expression matrices were prepared using the featureCounts package
Counts data was processed and analyzed using Seurat and pagoda2 packages in R-software
Assembly: GRCz11
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: polyA RNA

organism: Danio rerio

source_name: meninges

extract_protocol:
3 brains per group were dissected and put in a buffer containing 0.5% Trypsin, 1mM EDTA, and 10U DNaseI (Promega) for 10 min at 30°C and shaken at 600rpm every 3 minutes until the BLECs were detached from the brain. Brains were removed, and the cells were centrifuged at 2000 rpm for 5 min. The pellet was washed and resuspended in PBS containing 3 % FCS and then filtered through a 40 µm nylon cell strainer. Cells were FACS-sorted into 384-well plates containing lysis buffer.
RNA libraries were prepared using the Smart-Seq3 protocol at SICOF Huddinge, Sweden.

value: meninges

value: Fibroblast

tag: group

value: treated

tag: batch


title: ss3_23_058s_P22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 525
Smart-seq3

value: Immune


title: hapo_newborn_cordblood_F0398


title: ss3_23_058s_P16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 522
Smart-seq3


title: ss3_23_058s_P17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 523
Smart-seq3


title: hapo_newborn_cordblood_F0395


title: hapo_newborn_cordblood_F0394


title: hapo_newborn_cordblood_F0389


title: ss3_23_058s_P15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 521
Smart-seq3


title: ss3_23_058s_P14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 520
Smart-seq3


title: hapo_newborn_cordblood_F0373


title: ss3_23_058s_P13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 519
Smart-seq3


title: hapo_newborn_cordblood_F0372


title: ss3_23_058s_P12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 518
Smart-seq3


title: hapo_newborn_cordblood_F0370


title: hapo_newborn_cordblood_F0365


title: hapo_newborn_cordblood_F0368


title: ss3_23_058s_P10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 516
Smart-seq3


title: ss3_23_058s_P11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 517
Smart-seq3


title: ss3_23_058s_P09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 515
Smart-seq3


title: ss3_23_058s_P08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 514
Smart-seq3

value: Network


title: hapo_newborn_cordblood_F0362


title: hapo_newborn_cordblood_F0359


title: ss3_23_058s_P07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 513
Smart-seq3


title: hapo_newborn_cordblood_F0358


title: ss3_23_058s_O23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 512
Smart-seq3

value: Neuronal/Glia


title: ss3_23_058s_O21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 510
Smart-seq3


title: hapo_newborn_cordblood_F0355


title: ss3_23_058s_O20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 509
Smart-seq3


title: hapo_newborn_cordblood_F0357

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: ss3_23_058s_O22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 511
Smart-seq3


title: hapo_newborn_cordblood_F0353


title: ss3_23_058s_O18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 508
Smart-seq3


title: hapo_newborn_cordblood_F0356


title: hapo_newborn_cordblood_F0341


title: ss3_23_058s_O17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 507
Smart-seq3


title: hapo_newborn_cordblood_F0340


title: hapo_newborn_cordblood_F0338


title: ss3_23_058s_O16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 506
Smart-seq3


title: hapo_newborn_cordblood_F0336


title: ss3_23_058s_O15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 505
Smart-seq3


title: ss3_23_058s_O14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 504
Smart-seq3


title: hapo_newborn_cordblood_F0335


title: ss3_23_058s_O13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 503
Smart-seq3


title: ss3_23_058s_O11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 502
Smart-seq3


title: hapo_newborn_cordblood_F0322


title: ss3_23_058s_O10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 501
Smart-seq3


title: hapo_newborn_cordblood_F0321


title: ss3_23_058s_O09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 500
Smart-seq3


title: hapo_newborn_cordblood_F0318


title: hapo_newborn_cordblood_F0309


title: ss3_23_058s_O06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 498
Smart-seq3


title: ss3_23_058s_O05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 497
Smart-seq3


title: hapo_newborn_cordblood_F0306


title: hapo_newborn_cordblood_F0303


title: ss3_23_058s_O04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 496
Smart-seq3


title: hapo_newborn_cordblood_F0296


title: hapo_newborn_cordblood_F0295


title: ss3_23_058s_O03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 495
Smart-seq3


title: hapo_newborn_cordblood_F1060


title: ss3_23_058s_N21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 494
Smart-seq3


title: ss3_23_058s_N20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 493
Smart-seq3


title: ss3_23_058s_N19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 492
Smart-seq3


title: ss3_23_058s_N18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 491
Smart-seq3


title: hapo_newborn_cordblood_F0294

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_F0286


title: ss3_23_058s_N17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 490
Smart-seq3


title: hapo_newborn_cordblood_F0291


title: hapo_newborn_cordblood_F0282


title: ss3_23_058s_N15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 489
Smart-seq3


title: hapo_newborn_cordblood_F0278


title: ss3_23_058s_N14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 488
Smart-seq3


title: hapo_newborn_cordblood_F0289


title: hapo_newborn_cordblood_F0275


title: ss3_23_058s_N13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 487
Smart-seq3


title: ss3_23_058s_N12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 486
Smart-seq3


title: ss3_23_058s_N10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 485
Smart-seq3


title: hapo_newborn_cordblood_F0269


title: hapo_newborn_cordblood_F0268


title: ss3_23_058s_N08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 484
Smart-seq3


title: hapo_newborn_cordblood_F0258


title: ss3_23_058s_N07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 483
Smart-seq3


title: ss3_23_058s_N06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 482
Smart-seq3


title: hapo_newborn_cordblood_F0272


title: hapo_newborn_cordblood_F0257


title: hapo_newborn_cordblood_F0260


title: hapo_newborn_cordblood_F0256


title: hapo_newborn_cordblood_F0255


title: ss3_23_058s_M23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 480
Smart-seq3


title: ss3_23_058s_M22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 479
Smart-seq3


title: hapo_newborn_cordblood_F0252


title: ss3_23_058s_M21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 478
Smart-seq3


title: ss3_23_058s_M20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 477
Smart-seq3


title: hapo_newborn_cordblood_F0250


title: ss3_23_058s_M18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 476
Smart-seq3


title: hapo_newborn_cordblood_F0245


title: ss3_23_058s_M17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 475
Smart-seq3


title: hapo_newborn_cordblood_F0240


title: ss3_23_058s_M15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 474
Smart-seq3


title: ss3_23_058s_M13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 473
Smart-seq3


title: hapo_newborn_cordblood_F0235

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: ss3_23_058s_M12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 472
Smart-seq3


title: ss3_23_058s_M11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 471
Smart-seq3


title: hapo_newborn_cordblood_F0231


title: hapo_newborn_cordblood_F0237


title: ss3_23_058s_M10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 470
Smart-seq3


title: hapo_newborn_cordblood_F0229


title: ss3_23_058s_M09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 469
Smart-seq3


title: hapo_newborn_cordblood_F0227


title: hapo_newborn_cordblood_F0226


title: ss3_23_058s_M08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 468
Smart-seq3


title: hapo_newborn_cordblood_F0223


title: ss3_23_058s_M06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 466
Smart-seq3


title: hapo_newborn_cordblood_F0220


title: ss3_23_058s_M04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 465
Smart-seq3


title: ss3_23_058s_M07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 467
Smart-seq3


title: ss3_23_058s_M03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 464
Smart-seq3


title: hapo_newborn_cordblood_F0202


title: ss3_23_058s_L24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 463
Smart-seq3


title: hapo_newborn_cordblood_F0194


title: ss3_23_058s_L22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 462
Smart-seq3


title: hapo_newborn_cordblood_F0193


title: hapo_newborn_cordblood_F0190


title: ss3_23_058s_L21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 461
Smart-seq3


title: ss3_23_058s_L19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 460
Smart-seq3


title: hapo_newborn_cordblood_F0189


title: ss3_23_058s_L18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 459
Smart-seq3


title: hapo_newborn_cordblood_F0171


title: ss3_23_058s_L17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 458
Smart-seq3


title: hapo_newborn_cordblood_F0165


title: ss3_23_058s_L16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 457
Smart-seq3


title: hapo_newborn_cordblood_F0163

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: ss3_23_058s_L15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 456
Smart-seq3


title: hapo_newborn_cordblood_F0156


title: ss3_23_058s_L13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 454
Smart-seq3


title: hapo_newborn_cordblood_F0161


title: ss3_23_058s_L14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 455
Smart-seq3


title: hapo_newborn_cordblood_F0151


title: ss3_23_058s_L12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 453
Smart-seq3


title: hapo_newborn_cordblood_F0139


title: hapo_newborn_cordblood_F0131


title: hapo_newborn_cordblood_F0150


title: hapo_newborn_cordblood_F0127


title: ss3_23_058s_L08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 449
Smart-seq3


title: ss3_23_058s_L10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 451
Smart-seq3


title: ss3_23_058s_L11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 452
Smart-seq3


title: ss3_23_058s_L07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 448
Smart-seq3


title: ss3_23_058s_L09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 450
Smart-seq3


title: hapo_newborn_cordblood_F0123


title: hapo_newborn_cordblood_F0109


title: ss3_23_058s_L06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 447
Smart-seq3


title: hapo_newborn_cordblood_F0106


title: ss3_23_058s_L03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 445
Smart-seq3


title: hapo_newborn_cordblood_F0103


title: ss3_23_058s_L02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 444
Smart-seq3


title: ss3_23_058s_L04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 446
Smart-seq3


title: hapo_newborn_cordblood_F0104


title: hapo_newborn_cordblood_F0099


title: hapo_newborn_cordblood_F0094


title: hapo_newborn_cordblood_F0093


title: ss3_23_058s_K22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 441
Smart-seq3


title: hapo_newborn_cordblood_F0074


title: ss3_23_058s_K23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 442
Smart-seq3


title: ss3_23_058s_K19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 439
Smart-seq3


title: hapo_newborn_cordblood_F0067

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_F0065


title: ss3_23_058s_K17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 437
Smart-seq3


title: ss3_23_058s_K18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 438
Smart-seq3


title: hapo_newborn_cordblood_F0064


title: hapo_newborn_cordblood_F0062


title: ss3_23_058s_K16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 436
Smart-seq3


title: ss3_23_058s_K15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 435
Smart-seq3


title: hapo_newborn_cordblood_F0061


title: ss3_23_058s_K14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 434
Smart-seq3


title: hapo_newborn_cordblood_F0056


title: hapo_newborn_cordblood_F0254


title: ss3_23_058s_K13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 433
Smart-seq3


title: hapo_newborn_cordblood_F0039


title: hapo_newborn_cordblood_F0041


title: ss3_23_058s_K12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 432
Smart-seq3


title: ss3_23_058s_N05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 481
Smart-seq3


title: hapo_newborn_cordblood_F0244


title: hapo_newborn_cordblood_F0038


title: ss3_23_058s_K11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 431
Smart-seq3


title: hapo_newborn_cordblood_F0034


title: ss3_23_058s_K08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 429
Smart-seq3


title: ss3_23_058s_K09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 430
Smart-seq3


title: ss3_23_058s_K07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 428
Smart-seq3


title: hapo_newborn_cordblood_F0030


title: hapo_newborn_cordblood_F0036


title: ss3_23_058s_K06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 427
Smart-seq3


title: ss3_23_058s_K05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 426
Smart-seq3


title: hapo_newborn_cordblood_F0021


title: hapo_newborn_cordblood_F0020


title: ss3_23_058s_K04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 425
Smart-seq3


title: hapo_newborn_cordblood_F0012


title: ss3_23_058s_K02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 424
Smart-seq3


title: hapo_newborn_cordblood_F0009

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_F0002


title: hapo_newborn_cordblood_E2443


title: ss3_23_058s_J24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 423
Smart-seq3


title: hapo_newborn_cordblood_F0216


title: ss3_23_058s_J23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 422
Smart-seq3


title: ss3_23_058s_J20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 421
Smart-seq3


title: hapo_newborn_cordblood_E2433


title: ss3_23_058s_J19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 420
Smart-seq3


title: hapo_newborn_cordblood_E2414


title: hapo_newborn_cordblood_E2426


title: hapo_newborn_cordblood_E2405


title: ss3_23_058s_J17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 418
Smart-seq3


title: ss3_23_058s_J18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 419
Smart-seq3


title: ss3_23_058s_J16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 417
Smart-seq3


title: hapo_newborn_cordblood_E2404


title: hapo_newborn_cordblood_F1160


title: ss3_23_058s_J15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 416
Smart-seq3


title: hapo_newborn_cordblood_E2395


title: hapo_newborn_cordblood_E2380


title: ss3_23_058s_J14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 415
Smart-seq3


title: hapo_newborn_cordblood_E2389


title: ss3_23_058s_J13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 414
Smart-seq3


title: ss3_23_058s_J12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 413
Smart-seq3


title: hapo_newborn_cordblood_E2378


title: ss3_23_058s_J10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 412
Smart-seq3


title: hapo_newborn_cordblood_E2377


title: ss3_23_058s_J09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 411
Smart-seq3


title: hapo_newborn_cordblood_E2353


title: ss3_23_058s_J08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 410
Smart-seq3


title: ss3_23_058s_J07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 409
Smart-seq3


title: hapo_newborn_cordblood_E2342


title: hapo_newborn_cordblood_E2351


title: hapo_newborn_cordblood_E2344


title: ss3_23_058s_J06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 408
Smart-seq3


title: ss3_23_058s_J04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 407
Smart-seq3


title: hapo_newborn_cordblood_E2331

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: ss3_23_058s_J03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 406
Smart-seq3


title: hapo_newborn_cordblood_E2327


title: hapo_newborn_cordblood_E2310


title: ss3_23_058s_J02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 405
Smart-seq3


title: ss3_23_058s_I24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 404
Smart-seq3


title: ss3_23_058s_I21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 402
Smart-seq3


title: ss3_23_058s_I22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 403
Smart-seq3


title: hapo_newborn_cordblood_E2319


title: hapo_newborn_cordblood_E2313


title: ss3_23_058s_I20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 401
Smart-seq3


title: hapo_newborn_cordblood_E2307


title: hapo_newborn_cordblood_E2305


title: hapo_newborn_cordblood_E2292


title: hapo_newborn_cordblood_E2291


title: ss3_23_058s_I17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 399
Smart-seq3


title: ss3_23_058s_I16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 398
Smart-seq3


title: ss3_23_058s_I19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 400
Smart-seq3


title: hapo_newborn_cordblood_E2277


title: hapo_newborn_cordblood_E2271


title: ss3_23_058s_I14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 396
Smart-seq3


title: hapo_newborn_cordblood_E2261


title: hapo_newborn_cordblood_E2259


title: ss3_23_058s_I12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 394
Smart-seq3


title: ss3_23_058s_I13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 395
Smart-seq3


title: hapo_newborn_cordblood_E2233


title: hapo_newborn_cordblood_E2243


title: hapo_newborn_cordblood_E2220


title: ss3_23_058s_K24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 443
Smart-seq3


title: ss3_23_058s_I09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 392
Smart-seq3


title: ss3_23_058s_I08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 391
Smart-seq3


title: hapo_newborn_cordblood_E2213


title: ss3_23_058s_I05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 390
Smart-seq3


title: ss3_23_058s_I04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 389
Smart-seq3


title: hapo_newborn_cordblood_F0071

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_E2212


title: ss3_23_058s_I03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 388
Smart-seq3


title: ss3_23_058s_I02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 387
Smart-seq3


title: hapo_newborn_cordblood_E2200


title: hapo_newborn_cordblood_E2208


title: hapo_newborn_cordblood_E2216


title: hapo_newborn_cordblood_E2199


title: ss3_23_058s_H23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 385
Smart-seq3


title: hapo_newborn_cordblood_E2193


title: ss3_23_058s_H22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 384
Smart-seq3


title: hapo_newborn_cordblood_E2184


title: ss3_23_058s_H20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 382
Smart-seq3


title: ss3_23_058s_H24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 386
Smart-seq3


title: hapo_newborn_cordblood_E2166


title: hapo_newborn_cordblood_E2165


title: ss3_23_058s_H18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 380
Smart-seq3


title: hapo_newborn_cordblood_E2152


title: ss3_23_058s_H17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 379
Smart-seq3


title: hapo_newborn_cordblood_E2135


title: hapo_newborn_cordblood_E2142


title: ss3_23_058s_H19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 381
Smart-seq3


title: ss3_23_058s_H16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 378
Smart-seq3


title: hapo_newborn_cordblood_E2132


title: ss3_23_058s_H14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 376
Smart-seq3


title: hapo_newborn_cordblood_E2108


title: hapo_newborn_cordblood_E2107


title: ss3_23_058s_H13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 375
Smart-seq3


title: ss3_23_058s_H12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 374
Smart-seq3


title: hapo_newborn_cordblood_E2102


title: ss3_23_058s_H11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 373
Smart-seq3


title: ss3_23_058s_H10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 372
Smart-seq3


title: hapo_newborn_cordblood_E2069


title: ss3_23_058s_H09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 371
Smart-seq3


title: hapo_newborn_cordblood_E2064

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: ss3_23_058s_H08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 370
Smart-seq3


title: hapo_newborn_cordblood_E2048


title: hapo_newborn_cordblood_E2036


title: ss3_23_058s_H06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 368
Smart-seq3


title: hapo_newborn_cordblood_E2023


title: ss3_23_058s_H07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 369
Smart-seq3


title: ss3_23_058s_H05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 367
Smart-seq3


title: hapo_newborn_cordblood_E1991


title: ss3_23_058s_H04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 366
Smart-seq3


title: hapo_newborn_cordblood_E1980


title: ss3_23_058s_H02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 365
Smart-seq3


title: hapo_newborn_cordblood_E1979


title: ss3_23_058s_G24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 364
Smart-seq3


title: hapo_newborn_cordblood_E1976


title: ss3_23_058s_G23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 363
Smart-seq3


title: ss3_23_058s_G22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 362
Smart-seq3


title: hapo_newborn_cordblood_E1966


title: hapo_newborn_cordblood_E1922


title: ss3_23_058s_G21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 361
Smart-seq3


title: hapo_newborn_cordblood_E1911


title: hapo_newborn_cordblood_E1907


title: hapo_newborn_cordblood_E1902


title: ss3_23_058s_G18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 359
Smart-seq3


title: ss3_23_058s_G19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 360
Smart-seq3


title: ss3_23_058s_G17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 358
Smart-seq3


title: hapo_newborn_cordblood_E1894


title: hapo_newborn_cordblood_E1884


title: ss3_23_058s_G15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 356
Smart-seq3


title: hapo_newborn_cordblood_E1875


title: ss3_23_058s_G16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 357
Smart-seq3


title: ss3_23_058s_G14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 355
Smart-seq3


title: hapo_newborn_cordblood_E1866

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_E1857


title: ss3_23_058s_G13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 354
Smart-seq3


title: hapo_newborn_cordblood_E1840


title: ss3_23_058s_G11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 352
Smart-seq3


title: hapo_newborn_cordblood_E1788


title: ss3_23_058s_G09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 350
Smart-seq3


title: hapo_newborn_cordblood_E1774


title: ss3_23_058s_I10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 393
Smart-seq3


title: ss3_23_058s_G10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 351
Smart-seq3


title: hapo_newborn_cordblood_F1813


title: hapo_newborn_cordblood_F1880


title: ss3_23_058s_G07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 349
Smart-seq3


title: hapo_newborn_cordblood_E1764


title: hapo_newborn_cordblood_E1760


title: ss3_23_058s_F24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 347
Smart-seq3


title: ss3_23_058s_G05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 348
Smart-seq3


title: hapo_newborn_cordblood_E1734


title: ss3_23_058s_F22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 346
Smart-seq3


title: hapo_newborn_cordblood_E1722


title: hapo_newborn_cordblood_E1720


title: ss3_23_058s_F21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 345
Smart-seq3


title: ss3_23_058s_F20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 344
Smart-seq3


title: hapo_newborn_cordblood_E2173


title: ss3_23_058s_H21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 383
Smart-seq3


title: hapo_newborn_cordblood_E1717


title: ss3_23_058s_F19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 343
Smart-seq3


title: hapo_newborn_cordblood_E1710


title: ss3_23_058s_F18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 342
Smart-seq3


title: hapo_newborn_cordblood_E1702


title: ss3_23_058s_F17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 341
Smart-seq3


title: hapo_newborn_cordblood_E1694


title: ss3_23_058s_F16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 340
Smart-seq3


title: hapo_newborn_cordblood_E1681

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: ss3_23_058s_F15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 339
Smart-seq3


title: hapo_newborn_cordblood_E1677


title: ss3_23_058s_F13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 338
Smart-seq3


title: hapo_newborn_cordblood_E1662


title: ss3_23_058s_H15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 377
Smart-seq3


title: ss3_23_058s_F11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 337
Smart-seq3


title: hapo_newborn_cordblood_E1656


title: hapo_newborn_cordblood_E1653


title: ss3_23_058s_F10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 336
Smart-seq3


title: ss3_23_058s_F09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 335
Smart-seq3


title: hapo_newborn_cordblood_E1634


title: hapo_newborn_cordblood_E1639


title: ss3_23_058s_F08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 334
Smart-seq3


title: hapo_newborn_cordblood_E1630


title: ss3_23_058s_F07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 333
Smart-seq3


title: ss3_23_058s_F06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 332
Smart-seq3


title: ss3_23_058s_F05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 331
Smart-seq3


title: ss3_23_058s_F04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 330
Smart-seq3


title: hapo_newborn_cordblood_E1587


title: ss3_23_058s_F03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 329
Smart-seq3


title: hapo_newborn_cordblood_E1594


title: hapo_newborn_cordblood_E2091


title: hapo_newborn_cordblood_E1610


title: hapo_newborn_cordblood_E1611


title: ss3_23_058s_F02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 328
Smart-seq3


title: hapo_newborn_cordblood_E1585


title: ss3_23_058s_E24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 327
Smart-seq3


title: ss3_23_058s_E23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 326
Smart-seq3


title: hapo_newborn_cordblood_E1583


title: hapo_newborn_cordblood_E1574


title: ss3_23_058s_E21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 325
Smart-seq3


title: hapo_newborn_cordblood_E1579

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_E1561


title: ss3_23_058s_E20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 324
Smart-seq3


title: ss3_23_058s_E19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 323
Smart-seq3


title: hapo_newborn_cordblood_E1539


title: ss3_23_058s_E18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 322
Smart-seq3


title: hapo_newborn_cordblood_E1534


title: ss3_23_058s_E17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 321
Smart-seq3


title: hapo_newborn_cordblood_E1532


title: hapo_newborn_cordblood_E1531


title: ss3_23_058s_E16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 320
Smart-seq3


title: hapo_newborn_cordblood_E1528


title: ss3_23_058s_E15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 319
Smart-seq3


title: ss3_23_058s_E14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 318
Smart-seq3


title: hapo_newborn_cordblood_E1525


title: ss3_23_058s_E13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 317
Smart-seq3


title: hapo_newborn_cordblood_E1520


title: ss3_23_058s_E12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 316
Smart-seq3


title: ss3_23_058s_E11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 315
Smart-seq3


title: hapo_newborn_cordblood_E1509


title: ss3_23_058s_E10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 314
Smart-seq3


title: hapo_newborn_cordblood_E1504


title: hapo_newborn_cordblood_E1503


title: ss3_23_058s_E09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 313
Smart-seq3


title: hapo_newborn_cordblood_E1500


title: ss3_23_058s_E08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 312
Smart-seq3


title: hapo_newborn_cordblood_E1497


title: ss3_23_058s_E07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 311
Smart-seq3


title: hapo_newborn_cordblood_E1483


title: ss3_23_058s_E06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 310
Smart-seq3


title: ss3_23_058s_D23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 309
Smart-seq3


title: hapo_newborn_cordblood_E1477

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_E1479


title: hapo_newborn_cordblood_E1476


title: ss3_23_058s_D22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 308
Smart-seq3


title: ss3_23_058s_D20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 307
Smart-seq3


title: ss3_23_058s_D19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 306
Smart-seq3


title: hapo_newborn_cordblood_E1472


title: hapo_newborn_cordblood_E1461


title: ss3_23_058s_D18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 305
Smart-seq3


title: hapo_newborn_cordblood_E1458


title: hapo_newborn_cordblood_E1456


title: hapo_newborn_cordblood_E1457


title: ss3_23_058s_D17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 304
Smart-seq3


title: ss3_23_058s_D16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 303
Smart-seq3


title: ss3_23_058s_D15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 302
Smart-seq3


title: hapo_newborn_cordblood_E1452


title: ss3_23_058s_D14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 301
Smart-seq3


title: hapo_newborn_cordblood_F0784


title: hapo_newborn_cordblood_E1436


title: ss3_23_058s_D13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 300
Smart-seq3


title: ss3_23_058s_D12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 299
Smart-seq3


title: ss3_23_058s_D11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 298
Smart-seq3


title: ss3_23_058s_D09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 297
Smart-seq3


title: ss3_23_058s_D08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 296
Smart-seq3


title: hapo_newborn_cordblood_E1431


title: hapo_newborn_cordblood_E1383


title: ss3_23_058s_D07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 295
Smart-seq3


title: ss3_23_058s_G12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 353
Smart-seq3


title: hapo_newborn_cordblood_E1831


title: hapo_newborn_cordblood_E1382


title: hapo_newborn_cordblood_E1385


title: ss3_23_058s_D06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 294
Smart-seq3


title: hapo_newborn_cordblood_F0332

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_G0910


title: hapo_newborn_cordblood_E1376


title: hapo_newborn_cordblood_E1348


title: ss3_23_058s_C24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 292
Smart-seq3


title: hapo_newborn_cordblood_E1370


title: ss3_23_058s_I15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 397
Smart-seq3


title: hapo_newborn_cordblood_E1352


title: ss3_23_058s_C23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 291
Smart-seq3


title: hapo_newborn_cordblood_E1349


title: hapo_newborn_cordblood_E1313


title: ss3_23_058s_C16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 286
Smart-seq3


title: ss3_23_058s_C21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 290
Smart-seq3


title: hapo_newborn_cordblood_E1296


title: ss3_23_058s_C19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 289
Smart-seq3


title: hapo_newborn_cordblood_E1328


title: ss3_23_058s_C18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 288
Smart-seq3


title: Mnk3_Ctrl_RNA_Seq_rep1

city: Columbus

first: Ankita

last: Saini

state: Ohio

address: 460 W 12th Ave

department: Microbial Infection and Immunity

institute: The Ohio State University Wexner Medical Center

description:
Library name: Mnk3_Ctrl_RNA_rep1
Ribo-depletion

library_source: other

data_processing:
Aligned using STAR
Assembly: Reference build Ensembl_R76
Supplementary files format and content: Text file generated by Subread featureCounts containing counts of uniquely aligned unambigous reads per gene.

molecule: other

organism: Mus musculus

extract_protocol:
Total RNA was prepped using Qiagen kit followed by Ribo depletion
RNA-seq

treatment_protocol: Cells were either stimulated with 10ng/ml each of IL-1b+IL-23 or left untreated for ~16 hours

tag: cell line

tag: treatment

value: Control


title: ss3_23_058s_C17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 287
Smart-seq3


title: hapo_newborn_cordblood_E1303


title: P7657_1192

city: Stockholm

first: Andreas

last: Liontos

state: Stockholm

address: Svante Arrheniusväg 20C

department: Molecular Biosciences-The Wenner Gren Institute

institute: Stockholm University

description:
single cell library
Smart-Seq2

data_processing:
Sequencing was done with Illumina 2500 HiSeq Rapid mode using paired-end (2x125 bp) and single-end (1x50 bp). For downstream analysis, we used the one strand sequencing out of paired-end libraries and trimmed the reads to 50 bp
High quality transcriptomic libraries were obtained after filtering, for doublet cells included in our experiment as sequencing controls, for cells obtaining less than 40% uniquely mapped reads, for cells that had number of detected genes outside mean ± 2s.d range and for cells whose GFP  expression ratio was lower than the GFP ration determined in embryonic epithelial cells.
The following single cells were removed as known doublets in our analysis: "P7657_1067", "P7657_1189", "P2661_1003", "P4730_1029". The following single cells were removed because they had <40% uniquely mapped reads: "P2272_1042", "P2661_1042", "P3504_1071", "P3504_1082", "P4730_1040", "P7657_1022", "P7657_1024", "P7657_1025", "P7657_1032", "P7657_1070".
Assembly: Custom Mus Musculus (GRCm38) reference genome that contained GFP sequence and Ai14 cassette (RFP and WPRE sequences). The reference genome was created with the 10x Genomics "cell ranger mkref" and the mapping of the reads was done with the "cellranger count" function, using default settings.
Supplementary files format and content: raw count matrix and metadata files for the 464/478 single cells remaining after removal of doublet cells (4 cells removed) and removal of cells that failed uniquely map read filtering (10 cells removed) step.

molecule: total RNA

source_name: lung

extract_protocol:
For full-length (Smart-Seq2) library preparation (Picelli et al., 2014), the left lungs were used for enzymatic digestion and right lungs were treated as described above for histological analysis. Briefly, we cut the lungs in small pieces using a razor blade and digested with elastase (Worthington, LS002292) and DNase I 0.5 mg/ml (Sigma-Aldrich, DN25) in HBSS (Gibco, 14175), at 37oC for 1 hour with rotation. Equal volume of HBSS++ [HBSS (Gibco, 14175), supplemented with 2% 0.2µm filtered FCS (Gibco, 10500), 0.1 M HEPES (Sigma-Aldrich, H0887), antibiotics (Gibco, 15240096) and EGTA 2 mM] was added and the suspension was mixed gently. Then cells were centrifuged at 800g for 10 minutes at 4oC. Supernatant was removed with a serological pipette and cells were resuspended in HBSS++. Viability was tested using trypan blue (Sigma-Aldrich, T8154) (1:1 dilution) and presence of fluorescence positive cells was evaluated using a normal fluorescence microscope. Just before sorting, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) in order to remove cell aggregates. For E16.5 lungs, after digestion, centrifuge and cell resuspension in HBSS++, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) and counted. We resuspented the cells in the proper amount of HBSS++ in order to obtain 20x106 cells/ml cell concentration. 100 µl of cell suspension were stained with 0.5 µl of anti-EpCam-PE antibody (Biolegend, 118205) and 0.5 µl anti-CD45-APC antibody (Biolegend, 103112). Replicates of the above reactions were set in separate tubes; in order to prevent the formation of cell aggregates, which is typical when we centrifuge large amount of epithelial cells.
For cell-sorting, we used a BD FACSARIA III cell-sorter, using 100 µm nozzle, applying single-cell sorting purity setting. For E16.5 lungs, EpCampos CD45neg cells were sorted. Cells from all other stages were isolated according to GFP expression.
Cell sorting and single-cell library preparation were done according to Smart Seq2 protocol (Picelli et al., 2013; Picelli et al., 2014) with some modifications. Cells were sorted in 96-well plates (Piko PCR Plates 24-well, Thermo Scientific, SPL0240 and Plate Frame for 24-well PikoPCR Plates, Thermo Scientific, SFR0241).  Each well contained Triton-X100 (0.2%) (Sigma-Aldrich, T9284-100ML), ERCC RNA Spike-In Mix (1:400.000) (Life-Technologies, 4456740), Oligo-dT30 VN (1,25uM) AAGCAGTGGTATCAACGCAGAGTAC (30 x T) VN, dNTPs (2.5mM/each) (Thermo Scientific-Fermentas, R0192) and Rnase Inhibitor (1U/ul) (Clontech, 2313A) in 4 µl final volume. After sorting, strips were covered with Axygen PCR-tube caps (VWR, PCR-02-FCP-C), centrifuged and placed on dry ice until storage at -80oC for further use. For cell culture cells were sorted into HBSS++ buffer and kept on ice until they were placed in culture.
Smart Seq2 protocol is optimal for cell lines and/or large human cells (Picelli et al., 2014). Mouse primary pulmonary cells are smaller and they contain smaller amount of RNA, as a result high amount of primer concatamers were formed during cDNA library preparation, compromising its efficiency. Our optimized protocol contains 50% less Oligo-dT30 VN and cDNA synthesis was divided into two steps, the first was without TSO LNA and the second contained 1µM TSO LNA and additional 40 U of SuperScript II RT (Thermo-Fisher Scientific, 18064071). Reaction lasted 30 minutes at 42oC. Then enzyme was deactivated at 70oC for 15 minutes. For Pre-Amplification PCR, we used the KAPA HiFi Hotstart ReadyMix (2x) (KAPA Biosystems, KK2602) and the ISPCR-primer AAGCAGTGGTATCAACGCAGAGT. PCR included 21 cycles and the total volume increased to 50ul in order to reduce the concentration of the unused Oligo-dT30 VN and TSO-LNA primers.
Tagmentation and indexed library amplification were done with Nextera® XT DNA Library Preparation Kit (Illumina, FC-131-1096) and Nextera® XT Index Kit (96 indexes, 384 samples), (Illumina, FC-131-1002) according to the manufacturer protocol (with 2.5 x volume reduction in all reactions). The quantity of the used library for tagmentation was 50 pg of the 500-9000 bp fraction of the library, as indicated by its Bioanalyzer profile.

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_E1240

tag: Sex

value: Male

tag: tissue

value: cord clood

tag: developmental stage

tag: cell type


title: P7657_1191

description:
single cell library
Smart-Seq2

tag: strain


title: ss3_23_058s_C15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 285
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_E1291

value: newborn

value: whole blood cells


title: hapo_newborn_cordblood_E1234


title: ss3_23_058s_C12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 282
Smart-seq3

value: meninges


title: hapo_newborn_cordblood_E1287


title: ss3_23_058s_C14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 284
Smart-seq3


title: hapo_newborn_cordblood_E1263

value: Female


title: ss3_23_058s_C13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 283
Smart-seq3

value: treated


title: hapo_newborn_cordblood_E1214


title: P7657_1190

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date


title: hapo_newborn_cordblood_E1220


title: hapo_newborn_cordblood_E1197


title: hapo_newborn_cordblood_E1193


title: P7657_1189

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: ss3_23_058s_C11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 281
Smart-seq3

value: Immune


title: hapo_newborn_cordblood_E1186


title: ss3_23_058s_C10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 280
Smart-seq3


title: P7657_1188

description:
single cell library
Smart-Seq2

tag: type of_sequencing

tag: lane

tag: plate well


title: P7657_1187

description:
single cell library
Smart-Seq2

tag: internal number

tag: n primer

tag: s primer


title: ss3_23_058s_C09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 279
Smart-seq3

tag: tissue


title: ss3_23_058s_C08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 278
Smart-seq3

tag: cell type

value: Network


title: P7657_1186

description:
single cell library
Smart-Seq2

tag: strain

tag: developmental stage


title: hapo_newborn_cordblood_E1164

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex


title: hapo_newborn_cordblood_E1183


title: hapo_newborn_cordblood_E1135


title: P7657_1185

description:
single cell library
Smart-Seq2

tag: genotype


title: hapo_newborn_cordblood_E1138


title: ss3_23_058s_C05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 276
Smart-seq3

tag: group

tag: batch


title: ss3_23_058s_C07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 277
Smart-seq3


title: hapo_newborn_cordblood_E1133


title: hapo_newborn_cordblood_E1127


title: hapo_newborn_cordblood_E1125


title: P7657_1184

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria


title: ss3_23_058s_C04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 275
Smart-seq3

value: Neuronal/Glia


title: hapo_newborn_cordblood_E1115


title: hapo_newborn_cordblood_E1112


title: P7657_1183

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: hapo_newborn_cordblood_E1102


title: ss3_23_058s_B23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 274
Smart-seq3


title: P7657_1182

description:
single cell library
Smart-Seq2

tag: lane

tag: plate well

tag: internal number


title: hapo_newborn_cordblood_E1100

tag: tissue


title: hapo_newborn_cordblood_E1098

tag: cell type


title: P7657_1181

description:
single cell library
Smart-Seq2

tag: strain

tag: n primer

tag: s primer


title: ss3_23_058s_B22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 273
Smart-seq3


title: hapo_newborn_cordblood_E1095

tag: Sex

tag: developmental stage


title: ss3_23_058s_B21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 272
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_E1080


title: hapo_newborn_cordblood_E1066


title: P7657_1180

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date


title: ss3_23_058s_B20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 271
Smart-seq3


title: hapo_newborn_cordblood_E1036


title: P7657_1179

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: hapo_newborn_cordblood_E1024


title: ss3_23_058s_B19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 270
Smart-seq3

value: Fibroblast


title: hapo_newborn_cordblood_E1009


title: P7657_1178

description:
single cell library
Smart-Seq2

value: lung

tag: type of_sequencing

tag: lane

tag: plate well


title: hapo_newborn_cordblood_E0999

tag: tissue

tag: cell type


title: ss3_23_058s_B18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 269
Smart-seq3


title: hapo_newborn_cordblood_E0996


title: P7657_1177

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: internal number

tag: n primer


title: hapo_newborn_cordblood_E0984

tag: Sex

tag: developmental stage


title: P7657_1176

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: s primer


title: ss3_23_058s_B17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 268
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_E0976


title: ss3_23_058s_B16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 267
Smart-seq3


title: hapo_newborn_cordblood_E0972


title: P7657_1175

description:
single cell library
Smart-Seq2

tag: genotype

value: WT

tag: individual

tag: sorting date


title: hapo_newborn_cordblood_E0970


title: ss3_23_058s_B15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 266
Smart-seq3


title: hapo_newborn_cordblood_E0961


title: P7657_1174

description:
single cell library
Smart-Seq2

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: hapo_newborn_cordblood_E0936


title: ss3_23_058s_B14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 265
Smart-seq3


title: P7657_1173

description:
single cell library
Smart-Seq2

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well


title: hapo_newborn_cordblood_E0931

value: Male

tag: tissue

tag: cell type


title: hapo_newborn_cordblood_E0930

value: cord clood


title: P7657_1172

description:
single cell library
Smart-Seq2

tag: strain

tag: internal number

tag: n primer


title: hapo_newborn_cordblood_E0928

tag: Sex

tag: developmental stage

value: newborn


title: hapo_newborn_cordblood_E0975

value: whole blood cells


title: hapo_newborn_cordblood_E0899


title: ss3_23_058s_B12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 263
Smart-seq3

value: meninges

tag: group

tag: batch


title: P7657_1171

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: s primer


title: hapo_newborn_cordblood_E1305

value: Female


title: hapo_newborn_cordblood_E0895


title: ss3_23_058s_B11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 262
Smart-seq3

value: treated


title: P7657_1170

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no


title: hapo_newborn_cordblood_E0879


title: ss3_23_058s_B10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 261
Smart-seq3

value: Immune


title: Mnk3_Stim_RNA_Seq_rep1

description:
Library name: Mnk3_Stim_RNA_rep1
Ribo-depletion

tag: cell line

tag: treatment

value: Stimulated with IL-1b+IL-23


title: hapo_newborn_cordblood_E0876

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: tissue


title: hapo_newborn_cordblood_E0855

tag: cell type


title: ss3_23_058s_B09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 260
Smart-seq3


title: hapo_newborn_cordblood_E0872


title: P7657_1169

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: plate well


title: P7657_1168

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: internal number

tag: n primer


title: hapo_newborn_cordblood_E0854

tag: Sex


title: hapo_newborn_cordblood_E0842


title: ss3_23_058s_B08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 259
Smart-seq3

value: Network

tag: group

tag: batch


title: hapo_newborn_cordblood_E0841


title: hapo_newborn_cordblood_E0834


title: ss3_23_058s_B07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 258
Smart-seq3


title: P7657_1167

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date

tag: isolation criteria

tag: s primer


title: P7657_1166

description:
single cell library
Smart-Seq2

tag: tissue

tag: cell type

tag: ercc spike-in_lot_no


title: hapo_newborn_cordblood_E0833


title: ss3_23_058s_B05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 257
Smart-seq3


title: hapo_newborn_cordblood_E0831


title: hapo_newborn_cordblood_E0813


title: ss3_23_058s_A24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 256
Smart-seq3


title: P7657_1165

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date

tag: type of_sequencing


title: hapo_newborn_cordblood_E0802

tag: developmental stage


title: hapo_newborn_cordblood_E0793


title: hapo_newborn_cordblood_E0792


title: ss3_23_058s_A23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 255
Smart-seq3


title: P7657_1163

description:
single cell library
Smart-Seq2

tag: lane

tag: plate well

tag: internal number


title: hapo_newborn_cordblood_E0791

tag: Sex


title: ss3_23_058s_A22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 254
Smart-seq3

value: Neuronal/Glia

tag: group

tag: batch


title: hapo_newborn_cordblood_E0775


title: P7657_1162

description:
single cell library
Smart-Seq2

value: lung

tag: genotype

tag: individual

tag: n primer


title: hapo_newborn_cordblood_E0761


title: ss3_23_058s_A21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 253
Smart-seq3

value: Fibroblast


title: hapo_newborn_cordblood_E0759


title: P7657_1161

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: sorting date

tag: isolation criteria

tag: s primer


title: hapo_newborn_cordblood_E0757

tag: tissue

tag: cell type


title: ss3_23_058s_A18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 252
Smart-seq3


title: hapo_newborn_cordblood_E0754


title: hapo_newborn_cordblood_E0752


title: P7657_1160

description:
single cell library
Smart-Seq2

tag: strain

value: WT

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: ss3_23_058s_A16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 251
Smart-seq3


title: hapo_newborn_cordblood_E0747

value: Male

tag: developmental stage


title: P7657_1159

description:
single cell library
Smart-Seq2

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well


title: hapo_newborn_cordblood_E0737

tag: Sex

value: cord clood

value: newborn


title: ss3_23_058s_A15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 250
Smart-seq3

value: meninges

tag: group

tag: batch


title: hapo_newborn_cordblood_E0722

value: whole blood cells


title: P7657_1158

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: internal number


title: ss3_23_058s_A14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 249
Smart-seq3

value: treated


title: hapo_newborn_cordblood_E0714

value: Female


title: hapo_newborn_cordblood_E0708


title: P7657_1157

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: n primer


title: hapo_newborn_cordblood_E0704

tag: tissue

tag: cell type


title: ss3_23_058s_A13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 248
Smart-seq3

value: Immune


title: hapo_newborn_cordblood_E0700


title: P7657_1156

description:
single cell library
Smart-Seq2

tag: strain

tag: ercc spike-in_lot_no

tag: s primer


title: hapo_newborn_cordblood_E0694

tag: developmental stage


title: ss3_23_058s_A12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 247
Smart-seq3


title: hapo_newborn_cordblood_E0692


title: hapo_newborn_cordblood_E0689


title: P7657_1155

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: ss3_23_058s_A11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 246
Smart-seq3

tag: group


title: hapo_newborn_cordblood_E0679

tag: Sex


title: P7657_1154

description:
single cell library
Smart-Seq2

tag: genotype

tag: plate well


title: hapo_newborn_cordblood_E0639


title: ss3_23_058s_A10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 245
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_E0633

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_E0627


title: P7657_1153

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: internal number


title: ss3_23_056s_P22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 244
Smart-seq3

tag: tissue

value: control


title: hapo_newborn_cordblood_E0614

tag: cell type


title: P7657_1152

description:
single cell library
Smart-Seq2

tag: strain

tag: isolation criteria

tag: n primer


title: hapo_newborn_cordblood_E0598

tag: developmental stage


title: ss3_23_056s_P19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 242
Smart-seq3


title: hapo_newborn_cordblood_E0588


title: ss3_23_058s_B13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 264
Smart-seq3

value: Network


title: hapo_newborn_cordblood_E0586


title: hapo_newborn_cordblood_E0585


title: ss3_23_056s_P17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 241
Smart-seq3

value: Neuronal/Glia


title: hapo_newborn_cordblood_E0883


title: P7657_1149

description:
single cell library
Smart-Seq2

value: lung

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: s primer


title: hapo_newborn_cordblood_E0584


title: ss3_23_056s_P16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 240
Smart-seq3

tag: group


title: hapo_newborn_cordblood_E0566

tag: Sex


title: P7657_1148

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_E0560


title: ss3_23_056s_P15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 239
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_E0519


title: P7657_1147

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: individual

tag: sorting date

tag: plate well


title: hapo_newborn_cordblood_E0485

tag: tissue

tag: cell type


title: ss3_23_056s_P14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 238
Smart-seq3


title: hapo_newborn_cordblood_E0484


title: P7657_1146

description:
single cell library
Smart-Seq2

tag: strain

value: WT

tag: isolation criteria

tag: internal number


title: hapo_newborn_cordblood_E0474

tag: developmental stage


title: ss3_23_056s_P08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 237
Smart-seq3


title: hapo_newborn_cordblood_E0471


title: hapo_newborn_cordblood_E0466


title: ss3_23_056s_P04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 236
Smart-seq3


title: P7657_1145

description:
single cell library
Smart-Seq2

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: n primer


title: hapo_newborn_cordblood_E0462

tag: Sex

value: Male


title: P7657_1144

description:
single cell library
Smart-Seq2

tag: genotype

value: single-end 50bp

tag: s primer


title: hapo_newborn_cordblood_E0448

value: cord clood


title: ss3_23_056s_P03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 235
Smart-seq3

tag: group


title: hapo_newborn_cordblood_E0447

value: newborn


title: hapo_newborn_cordblood_E0445


title: P7657_1143

description:
single cell library
Smart-Seq2

tag: type of_sequencing

tag: lane


title: ss3_23_056s_P02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 234
Smart-seq3

value: meninges

tag: batch


title: hapo_newborn_cordblood_E0438

value: whole blood cells


title: P7657_1142

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: plate well


title: hapo_newborn_cordblood_E0436

tag: tissue

tag: cell type


title: ss3_23_056s_P01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 233
Smart-seq3


title: hapo_newborn_cordblood_E0432


title: hapo_newborn_cordblood_E0403


title: P7657_1141

description:
single cell library
Smart-Seq2

tag: strain

tag: isolation criteria

tag: internal number


title: ss3_23_056s_O23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 232
Smart-seq3


title: hapo_newborn_cordblood_E0401

tag: developmental stage


title: hapo_newborn_cordblood_E0382


title: hapo_newborn_cordblood_E1250


title: hapo_newborn_cordblood_E0371


title: hapo_newborn_cordblood_E1205


title: P7657_1164

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: n primer


title: ss3_23_056s_O21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 230
Smart-seq3


title: hapo_newborn_cordblood_E0364

tag: Sex


title: hapo_newborn_cordblood_E1169


title: hapo_newborn_cordblood_E0355


title: P7657_1138

description:
single cell library
Smart-Seq2

tag: genotype

tag: s primer


title: ss3_23_056s_O17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 229
Smart-seq3

tag: group


title: hapo_newborn_cordblood_E0336


title: ss3_23_056s_O16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 228
Smart-seq3

value: Fibroblast

tag: batch


title: hapo_newborn_cordblood_E0326

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Female


title: P7657_1137

description:
single cell library
Smart-Seq2

tag: individual

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_E0318

tag: tissue


title: P7657_1136

description:
single cell library
Smart-Seq2

tag: cell type

tag: sorting date

tag: plate well


title: hapo_newborn_cordblood_E0317


title: ss3_23_056s_O15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 227
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_E0309


title: hapo_newborn_cordblood_E0267


title: P7657_1135

description:
single cell library
Smart-Seq2

tag: strain

tag: isolation criteria

tag: internal number


title: ss3_23_056s_O14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 226
Smart-seq3

value: control


title: hapo_newborn_cordblood_E0236

tag: developmental stage


title: hapo_newborn_cordblood_E0225


title: P7657_1134

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: n primer


title: ss3_23_056s_O12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 225
Smart-seq3


title: hapo_newborn_cordblood_E1416

tag: Sex


title: hapo_newborn_cordblood_E0189


title: P7657_1133

description:
single cell library
Smart-Seq2

tag: genotype

tag: s primer


title: hapo_newborn_cordblood_E0185