title: Tcell_person1_P1902_1622


title: Tcell_person1_P1902_1613

status: Public on Sep 26 2016

type: SRA

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
genome build:  hg19
Aligned reads with rna-star
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track
Supplementary_files_format_and_content: Tab-delimited text files report RPKMs and read counts.

molecule: total RNA

organism: Homo sapiens

extract_protocol: SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)

tag: age

value: adult

tag: Sex

value: male

tag: cell type

value: ex vivo single Tcell


title: Tcell_person1_P1902_1621


title: Tcell_person1_P1902_1614


title: Tcell_person1_P1902_1623


title: Tcell_person1_P1902_1616


title: Tcell_person1_P1902_1608


title: Tcell_person1_P1902_1598


title: Tcell_person1_P1902_1607


title: Tcell_person1_P1902_1606


title: Tcell_person1_P1902_1597


title: Tcell_person1_P1902_1605


title: Tcell_person1_P1902_1599


title: Tcell_person1_P1902_1600


title: Tcell_person1_P1902_1638


title: Tcell_person1_P1902_1592


title: Tcell_person1_P1902_1590


title: Tcell_person1_P1902_1645


title: Tcell_person1_P1902_1591


title: Tcell_person1_P1902_1584


title: Tcell_person1_P1902_1589


title: Tcell_person1_P1902_1581


title: Tcell_person1_P1902_1583


title: Tcell_person1_P1902_1379


title: Tcell_person1_P1902_1378


title: Tcell_person1_P1902_1377


title: Tcell_person1_P1902_1372


title: Tcell_person1_P1902_1371


title: Tcell_person1_P1902_1361


title: Tcell_person1_P1902_1364


title: Tcell_person1_P1902_1370


title: Tcell_person1_P1902_1363


title: Tcell_person1_P1902_1369


title: Tcell_person1_P1902_1356


title: Tcell_person1_P1902_1362


title: Tcell_person1_P1902_1347


title: Tcell_person1_P1902_1353


title: Tcell_person1_P1902_1345


title: Tcell_person1_P1902_1340


title: Tcell_person1_P1902_1355


title: Tcell_person1_P1902_1348


title: Tcell_person1_P1902_1354


title: Tcell_person1_P1902_1338


title: Tcell_person1_P1902_1582


title: Tcell_person1_P1902_1339


title: Tcell_person1_P1902_1332


title: Tcell_person1_P1902_1337


title: Tcell_person1_P1902_1322


title: Tcell_person1_P1902_1323


title: Tcell_person1_P1902_1321


title: Tcell_person1_P1902_1324


title: Tcell_person1_P1902_1316


title: Tcell_person1_P1902_1308


title: Tcell_person1_P1902_1315


title: Tcell_person1_P1902_1298


title: Tcell_person1_P1902_1305


title: Tcell_person1_P1902_1299


title: Tcell_person1_P1902_1297


title: Tcell_person1_P1902_1291


title: Tcell_person1_P1902_1331


title: Tcell_person1_P1902_1660


title: Tcell_person1_P1902_1665


title: Tcell_person1_P1902_1658


title: Tcell_person1_P1902_1651


title: Tcell_person1_P1902_1652


title: Tcell_person1_P1902_1649


title: Tcell_person1_P1902_1346


title: Tcell_person1_P1902_1330


title: Tcell_person1_P1902_1329


title: Tcell_person1_P1902_1642


title: Tcell_person1_P1902_1657


title: Tcell_person1_P1902_1644


title: Tcell_person1_P1902_1643


title: Tcell_person1_P1902_1635


title: Tcell_person1_P1902_1636


title: Tcell_person1_P1902_1634


title: Tcell_person1_P1902_1641


title: Tcell_person1_P1902_1650


title: Tcell_person1_P1902_1306


title: Tcell_person1_P1902_1659


title: Tcell_person1_P1902_1633


title: Tcell_person1_P1902_1290


title: Tcell_person1_P1902_1628


title: Tcell_person1_P1902_1625


title: Tcell_person1_P1902_1627


title: Tcell_person1_P1902_1620


title: Tcell_person1_P1902_1626


title: Tcell_person1_P1902_1619


title: Tcell_person1_P1902_1618


title: Tcell_person1_P1902_1617


title: Tcell_person1_P1902_1612


title: Tcell_person1_P1902_1610


title: Tcell_person1_P1902_1604


title: Tcell_person1_P1902_1603


title: Tcell_person1_P1902_1601


title: Tcell_person1_P1902_1596


title: Tcell_person1_P1902_1595


title: Tcell_person1_P1902_1593


title: Tcell_person1_P1902_1594


title: Tcell_person1_P1902_1602


title: Tcell_person1_P1902_1587


title: Tcell_person1_P1902_1585


title: Tcell_person1_P1902_1580


title: Tcell_person1_P1902_1579


title: Tcell_person1_P1902_1578


title: Tcell_person1_P1902_1577


title: Tcell_person1_P1902_1588


title: Tcell_person1_P1902_1586


title: Tcell_person1_P1902_1414


title: Tcell_person1_P1902_1416


title: Tcell_person1_P1902_1411


title: Tcell_person1_P1902_1413


title: Tcell_person1_P1902_1415


title: Tcell_person1_P1902_1611


title: Tcell_person1_P1902_1609


title: Tcell_person1_P1902_1410


title: Tcell_person1_P1902_1406


title: Tcell_person1_P1902_1402


title: Tcell_person1_P1902_1403


title: Tcell_person1_P1902_1407


title: Tcell_person1_P1902_1404


title: Tcell_person1_P1902_1399


title: Tcell_person1_P1902_1398


title: Tcell_person1_P1902_1401


title: Tcell_person1_P1902_1397


title: Tcell_person1_P1902_1396


title: Tcell_person1_P1902_1390


title: Tcell_person1_P1902_1394


title: Tcell_person1_P1902_1395


title: Tcell_person1_P1902_1391


title: Tcell_person1_P1902_1412


title: Tcell_person1_P1902_1387


title: Tcell_person1_P1902_1409


title: Tcell_person1_P1902_1386


title: Tcell_person1_P1902_1385


title: Tcell_person1_P1902_1388


title: Tcell_person1_P1902_1405


title: Tcell_person1_P1902_1389


title: Tcell_person1_P1902_1374


title: Tcell_person1_P1902_1375


title: Tcell_person1_P1902_1368


title: Tcell_person1_P1902_1373


title: Tcell_person1_P1902_1381


title: Tcell_person1_P1902_1367


title: Tcell_person1_P1902_1366


title: Tcell_person1_P1902_1359


title: Tcell_person1_P1902_1358


title: Tcell_person1_P1902_1365


title: Tcell_person1_P1902_1351


title: Tcell_person1_P1902_1352


title: Tcell_person1_P1902_1357


title: Tcell_person1_P1902_1393


title: Tcell_person1_P1902_1350


title: Tcell_person1_P1902_1349


title: Tcell_person1_P1902_1341


title: Tcell_person1_P1902_1344


title: Tcell_person1_P1902_1343


title: Tcell_person1_P1902_1342


title: Tcell_person1_P1902_1336


title: Tcell_person1_P1902_1376


title: Tcell_person1_P1902_1334


title: Tcell_person1_P1902_1335


title: Tcell_person1_P1902_1360


title: Tcell_person1_P1902_1325


title: Tcell_person1_P1902_1319


title: Tcell_person1_P1902_1333


title: Tcell_person1_P1902_1312


title: Tcell_person1_P1902_1318


title: Tcell_person1_P1902_1326


title: Tcell_person1_P1902_1320


title: Tcell_person1_P1902_1303


title: Tcell_person1_P1902_1327


title: Tcell_person1_P1902_1296


title: Tcell_person1_P1902_1304


title: Tcell_person1_P1902_1295


title: Tcell_person1_P1902_1294


title: Tcell_person1_P1299_2152

value: in vivo single Tcell


title: Tcell_person1_P1902_1293


title: Tcell_person1_P1299_2150


title: Tcell_person1_P1299_2149


title: Tcell_person1_P1299_2146


title: Tcell_person1_P1299_2142


title: Tcell_person1_P1299_2138


title: Tcell_person1_P1299_2133


title: Tcell_person1_P1299_2135


title: Tcell_person1_P1902_1328


title: Tcell_person1_P1299_2129


title: Tcell_person1_P1299_2121


title: Tcell_person1_P1299_2114


title: Tcell_person1_P1299_2111


title: Tcell_person1_P1902_1311


title: Tcell_person1_P1299_2103


title: Tcell_person1_P1299_2102


title: Tcell_person1_P1299_2096


title: Tcell_person1_P1299_2088


title: Tcell_person1_P1299_2086


title: Tcell_person1_P1299_2081


title: Tcell_person1_P1902_1302


title: Tcell_person1_P1299_2099


title: Tcell_person1_P1299_2090


title: Tcell_person1_P1299_2087


title: Tcell_person1_P1299_2070


title: Tcell_person1_P1299_2082


title: Tcell_person1_P1299_2064


title: Tcell_person1_P1299_2061


title: Tcell_person1_P1299_2065


title: Tcell_person1_P1299_2080


title: Tcell_person1_P1299_2058


title: Tcell_person1_P1299_2057


title: Tcell_person1_P1299_2040


title: Tcell_person1_P1299_2042


title: Tcell_person1_P1299_2037


title: Tcell_person1_P1299_2033


title: Tcell_person1_P1299_2035


title: Tcell_person1_P1299_2011


title: Tcell_person1_P1299_2018


title: Tcell_person1_P1299_2016


title: Tcell_person1_P1299_2027


title: Tcell_person1_P1299_2032


title: Tcell_person1_P1299_2010


title: Tcell_person1_P1299_2015


title: Tcell_person1_P1299_1958


title: Tcell_person1_P1299_2005


title: Tcell_person1_P1299_1960


title: Tcell_person1_P1299_2003


title: Tcell_person1_P1299_2059


title: Tcell_person1_P1299_1956


title: Tcell_person1_P1299_1950


title: Tcell_person1_P1299_1955


title: Tcell_person1_P1299_2045


title: Tcell_person1_P1299_1948


title: Tcell_person1_P1299_1953


title: Tcell_person1_P1299_1944


title: Tcell_person1_P1299_2053


title: Tcell_person1_P1299_1946


title: Tcell_person1_P1299_1945


title: Tcell_person1_P1299_2023


title: Tcell_person1_P1299_1937


title: Tcell_person1_P1299_1932


title: Tcell_person1_P1299_1939


title: Tcell_person1_P1299_1931


title: Tcell_person1_P1299_2013


title: Tcell_person1_P1299_1930


title: Tcell_person1_P1299_1927


title: Tcell_person1_P1299_1926


title: Tcell_person1_P1299_1912


title: Tcell_person1_P1299_1929


title: Tcell_person1_P1299_1916


title: Tcell_person1_P1299_1915


title: Tcell_person1_P1299_1905


title: Tcell_person1_P1299_1911


title: Tcell_person1_P1299_1899


title: Tcell_person1_P1299_1893


title: Tcell_person1_P1299_1880


title: Tcell_person1_P1299_1900


title: Tcell_person1_P1299_1933


title: Tcell_person1_P1299_1891


title: Tcell_person1_P1299_1872


title: Tcell_person1_P1299_1866


title: Tcell_person1_P1299_1865


title: Tcell_person1_P1299_1874


title: Tcell_person1_P1299_1864


title: Tcell_person1_P1299_1863


title: Tcell_person1_P1299_1848


title: Tcell_person1_P1299_1851


title: Tcell_person1_P1299_1858


title: Tcell_person1_P1299_1837


title: Tcell_person1_P1299_1860


title: Tcell_person1_P1299_1854


title: Tcell_person1_P1299_1823


title: Tcell_person1_P1299_1909


title: Tcell_person1_P1299_1821


title: Tcell_person1_P1299_1895


title: Tcell_person1_P1299_1807


title: Tcell_person1_P1299_1816


title: Tcell_person1_P1299_1820


title: Tcell_person1_P1299_1806


title: Tcell_person1_P1299_1814


title: Tcell_person1_P1299_1804


title: Tcell_person1_P1299_1805


title: Tcell_person1_P1299_2002


title: Tcell_person1_P1299_1799


title: Tcell_person1_P1299_1793


title: Tcell_person1_P1299_1792


title: Tcell_person1_P1299_1791


title: Tcell_person1_P1299_1779


title: Tcell_person1_P1299_1786


title: Tcell_person1_P1299_1777


title: Tcell_person1_P1299_1801


title: Tcell_person1_P1299_1798


title: Tcell_person1_P1299_1783


title: WT2

city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

country: France

institute: CNRS-AMU

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component..
Demultiplexing was performed using CASAVA 1.8.2 (Illumina).
Alignment was performed with TopHat 2.0.9 (with bowtie 2.1.0) to the mm10 version of the Mus muculus genome. The transcript annotation was retrieved from UCSC on March 6, 2013.
Counting of reads aligned to a gene was performed with HTSeq-count 0.5.3p9.
Genome_build: Mus musculus 10 (mm10)
Supplementary_files_format_and_content: Excel file with a first column for gene identification. The next columns correspond to the raw counts (non-normalized) for each sample.

organism: Mus musculus

source_name: mouse cortex

extract_protocol:
1 µg of total RNA from wild-type and Tshz3 mutant neocortex at E18.5 was prepared using Rneasy Plus Universal Mini Kit gDNA eliminator (Qiagen ™).   Three independent replicates, each containing cortices from 3-4 embryos from multiple litters, were prepared from wild-type and Tshz3 mutant neocortex at E18.5.
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

tag: developmental stage

value: embryonic stage 18.5

tag: tissue

value: cortex

tag: genotype

value: wild type


title: WT3


title: KO1

value: Tshz3 mutant


title: KO3


title: Tcell_person1_P1299_1775


title: Tcell_person1_P1299_1785


title: fibroblast.342

data_processing:
Aligned reads with rna-star
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text

source_name: Single fibroblast

value: single fibroblast

tag: strain

value: female


title: Tcell_person1_P1299_1774


title: Tcell_person1_P1299_1773


title: Tcell_person1_P1299_1771


title: fibroblast.341


title: fibroblast.338


title: Tcell_person1_P1299_1480


title: fibroblast.339


title: fibroblast.340


title: fibroblast.337


title: Tcell_person1_P1299_1479


title: WT1


title: Tcell_person1_P1299_1477


title: KO2


title: Tcell_person1_P1299_1476


title: Tcell_person1_P1299_1475


title: 3NY, replicate 3

city: Orlando

first: Augusto

last: Schneider

state: FL

address: 6900 Lake Nona Blvd

department: Burnett School of Biomedical Sciences

country: USA

institute: University of Central Florida

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the mRNA transcriptome, defined by a gtf for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
This gtf is supplied as a 'processed data file'.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq Count .txt file

molecule: polyA RNA

source_name: Normal_6 months_Ovary

extract_protocol:
Ovaries were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA was extracted according to Matkovich & Dorn (2015; Gary R. Skuse and Maureen C. Ferran (eds.), Cardiomyocytes: Methods and Protocols, Methods in Molecular Biology, vol. 1299, DOI 10.1007/978-1-4939-2572-8_3) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ames dwarf

tag: genotype/variation

value: Normal (N/df)

value: 6 months old

value: Ovary


title: 21NY, replicate 5


title: 5NY, replicate 4


title: 4NY, replicate 2


title: Tcell_person1_P1299_1463


title: Tcell_person1_P1299_1464


title: 2NY, replicate 1


title: 13NO, replicate 4

source_name: Normal_22 months_Ovary

value: 22 months old


title: Tcell_person1_P1299_1462


title: Tcell_person1_P1299_1461


title: 22NO, replicate 3


title: 15NO, replicate 5


title: 12NO, replicate 1


title: 14NO, replicate 2


title: Tcell_person1_P1299_1458


title: 6YD, replicate 5

source_name: dwarf_6 months_Ovary

value: dwarf (df/df)


title: Tcell_person1_P1299_1455


title: 8YD, replicate 4


title: Tcell_person1_P1299_1454


title: 10YD, replicate 3


title: Tcell_person1_P1299_1452


title: Tcell_person1_P1299_1456


title: Tcell_person1_P1299_1453


title: Tcell_person1_P1299_1472


title: 9YD, replicate 2


title: Tcell_person1_P1299_1450


title: Tcell_person1_P1299_1447


title: Tcell_person1_P1299_1442


title: 23OD, replicate 5

source_name: dwarf_22 months_Ovary


title: 19OD, replicate 4


title: Tcell_person1_P1299_1441


title: 16OD, replicate 3


title: Tcell_person1_P1299_1439


title: Tcell_person1_P1299_1440


title: 20OD, replicate 2


title: 18OD, replicate 1


title: Tcell_person1_P1299_1434


title: hoechst.fibroblast.dia.82

data_processing:
Genome Build: mm9
Aligned reads with rna-star
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track
For the sample Bf37_mRNA_Fibroblast_Total_fraction we also used the  rpkmforgenes.py option -stranded
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text

extract_protocol:
SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)
SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)

tag: cross


title: Tcell_person1_P1299_1435


title: Bf37_mRNA_Fibroblast_Total_fraction

description: Stranded mRNA-sequencing of RNA from primary fibroblast culture using Illumina mRNA Stranded TruSeq

source_name: Fibroblasts


title: Tcell_person1_P1299_1431


title: Tcell_person1_P1299_1432


title: 7YD, replicate 1


title: Tcell_person1_P1299_1430


title: hoechst.fibroblast.dia.78


title: hoechst.fibroblast.dia.81


title: hoechst.fibroblast.dia.77


title: hoechst.fibroblast.dia.75


title: hoechst.fibroblast.dia.79


title: hoechst.fibroblast.dia.76


title: Tcell_person1_P1299_1427


title: Tcell_person1_P1299_1424


title: Tcell_person1_P1299_1423


title: Tcell_person1_P1299_1428


title: hoechst.fibroblast.dia.73


title: Tcell_person1_P1299_1436


title: hoechst.fibroblast.dia.74


title: hoechst.fibroblast.dia.71


title: Tcell_person1_P1299_1419


title: hoechst.fibroblast.dia.70


title: Tcell_person1_P1299_1420


title: hoechst.fibroblast.dia.69


title: Tcell_person1_P1299_1417


title: hoechst.fibroblast.dia.80


title: Tcell_person1_P1299_1418


title: hoechst.fibroblast.dia.68


title: hoechst.fibroblast.dia.66


title: hoechst.fibroblast.dia.67


title: Tcell_person1_P1299_1415


title: hoechst.fibroblast.dia.65


title: hoechst.fibroblast.dia.64


title: Tcell_person1_P1299_1413


title: hoechst.fibroblast.dia.72


title: Tcell_person1_P1299_1421


title: Tcell_person1_P1299_1422


title: Tcell_person1_P1299_1407


title: Tcell_person1_P1299_1410


title: Tcell_person1_P1299_1408


title: hoechst.fibroblast.dia.62


title: Tcell_person1_P1299_1405


title: hoechst.fibroblast.dia.61


title: hoechst.fibroblast.dia.60


title: Tcell_person1_P1299_1406


title: hoechst.fibroblast.dia.59


title: hoechst.fibroblast.dia.58


title: Tcell_person1_P1299_1403


title: Tcell_person1_P1299_1402


title: hoechst.fibroblast.dia.57


title: Tcell_person1_P1299_1416


title: hoechst.fibroblast.dia.56


title: Tcell_person1_P1299_1400


title: hoechst.fibroblast.dia.55


title: Tcell_person1_P1299_1401


title: Tcell_person1_P1299_1414


title: Tcell_person1_P1299_1398


title: hoechst.fibroblast.dia.54


title: Tcell_person1_P1299_1396


title: hoechst.fibroblast.dia.63


title: hoechst.fibroblast.dia.51


title: Tcell_person1_P1299_1395


title: Tcell_person1_P1299_1394


title: Tcell_person1_P1299_1392


title: hoechst.fibroblast.dia.50


title: Tcell_person1_P1299_1388


title: Tcell_person1_P1299_1386


title: hoechst.fibroblast.dia.49


title: hoechst.fibroblast.dia.46


title: Tcell_person1_P1299_1385


title: Tcell_person1_P1299_1384


title: Tcell_person1_P1299_1383


title: Tcell_person1_P1299_1387


title: hoechst.fibroblast.dia.48


title: hoechst.fibroblast.dia.45


title: hoechst.fibroblast.dia.47


title: Tcell_person1_P1299_1381


title: hoechst.fibroblast.dia.44


title: hoechst.fibroblast.dia.43


title: hoechst.fibroblast.dia.42


title: Tcell_person1_P1299_1379


title: Tcell_person1_P1299_1377


title: hoechst.fibroblast.dia.41


title: hoechst.fibroblast.dia.53


title: hoechst.fibroblast.dia.40


title: Tcell_person1_P1299_1373


title: hoechst.fibroblast.dia.39


title: hoechst.fibroblast.dia.37


title: Tcell_person1_P1299_1374


title: Tcell_person1_P1299_1368


title: Tcell_person1_P1299_1369


title: Tcell_person1_P1299_1380


title: Tcell_person1_P1299_1367


title: hoechst.fibroblast.dia.36


title: hoechst.fibroblast.dia.38


title: hoechst.fibroblast.dia.35


title: Tcell_person1_P1299_1363


title: Tcell_person1_P1299_1359


title: Tcell_person1_P1299_1362


title: hoechst.fibroblast.dia.34


title: Tcell_person1_P1299_1358


title: Tcell_person1_P1299_1355


title: hoechst.fibroblast.dia.31


title: hoechst.fibroblast.dia.33


title: hoechst.fibroblast.dia.29


title: hoechst.fibroblast.dia.52


title: hoechst.fibroblast.dia.30


title: Tcell_person1_P1299_1352


title: hoechst.fibroblast.dia.28


title: hoechst.fibroblast.dia.26


title: Tcell_person1_P1299_1354


title: hoechst.fibroblast.dia.27


title: Tcell_person1_P1299_1349


title: hoechst.fibroblast.dia.23


title: Tcell_person1_P1299_1348


title: Tcell_person1_P1299_1346


title: hoechst.fibroblast.dia.24


title: Tcell_person1_P1299_1366


title: hoechst.fibroblast.dia.22


title: Tcell_person1_P1299_1357


title: hoechst.fibroblast.dia.21


title: Tcell_person1_P1299_1341


title: Tcell_person1_P1299_1344


title: hoechst.fibroblast.dia.32


title: Tcell_person1_P1299_1340


title: hoechst.fibroblast.dia.20


title: hoechst.fibroblast.dia.17


title: hoechst.fibroblast.dia.16


title: Tcell_person1_P1299_1339


title: Tcell_person1_P1299_1335


title: hoechst.fibroblast.dia.19


title: hoechst.fibroblast.dia.18


title: hoechst.fibroblast.dia.25


title: hoechst.fibroblast.dia.15


title: Tcell_person1_P1299_1333


title: Tcell_person1_P1299_1331


title: Tcell_person1_P1299_1337


title: hoechst.fibroblast.dia.12


title: hoechst.fibroblast.dia.13


title: hoechst.fibroblast.dia.14


title: Tcell_person1_P1299_1329


title: hoechst.fibroblast.dia.11


title: Tcell_person1_P1299_1326


title: Tcell_person1_P1299_1327


title: Tcell_person1_P1299_1325


title: Tcell_person1_P1299_1323


title: hoechst.fibroblast.dia.8


title: hoechst.fibroblast.dia.9


title: hoechst.fibroblast.dia.10


title: Tcell_person1_P1299_1338


title: Tcell_person1_P1299_1322


title: hoechst.fibroblast.dia.7


title: hoechst.fibroblast.dia.4


title: hoechst.fibroblast.dia.6


title: Tcell_person1_P1299_1317


title: Tcell_person1_P1299_1316


title: Tcell_person1_P1299_1318


title: Tcell_person1_P1299_1330


title: hoechst.fibroblast.dia.3


title: hoechst.fibroblast.dia.5


title: hoechst.fibroblast.dia.2


title: Tcell_person1_P1299_1314


title: Tcell_person1_P1299_1328


title: Tcell_person1_P1299_1311


title: Tcell_person1_P1299_1312


title: Adult HSC_replicate3

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

data_processing:
RNA-Seq: Reads were aligned using Bowtie against the murine transcriptome (mouse NCBI build37 Refseq transcripts)
RNA-Seq: Non-uniquely mapped reads were discarded. Count number of reads for each transcript and reads per kilobase of a transcript per million mapped reads (RPKMs) were calculated and assigned to each transcript.
RNA-Seq: Overlapping Refseq transcripts were collapsed giving the highest one expression value per gene loci.
RNA-Seq: Gene expression levels for Refseq genes were summarized as reads per kilobase of exon model per million mapped reads (RPKM) and read counts using custom R scripts
Genome_build: mm9
Supplementary_files_format_and_content: Read counts and RPKM values from RNA sequencing

source_name: Adult bone marrow

extract_protocol:
cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
For RNA-Seq NEBNext® DNA Library Prep Reagent Set for Illumina®

treatment_protocol: Cell populations isolated by FACS sorting

value: Adult bone marrow

value: C57 BL6, Rag1-GFP reporter mouse

tag: phenotype


title: Adult HSC_replicate2


title: Tcell_person1_P1299_1307

value: adult

value: male


title: Adult HSC_replicate1


title: Tcell_person1_P1299_1310

value: in vivo single Tcell


title: Adult LMPP_replicate2


title: Tcell_person1_P1299_1306


title: Adult LMPP_replicate1


title: Tcell_person1_P1299_1305


title: Tcell_person1_P1299_1319


title: Adult ETP_replicate3

source_name: Adult thymus

value: Adult thymus


title: Tcell_person1_P1299_1300


title: Tcell_person1_P1299_1301


title: Adult ETP_replicate1


title: Tcell_person1_P1299_1302


title: Tcell_person1_P1299_1296


title: hoechst.fibroblast.dia.1


title: Tcell_person1_P1299_1294


title: Neonatal HSC_replicate3

source_name: Neonatal bone marrow

value: Neonatal bone marrow


title: Adult ETP_replicate2


title: Tcell_person1_P1299_1289


title: Neonatal HSC_replicate2


title: Neonatal LMPP_replicate2


title: Neonatal HSC_replicate1


title: Tcell_person1_P1299_1284


title: Neonatal LMPP_replicate1


title: Neonatal ETP_replicate3

source_name: Neonatal thymus

value: Neonatal thymus


title: Neonatal ETP_replicate2


title: Tcell_person1_P1299_1293


title: Tcell_person1_P1299_1283


title: Tcell_person1_P1299_1282


title: E11.5 HSPC_replicate3

source_name: E11.5 Aorta-Gonads_Mesonephros

value: E11.5 Aorta-Gonads_Mesonephros


title: Tcell_person1_P1299_1279


title: Tcell_person1_P1299_1278


title: E11.5 HSPC_replicate2


title: E11.5 HSPC_replicate1


title: E11.5 LMPP_replicate2

source_name: E11.5 Fetal liver

value: E11.5 Fetal liver


title: Tcell_person1_P1299_1291


title: Neonatal LMPP_replicate3


title: E11.5 LMPP_replicate1


title: E11.5 LMPP_replicate3


title: Tcell_person1_P1299_1277


title: E11.5 T-IP_replicate3

source_name: E11.5 Thymus rudiment

value: E11.5 Thymus rudiment


title: Tcell_person1_P1299_1270


title: Tcell_person1_P1299_1271


title: Tcell_person1_P1299_1272


title: E11.5 T-IP_replicate2


title: Tcell_person1_P1299_1275


title: Tcell_person1_P1299_1268


title: Tcell_person1_P1299_1267


title: E11.5 T-IP_replicate1


title: Tcell_person1_P1299_1265


title: Neonatal ETP_replicate1


title: Tcell_person1_P1299_1280


title: Tcell_person1_P1299_1262


title: liver.336

data_processing:
genome build:  mm9
Aligned reads with rna-star
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track
Supplementary_files_format_and_content: Tab-delimited text files report RPKMs and read counts.

value: C57BL/6J (mother) x CAST/EiJ (father)

value: E15 liver cell


title: liver.333


title: liver.335


title: liver.334


title: liver.332


title: Tcell_person1_P1299_1260


title: liver.331


title: liver.330


title: Tcell_person1_P1299_1269


title: liver.327


title: liver.329


title: liver.328


title: Tcell_person1_P1299_1258


title: Tcell_person1_P1299_1257


title: Tcell_person1_P1299_1253


title: liver.324


title: Tcell_person1_P1299_1252


title: Tcell_person1_P1299_1248


title: Tcell_person1_P1299_1254


title: liver.325


title: Tcell_person1_P1299_1250


title: liver.323


title: Tcell_person1_P1299_1259


title: Tcell_person1_P1299_1247


title: Tcell_person1_P1299_1246


title: liver.322


title: liver.321


title: Tcell_person1_P1299_1245


title: Tcell_person1_P1299_1242


title: liver.320


title: Tcell_person1_P1299_1261


title: liver.319


title: liver.318


title: Tcell_person1_P1299_1241


title: Tcell_person1_P1299_1244


title: liver.326


title: liver.317


title: Tcell_person1_P1299_1240


title: liver.314


title: liver.315


title: Tcell_person1_P1299_1234


title: Tcell_person1_P1299_1238


title: Tcell_person1_P1299_1231


title: liver.312


title: Tcell_person1_P1299_1239


title: liver.316


title: Tcell_person1_P1299_1235


title: liver.311


title: Tcell_person1_P1299_1236


title: liver.309


title: Tcell_person1_P1299_1228


title: liver.310


title: liver.308


title: liver.306


title: Tcell_person1_P1299_1226


title: brain.305

value: E15 brain cell


title: brain.304


title: Tcell_person1_P1299_1216


title: Tcell_person1_P1299_1215


title: Tcell_person1_P1299_1225


title: Tcell_person1_P1299_1214


title: liver.307


title: brain.303


title: liver.313


title: brain.302


title: Tcell_person1_P1299_1211


title: Tcell_person1_P1299_1213


title: fibroblast.split.G.301

value: female

value: splitted fibroblast


title: Tcell_person1_P1299_1227


title: Tcell_person1_P1299_1209


title: Tcell_person1_P1299_1208


title: fibroblast.split.F.298


title: fibroblast.split.E.296


title: E13.5 DN2_replicate2

source_name: E13.5 Thymus rudiment

extract_protocol:
cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
For RNA-Seq NEBNext® DNA Library Prep Reagent Set for Illumina®
RNA-Seq samples were sequenced on Illumina HiSeq 4000

value: E13.5 Thymus rudiment


title: fibroblast.split.D.295


title: Tcell_person1_P1299_1207


title: Tcell_person1_P1299_1210


title: fibroblast.split.E.297


title: E13.5 DN2_replicate1


title: E12.5 ETP_replicate3

source_name: E12.5 Thymus rudiment

value: E12.5 Thymus rudiment


title: fibroblast.split.D.294


title: fibroblast.split.C.292


title: E12.5 ETP_replicate2

value: C57 BL6, Rag1-GFP reporter mouse


title: fibroblast.split.C.293

value: adult


title: fibroblast.split.B.290


title: Tcell_person1_P1299_1204

value: male


title: fibroblast.split.B.291


title: fibroblast.split.A.289


title: Tcell_person1_P1299_1205

value: in vivo single Tcell


title: E13.5 DN2_replicate3


title: fibroblast.split.A.288


title: fibroblast.split.F.299


title: Tcell_person1_P1299_1206


title: Tcell_person1_P1299_1203


title: fibroblast.split.P.287

value: CAST/EiJ (mother) x C57BL/6J (father)


title: E11.5 T-IP_replicate3_NewSeq


title: fibroblast.split.P.286


title: E11.5 T-IP_replicate2_NewSeq


title: fibroblast.split.O.285


title: Tcell_person1_P1299_1201


title: fibroblast.split.L.283


title: fibroblast.split.L.282


title: E11.5 T-IP_replicate1_NewSeq


title: Tcell_person1_P1299_1200


title: fibroblast.split.O.284


title: fibroblast.split.K.280


title: Tcell_person1_P1299_1199


title: E12.5 ETP_replicate1


title: fibroblast.split.J.279


title: Tcell_person1_P1299_1197


title: fibroblast.split.J.278


title: Tcell_person1_P1299_1196


title: fibroblast.split.I.276


title: fibroblast.split.T.274


title: Tcell_person1_P1299_1194


title: fibroblast.split.G.300


title: Tcell_person1_P1299_1202


title: fibroblast.split.Q.271


title: Tcell_person1_P1299_1192


title: fibroblast.split.S.272


title: fibroblast.split.Q.270


title: Tcell_person1_P1299_1191


title: fibroblast.269

value: CAST/EiJ x C57BL/6J or C57BL/6J x CAST/EiJ


title: Tcell_person1_P1299_1190


title: fibroblast.267

value: single fibroblast


title: Tcell_person1_P1299_1189


title: fibroblast.265


title: fibroblast.split.K.281


title: Tcell_person1_P1299_1187


title: fibroblast.263


title: fibroblast.262


title: fibroblast.split.T.275


title: fibroblast.261


title: fibroblast.split.I.277


title: fibroblast.264


title: fibroblast.260


title: Tcell_person1_P1299_1185


title: Tcell_person1_P1299_1186


title: fibroblast.258


title: fibroblast.259


title: fibroblast.257


title: fibroblast.split.S.273


title: fibroblast.256


title: Tcell_person1_P1299_1179


title: fibroblast.253


title: fibroblast.255


title: Tcell_person1_P1299_1181


title: fibroblast.268


title: fibroblast.252


title: fibroblast.266


title: Tcell_person1_P1299_1177


title: fibroblast.251


title: fibroblast.250


title: fibroblast.249


title: Tcell_person1_P1299_1176


title: Tcell_person1_P1299_1175


title: fibroblast.246


title: fibroblast.244


title: fibroblast.247


title: Tcell_person1_P1299_1174


title: fibroblast.248


title: Tcell_person1_P1299_1173


title: fibroblast.242


title: Tcell_person1_P1299_1171


title: Tcell_person1_P1299_1182


title: fibroblast.245


title: fibroblast.254


title: fibroblast.239


title: fibroblast.240


title: fibroblast.238


title: Tcell_person1_P1299_1170


title: fibroblast.241


title: fibroblast.237


title: Tcell_person1_P1299_1169


title: Tcell_person1_P1299_1167


title: fibroblast.235


title: fibroblast.236


title: Tcell_person1_P1299_1166


title: fibroblast.234


title: fibroblast.233


title: fibroblast.232


title: fibroblast.243


title: fibroblast.230


title: fibroblast.227


title: Tcell_person1_P1299_1155


title: fibroblast.228


title: fibroblast.231


title: Tcell_person1_P1299_1158


title: Tcell_person1_P1299_1159


title: fibroblast.226


title: fibroblast.229


title: Tcell_person1_P1299_1154


title: fibroblast.224


title: Tcell_person1_P1299_1153


title: fibroblast.220


title: fibroblast.222


title: Tcell_person1_P1299_1152


title: fibroblast.225


title: fibroblast.221


title: Tcell_person1_P1299_1149


title: fibroblast.218


title: fibroblast.216


title: Tcell_person1_P1299_1147


title: fibroblast.219


title: fibroblast.217


title: fibroblast.215


title: Tcell_person1_P1299_1162


title: Tcell_person1_P1299_1146


title: fibroblast.213


title: fibroblast.212


title: fibroblast.223


title: fibroblast.211


title: Tcell_person1_P1299_1145


title: Tcell_person1_P1299_1144


title: Tcell_person1_P1299_1143


title: fibroblast.210


title: fibroblast.206


title: fibroblast.208


title: fibroblast.207


title: Tcell_person1_P1299_1141


title: fibroblast.205


title: fibroblast.204


title: fibroblast.203


title: Tcell_person1_P1299_1136


title: fibroblast.201


title: Tcell_person1_P1299_1134


title: fibroblast.198


title: fibroblast.199


title: fibroblast.214


title: fibroblast.200


title: Tcell_person1_P1299_1135


title: fibroblast.196


title: Tcell_person1_P1299_1133


title: fibroblast.197


title: fibroblast.194


title: Tcell_person1_P1299_1130


title: fibroblast.209


title: fibroblast.195


title: Tcell_person1_P1299_1129


title: fibroblast.193


title: fibroblast.192


title: fibroblast.191


title: fibroblast.189


title: fibroblast.202


title: fibroblast.190


title: fibroblast.188


title: Tcell_person1_P1299_1121


title: Tcell_person1_P1299_1126


title: Tcell_person1_P1299_1118


title: fibroblast.187


title: fibroblast.186


title: fibroblast.183


title: Tcell_person1_P1299_1115


title: fibroblast.185


title: fibroblast.181


title: fibroblast.180


title: fibroblast.178


title: fibroblast.179


title: fibroblast.177


title: Tcell_person1_P1299_1113


title: fibroblast.176


title: Tcell_person1_P1299_1125


title: Tcell_person1_P1299_1108


title: Tcell_person1_P1299_1107


title: fibroblast.175


title: fibroblast.173


title: Tcell_person1_P1299_1104


title: fibroblast.171


title: fibroblast.184


title: fibroblast.174


title: fibroblast.169


title: fibroblast.182


title: Tcell_person1_P1299_1117


title: fibroblast.172


title: Tcell_person1_P1299_1103


title: Tcell_person1_P1299_1114


title: Tcell_person1_P1299_1101


title: fibroblast.170


title: fibroblast.166


title: fibroblast.167


title: fibroblast.165


title: fibroblast.162


title: fibroblast.168


title: Tcell_person1_P1299_1102


title: fibroblast.164


title: Tcell_person1_P1299_1099


title: fibroblast.161


title: fibroblast.160


title: Tcell_person1_P1299_1097


title: fibroblast.163


title: fibroblast.159


title: fibroblast.157


title: fibroblast.156


title: fibroblast.158


title: Tcell_person1_P1299_2153


title: Tcell_person1_P1299_1098


title: Tcell_person1_P1299_2143


title: fibroblast.153


title: fibroblast.154


title: fibroblast.155


title: Tcell_person1_P1299_2130


title: Tcell_person1_P1299_2127


title: fibroblast.149


title: Tcell_person1_P1299_2112


title: fibroblast.150


title: fibroblast.146


title: fibroblast.151


title: fibroblast.152


title: fibroblast.143


title: fibroblast.147


title: fibroblast.144


title: fibroblast.141


title: Tcell_person1_P1299_2105


title: Tcell_person1_P1299_2095


title: fibroblast.140


title: Tcell_person1_P1299_2145


title: Tcell_person1_P1299_2089


title: fibroblast.139


title: Tcell_person1_P1299_2085


title: fibroblast.138


title: WT rep2 T8h

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
cleaning with clean_ngs (v 0.7)
alignment with tophat (v 1.4.1)
counting with htseq-count (v 0.1)
Genome_build: Aspergillus fumigatus A1163
Supplementary_files_format_and_content: Htseq-count file; txt file with name of gene and corresponding counting

organism: Aspergillus fumigatus

source_name: Glucose (3%) + Yeast Extract (1%) medium

growth_protocol: Parental strain conidia (10^8) were inoculated in Glucose (3%) + Yeast Extract (1%) at 37°C for 4 or 8 h at 150 rpm.

extract_protocol:
For RNAseq analysis, we used 2 to 5 μg of total RNA to purify polyadenylated mRNAs and construct the sequencing libraries using the TruSeq RNA Sample Prep Kit v2
Non-directional libraries were prepared using the TruSeq RNA Sample preparation kit v2 following the manufacturer’s instructions (Illumina). The nondirectional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies). 50-bp Single Read sequences were generated on the Hiseq2000 sequencer according to manufacturer’s instructions (Illumina). Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1.7) giving FASTQ formatted reads.

treatment_protocol: Dormant (0h), swollen (4h) and germinated (8h) conidia thus obtained were disrupted with 0.5 mm diameter glass beads in a volume of 500 µl and then RNA was isolated using the QIAGEN RNA/DNA kit.

value: Germinated conidia T8h


title: WT rep3 T8h


title: fibroblast.148


title: fibroblast.137


title: fibroblast.135


title: Tcell_person1_P1299_2074


title: Tcell_person1_P1299_2109


title: fibroblast.136


title: fibroblast.145


title: Tcell_person1_P1299_2071


title: WT rep3 T4h

value: Swollen conidia T4h


title: Tcell_person1_P1299_2069


title: WT rep1 T4h


title: WT rep2 T4h


title: fibroblast.130


title: fibroblast.132


title: Tcell_person1_P1299_2004


title: WT rep1 T8h


title: WT rep3 T0

source_name: Malt agar medium

value: dormant conidia T0


title: fibroblast.142

value: C57BL/6J (mother) x CAST/EiJ (father)


title: fibroblast.129


title: Tcell_person1_P1299_1943


title: fibroblast.128


title: fibroblast.131


title: fibroblast.127


title: fibroblast.126


title: WT rep2 T0


title: fibroblast.134


title: fibroblast.125


title: Tcell_person1_P1299_1833


title: Tcell_person1_P1299_1855


title: fibroblast.124


title: WT rep1 T0


title: fibroblast.133


title: fibroblast.123.cl7_5.pooled.cells


title: Tcell_person1_P1299_1782


title: fibroblast.121.cl7_15.pooled.cells

value: 5pooled fibroblasts


title: L. major H3VKO

city: Athens

first: David

last: Reynolds

state: Georgia

address: 120 E Green St

department: Biochemistry and Molecular Biology

institute: University of Georgia

description: Small RNAs

data_processing:
Sequenced reads were mapped using Bowtie2 version 2.2.3 with local sensitive mode, all other parameters default
Reads were further processed using Samtools 1.2. Reads shorter than 18bp were discarded before mapping
Genome_build: Leishmania major Friedlin (v4.2 from TriTrypDB.org) [http://tritrypdb.org/common/downloads/release-4.2/Lmajor/fasta/LmajorFriedlinGenomic_TriTrypDB-4.2.fasta]
Supplementary_files_format_and_content: wig format containing RPM calculated using a window size of 101bp and a step size of 101bp

organism: Leishmania major

source_name: H3V KO parasite

growth_protocol: Leishmania major Friedlin strain promastigotes were grown at 26°C in M199 media supplemented with 10% FBS, as described by Kapler et al., 1990

extract_protocol:
Small RNA was isolated from log phase Leishmania major cultures using the Qiagen miRNeasy kit, according to the manufacturer’s instructions. 5x107 cells were used for each prep.
Small RNA-seq libraries were constructed by Vertis Biotechnology AG, Germany. Approximately 250ng of small RNA was poly A-tailed using poly A polymerase. The 5' triphosphate and cap structures were removed using tobacco acid pyrophosphatase. An RNA adapter was ligated to the 5' monophosphate. First strand cDNA synthesis was performed using an oligo dT adapter primer and the M-MLV reverse transcriptase. cDNAs were then PCR amplified to about 10-20 ng/uL using high fidelity DNA polymerase and purified using the Agencourt AMPure XP kit.

treatment_protocol: DMOG treatment of H3.V knockout cells was performed by supplementing media with 5mM DMOG for 10 days. Control cells were treated with equal concentrations of vehicle (DMSO)

value: Friedlin

tag: lifestage

value: promastigote form

value: H3V KO

tag: treatment

value: vehicle (DMSO)

tag: sample

value: small RNA


title: fibroblast.120.cl7

value: female

value: 15pooled fibroblasts


title: Tcell_person1_P1299_1780

value: adult

value: male


title: fibroblast.119.cl7

value: CAST/EiJ (mother) x C57BL/6J (father)


title: fibroblast.118.cl7


title: L. major H3VKO DMOG

description: Small RNAs

source_name: H3V KO parasite, DMOG

value: dimethyloxalylglycine (DMOG)


title: fibroblast.114.cl7

value: single fibroblast


title: Tcell_person1_P1299_2098

value: in vivo single Tcell


title: fibroblast.117.cl7


title: Tcell_person1_P1299_2122


title: fibroblast.115.cl7


title: fibroblast.116.cl7


title: Tcell_person1_P1299_2093


title: Tcell_person1_P1299_2075


title: fibroblast.113.cl7


title: fibroblast.110.cl7


title: Tcell_person1_P1299_2067


title: fibroblast.112.cl7


title: fibroblast.109.cl7


title: fibroblast.107.cl7


title: fibroblast.108.cl7


title: fibroblast.106.cl7


title: Tcell_person1_P1299_2039


title: Tcell_person1_P1299_2051


title: fibroblast.105.cl7


title: fibroblast.104.cl7


title: Tcell_person1_P1299_2036


title: fibroblast.103.cl7


title: Tcell_person1_P1299_2025


title: Tcell_person1_P1299_1910


title: fibroblast.101.cl7


title: fibroblast.97.cl7


title: fibroblast.99.cl7


title: Tcell_person1_P1299_2008


title: fibroblast.98.cl7


title: Tcell_person1_P1299_1827


title: fibroblast.96.cl7


title: fibroblast.100.cl7


title: fibroblast.111.cl7


title: fibroblast.94.cl7


title: fibroblast.95.cl7


title: Tcell_person1_P1299_1813


title: fibroblast.92.cl7


title: fibroblast.93.cl7


title: Tcell_person1_P1299_1812


title: fibroblast.91.cl7


title: Tcell_person1_P1299_2154


title: fibroblast.90.cl7


title: Patient 69, pre-treatment

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 69, pre-treatment
SL-62

data_processing:
Demultiplexing and creation of FASTQ files were performed using Illumina CASAVA (v1.8.2), trimming off the last base of each read.
Alignment and gene-level counts were generated using RSEM (v1.2.10) and Ensembl v74 annotation.
Genes were filtered out based on a modified version of the mixture model in the SCAN.UPC package; a gene was included in downstream analyses if the mixture model classified it as "signal" in at least 15% of the samples.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] RSEM-generated gene counts

source_name: Cytologically normal bronchial airway epithelial cells

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (QIAgen).
Sequencing libraries were prepared using the Illumina® TruSeq® RNA Kit v2.
The libraries were multiplexed in groups of six using the Illumina® TruSeq® Paired-End Cluster Kit. Each sample was sequenced on an Illumina® HiSeq® 2500 to generate paired-end 100-nucleotide reads.

tag: disease state

value: bronchial dysplasia

tag: patient id

tag: timepoint

value: Pre

tag: arm

value: Placebo

tag: response

value: Stable Disease


title: Patient 68, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 68, post-treatment
SL2-61

value: Post

value: Myo-Inositol

value: Complete Response

value: Cytologically normal bronchial airway epithelial cells


title: Patient 69, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 69, post-treatment
SL2-62


title: fibroblast.102.cl7

tag: age

tag: Sex


title: fibroblast.122.cl7_5.pooled.cells

tag: cell type

value: 5pooled fibroblasts


title: fibroblast.88.cl7

value: female


title: Tcell_person1_P1299_2144


title: Patient 68, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 68, pre-treatment
SL-61


title: fibroblast.87.cl7


title: fibroblast.86.cl7


title: Patient 67, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 67, post-treatment
SL2-60


title: fibroblast.82.cl7


title: fibroblast.85.cl7


title: fibroblast.84.cl7


title: fibroblast.83.cl7


title: fibroblast.80.cl7


title: Tcell_person1_P1299_2113


title: Tcell_person1_P1299_2120


title: fibroblast.81.cl7


title: Tcell_person1_P1299_2117


title: Patient 66, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 66, post-treatment
SL2-59


title: Tcell_person1_P1299_2041


title: fibroblast.89.cl7


title: Tcell_person1_P1299_2030


title: fibroblast.78.cl7


title: fibroblast.77.cl7


title: Patient 66, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 66, pre-treatment
SL-59


title: fibroblast.75.cl7


title: Tcell_person1_P1299_1954


title: fibroblast.76.cl7


title: fibroblast.74.cl7


title: Tcell_person1_P1299_1876


title: Patient 65, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 65, pre-treatment
SL-58


title: Patient 64, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 64, post-treatment
SL2-57


title: Patient 65, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 65, post-treatment
SL2-58


title: fibroblast.72.cl7


title: Patient 67, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 67, pre-treatment
SL-60


title: Tcell_person1_P1299_1835


title: fibroblast.73.cl7


title: fibroblast.68.cl7


title: fibroblast.67.cl7


title: fibroblast.79.cl7


title: fibroblast.69.cl7


title: Patient 63, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 63, post-treatment
SL2-56

value: Progressive Disease


title: Tcell_person1_P1299_1875

value: adult


title: fibroblast.66.cl7


title: Tcell_person1_P1299_2034

value: male


title: fibroblast.65.cl7

value: CAST/EiJ (mother) x C57BL/6J (father)


title: fibroblast.64.cl7


title: Patient 62, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 62, post-treatment
SL2-55


title: Tcell_person1_P1299_2029


title: fibroblast.62.cl7


title: fibroblast.63.cl7


title: Tcell_person1_P1299_2026


title: Patient 61, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 61, post-treatment
SL2-54


title: fibroblast.61.cl7


title: Tcell_person1_P1299_2019


title: fibroblast.60.cl6

value: C57BL/6J (mother) x CAST/EiJ (father)


title: Patient 64, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 64, pre-treatment
SL-57


title: Tcell_person1_P1299_1822


title: Patient 61, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 61, pre-treatment
SL-54


title: Patient 63, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 63, pre-treatment
SL-56


title: fibroblast.59.cl6

value: single fibroblast


title: Tcell_person1_P1299_1938

value: in vivo single Tcell


title: fibroblast.58.cl6


title: fibroblast.57.cl6


title: Tcell_person1_P1299_1919


title: fibroblast.71.cl7


title: Patient 60, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 60, pre-treatment
SL-53

value: bronchial dysplasia


title: fibroblast.55.cl6


title: fibroblast.56.cl6


title: Patient 62, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 62, pre-treatment
SL-55

value: Pre


title: fibroblast.54.cl6


title: fibroblast.53.cl6


title: Patient 59, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 59, post-treatment
SL2-52

value: Placebo


title: fibroblast.52.cl6


title: Tcell_person1_P1299_1868


title: fibroblast.51.cl6


title: Tcell_person1_P1299_1862


title: fibroblast.50.cl6


title: Patient 58, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 58, post-treatment
SL2-51


title: fibroblast.49.cl6


title: fibroblast.48.cl6


title: Tcell_person1_P1299_1790


title: Patient 60, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 60, post-treatment
SL2-53


title: Tcell_person1_P1299_1784


title: fibroblast.47.cl6


title: fibroblast.46.cl6


title: Patient 57, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 57, post-treatment
SL2-50

value: Partial Response


title: Patient 58, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 58, pre-treatment
SL-51


title: fibroblast.45.cl6


title: fibroblast.44.cl6


title: Tcell_person1_P1299_1907


title: Tcell_person1_P1299_1459


title: Tcell_person1_P1299_1393


title: fibroblast.41.cl6


title: Patient 56, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 56, post-treatment
SL2-49

value: Post


title: fibroblast.43.cl6


title: fibroblast.40.cl6


title: Patient 57, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 57, pre-treatment
SL-50

value: Myo-Inositol


title: Patient 59, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 59, pre-treatment
SL-52


title: fibroblast.70.cl7


title: Tcell_person1_P1299_1332


title: fibroblast.39.cl6


title: fibroblast.38.cl6


title: Tcell_person1_P1299_1308


title: Patient 56, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 56, pre-treatment
SL-49


title: Patient 55, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 55, post-treatment
SL2-48


title: Patient 55, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 55, pre-treatment
SL-48


title: fibroblast.36.cl6


title: fibroblast.34.cl6


title: Tcell_person1_P1299_1266


title: fibroblast.35.cl6


title: Tcell_person1_P1299_1229


title: fibroblast.33.cl6


title: Tcell_person1_P1299_1249


title: Patient 54, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 54, post-treatment
SL2-47


title: fibroblast.31.cl6


title: fibroblast.42.cl6


title: Patient 54, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 54, pre-treatment
SL-47


title: fibroblast.32.cl6


title: fibroblast.30.cl6


title: fibroblast.29.cl6


title: Patient 53, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 53, post-treatment
SL2-46


title: Tcell_person1_P1299_1224


title: Patient 53, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 53, pre-treatment
SL-46


title: fibroblast.28.cl6


title: fibroblast.27.cl6


title: fibroblast.37.cl6


title: fibroblast.26.cl6


title: fibroblast.24.cl6


title: Patient 52, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 52, post-treatment
SL2-45


title: Tcell_person1_P1299_1178


title: fibroblast.23.cl6


title: Tcell_person1_P1299_2126


title: Tcell_person1_P1299_1119


title: Patient 52, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 52, pre-treatment
SL-45


title: fibroblast.22.cl5


title: Tcell_person1_P1299_2125


title: fibroblast.21.cl5


title: Patient 51, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 51, post-treatment
SL2-44


title: Patient 51, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 51, pre-treatment
SL-44


title: fibroblast.20.cl5


title: Patient 50, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 50, post-treatment
SL2-43


title: fibroblast.17.cl5


title: fibroblast.18.cl5


title: fibroblast.25.cl6


title: fibroblast.19.cl5


title: Tcell_person1_P1299_2110


title: Tcell_person1_P1299_2104


title: Patient 50, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 50, pre-treatment
SL-43


title: fibroblast.13.cl4


title: Patient 49, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 49, post-treatment
SL2-42


title: fibroblast.15.cl5


title: fibroblast.14.cl4


title: Tcell_person1_P1299_2077


title: fibroblast.12.cl4


title: Tcell_person1_P1299_2063


title: Patient 49, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 49, pre-treatment
SL-42


title: fibroblast.10.cl3


title: fibroblast.9.cl3


title: fibroblast.11.cl3


title: Patient 48, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 48, post-treatment
SL2-41


title: Patient 48, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 48, pre-treatment
SL-41


title: Tcell_person1_P1299_2106


title: fibroblast.8.cl3


title: fibroblast.16.cl5


title: Tcell_person1_P1299_1873


title: fibroblast.7.cl2


title: fibroblast.6.cl2


title: Tcell_person1_P1299_1769


title: fibroblast.5.cl2


title: Patient 47, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 47, post-treatment
SL2-40


title: fibroblast.4.cl2


title: fibroblast.3.cl1


title: Patient 47, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 47, pre-treatment
SL-40


title: fibroblast.1.cl1


title: fibroblast.2.cl1


title: Patient 46, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 46, post-treatment
SL2-39


title: Tcell_person1_P1299_1941


title: Tcell_person1_P1299_1925


title: Patient 46, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 46, pre-treatment
SL-39


title: Tcell_person1_P1299_1890


title: Patient 45, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 45, post-treatment
SL2-38

value: Stable Disease


title: GRS-9

city: Turku

first: Riikka

last: Lund

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology, University of Turku

data_processing:
Sequenced reads were mapped to the hg19 genome reference using bowtie allowing for a maximum two mismatches in the seed region (length of 17nt) and discarding reads that map to more than five genomic locations.
The alignments were then used as input to miRDeep2 to generate the coverage for mature microRNAs. Default parameter values were used.
In cases where a mature microRNA corresponded with multiple precursor microRNAs, only the counts from the precursor microRNA with the highest number of mapped reads were included
Reads per million microRNAs mapped (rpm) were obtained and averaged for the three samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing rpm values for each sample

source_name: hESC

growth_protocol: Cells are grown in matrigel with mTeser

extract_protocol: RNA is extracted with TRI-reagent.

tag: cell line


title: Tcell_person1_P1299_1902


title: Tcell_person1_P1299_1883


title: Patient 45, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 45, pre-treatment
SL-38

value: Cytologically normal bronchial airway epithelial cells


title: Patient 44, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 44, post-treatment
SL2-37


title: Patient 43, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 43, post-treatment
SL2-36


title: Tcell_person1_P1299_1846


title: Patient 43, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 43, pre-treatment
SL-36


title: Tcell_person1_P1299_1852


title: Patient 44, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 44, pre-treatment
SL-37


title: Tcell_person1_P1299_1898


title: Tcell_person1_P1299_1789


title: Patient 42, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 42, pre-treatment
SL-35


title: Tcell_person1_P1299_2024


title: Tcell_person1_P1299_2007


title: Patient 42, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 42, post-treatment
SL2-35


title: Tcell_person1_P1299_1952


title: Tcell_person1_P1299_1947


title: Patient 41, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 41, post-treatment
SL2-34


title: GRS-13


title: GRS-11


title: Patient 41, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 41, pre-treatment
SL-34


title: Tcell_person1_P1299_1903


title: Patient 40, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 40, post-treatment
SL2-33


title: Patient 40, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 40, pre-treatment
SL-33


title: Tcell_person1_P1299_1897


title: Patient 39, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 39, post-treatment
SL2-32


title: Patient 38, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 38, post-treatment
SL2-31


title: Tcell_person1_P1299_1425


title: Patient 39, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 39, pre-treatment
SL-32


title: Tcell_person1_P1299_1809


title: Tcell_person1_P1299_1836


title: Tcell_person1_P1299_1794


title: Patient 38, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 38, pre-treatment
SL-31


title: Patient 37, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 37, pre-treatment
SL-30

value: Complete Response


title: Tcell_person1_P1299_1232


title: Tcell_person1_P1299_1298


title: Tcell_person1_P1299_1320


title: Tcell_person1_P1299_1138


title: Patient 36, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 36, pre-treatment
SL-29


title: Tcell_person1_P1299_1426


title: Patient 36, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 36, post-treatment
SL2-29


title: Patient 35, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 35, post-treatment
SL2-28


title: Patient 34, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 34, post-treatment
SL2-27


title: Patient 34, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 34, pre-treatment
SL-27


title: Tcell_person1_P1299_1221


title: Tcell_person1_P1299_1230


title: Tcell_person1_P1299_1467


title: Tcell_person1_P1299_1223


title: Tcell_person1_P1299_1342


title: Tcell_person1_P1299_1193


title: Patient 33, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 33, post-treatment
SL2-26


title: Tcell_person1_P1299_1399


title: Patient 32, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 32, post-treatment
SL2-25


title: Patient 31, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 31, pre-treatment
SL-24


title: Tcell_person1_P1299_1474


title: Patient 32, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 32, pre-treatment
SL-25


title: Tcell_person1_P1299_1139


title: Patient 31, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 31, post-treatment
SL2-24


title: Patient 37, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 37, post-treatment
SL2-30


title: Patient 35, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 35, pre-treatment
SL-28


title: Patient 30, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 30, pre-treatment
SL-23


title: Tcell_person1_P1299_1315


title: Patient 30, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 30, post-treatment
SL2-23


title: Patient 29, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 29, post-treatment
SL2-21


title: Tcell_person1_P1299_2141


title: Patient 29, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 29, pre-treatment
SL-21


title: Tcell_person1_P1299_1110


title: Patient 33, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 33, pre-treatment
SL-26


title: Patient 28, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 28, post-treatment
SL2-20


title: Patient 27, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 27, post-treatment
SL2-19


title: Tcell_person1_P1299_1324


title: Patient 27, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 27, pre-treatment
SL-19


title: Tcell_person1_P1299_2078


title: Tcell_person1_P1299_2062


title: Tcell_person1_P1299_1183


title: Tcell_person1_P1299_1122


title: Patient 26, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 26, post-treatment
SL2-18


title: Tcell_person1_P1299_1808


title: Tcell_person1_P1299_1471


title: Patient 28, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 28, pre-treatment
SL-20


title: Patient 26, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 26, pre-treatment
SL-18


title: Tcell_person1_P1299_1776


title: Patient 25, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 25, post-treatment
SL2-17


title: Tcell_person1_P1299_2097


title: Tcell_person1_P1299_1934


title: Patient 24, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 24, post-treatment
SL2-16


title: Tcell_person1_P1299_2048


title: Patient 25, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 25, pre-treatment
SL-17


title: Tcell_person1_P1299_2119


title: Patient 23, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 23, post-treatment
SL2-15


title: Tcell_person1_P1299_1796


title: Patient 23, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 23, pre-treatment
SL-15


title: Patient 22, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 22, post-treatment
SL2-14


title: Patient 22, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 22, pre-treatment
SL-14


title: Patient 24, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 24, pre-treatment
SL-16


title: Tcell_person1_P1299_2020


title: Tcell_person1_P1299_2021


title: Tcell_person1_P1299_2079


title: Patient 21, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 21, post-treatment
SL2-12


title: Patient 21, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 21, pre-treatment
SL-12


title: Tcell_person1_P1299_1951


title: Patient 20, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 20, pre-treatment
SL-11


title: Tcell_person1_P1299_1829


title: Tcell_person1_P1299_2043


title: Patient 19, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 19, pre-treatment
SL-10


title: Tcell_person1_P1299_1844


title: Patient 19, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 19, post-treatment
SL2-10


title: Tcell_person1_P1299_1815


title: Tcell_person1_P1299_2134


title: Tcell_person1_P1299_1811


title: Patient 18, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 18, post-treatment
SL2-9


title: Tcell_person1_P1299_2014


title: Tcell_person1_P1299_1832


title: Patient 18, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 18, pre-treatment
SL-9


title: Patient 17, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 17, pre-treatment
SL-7


title: Patient 17, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 17, post-treatment
SL2-7


title: Patient 16, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 16, post-treatment
SL2-6


title: Tcell_person1_P1299_1787


title: Tcell_person1_P1299_2094


title: Tcell_person1_P1299_1800


title: Patient 16, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 16, pre-treatment
SL-6


title: Patient 20, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 20, post-treatment
SL2-11


title: Patient 15, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 15, post-treatment
SL2-5


title: Tcell_person1_P1299_2066


title: Tcell_person1_P1299_1892


title: Patient 15, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 15, pre-treatment
SL-5


title: Tcell_person1_P1299_1841


title: Patient 14, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 14, post-treatment
SL2-4


title: Patient 14, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 14, pre-treatment
SL-4


title: Tcell_person1_P1299_2006


title: Patient 13, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 13, pre-treatment
SL-3


title: Patient 13, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 13, post-treatment
SL2-3


title: Tcell_person1_P1299_1375


title: Patient 12, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 12, post-treatment
SL2-2


title: Patient 11, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 11, post-treatment
SL2-1


title: Tcell_person1_P1299_1877


title: Patient 11, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 11, pre-treatment
SL-1


title: Tcell_person1_P1299_1276


title: Patient 12, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 12, pre-treatment
SL-2


title: Tcell_person1_P1299_1818


title: Patient 10, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 10, post-treatment
BEC-23


title: Tcell_person1_P1299_1160


title: Tcell_person1_P1299_1409


title: Tcell_person1_P1299_1451


title: Patient 10, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 10, pre-treatment
BEC-22


title: Patient 9, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 9, post-treatment
BEC-21


title: Tcell_person1_P1299_1382


title: Tcell_person1_P1299_1365


title: Patient 9, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 9, pre-treatment
BEC-10


title: Tcell_person1_P1299_1303


title: Patient 8, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 8, pre-treatment
BEC-17


title: Tcell_person1_P1299_2028


title: Tcell_person1_P1299_1292


title: Tcell_person1_P1299_1449


title: Patient 7, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 7, post-treatment
BEC-19


title: Patient 7, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 7, pre-treatment
BEC-16


title: Tcell_person1_P1299_1256


title: Patient 8, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 8, post-treatment
BEC-20


title: Tcell_person1_P1299_1184


title: Tcell_person1_P1299_2047


title: Tcell_person1_P1299_1372


title: Patient 6, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 6, post-treatment
BEC-18


title: Patient 5, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 5, post-treatment
BEC-12


title: Patient 5, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 5, pre-treatment
BEC-8


title: Tcell_person1_P1299_1924


title: Tcell_person1_P1299_1904


title: Tcell_person1_P1299_2118


title: Patient 3, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 3, post-treatment
BEC-11


title: Tcell_person1_P1299_1842


title: Patient 4, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 4, pre-treatment
BEC-7


title: Tcell_person1_P1299_2151


title: Tcell_person1_P1299_1824


title: Patient 2, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 2, post-treatment
BEC-5


title: Patient 3, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 3, pre-treatment
BEC-4


title: Patient 2, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 2, pre-treatment
BEC-3


title: Tcell_person1_P1299_2083


title: Patient 1, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 1, post-treatment
BEC-2


title: Tcell_person1_P1299_2031


title: Patient 6, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 6, pre-treatment
BEC-15


title: Patient 1, pre-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 1, pre-treatment
BEC-1


title: Tcell_person1_P1299_1940


title: Tcell_person1_P1299_1817


title: Adult female Culex quinquefasciatus 60h post-eclosion

city: Auburn

first: Nannan

last: Liu

state: AL

address: 301 Funchess Hall

department: Entomology

institute: Auburn University

description:
mRNA profiling
Sample 6

data_processing:
Base-calling, filtering, and conversion to fastq files were conducted by the Hudson Alpha Institute of Biotechnology using CASAVA version 1.8.
Paired end fastq data were trimmed for adapter using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic)
Cleaned reads were mapped to the Cx. quinquefasciatusburg v1.2 (www.vectorbase.org) using Tophat as paired end reads with no novel junction discovery, an average insert size of 200 nt and a standard deviation of 50 (http://www.cbcb.umd.edu/).
Gene expression and differential gene expression estimations were performed using the Cufflinks-Cuffdiff pipeline as a time series (http://www.cbcb.umd.edu/).
Genome_build: Culex quinquefasciatus strain Johannesburg version 1.2 (www.vectorbase.org)
Supplementary_files_format_and_content: Tab-delimited text file of FPKM values of all gene expression by time point

organism: Culex quinquefasciatus

growth_protocol: Cx. quinquefasciatus were reared under a 12:12 (L:D) photoperiod

extract_protocol:
A total of 200 females were pooled for each sample, homogenized in quanidinium isothiocyanate buffer and extracted using the hot acid phenol extraction method as outlined by Chomczynski and Sacchi (1987). RNA was extracted over 1:1 acid phenol twice, precipitated over two volumes of 100% ethanol, then resuspended in buffer and treated with Proteinase K to remove remaining protein, re-extracted over 1:1 phenol:chloroform, extracted 1x over chloroform and precipitated over two volumes of ethanol and 0.3M sodium acetate. From this, a total of 30 micrograms of RNA was used for DNase I treatment using the Ambion DNA-Free kit to remove residual DNA. DNA-free RNA was then re-extracted over 1:1 phenol:chloroform followed by final extraction over chloroform, precipitation over two volumes of 100% ethanol and 0.3M sodium acetate. The precipitated pellet was washed two times over 80% ethanol, resuspended in sterile deionized water and sent for sequencing.
Paired end libraries were prepared according to Illumina's instructions accompanying the mRNA Seq 8-sample kit by the Hudson Alpha Institute of Biotechnology, Huntsville, AL. Libraries were then sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols. Lengths of 51 nucleotides were sequenced for each of the paired ends and the average insert size was 200 nucleotides.

tag: developmental stage

tag: gender

value: female

value: 60h post-eclosion

tag: tissue

value: whole body


title: Adult female Culex quinquefasciatus 48h post-eclosion

description:
mRNA profiling
Sample 5

value: adult

value: 48h post-eclosion


title: Adult female Culex quinquefasciatus 72h post-eclosion

description:
mRNA profiling
Sample 7

value: 72h post-eclosion


title: Adult female Culex quinquefasciatus 36h post-eclosion

description:
mRNA profiling
Sample 4

value: 36h post-eclosion


title: Tcell_person1_P1299_2091

value: male

value: in vivo single Tcell


title: Patient 4, post-treatment

description:
Gene expression from cytologically normal bronchial airway epithelial cells from patient 4, post-treatment
BEC-13

value: bronchial dysplasia


title: Adult female Culex quinquefasciatus 24h post-eclosion

description:
mRNA profiling
Sample 3

value: 24h post-eclosion


title: Adult female Culex quinquefasciatus 2h post-eclosion

description:
mRNA profiling
Sample 1

value: 2h post-eclosion


title: Adult female Culex quinquefasciatus 12h post-eclosion

description:
mRNA profiling
Sample 2

value: 12h post-eclosion


title: Tcell_person1_P1299_2137


title: Tcell_person1_P1299_1901


title: Tcell_person1_P1299_2038


title: NPC1

city: Cambridge

first: Julien

last: Muffat

address: 9 Cambridge center

institute: Whitehead Institute

description: IPS-derived differentiated neurons and glia

data_processing:
RNASeq paired-end reads from Illumina 1.5 encoding were aligned using TopHat (v 2.0.13) to the human genome (GRCh37) with Ensembl annotation (GRCh37.75) in gtf format: default parameters were used, except for base encoding.
Cufflinks (v 2.2.1) was used to quantify gene expression (FPKM) using default parameters, GENCODE (v19) gtf annotation was used as transcript reference annotation.  The median expression value for each gene is reported.
Genome_build: GRCh37
Supplementary_files_format_and_content: fpkm (text)

source_name: differentiated NPC

growth_protocol: Colonies were treated with collagenase IV (1.5mg/mL) and mildly triturated to form a suspension of uniform clumps, transferred directly to 5mL NGD + 10ng/mL IL-34 + 10ng/mL CSF1, in ultra-low attachment 6-well plates (corning). 6 confluent wells (~3x106 cells) were pooled into one su0spension well. Embryoid bodies were monitored for appearance of two main identifiable types. The first group was composed of compact phase-bright neuralized spheroids, the second group were large, expanding cystic bodies, YS-EBs. Every 5 days, EBs were gently triturated to shear off loose cells of interest, settled, and the supernatant placed in a single well of a Primaria 6-well plate. Unattached cells and small EBs were washed with freshNGD. Attached cells were monitored for morphological characteristics of microglia/microglial precursors (compact nucleus, vacuoles, membrane ruffles, motility), and wells from 6 consecutive productions (one month) were pooled to constitute one synchronized population. Further maintenance for 2  weeks  was performed in NGD + 100ng/mL IL-34 + 5ng/mL CSF1).

extract_protocol:
RLT+ with bME, following the Rneasy micro plus protocol form Qiagen, per the manufacturer's instruction
Samples were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech), according to manufacturer’s protocols and using 10 ng of input. Final libraries were evaluated for size using a Fragment Analyzer (Advanced Analytical Technologies) and quantified using both Qubit (Thermo Fisher) and qPCR (Roche LightCycler 480, KAPA Illumina Library Quantification Kit) before sequencing.

tag: growth conditions

value: grown in basal medium

tag: source/differentiation

value: iPS-derived

value: neural co-culture, control genetic bakcground


title: pMGL3+NCM

description: iPS-derived microglia like cells co-cultured with differentiated neurons and glia

source_name: induced microglia-like cell

value: grown in neural conditioned medium NCM (Transwell co-culture)

value: induced, AMN2 genetic background


title: pMGL2+NCM

value: induced, AMN1 genetic background


title: Tcell_person1_P1299_1888


title: Tcell_person1_P1299_1778


title: Tcell_person1_P1299_1869


title: RsaFaFb RsaA rep2

city: Livermore

first: K.

middle: Wesley

last: Overton

state: CA

address: 7000 East Avenue

department: Biosciences and Biotechnology Division

institute: Lawrence Livermore National Laboratory

data_processing:
Sequencing data was mapped to the C. crescentus NA1000 reference genome sequence (GenBank accession number NC_011916.1) using Bowtie v1.1.1 with parameters -t -S -m 1
HTSeq-0.6.1p1 was used to quantify the number of counts per genomic feature
the counts per genomic feature output was converted to a .bam file, sorted, and indexed using samtools-0.1.19
RSeQC-2.3.9 was used to normalize the counts data and generate .wig files
Genome_build: GenBank accession number NC_011916.1
Supplementary_files_format_and_content: .wig files were generated using RSeQC-2.3.9. Values were normalized to 200,000,000. Each sample has a forward and reverse wig file associated with it. The first line of the wig files was modified for successful loading into the genome browser Mochiview.

organism: Caulobacter vibrioides

source_name: RsaFaFb RsaA

growth_protocol: Cultures were grown to early log phase in PYE (peptone, yeast extract) rich media

extract_protocol:
Cells were harvested and immediately added to ice-cold ethanol containing 5% (vol/vol) water-saturated phenol (pH 6.6). Total RNA was isolated using hot phenol and phenol/chloroform extractions.
5 ug of total RNA was treated with the ScriptSeq Complete Kit - Bacteria from Epicentre, an Illumina company (Cat# BB1224) for ribosomal RNA depletion and library generation with ScriptSeq Index Primers.

tag: strain

tag: genotype

value: delta_rsaFaFb rsaA


title: RsaFaFb RsaA rep1


title: Tcell_person1_P1299_2046

value: adult


title: RsaFaFb rep3

source_name: RsaFaFb


title: pMGL5

description: hES-derived microglia like cells grown in minimal medium

value: hES-derived

value: Induced, MECP2 ko genetic background


title: Tcell_person1_P1299_2001


title: pMGL4

description: iPS-derived microglia like cells grown in minimal medium

value: induced, AMN3 genetic background


title: NPC3

value: neural co-culture, AMN2 genetic background


title: pMGL3.2


title: NPC2

value: neural co-culture, AMN1 genetic background


title: Tcell_person1_P1299_1831

value: male

value: in vivo single Tcell


title: RsaFaFb rep1


title: Tcell_person1_P1299_2101


title: pMGL3.1


title: RsaFaFb rep2


title: RsaFb rep3

source_name: RsaFb


title: RsaFaFb RsaA rep3


title: pMGL1

value: induced, control genetic background


title: pMGL2


title: Tcell_person1_P1299_1918


title: pMGL1+NCM


title: RsaFb rep1


title: Tcell_person1_P1299_1942


title: RsaFa rep3

source_name: RsaFa


title: RsaFb rep2


title: Tcell_person1_P1299_1887


title: Tcell_person1_P1299_1886


title: FMG2

description: Fetal primary cells used as reference

source_name: primary  fetal microglia

value: commercial purification

value: primary, undetermined control reference


title: FMG1

description: Fetal primary cells used as reference

value: grown in basal medium


title: Tcell_person1_P1299_1878


title: RsaFa rep1


title: human pancreatic islets, sample 4

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

institute: Harvard University

data_processing:
Reads were first filtered based on presence in read 1 of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015)
Read 2 was then trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 80 -m 200 -best -strata -a) to the human or mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (Homo sapiens: GRCh38.82,  Mus musculus: GRCm38.84) including all annotations with "Transcript Support Levels" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Klein et al., Cell 2015)
Genome_build: GRCh38 (human sample), GRCm38 (mouse samples)
Supplementary_files_format_and_content: Columns = gene; rows = cells. Column 1 contains cell identifier. Column 2 contains matching cell barcode. Column 3 contains cell-type assignment for analysis. Columns 4+ contain counts for each gene. Values show unique molecular identifier (UMI)-filtered counts per cell detected in the raw data. No normalization is performed.

source_name: Female donor, age 59, BMI: 29.9

extract_protocol:
Cells were encapsulated using the inDrop platform, into droplets on ice and lysed  in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Cells were barcoded using the inDrop platform (Klein et al., Cell 2015), which makes use of the CEL-Seq protocol for library construction Hashimshony et al., Cell Reports 2012)

treatment_protocol: Human pancreatic islets were obtained from Prodo or NDRI and recovered in CMRLS at 37°C for 24h-48h hours after receipt. Mouse islets were prepared using gradient centrifugation and islets from the same strain were pooled, then recovered in XX for 24h.

value: female

tag: bmi

tag: type 2 diabetes mellitus

value: Yes


title: WT rep3

source_name: WT

value: wild type


title: Tcell_person1_P1299_1914


title: Tcell_person1_P1299_1936


title: human pancreatic islets, sample 2

source_name: Female donor, age 51, BMI: 21.1

value: No


title: WT rep1


title: human pancreatic islets, sample 3

source_name: Male donor, age 38, BMI: 27.5


title: WT rep2


title: Tcell_person1_P1299_1867


title: FMG1+NCM

description: Fetal primary cells used as reference

value: grown in neural conditioned medium NCM


title: IBxDU-429

status: Public on Sep 25 2016

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

data_processing:
Sequence reads were analyzed using CLCBio Genomic workbench software 7.0 (CLC Bio, Aarhus, Denmark).
Quality control analysis was performed using the NGS quality control tool. A hierarchical clustering of the samples was also performed. One IBxDU pig was discarded for further analysis because the sample deviated largely from the expected grouping in the clustering analysis, probably due to RNA sampling or processing problems (sample 9- IBxDU-425)
Sequence paired-end reads (76bp) were assembled against the annotated Sscrofa10.2 reference genome using the genome, annotated genes and mRNA tracks
Data was normalized by calculating the reads per kilo base per million mapped reads’ (RPKM) for each gene
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Processed data file includes normalized expression values (RPKM) for all genes in all 11 samples passing the quality control, fold changes and P values for differential expression

organism: Sus scrofa

source_name: Biceps femoris muscle_Iberian x Duroc

growth_protocol: All tissues were collected within 15 min postmortem, snap-frozen in liquid nitrogen, and then stored at -80° C until processing.

extract_protocol:
Total RNA was extracted from 50-100mg samples of BF muscle using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of the RNA was evaluated using the RNA Integrity Number (RIN) value from the Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA). The RIN values ranged from 7.5 to 9.8
Sequencing libraries were made using the mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-100-0801) according to manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp on a on a HiSeq2000 sequence analyzer (Illumina, Inc). Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

treatment_protocol: 50-100 mg samples of each tissue were ground in liquid nitrogen with mortar and pestle.

value: postnatal day 1

value: crossbred Iberian x Duroc

value: Biceps femoris muscle


title: IBxDU-426


title: IBxDU-427


title: IB-431

source_name: Biceps femoris muscle_Iberian

value: pure Iberian


title: IB-504


title: IB-503


title: IBxDU-402


title: IB-345


title: RsaFa rep2


title: IBxDU-425


title: IBxDU-412


title: human pancreatic islets, sample 1

source_name: Male donor, age 17, BMI: 21.5


title: 50-3-IP

city: LA

first: Li

last: Qinqun

state: LA

address: 421 HongCao Rd., Building 63, 2nd floor

department: TS

institute: Kangchen

library_source: genomic

data_processing:
Base calling were performed using Off-Line Basecaller software (OLB V1.8).
Date were filtered using the Solexa CHASTITY
The clean reads were aligned to Zebrafish genome (UCSC danRer7) using BOWTIE software (V2.1.0).
Aligned reads were used for peak calling of the MeDIP regions using MACS V2.
Genome_build: UCSC danRer7
Supplementary_files_format_and_content: wig

molecule: genomic DNA

organism: Danio rerio

source_name: larvae

growth_protocol: Wild-type TU zebrafish were maintained using routine procedures (Westerfield, 2000). Collection and exposure of fertilized eggs were all carried out in zebrafish medium (3.5 g/L NaCl, 0.05 g/L NaHCO3, 0.05 g/L KCl, 0.05 g/L CaCl2).

extract_protocol:
Genomic DNA was sonicated to ~200 - 900bp fragments, and 1 μg of fragmented sample was ligated to Illumina’s genomic adapters with Genomic DNA Sample Kit (#FC-102-1002, Illumina), following the manufacturer’s instructions. ~300 - 1000 bp ligated DNA fragments were further immunoprecipitated by anti-5-methylcytosine antibody (Diagenode).
Fragmented DNA was prepared for Illumina HiSeq 2000 sequencing as the following steps: 1) End repair of DNA samples with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK; 2) A single ‘A’ base was added to the 3' ends with Klenow (exo minus) polymerase; 3) Ligation of Illumina's genomic adapters to DNA fragments; 4) MeDIP to enrich methylated DNA by anti-5-methylcytosine antibody; 5) PCR amplification to enrich precipitated fragments; 6) Gel purification to extract ~300 - 1000 bp DNA fragments. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Illumina HiSeq 2000 following the TruSeq SBS Kit v5 protocol.

treatment_protocol: Embryos between 0 and 0.5 hpf were exposed to BaP with the concentration of 50 nmol/L in glass petri dishes.Similar criteria were applied to the control group, which received an equal volume of the DMSO solvent (504μL/L)instead of BaP. At 96 hpf,zebrafish were collected in liquid nitrogen for MeDIP-sequencing.

value: TU

value: 96 hour post-fertilization (hpf) zebrafish

tag: treatment

value: 50 nmol/L BaP

tag: medip antibody

value: 5-mC monoclonal antibody


title: 50-Input


title: 50-2-IP


title: 50-1-IP


title: C-1-IP

value: DMSO


title: C-3-IP


title: Suckling 2 Input

city: Chengdu

first: Shen

last: He

address: wenjiang, huimin road 211

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

data_processing:
library strategy: MeRIP-Seq
Base-calling with CASAVA.
Adaptor and low quality bases were trimmed with Skewer.
Aligned to pig reference genome Sscrofa10.2.81 downloading from Ensemble (www.ensembl.org) with BWA MEM
Duplicated reads were marked with Samblaster
Only the uniquely mapped (MAPQ>=13) and duplicated alignments were used for peak calling
MACS2 is employed to perform peak calling with a threshold of q 0.05 with insert size of 200 base pair.
Genome_build: Sscrofa10.2.81
Supplementary_files_format_and_content: bw files of paired MeRIP and Input of each replicate.

source_name: Suckling Input

extract_protocol:
Total RNA was subjected to two rounds of purification using oligo(dT)-coupled magnetic beads according to the manufacturer’s instructions (Ambion), for mRNA isolation. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol. Approximately 5 μg fragmented mRNA was subjected to immunoprecipitation, according to the reported MeRIP protocal.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (E7530L, New England Biolabs) was used to construct the library from immunoprecipitated RNA and input RNA according to manufacturer’s published protocol.

tag: breed

value: Rongchang pig

value: liver

value: Postnatal day 21

tag: rip antibody


title: IB-330

tag: age

value: male


title: C-Input


title: W_T3

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (hg38) by TopHat (version 2.0.10) and Bowtie2 (version 2.1.0).
The number of fragments in each known gene from GENCODE Release 21 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.16.0).
Genome_build: hg38
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq) for all the samples.

source_name: HPCa167N benign prostatic bulk cells cultured in WIT

growth_protocol: Either freshly disassociated bulk benign prostatic cells or purified subpopulations were culatured primarily in PrEGM or WIT

extract_protocol:
The PrEGM- and WIT-expanded cells from either bulk or FACS-purified human benign prostatic basal and luminal cells are subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient id

tag: patient age (yrs)

value: Prostate


title: W_T1

tag: cell type

value: HPCa167N benign prostatic bulk cells cultured in WIT


title: W_T2


title: Adult 3 Input

source_name: Adult Input

value: Two years old


title: Adult 2 Input


title: C-2-IP

tag: developmental stage


title: W_L2

source_name: Freshly purified HPCa167N benign prostatic luminal cells cultured in WIT


title: Adult 1 Input


title: W_B2

source_name: Freshly purified HPCa167N benign prostatic basal cells cultured in WIT


title: W_B1

value: Freshly purified HPCa167N benign prostatic basal cells cultured in WIT


title: Suckling 3 Input


title: Adult 3 MeRIP

source_name: Adult MeRIP

value: m6A (Synaptic Systems Cat. No.202011)


title: P_T3

source_name: HPCa167N benign prostatic bulk cells cultured in PrEGM


title: Suckling 1 Input


title: IB-323

value: postnatal day 1

tag: Sex


title: P_T1

tag: tissue

value: HPCa167N benign prostatic bulk cells cultured in PrEGM


title: Newborn 3 Input

source_name: Newborn Input

value: Postnatal day 0


title: Newborn 2 Input


title: P_B3

source_name: Freshly purified HPCa167N benign prostatic basal cells cultured in PrEGM


title: Suckling 3 MeRIP

source_name: Suckling MeRIP

value: m6A (Synaptic Systems Cat. No.202008)


title: Adult 1 MeRIP

value: m6A (Synaptic Systems Cat. No.202009)


title: W_L1

value: Freshly purified HPCa167N benign prostatic luminal cells cultured in WIT


title: Newborn 1 Input


title: Suckling 1 MeRIP

value: m6A (Synaptic Systems Cat. No.202006)


title: Newborn 2 MeRIP

source_name: Newborn MeRIP

value: m6A (Synaptic Systems Cat. No.202004)


title: Adult 2 MeRIP

value: Rongchang pig

value: m6A (Synaptic Systems Cat. No.202010)


title: P_T2


title: W_B3


title: Newborn 3 MeRIP

value: liver

value: m6A (Synaptic Systems Cat. No.202005)


title: W_L3

value: Prostate