title: WBC 45

city: Jerusalem

first: Tal

last: Michaeli

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_45_N

data_processing:
Adapter trimming using trim_galore
Read alignment and base calling: BSMAP v2.74
Tiles and DMRs calculation: MethylKit v0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: Processed file is in bed format containing genome wide 100bp tiles methylation data of all samples

source_name: WBC

extract_protocol:
A fetal blood sample (0.2-2 ml) was collected from the umbilical cord into two EDTA-containing tubes after the delivery of the baby and before placental removal. The placental sampled area was taken from the midway between the point of cord insertion into the placenta and the placental circumference. DNA extraction was performed according to standard protocols(Qiagen kit).
RRBS libraries were prepared as described (Boyle, P. et al. 2012)

tag: gestational age (weeks)


title: WBC 44

status: Public on Jul 18 2019

type: SRA

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_44_N

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: NOTNV36LH8B

city: Tallinn

first: Agne

last: Velthut-Meikas

address: Akadeemia tee 15

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

description: ESTcounts.csv

library_source: transcriptomic

data_processing:
Quality control and adapter trimming of raw sequences was performed using Trimmomatic version 0.36. All sequences were scanned with 4 base long sliding window and reads were dropped if the average quality of base pair was below 30 according to Phred +33 quality score system or if total read length was less than 17.
Identification of miRNAs from sequencing reads was performed by miRDeep2 algorithm according to miRBase version 21. Standard settings were used.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: counts

molecule: total RNA

source_name: blood

extract_protocol:
Qiagen miRNeasy protocol for endometrium samples and PaxGene Blood miRNA protocol for blood samples
Illumina TruSeq Small RNA Library Preparation Guide

tag: patient id

tag: lh day

tag: group

value: IVF

tag: country

value: Estonia

tag: age


title: 13A6LN23

type: RNA

city: La Jolla

first: Luc

last: Teyton

state: CA

address: 10550 North Torrey Pines Road

country: USA

institute: TSRI

description: 13-21 A 6weeks UPDATED.csv

data_processing: Custom R analysis pipeline

label: EVAGREEN

organism: Mus musculus

source_name: LymphNode

label_protocol: IAg7 tetramers with PE fluorphores. Stain at 4C for 60 minutes

extract_protocol: Tetramer used to stain CD4+ T cells specific to either 12-20 or 13-21 of the insulin Beta chain from various NOD mice tissues.

tag: cell type

value: CD4+ T cell

tag: strain

value: NOD/ShiLtJ

tag: iag7 tetramer

tag: age (in weeks)


title: NOTNV35LH8E

description: ESTcounts.csv

source_name: endometrium


title: 13A6LN32

description: 13-21 A 6weeks UPDATED.csv


title: clone_replicate1_66

city: Boston

first: Yang

last: Luo

state: Massachusetts

address: 77 avenue louis pasteur, room 255

institute: Harvard Medical School

data_processing:
Low input gene expression quantification was performed with Kallisto version 0.43.1 (Bray et al, Nature Biotechnology, 2016), using the Ensembl 83 annotation.
Normalized expression are log2(tpm+1) values. Expressed genes those with a log2(TMPM+1) > 1 in at least 95% of the samples.
Genome_build: hg19

source_name: THP1 clonal cell line

growth_protocol: 10% complete RPMI (1640 + 50mL FBS + 0.5mLBME + 5.5mL Pen/Strep + 5mL NEAA + 2mL Lglut + 7.5mL HEPES + 5mL NaPyruvate)

extract_protocol:
Qiagen Rneasy minikit (Qiagen, catalogue no. 74104)
Smartseq2 (Broad Institute Genomics Platform)

treatment_protocol: CRISPR/Cas9 disruption of 3q23 genomic region around rs73226617, and single-cell sorts of edited THP1 cells after 2 weeks

tag: cell line

tag: genotype

value: Detectable genomic deletion in amplicon


title: WBC 42

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_42_N


title: 13A6LN20

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN28

description: 13-21 A 6weeks UPDATED.csv


title: WBC 41

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_41_N


title: NOTNV35LH8B

description: ESTcounts.csv


title: NOTNV38LH8B

description: ESTcounts.csv


title: 13A6LN18

description: 13-21 A 6weeks UPDATED.csv


title: WBC 43

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_43_N


title: 13A6LN17

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN19

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV33LH8E

description: ESTcounts.csv


title: WBC 40

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_40_N


title: 13A6LN16

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV33LH8B

description: ESTcounts.csv


title: WBC 46

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_46_N


title: WBC 39

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_39_N


title: 13A6LN15

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV32LH8E

description: ESTcounts.csv


title: 13A6LN13

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN10

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV32LH8B

description: ESTcounts.csv


title: WBC 37

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_37_N


title: clone_replicate1_160


title: WBC 38

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_38_N


title: WBC 36

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_36_N


title: WBC 35

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_35_N


title: 13A6LN9

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN6

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN12

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV29LH8E

description: ESTcounts.csv


title: 13A6LN8

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV30LH8E

description: ESTcounts.csv


title: 13A6LN7

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV30LH8B

description: ESTcounts.csv


title: WBC 34

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_34_N


title: 13A6LN4

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV27LH8E

description: ESTcounts.csv


title: 13A6LN3

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN5

description: 13-21 A 6weeks UPDATED.csv


title: WBC 33

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_33_N


title: 13A6LN14

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV27LH8B

description: ESTcounts.csv


title: 13A6LN11

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV25LH8E

description: ESTcounts.csv

value: CONTROL


title: WBC 32

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_32_N


title: 13A6S41

description: 13-21 A 6weeks UPDATED.csv

source_name: Spleen


title: 13A6S40

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN1

description: 13-21 A 6weeks UPDATED.csv


title: WBC 31

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_31_N


title: 13A6S42

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S39

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S38

description: 13-21 A 6weeks UPDATED.csv


title: WBC 30

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_30_N


title: 13A6S37

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S36

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV25LH2E

description: ESTcounts.csv


title: NOTNV25LH8B

description: ESTcounts.csv


title: 13A6S35

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV25LH2B

description: ESTcounts.csv


title: 13A6LN2

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S34

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S33

description: 13-21 A 6weeks UPDATED.csv


title: WBC 25

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_25_N


title: 13A6S32

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV24LH8E

description: ESTcounts.csv


title: WBC 26

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_26_N


title: 13A6S30

description: 13-21 A 6weeks UPDATED.csv


title: WBC 24

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_24_N


title: 13A6S29

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S31

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S28

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV24LH8B

description: ESTcounts.csv


title: WBC 21

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_21_N


title: NOTNV24LH2E

description: ESTcounts.csv


title: 13A6S26

description: 13-21 A 6weeks UPDATED.csv


title: WBC 18

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_18_N


title: NOTNV18LH8E

description: ESTcounts.csv


title: 13A6S25

description: 13-21 A 6weeks UPDATED.csv


title: WBC 27

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_27_N


title: 13A6S24

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S23

description: 13-21 A 6weeks UPDATED.csv


title: WBC 17

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_17_N


title: 13A6S21

description: 13-21 A 6weeks UPDATED.csv


title: WBC 15

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_15_N


title: NOTNV18LH8B

description: ESTcounts.csv


title: 13A6S22

description: 13-21 A 6weeks UPDATED.csv


title: WBC 16

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_16_N


title: NOTNV18LH2B

description: ESTcounts.csv


title: WBC 14

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_14_N


title: 13A6S20

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S18

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV16LH8E

description: ESTcounts.csv


title: 13A6S17

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S16

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S15

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV24LH2B

description: ESTcounts.csv


title: 13A6S27

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV16LH2E

description: ESTcounts.csv


title: WBC 12

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_12_N


title: 13A6S14

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S13

description: 13-21 A 6weeks UPDATED.csv


title: WBC 11

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_11_N


title: 13A6S12

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S11

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV16LH2B

description: ESTcounts.csv


title: NOTNV18LH2E

description: ESTcounts.csv


title: 13A6S10

description: 13-21 A 6weeks UPDATED.csv


title: WBC 10

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_10_N


title: 13A6S9

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV15LH8E

description: ESTcounts.csv


title: 13A6S19

description: 13-21 A 6weeks UPDATED.csv


title: WBC 9

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_9_N


title: 13A6S8

description: 13-21 A 6weeks UPDATED.csv


title: 13A6S7

description: 13-21 A 6weeks UPDATED.csv


title: WBC 13

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_13_N


title: 13A6S5

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV15LH8B

description: ESTcounts.csv


title: NOTNV16LH8B

description: ESTcounts.csv


title: 13A6S4

description: 13-21 A 6weeks UPDATED.csv


title: WBC 8

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_8_N


title: WBC 7

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_7_N


title: NOTNV15LH2B

description: ESTcounts.csv


title: 13A6S2

description: 13-21 A 6weeks UPDATED.csv


title: WBC 6

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_6_N


title: 13A6S1

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV15LH2E

description: ESTcounts.csv


title: 12B12S44

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN44

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S43

description: 12-20B 12 weeks UPDATED.csv


title: WBC 5

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_5_N


title: NOTNV13LH8B

description: ESTcounts.csv


title: 12B12LN43

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV13LH8E

description: ESTcounts.csv


title: WBC 3

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_3_N


title: WBC 4

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_4_N


title: 13A6S6

description: 13-21 A 6weeks UPDATED.csv


title: 12B12LN42

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV13LH2B

description: ESTcounts.csv


title: NOTNV12LH8E

description: ESTcounts.csv


title: 12B12LN40

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN39

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN41

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN36

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV12LH2E

description: ESTcounts.csv


title: NOTNV13LH2E

description: ESTcounts.csv


title: WBC 2

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_2_N


title: Placenta 45

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_45_N

source_name: Placenta


title: 12B12LN37

description: 12-20B 12 weeks UPDATED.csv


title: 13A6S3

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV12LH8B

description: ESTcounts.csv


title: WBC 1

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
WBC_1_N


title: 12B12LN38

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN35

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN34

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 46

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_46_N


title: NOTNV12LH2B

description: ESTcounts.csv


title: Placenta 44

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_44_N


title: 12B12LN32

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV11LH8E

description: ESTcounts.csv


title: 12B12LN31

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN33

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV11LH8B

description: ESTcounts.csv


title: Placenta 43

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_43_N


title: 12B12LN30

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN28

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 42

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_42_N


title: NOTNV11LH2E

description: ESTcounts.csv


title: 12B12LN26

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN27

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN29

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 41

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_41_N


title: NOTNV11LH2B

description: ESTcounts.csv


title: 12B12LN25

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 40

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_40_N


title: NOTNV09LH8E

description: ESTcounts.csv


title: 12B12LN24

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN23

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN22

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 39

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_39_N


title: 12B12LN20

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV09LH2E

description: ESTcounts.csv


title: Placenta 38

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_38_N


title: Placenta 37

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_37_N


title: 12B12LN18

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN16

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN17

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV09LH2B

description: ESTcounts.csv


title: NOTNV06LH8E

description: ESTcounts.csv


title: Placenta 36

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_36_N


title: NOTNV09LH8B

description: ESTcounts.csv


title: 12B12LN14

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 35

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_35_N


title: 12B12LN13

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV06LH8B

description: ESTcounts.csv


title: Placenta 34

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_34_N


title: 12B12LN11

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN10

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 32

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_32_N


title: 12B12LN21

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV06LH2B

description: ESTcounts.csv


title: NOTNV06LH2E

description: ESTcounts.csv


title: 12B12LN19

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN8

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN7

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN9

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 30

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_30_N


title: NOTNV04LH8E

description: ESTcounts.csv


title: 12B12LN5

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN15

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 27

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_27_N


title: 12B12LN3

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 31

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_31_N


title: 12B12LN12

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN1

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S42

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV04LH2B

description: ESTcounts.csv


title: Placenta 25

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_25_N


title: NOTNV03LH8E

description: ESTcounts.csv


title: 12B12S41

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV03LH8B

description: ESTcounts.csv


title: 12B12S39

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 24

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_24_N


title: NOTNV03LH2E

description: ESTcounts.csv


title: Placenta 23

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_23_N


title: 12B12S37

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN6

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S36

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV04LH8B

description: ESTcounts.csv


title: NOTNV03LH2B

description: ESTcounts.csv


title: 12B12S35

description: 12-20B 12 weeks UPDATED.csv


title: 12B12LN4

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 21

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_21_N


title: 12B12S38

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 20

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_20_N


title: 12B12LN2

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV02LH8E

description: ESTcounts.csv


title: 12B12S33

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S34

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S32

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 18

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_18_N


title: NOTNV04LH2E

description: ESTcounts.csv


title: 12B12S31

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV02LH8B

description: ESTcounts.csv


title: 12B12S30

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S29

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 17

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_17_N


title: Placenta 26

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_26_N


title: 12B12S40

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV02LH2E

description: ESTcounts.csv


title: 12B12S28

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 16

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_16_N


title: NOTNV02LH2B

description: ESTcounts.csv


title: NOTNV01LH8E

description: ESTcounts.csv


title: 12B12S27

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S26

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S25

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 14

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_14_N


title: Placenta 15

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_15_N


title: 12B12S23

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S24

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S22

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV01LH8B

description: ESTcounts.csv


title: 12B12S21

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV01LH2E

description: ESTcounts.csv


title: Placenta 12

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_12_N


title: 12B12S20

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S19

description: 12-20B 12 weeks UPDATED.csv


title: NOTNV01LH2B

description: ESTcounts.csv


title: Placenta 13

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_13_N


title: 12B12S18

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S16

description: 12-20B 12 weeks UPDATED.csv


title: NOT1325LH8E

description: ESTcounts.csv


title: Placenta 11

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_11_N


title: NOT1325LH8B

description: ESTcounts.csv


title: 12B12S15

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S17

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 10

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_10_N


title: 12B12S14

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 9

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_9_N


title: 12B12S13

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 8

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_8_N


title: NOT1213LH8B

description: ESTcounts.csv


title: 12B12S12

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 7

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_7_N


title: 12B12S9

description: 12-20B 12 weeks UPDATED.csv


title: NOT1213LH2E

description: ESTcounts.csv


title: NOT1213LH8E

description: ESTcounts.csv


title: Placenta 6

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_6_N


title: 12B12S10

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S11

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S8

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S7

description: 12-20B 12 weeks UPDATED.csv


title: 12B12S5

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 5

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_5_N


title: 12B12S3

description: 12-20B 12 weeks UPDATED.csv


title: Placenta 4

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_4_N


title: NOT1210LH8B

description: ESTcounts.csv


title: 12B12S2

description: 12-20B 12 weeks UPDATED.csv


title: NOT1213LH2B

description: ESTcounts.csv


title: NOT1210LH2E

description: ESTcounts.csv


title: 12B12S1

description: 12-20B 12 weeks UPDATED.csv


title: NOT1210LH2B

description: ESTcounts.csv


title: 12A12S44

description: 12-20A 12weeks UPDATED.csv


title: 12A12S43

description: 12-20A 12weeks UPDATED.csv


title: NOT1209LH8E

description: ESTcounts.csv


title: NOT1209LH8B

description: ESTcounts.csv


title: Placenta 1

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_1_N


title: 12A12LN44

description: 12-20A 12weeks UPDATED.csv


title: 12B12S6

description: 12-20B 12 weeks UPDATED.csv


title: NOT1209LH2E

description: ESTcounts.csv


title: NOT1210LH8E

description: ESTcounts.csv


title: Placenta 3

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_3_N


title: 12A12LN43

description: 12-20A 12weeks UPDATED.csv


title: Placenta 2

description:
100bpTiles_Tiles_Cov10_All.bed.zip
Cov10_Tiles_YoungWBC_More_Meth_0.50.xlsx
Cov10_Tiles_YoungPL_More_Meth_0.50.xlsx
Cov10_Tiles_OldWBC_More_Meth_0.50.xlsx
PL_2_N


title: ERTK11LH8E

description: ESTcounts.csv


title: 12A12LN42

description: 12-20A 12weeks UPDATED.csv


title: ERTK11LH2E

description: ESTcounts.csv


title: 12A12LN41

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN40

description: 12-20A 12weeks UPDATED.csv


title: GW-516 treatment-1

city: New York

first: Wenjing

last: Su

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description:
Sample 9
PC3-GW516-1

data_processing:
50-bp sequences were aligned to hg19 using STAR and counts generated from STAR output --quantMode GeneCounts.
Differential gene expression was analyzed using the DESeq2 (1.8.1) package in R using default settings.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files containing DESeq2 normalized to shcon.

source_name: PC3 prostate cancer cell line, GW-516 treatment

growth_protocol: Sample 1-10: Cells were cultured in DMEM/F-12 supplemented with 10% Fetal Bovine Serum, 2 mM L-Glutamine (Glu), 100 IU/ml Penicillin/Streptomycin.

extract_protocol:
Total RNA extracted via Trizol/Zymo RNA extraction kit.
Illumina TruSeq RNA Sample Preparation.
Paired-end Read, mRNA TruSeq stranded 175bp.

treatment_protocol:
Sample 1-6: Cells stably expressed indicated shRNAs.
Sample 7-10: Cells treated with indicated compounds for 48 hours.

value: prostate cancer cell line

tag: treatment


title: 12A12LN39

description: 12-20A 12weeks UPDATED.csv


title: NOT1209LH2B

description: ESTcounts.csv


title: Macrophage-like cells, single-DH82_2h_2

city: Seoul

first: Woo Bin

last: Park

address: Gwan-ak ro 1

country: South Korea

institute: Veterinary medicine, Seoul national university

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat v2.0.12
Gene expression level was measured with Cufflinks v2.1.1
Differential expression analysis was performed by Cuffdiff
Genome_build: Ensembl ver.76 (Canine lupus familiaris)
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

organism: Canis lupus familiaris

source_name: Macrophage-like cells, single-DH82_2h

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Prep Kit

value: Macrophage-like cell

value: 10 years

value: stimulation with Brucella canis

tag: time


title: Macrophage-like cells, single-DH82_24h_2

source_name: Macrophage-like cells, single-DH82_24h


title: Macrophage-like cells, single-DH82_12h_1

source_name: Macrophage-like cells, single-DH82_12h


title: Macrophage-like cells, single-DH82_12h_2


title: Macrophage-like cells, single-DH82_2h_1


title: Macrophage-like cells, single-DH82_24h_1


title: PRT4165 treatment-2

description:
Sample 8
PC3-PRT-2

source_name: PC3 prostate cancer cell line, PRT4165 treatment


title: 12A12LN38

description: 12-20A 12weeks UPDATED.csv


title: Macrophage-like cells, co-DH82_24h_2

source_name: Macrophage-like cells, co-DH82_24h

value: D17 and DH82 co-culture model


title: Yeats4_WT

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

country: China

institute: Institute of Biophysics, CAS

description: This is wild-type progenitors

hyb_protocol: hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000.

data_processing: All resulting .CEL files for each array type were processed as a single group via the Affymetrix Power Tools (APT) package using sketch normalization and the RMA algorithm to summarize probeset signal.

label: biotin

source_name: WT ILC progenitors

label_protocol: 10 mg of cRNA was carried into the second cycle, first strand cDNA synthesis reaction. 5.5 mg of single-stranded cDNA was fragmented and biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit according to The GeneChip® WT Terminal Labeling and Hybridization User Manual

extract_protocol:
2x105 progenitors were isolated from WT or Yeats4-deleted mice by FACS
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Wild-type


title: GW-516 treatment-2

description:
Sample 10
PC3-GW516-2


title: PRT4165 treatment-1

description:
Sample 7
PC3-PRT-1


title: 12A12LN37

description: 12-20A 12weeks UPDATED.csv


title: Yeats4_KO

description: This is Yeats4-deficient progenitors

source_name: Yeats4-deficient ILC progenitors

value: Yeats4 knockout


title: Macrophage-like cells, co-DH82_24h_1


title: tumor from IDB-05 triple-positive PDX model (956_14)

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

description:
IDB-05 triple-positive PDX model
Sample name: 956_14

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: tissue


title: 12A12LN36

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN35

description: 12-20A 12weeks UPDATED.csv


title: tumor from IDB-05 triple-positive PDX model (956_7)

description:
IDB-05 triple-positive PDX model
Sample name: 956_7


title: RNF2 shRNA2-1

description:
Sample 5
PC3-sh2-1

source_name: PC3 prostate cancer cell line, RNF2 shRNA2

tag: shRNA


title: Macrophage-like cells, co-DH82_12h_1

source_name: Macrophage-like cells, co-DH82_12h


title: Macrophage-like cells, co-DH82_12h_2


title: RNF2 shRNA1-2

description:
Sample 4
PC3-sh1-2

source_name: PC3 prostate cancer cell line, RNF2 shRNA1


title: 12A12LN34

description: 12-20A 12weeks UPDATED.csv


title: RNF2 shRNA2-2

description:
Sample 6
PC3-sh2-2


title: Macrophage-like cells, co-DH82_2h_2

source_name: Macrophage-like cells, co-DH82_2h


title: tumor from IDB-04 luminal PDX model resistant but not treated with docetaxel (25_5_29)

description:
IDB-04 luminal PDX model resistant but not treated with docetaxel
Sample name: 25_5_29


title: 12A12LN33

description: 12-20A 12weeks UPDATED.csv

source_name: LymphNode


title: RNF2 shRNA1-1

description:
Sample 3
PC3-sh1-1


title: Scramble shRNA-2

description:
Sample 2
PC3-shcon-2

source_name: PC3 prostate cancer cell line, Scramble shRNA

value: Scramble


title: Macrophage-like cells, co-DH82_2h_1


title: tumor from IDB-03 luminal PDX model resistant but not treated with docetaxel (1070_81)

description:
IDB-03 luminal PDX model resistant but not treated with docetaxel
Sample name: 1070_81


title: tumor from IDB-04 luminal PDX model resistant and treated with docetaxel (Q25_5_23)

description:
IDB-04 luminal PDX model resistant and treated with docetaxel
Sample name: Q25_5_23


title: tumor from IDB-04 luminal PDX model resistant and treated with docetaxel (Q25_5_26)

description:
IDB-04 luminal PDX model resistant and treated with docetaxel
Sample name: Q25_5_26


title: LuCaP_176_s5_ET1374

status: Public on Jul 17 2019

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 176 PDX tumor

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X. For PDX samples, sequences aligning to the mm10 mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 176 PDX tumor

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).

extract_protocol:
Total RNA was isolated from 98 CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) from 55 patients with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from flash frozen LuCaP xenograft tissue or cell lines with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended in solution DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol. Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: gender

value: male

value: prostate cancer

tag: molecular phenotype


title: Macrophage-like cells, control-DH82_0h_1

source_name: Macrophage-like cells, control-DH82_0h

value: control


title: LuCaP_49_p70s18n16

description: LuCaP 49 PDX tumor

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.  For PDX samples, sequences aligning to the mm10 mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 49 PDX tumor


title: tumor from IDB-03 luminal PDX model resistant and treated with docetaxel (Q1070_22)

description:
IDB-03 luminal PDX model resistant and treated with docetaxel
Sample name: Q1070_22


title: 12A12LN32

description: 12-20A 12weeks UPDATED.csv


title: LuCaP_49_p70s16n16

description: LuCaP 49 PDX tumor


title: tumor from IDB-02 TNBC PDX model resistant to docetaxel (Q13_5_34)

description:
IDB-02 TNBC PDX model resistant to docetaxel
Sample name: Q13_5_34


title: tumor from IDB-02 TNBC PDX model resistant to docetaxel (Q1305_39)

description:
IDB-02 TNBC PDX model resistant to docetaxel
Sample name: Q1305_39


title: LuCaP_176_s5_ET1489

description: LuCaP 176 PDX tumor


title: PC3_siREST_1

description: PC-3 human prostate tumor cell line transfected with REST siRNA

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

growth_protocol: Cells were cultured in RPMI-1640 Media (Gibco, Life Technologies) with 10% fetal bovine serum (Atlanta Biologicals).

value: PC-3 (ATCC CRL-1435)


title: PC3-siREST_2

source_name: PC-3 human prostate tumor cell line transfected with REST siRNA


title: tumor from IDB-02 TNBC PDX model resistant to docetaxel (Q13_5_38)

description:
IDB-02 TNBC PDX model resistant to docetaxel
Sample name: Q13_5_38


title: tumor from IDB-03 luminal PDX model resistant but not treated with docetaxel (1070_79)

description:
IDB-03 luminal PDX model resistant but not treated with docetaxel
Sample name: 1070_79


title: PacMetUT1-KO1-siNCT

description: PacMet AR-null human prostate tumor cell line transfected with control siRNA


title: PacMetUT1-KO2-siREST

description: PacMet AR-null human prostate tumor cell line transfected with REST siRNA


title: PC3-siNCT_2

description: PC-3 human prostate tumor cell line transfected with control siRNA


title: PC3_siNCT_1

source_name: PC-3 human prostate tumor cell line transfected with control siRNA


title: PacMetUT1-KO1-siREST

source_name: PacMet AR-null human prostate tumor cell line transfected with REST siRNA


title: C42B-siREST_2

description: C4-2B human prostate tumor cell line transfected with REST siRNA


title: tumor from IDB-04 luminal PDX model resistant but not treated with docetaxel (25_5_31)

description:
IDB-04 luminal PDX model resistant but not treated with docetaxel
Sample name: 25_5_31


title: Macrophage-like cells, control-DH82_0h_2


title: PacMetUT1-KO2-siNCT

source_name: PacMet AR-null human prostate tumor cell line transfected with control siRNA


title: Scramble shRNA-1

description:
Sample 1
PC3-shcon-1


title: C42B-siNCT_2

description: C4-2B human prostate tumor cell line transfected with control siRNA


title: tumor from IDB-02 TNBC PDX model sensitive to docetaxel (13_5_60)

description:
IDB-02 TNBC PDX model sensitive to docetaxel
Sample name: 13_5_60


title: 12A12LN31

description: 12-20A 12weeks UPDATED.csv


title: tumor from IDB-02 TNBC PDX model sensitive to docetaxel (13_5_59)

description:
IDB-02 TNBC PDX model sensitive to docetaxel
Sample name: 13_5_59


title: tumor from IDB-03 luminal PDX model resistant and treated with docetaxel (Q1070_19)

description:
IDB-03 luminal PDX model resistant and treated with docetaxel
Sample name: Q1070_19


title: C42B_siNCT_1

source_name: C4-2B human prostate tumor cell line transfected with control siRNA


title: C42B_siREST_1

source_name: C4-2B human prostate tumor cell line transfected with REST siRNA


title: tumor from IDB-01 TNBC PDX model resistant to docetaxel (Q24_11_45)

description:
IDB-01 TNBC PDX model resistant to docetaxel
Sample name: Q24_11_45


title: SKOV3-CON_CAS9-3

city: Ann Arbor

first: Armand

last: Bankhead

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan

data_processing:
Reads were mapped to GRCh38 using STAR v2.5.2
Gene quantifications were calculated using Cufflinks v2.2.1 to quantify refGene annotations. Gene read counts calculated using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and read counts per gene for each Sample

source_name: ovary

growth_protocol: OVCAR3, OVCAR8 and SKOV3 cells were purchased from National Cancer Institute, Bethesda, MD. HEY cells were kindly provided as a gift by Dr. Louis Dubeau (University of Southern California, CA). Mesenchymal stem cells were kindly provided as a gift by Dr. Karen McLean (University of Michigan, MI). All cells were grown as monolayers at 37°C in a humidified atmosphere of 5% CO2. All experiments were carried out using cells in the exponential growth phase. Cells were routinely checked for mycoplasma contamination with PlasmoTest (InvivoGen).

extract_protocol:
Cells were lysed with TRIzol® Reagent (ThermoFisher Scientific) at room temperature. RNA was further purified with DirectZol kit (Zymo Research, Irvine, CA).
RNA quality was assessed using the TapeStation (Agilent Technologies, Santa Clara, CA). Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared with TruSeq Stranded mRNA Library Prep (Illumina) per the supplier’s protocol with 1ug of RNA and 12 cycles of PCR amplification. Libraries were checked for size on the TapeStation and quantified using the Kapa Biosystems library quantification kit (Illumina). The libraries were barcoded, pooled and sequenced on the HiSeq 4000 at the University of Michigan DNA Sequencing Core using 50bp single-end 50bp (OVCAR3 and OVCAR8) and paired-end 50bp (SKOV3) sequencing.

treatment_protocol: Three STAT3 CRISPR guide sequences (1: ACAATCCGGGCAATCTCCAT, 2: CATTCGACTCTTGCAGGAAG, 3: GAAACTGCCGCAGCTCCATT) were designed and purchased from Invitrogen™, ThermoFisher Scientific. In vitro transcription of the gRNA template was carried out with the MEGAshortscript™ T7 Transcription Kit using the manufacturer’s recommended conditions. The gRNA product was purified with the MEGAclearTM Transcription Clean-Up kit as described in the manual. RNA concentration was determined using a NanoDrop spectrophotometer. The percentage of locus-specific indel formation was measured and selected using the GeneArt® Genomic Cleavage Selection Kit (Invitrogen™, ThermoFisher Scientific). Target sequences were cloned into a cleavage selection vector, which contains the orange fluorescence protein (OFP) as a reporter for fluorescence-based cell sorting. The percentage of OFP-positive cells indicates the cleavage activity of CRISPR-Cas9. CRISPR-Cas9 mediated genome editing was performed as previously reported [42]. At 48 h post-transfection, the cells were harvested for analysis of genome modification efficiency using the GeneArt Genomic Cleavage Detection kit (Invitrogen™, ThermoFisher Scientific). Additionally, cells were analyzed by flow cytometry to identify the OFP-positive population and were sorted by FACS. A single clone isolation was further performed on sorted OFP-positive cells. The clones were screened by Western blot to assess STAT3 protein expression levels. STAT3 sequence in KO cells was confirmed with a homozygous 1 bp deletion by Sanger sequencing.

tag: genotype/variation

value: Casp9 control


title: OV8-KO-3

value: STAT3 KO


title: SKOV3-CON_CAS9-1


title: SKOV3-CON_CAS9-2


title: tumor from IDB-01 TNBC PDX model resistant to docetaxel (Q24_1_41)

description:
IDB-01 TNBC PDX model resistant to docetaxel
Sample name: Q24_1_41


title: SKOV3-STAT3_KO-2


title: SKOV3-STAT3_KO-1


title: SKOV3-STAT3_KO-3


title: OV8-KO-1


title: tumor from IDB-01 TNBC PDX model sensitive to docetaxel (24_11_39)

description:
IDB-01 TNBC PDX model sensitive to docetaxel
Sample name: 24_11_39


title: OV3-KO-3


title: OV3-KO-2


title: OV8-WT-2

value: parental control


title: OV8-WT-3


title: OV3-WT-3


title: tumor from IDB-01 TNBC PDX model sensitive to docetaxel (24_11_40)

description:
IDB-01 TNBC PDX model sensitive to docetaxel
Sample name: 24_11_40


title: OV8-KO-2


title: OV3-WT-1


title: OV8-WT-1


title: OV3-WT-2


title: SKOV3-KO-3


title: tumor from IDB-01 TNBC PDX model resistant to docetaxel (Q24_11_39)

description:
IDB-01 TNBC PDX model resistant to docetaxel
Sample name: Q24_11_39


title: SKOV3-WT-3


title: SKOV3-WT-2


title: OV3-KO-1


title: SKOV3-KO-2


title: SKOV3-WT-1


title: NC [E0-D0-3_S1_L001]

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
kallisto to get read counts
DEseq2 to normalize and detect DE genes
star aligner to align reads
star-fusion to detect gene fusion
Genome_build: hg19
Supplementary_files_format_and_content: read count

source_name: NC

growth_protocol: MV4;11 cells were gown in RPMI supplemented with 10% FBS and 1% PenStrep under standard culture conditions. Cells were plated in 1ml at 50,000 cells/ml

extract_protocol:
mRNA was isolated from cells three days after sort using qiagen RNeasy kit
Library prep was performed using Illumina HiSeq, 2x150bp configuration. ~350M raw paired-end reads per lane, Illumina HiSeq 4000

treatment_protocol: MV4;11 AML cells were exposed to the DOT1L inhibitor EPZ5676 at 0.08 and 0.16 uM, and the EZH2 inhibitor GSK126 at 0.3 uM for 7 days. Fresh media and compound were supplied on day 4. RNA was isolated using RNeasy (Quiagen) and submitted for RNA-Seq

value: human KMT2A rearranged MV4;11 AML cell line


title: NC [E0-D0_S1_L001]


title: Dot1lhigh [E0-D0-16-3_S6_L001]

value: DOT1L inhibitor EPZ5676 at 0.16 uM


title: Dot1llow [E0-D0-08-2_S10_L002]

value: DOT1L inhibitor EPZ5676 at 0.08 uM


title: Dot1llow [E0-D0-08_S4_L001]


title: Dot1llow [E0-D0-08-3_S4_L001]


title: Combohigh [E0-3-D0-16_S5_L001]

source_name: Combohigh

value: DOT1L inhibitor EPZ5676 at 0.16 uM + EZH2 inhibitor GSK126 at 0.3 uM for 7 days


title: Ezh2 [E0-3-D0_S2_L001]

value: EZH2 inhibitor GSK126 at 0.3 uM for 7 days


title: Ezh2 [E0-3-D0-19_S8_L002]


title: Combolow [E0-3-D0-08-3_S3_L001]

source_name: Combolow

value: DOT1L inhibitor EPZ5676 at 0.08 uM + EZH2 inhibitor GSK126 at 0.3 uM for 7 days


title: Combolow [E0-3-D0-08_S3_L001]


title: Combohigh [E0-3-D0-16-3_S5_L001]


title: Combohigh [E0-3-D0-16-21_S11_L002]


title: Ezh2 [E0-3-D0-3_S2_L001]


title: F_Empagliflozin

first: Yong-ho

last: Lee

address: Yonsei-ro 50-1, SeoDaeMunGu

institute: Yonsei University College of Medicine

data_processing:
Original files generated by the sequencing instrument were imported to the CLC Genomic Workbench software 9.0.1., with a library size of 200-500 bp.
Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.0.1.
Genome_build: Genome_build: Homo sapiens (hg19)
Supplementary_files_format_and_content: RPKM

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 1% penicillin, 1% streptomycin, and 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated from macrophage lysates obtained from PBMCs of 7 individuals using a Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To generate human macrophages, cells were incubated with 20 ng/mL M-CSF for 3 days, followed by freshly replacing same medium with 10 ng/mL M-CSF every 2 days (total 7 days).

tag: subject status

value: diabetic patient

value: Empagliflozin

value: Macrophage


title: C_Glimepiride

value: Glimepiride


title: E_Empagliflozin


title: Combolow [E0-3-D0-08-20_S9_L002]


title: NC [E0-D0-1_S7_L002]


title: D_Empagliflozin


title: Dot1lhigh [E0-D0-16_S6_L001]


title: B_Glimepiride


title: G_Empagliflozin


title: A_Glimepiride


title: T47D_LTED

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description:
expression_matrix.rawCounts.txt.gz
expression_matrix.normalizedCounts.txt.gz

data_processing:
cellRanger (v2.1.1) was run on the raw data using GRCh38 annotation (v1.2.0). Output from cellRanger was loaded into R using the function load_cellranger_matrix_h5 from package cellranger (v1.1.0; genome = ”GRCh38”). Datasets were merged according to gene names.
A filter on cells showing at least 1,500 detected genes per cell and at least 5,000 UMIs per cell was then applied. After that, reads mapping on mitochondrial genes were excluded. Before normalization, data were imported in Seurat (v2.3.4; PMID: 29608179) and scaled (NormalizeData function using normalization.method = "LogNormalize", scale.factor = 10000, followed by the ScaleData function).
A filtering step was then performed based on the cumulative level of expression (the sum of the Seurat-scaled values) of three housekeeping genes (GAPDH, RPL26 and RPL36, http://doi.org/10.1101/229815). Cells showing housekeeping gene expression in the bottom 1% were then excluded from further analyses. At last, genes expressed in less than 20 cells were excluded. Across-cells normalization was performed using the R package Scran (v1.6.9) (PMID: 27909575).
Raw counts were imported into a SCE object using the newSCESet function; size factors were calculated using computeSumFactors (sizes = seq(20, 250, 10)), on data pre-clustered through quickCluster.
Genome_build: GRCh38
Supplementary_files_format_and_content: expression_matrix.rawCounts.txt: expression matrix (raw counts), flat text file with tab delimiters; expression_matrix.normalizedCounts.txt: expression matrix (normalized counts), flat text file with tab delimiters.

molecule: polyA RNA

source_name: ERα positive breast cancer cells

growth_protocol: T47D cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal calf serum (FCS). T47D Long-term oestrogen-deprived cells (LTED) were derived from T47D after one year oestrogen deprivation as previously described and were maintained in phenol-red free DMEM containing 10% charcoal stripped fetal calf serum (SFCS) (PMID: 2632259). Both media were supplemented with 2 mM L-glutamine, 100 units/mL penicillin and streptomycin.

extract_protocol:
Single cells were prepared from a full population of T47D or LTED, or from sorting T47D CD44-GFP reporter cells by the level of GFP expression after 2 days of E2 deprivation. After centrifugation, single cells were washed with PBS and were re-suspended with a buffer (Ca++/Mg++ free PBS + 0.04% BSA) at 1,000 cells/µl. Captures were performed using the 10x Genomics Chromium platform, according to manufacturer guidelines and in order to obtain 5,000 cells per capture.
Libraries were generated using the 10x Genomics Chromium platform.

treatment_protocol: T47D cells were treated with E2 depleted medium for 2 days.

value: Long-term estrogen deprivation

value: E2 starvation


title: Runx1KO Replicate 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from P0 ovaries Runx1 KO

hyb_protocol: 4.6 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 3.2) and Expression Console (Version 1.2).

source_name: P0 ovaries Runx1 KO

label_protocol: Fifty (50) nanograms of total RNA were amplified and labeled as directed in the WT-Ovation Pico RNA Amplification System and Encore Biotin Module protocols.

extract_protocol: A ovary (newborn P0) was separated from the mesonephros and was used as one biological replicate (4 biological replicates were included for each genotype). Total RNA was isolated using Picopure extraction kit (Arcturus). RNA quality and concentration were determined using N Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, California)

treatment_protocol: All newborn mice used in this study resulted from the crossing between Runx1f/f; Foxl2+/- females with Sf1-cre+/Tg ;Runx1+/-;Foxl2+/- males. The genotype of the gonads used in this study is as follows: control: Runx1+/f Foxl2+/+ Sf1-cre+/+ ;    Runx1 KO: Runx1-/f Foxl2+/+ Sf1-cre+/Tg;    Foxl2 KO: Runx1+/f Foxl2-/- Sf1-cre+/+;     Runx1/Foxl2 dKO: Runx1-/f Foxl2-/- Sf1-Cre+/Tg;

value: ovaries

value: newborn


title: Runx1/Foxl2 dKO Replicate 4

description: Gene expression from P0 ovaries Runx1/Foxl2 double KO

source_name: P0 ovaries Runx1/Foxl2 double KO


title: Runx1KO Replicate 3


title: T47D_WM2d_CD44H

value: T47D CD44high facs-sorted

value: E2 starvation for 2 days


title: T47D_RM

value: T47D full population

value: E2 supplement


title: T47D_RM_CD44H


title: Runx1KO Replicate 4


title: Runx1/Foxl2 dKO Replicate 2


title: Runx1/Foxl2 dKO Replicate 1


title: Runx1/Foxl2 dKO Replicate 3


title: MCF7_WM7d_CD44L

data_processing:
cellRanger (v2.1.1) was run on the raw data using GRCh38 annotation (v1.2.0). Output from cellRanger was loaded into R using the function load_cellranger_matrix_h5 from package cellranger (v1.1.0; genome = ”GRCh38”). Datasets were merged according to gene names.
All cells sampled were retained except for flow-sorted CD44high and CD44low either in +E2 media or starved for two days, for which the top 5,000 cells in terms of UMIs per cell were considered.
A filter on cells showing at least 1,500 detected genes per cell and at least 5,000 UMIs per cell was then applied. After that, reads mapping on mitochondrial genes were excluded. Before normalization, data were imported in Seurat (v2.3.4; PMID: 29608179) and scaled (NormalizeData function using normalization.method = "LogNormalize", scale.factor = 10000, followed by the ScaleData function).
A filtering step was then performed based on the cumulative level of expression (the sum of the Seurat-scaled values) of three housekeeping genes (GAPDH, RPL26 and RPL36, http://doi.org/10.1101/229815). Cells showing housekeeping gene expression in the bottom 1% were then excluded from further analyses. At last, genes expressed in less than 20 cells were excluded. Across-cells normalization was performed using the R package Scran (v1.6.9) (PMID: 27909575).
Raw counts were imported into a SCE object using the newSCESet function; size factors were calculated using computeSumFactors (sizes = seq(20, 250, 10)), on data pre-clustered through quickCluster.
Genome_build: GRCh38
Supplementary_files_format_and_content: expression_matrix.rawCounts.txt: expression matrix (raw counts), flat text file with tab delimiters; expression_matrix.normalizedCounts.txt: expression matrix (normalized counts), flat text file with tab delimiters.

growth_protocol: MCF7 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal calf serum (FCS). Long-term oestrogen-deprived cells (LTED) were derived from MCF7 after one year oestrogen deprivation as previously described and were maintained in phenol-red free DMEM containing 10% charcoal stripped fetal calf serum (SFCS) (PMID: 26610607). Both media were supplemented with 2 mM L-glutamine, 100 units/mL penicillin and streptomycin. 10−8 M estradiol (E2758 Sigma) was added routinely to MCF7.

extract_protocol:
Single cells were prepared from a full population of MCF7 or LTED, or from sorting MCF7 CD44-GFP reporter cells by the level of GFP expression at different time points of E2 deprivation. After centrifugation, single cells were washed with PBS and were re-suspended with a buffer (Ca++/Mg++ free PBS + 0.04% BSA) at 1,000 cells/µl. Captures were performed using the 10x Genomics Chromium platform, according to manufacturer guidelines and in order to obtain 5,000 cells per capture.
Libraries were generated using the 10x Genomics Chromium platform.

treatment_protocol: MCF7 cells were treated with E2 depleted medium at 2, 4, and 7 days and sorted into CD44high and CD44low subpopulation.

value: MCF7 CD44low facs-sorted

value: E2 starvation for 7 days


title: MCF7_WM4d_CD44L

value: E2 starvation for 4 days


title: MCF7_WM7d_CD44H

value: MCF7 CD44high facs-sorted


title: MCF7_LTED

value: LTED


title: MCF7_WM4d_CD44H


title: Differentiating NSCs/NPCs, biological rep1

city: Hyderabad

first: Arvind

last: Kumar

state: Telangana

address: Uppal Road, Habsiguda

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

description: miRNA expression data from differentiating NSCs/NPCs

hyb_protocol: Biotin-labeled RNA sample was mixed with the hybridization cocktail, injected in the GeneChip miRNA arrays (Affymetrix) and then incubated at 48°C at 60 rpm for 16h for hybridization.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Analysis was done using Expression Console software (Affymetrix), where the*.CEL files were uploaded and using ‘MicroRNA Arrays RMA + DABG’ workflow, summarization file was generated

label: Biotin

source_name: Differentiating NSCs/NPCs

label_protocol: 1ug of total RNA was biotin-labeled using the FlashTag Biotin HSR RNA labeling kit (Genisphere), as per manufacturer’s instructions

growth_protocol: For the primary culture of NSCs/NPCs from DG of adult mice, the protocol described by Reynolds et al. was followed. Hippocampi were dissected from the adult mice, single cells were obtained after enzymatic treatment, washed and seeded in Neurocult medium with growth factors in it.

extract_protocol: Total RNA was isolated using mirVana RNA isolation kit (Ambion) according to manufacturer's instructions

treatment_protocol: Cells after dissociation of proliferating neurospheres were passaged and plated on coated dishes and kept in proliferating medium for 2 days. Thereafter proliferating medium was replaced with differentating medium and cells were allowed to differentiate for 7 days

value: hippocampus/dentate gyrus

value: Differentiating NSCs/NPCs

tag: molecule subtype

value: microRNA


title: Differentiating NSCs/NPCs, biological rep3


title: FoxI2KO Replicate 1

description: Gene expression from P0 ovaries Foxl2 KO

source_name: P0 ovaries Foxl2 KO


title: Differentiating NSCs/NPCs, biological rep2


title: MCF7_RM_CD44H


title: ctr4 Replicate 4

description: Gene expression from P0 ovaries control

source_name: P0 ovaries control


title: FoxI2KO Replicate 4


title: Runx1KO Replicate 1


title: ctr2 Replicate 2

description: Gene expression from P0 ovaries control


title: FoxI2KO Replicate 3


title: MCF7_RM

value: MCF7 full population


title: MCF7_RM_CD44L


title: FoxI2KO Replicate 2


title: ctr3 Replicate 3

description: Gene expression from P0 ovaries control


title: 946716-2

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq data was analyzed by following the procedure described here. Briefly, after sequence quality filtering at a cutoff of a minimum quality score Q20 in ≥90% bases, the good quality reads were aligned to the University of California Santa Cruz’s Mus musculus reference genome and transcriptome (build mm10) using the Burrows-Wheeler Aligner.43 The reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were combined to calculate as expression level for a corresponding transcript and further normalized based on reads per kilobase per million reads44 in order to compare transcription levels among samples. The transcripts with a low raw read count <100 in all the samples were excluded for downstream analysis. Gene expression value was transformed to the log2 base scale. Principal component analysis was first performed to assess the sample correlations using the expression data of all the genes. The DEGs in diabetic mice versus control mice were identified by the R package DEGseq for sorted GECs, and we selected the genes based on DEGseq adjusted P < 0.05 and 1.5-fold change. The limma test45 was applied for analysis of data in isolated glomeruli with a cutoff of P < 0.05 and 1.5-fold change. The Gene Ontology and pathway analysis for the differentially expressed genes were then performed using INGENUITY IPA (http://www.ingenuity.com/products/ipa) and online tool Enrichr.19 The read coverage of gene functional elements was also visualized by IGV tool (Integrative Genome Viewer; http://www.broadinstitute.org/igv/) from the genome alignment file. Heat map analysis was performed for the top 50 fold-changed DEGs with DEGseq test after median center transformed using Multiple Experiment Viewer (Web MEV) software (mev.tm4.org).46
Genome_build: mm10

source_name: Kidney glomerulus

extract_protocol:
Total RNA was extracted from glomeruli using Trizol method. Purified RNA underwent DNA digestion using RNase-free DNase set (79254, Qiagen). mRNA sequencing was performed at Beijing Genomics Institute.
Following RNA isolation, Poly-A selection was performed for obtain the mRNA for sequecing.

treatment_protocol: Glomeruli were isolated by Dynabead perfusion and cells were dissociated as described previously.10 Briefly, animals were perfused with 8-ml bead solution and 2-ml bead solution with enzymatic digestion buffer containing collagenase type II 300 U/ml, pronase E (1 mg/ml), and Dynase I (50 μg/ml), which was prewarmed at 37 °C. At the end of perfusion, kidneys were removed, decapsulated, minced into 1- mm3 pieces, and digested in 3 ml digestion buffer at 37 °C for 15 minutes on a rotator (100 rpm). Digested tissue was then passed through a 100-μm cell strainer and collected by centrifugation. The pellet was resuspended in 2  ml of Hanks buffered salt solution and glomeruli were washed 3 times and collected using a magnet. Separated glomeruli were resuspended in 2 ml digestion buffer and incubated at 37 °C for additional 40 minutes at 1400 rpm/min on a thermomixer. During the digestion period, the solution was vortexed every 10 minutes and sheared with a 27G needle every 15 minutes. The solution was then put on magnetic particle concentrator, and supernatants were pooled. The suspension was sieved through 40-μm cell strainer and centrifuged at 1500 rpm for 5 minutes at 4 °C. After the 2-step approach for primary cell purification, single cells were resuspended in 0.5 ml of Hanks buffered salt solution supplemented with 2% fetal bovine serum, 25 mmol/l N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid and 4',6-diamidino-2-phenylindole. Single-cell suspension was then sorted into EYFP+ and EYFP– population with a BD Aria II cell sorter (BD Biosciences, San Jose, CA) with a laser excitation at 488 nm and a sheath pressure of 30 psi. On average, 200,000 sorted GECs were obtained per mouse.

value: Kidney glomerulus

value: Control, ATG-treated


title: ctr1 Replicate 1

description: Gene expression from P0 ovaries control

value: ovaries


title: 946716-1


title: MCF7_WM2d_CD44H


title: 946715-2

value: Control, 5% DMSO vehicle-treated


title: MCF7_WM2d_CD44L


title: 945352-2

value: Streptozotocin, ATG-treated


title: 946715-1


title: Proliferating neurospheres, biological rep1

description: miRNA expression data from proliferating neurospheres

source_name: Neurospheres

value: Neurospheres


title: 945352-1


title: 945352-3


title: 945351-3

value: Streptozotocin, 5% DMSO vehicle-treated


title: 945351-2


title: Ptpn2-null_CD8_Tim-3_Rep2

first: Brian

middle: Christopher

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

department: Immunology

description:
Transferred Ptpn2-guide P14+ Tim-3+ CD8+ T cells isolated from spleens of mice 8 days after infection with LCMV Clone 13.
Isolation of CD8+ T cells: CD8+ MACS positive selection (Miltenyi) followed by FACS.
Accessible chromatin.

data_processing:
Quality trimming of Fastqs was performed using Trimmomatic.
Trimmed reads were aligned to the mm9 mouse genome using Bowtie2.
Aligned reads were sorted and biological replicates were merged for peak-calling with samtools.
Peak-calling was performed on merged bams using MACS2.
Union and merging of peaks across all condition was done using BEDtools.
BEDtools was used to quantify raw ATAC cut-sites within each peak in universe for each biological replicate to obtain a raw counts matrix.
Library size normalization was performed using DESeq2 to obtain a final normalized counts matrix.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: TDF file is a chromatin accessibility visualization file that can be loaded onto IGV.

source_name: CD8+ T-cells

growth_protocol: C57BL/6 mice were infected with 4 x 10^6 pfu LCMV Clone 13 via IV injection. On day 8 after infection, mice were sacrificed and spleens removed for CD8+ T cell isolation.

extract_protocol:
CD8+ MACS positive selection was performed on single-cell suspensions of splenocytes from chronically infected mice, followed by FACS.
Library construction was performed as per standard ATAC-seq protocol, as outlined in Corces et al., Nature Genetics 2016.

treatment_protocol: Mice were treated with 200 microgram CD4 depleting antibody (clone GK1.5) on days -1 and 1.

value: CD4-depleting antibody

tag: infection

value: LCMV Clone 13

tag: time point

value: 8 days post-infection


title: 945351-1


title: 934479


title: 934568

value: Control, ATG treated


title: Ptpn2-null_CD8_Tim-3_Rep1

tag: cell type

value: Transferred Ptpn2-guide P14+ Tim-3+ CD8+ T cells


title: DCISCAF2cy rep3

city: Tokyo

first: Yoshihiro

last: Mezawa

address: 2-1-1 Hongo, Bunkyo-ku

country: Japan

institute: Juntendo University

hyb_protocol: Amplified double stranded cDNA was generated using the WT-Ovation Pico RNA Amplification system (NuGEN #3300-12) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module v2 (NuGEN #4200-60) to manufacturer’s instructions. Overnight hybridization to GeneChip™ Human Genome U133 Plus 2.0 Arrays (Affymetrix #900466) was performed according to NuGEN FL-Ovation cDNA Biotin Module v2 user guide. Arrays were washed and stained using the Affymetrix GeneChip Fluidics Station and scanned using the Affymetrix GeneChip Scanner 3000 system with Autoloader, running on Affymetrix GeneChip Command Console Software.

data_processing: The  data of each breast cancer were processed by Robust Multi-array Average (RMA) method on R console.

source_name: DCIS

growth_protocol: The cells were cultured in DMEM/F-12 with GlutaMAX™ (Gibco) supplemented  with 5% FBS and penicillin-streptomycin.

extract_protocol: Total RNA was extracted using NucleoSpin RNA II (Takara).

treatment_protocol: no treatment

value: CAFs


title: DCISCAF2cy rep4

scan_protocol: Amplified double stranded cDNA was generated using the WT-Ovation Pico RNA Amplification system (NuGEN #3300-12) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module v2 (NuGEN #4200-60) to manufacturer’s instructions. Overnight hybridization to GeneChip™ Human Genome U133 Plus 2.0 Arrays (Affymetrix #900466) was performed according to NuGEN FL-Ovation cDNA Biotin Module v2 user guide. Arrays were washed and stained using the Affymetrix GeneChip Fluidics Station and scanned using the Affymetrix GeneChip Scanner 3000 system with Autoloader, running on Affymetrix GeneChip Command Console Software.


title: DCISCAF2cy rep2

label_protocol: Amplified double stranded cDNA was generated using the WT-Ovation Pico RNA Amplification system (NuGEN #3300-12) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module v2 (NuGEN #4200-60) to manufacturer’s instructions. Overnight hybridization to GeneChip™ Human Genome U133 Plus 2.0 Arrays (Affymetrix #900466) was performed according to NuGEN FL-Ovation cDNA Biotin Module v2 user guide. Arrays were washed and stained using the Affymetrix GeneChip Fluidics Station and scanned using the Affymetrix GeneChip Scanner 3000 system with Autoloader, running on Affymetrix GeneChip Command Console Software.


title: Ptpn2-null_CD8_Slamf6_Rep1

description:
Transferred Ptpn2-guide P14+ Slamf6+ CD8+ T cells isolated from spleens of mice 8 days after infection with LCMV Clone 13.
Isolation of CD8+ T cells: CD8+ MACS positive selection (Miltenyi) followed by FACS.
Accessible chromatin.

tag: strain


title: Ptpn2-null_CD8_Slamf6_Rep2

value: Transferred Ptpn2-guide P14+ Slamf6+ CD8+ T cells


title: DCISCAF2cy rep1


title: Ctrl_CD8_Tim-3_Rep2

description:
Transferred control-guide P14+ Tim-3+ CD8+ T cells isolated from spleens of mice 8 days after infection with LCMV Clone 13.
Isolation of CD8+ T cells: CD8+ MACS positive selection (Miltenyi) followed by FACS.
Accessible chromatin.


title: DCIScnt2cy rep4

value: control


title: Ctrl_CD8_Tim-3_Rep1

value: Transferred control-guide P14+ Tim-3+ CD8+ T cells


title: DCIScnt2cy rep2


title: DCIScnt2cy rep1


title: Ctrl_CD8_Slamf6_Rep2

description:
Transferred control-guide P14+ Slamf6+ CD8+ T cells isolated from spleens of mice 8 days after infection with LCMV Clone 13.
Isolation of CD8+ T cells: CD8+ MACS positive selection (Miltenyi) followed by FACS.
Accessible chromatin.


title: DCIScnt2cy rep3


title: Ctrl_CD8_Slamf6_Rep1

value: Transferred control-guide P14+ Slamf6+ CD8+ T cells


title: 969_N

city: London

first: Long

last: Hoang

address: Dovehouse Street

department: Genomic Medicine

country: United Kingdom

institute: Imperial College London

description: Global gene expression data for each extracted RNA sample was generated using Affymetrix Human Gene 1.1ST arrays and the GeneTitan system following Affymetrix protocols (Affymetrix, California, USA). Briefly taking 200ng of RNA amplified sense-strand complementary DNA (cDNA) was generated using the Ambion® WT Expression Kit (Life Technologies, California, USA).  This was then fragmented and labelled using the Affymetrix GeneChip® WT Terminal Labeling Kit (Affymetrix, California, USA) before hybridization onto the arrays and subsequent scanning on the GeneTitan system.  Poly-A RNA controls were included as per Affymetrix’s recommendations.

scan_protocol: GeneTitan system

data_processing: Quality of the expression data generated was assessed through arrayQualityMetrics (3.30.0) and the RLE (Relative Log Expression) and NUSE (Normalised Unscaled Standard Errors) metrics calculated within the Bioconductor package Oligo (1.38.0)

source_name: Normal Tissue

extract_protocol: Total RNA was extracted from tissues (stored in RNAlater) using the Qiagen RNeasy fibrous midi kit including the recommended homogenisation step with the Qiagen TissueRuptor® and disposable probes (Qiagen, Crawley, UK)

treatment_protocol: stored at -80°C

tag: age

tag: group

value: LUAD


title: 82_T

hyb_protocol: hybridization onto the arrays and subsequent scanning on the GeneTitan system

source_name: Tumour

label_protocol: 200ng of RNA amplified sense-strand complementary DNA (cDNA) was generated using the Ambion® WT Expression Kit (Life Technologies, California, USA).  This was then fragmented and labelled using the Affymetrix GeneChip® WT Terminal Labeling Kit (Affymetrix, California, USA)

value: LUSC


title: 689_N


title: 969_T


title: 24_N


title: 617_N


title: 617_T


title: 674_N


title: 1002_T


title: 223_N


title: 1002_N


title: 674_T


title: SKOV3-KO-1

tag: cell line

value: STAT3 KO


title: Sample2_PTPN2N1_Tim_3

description:
processed data file:
GSE119270_lcmv_raw_count_matrix.txt.gz

data_processing:
Basecalls performed using Illumina NextSeq500 and converted to fastq files using Bcl2fastq
Fastq files trimmed for poor quality reads using Trimmomatic with the parameters LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:16
Trimmed Fastq files were aligned to the mouse genome mm10 using Bowtie2
Aligned reads aggregated to a gene count matrix using HTSeq
Count normalization and differential expression analysis performed using DESeq2 (quality filter: gene expression threshold of 100,000)
Genome_build: mm10
Supplementary_files_format_and_content: normalized count matrix, tab-delimited text

source_name: cells isolated from the mouse after infection or tumor extraction.

growth_protocol: Antigen specific T cells (OT-1 specific for SIINFEKL peptide within OVA) were transferred to MC38-OVA tumors and allowed to respond and proliferate in response to the tumor for 7 days

extract_protocol:
Cells were sorted in pools of 500 cells into 25uL Qiagen RLT + 1%beta-mercaptoethanol (v/v) and frozen at -80C
Lysates were converted to cDNA following capture with Agencourt RNA Clean beads using the SmartSeq2 protocol as previously described (Trombetta et al, Curr Protoc Mol Biol, 2014)

value: spleen

value: CD8+ T cells

tag: sgrna

tag: phenotype


title: Sample2_PTPN2N1_Slam_1


title: Sample2_PTPN2N1_Slam_3


title: Sample2_PTPN2N1_Tim_2


title: Sample2_Ctrl_Tim_3

value: Control


title: Sample2_Ctrl_Tim_2


title: 82_N


title: Sample2_PTPN2N1_Tim_1


title: Sample2_Ctrl_Tim_1


title: Sample2_PTPN2N1_Slam_2


title: 689_T


title: 24_T


title: 223_T


title: 282_N


title: 931_N


title: 627_N


title: Sample2_Ctrl_Slam_3


title: Sample1_PTPN2N1_Slam_3


title: Sample1_PTPN2N1_Tim_2


title: Sample1_PTPN2N1_Tim_1


title: Sample1_PTPN2N1_Slam_2


title: Sample2_Ctrl_Slam_1


title: Sample1_PTPN2N1_Tim_3


title: Sample2_Ctrl_Slam_2


title: Sample1_Ctrl_Tim_2


title: Sample1_Ctrl_Tim_3


title: Sample1_Ctrl_Slam_1


title: Sample1_Ctrl_Slam_2


title: Sample1_Ctrl_Slam_3


title: Input_PTPN2N1_na_4

source_name: aliquot of the cells lysed for RNAseq at the time of transfer

value: input


title: Sample1_Ctrl_Tim_1


title: Input_PTPN2N1_na_3


title: 931_T


title: 1022_N


title: 1012_N


title: 822_N


title: 921_N


title: 612_N


title: 921_T


title: 208_T


title: 282_T


title: 363_T


title: Input_PTPN2N1_na_1


title: 208_N


title: Input_Ctrl_na_4


title: 627_T


title: 363_N


title: 612_T


title: 822_T


title: 937_N


title: 1012_T


title: Input_Ctrl_na_3


title: Defeated Mice, biological rep2

data_processing: Analysis was done using miRNA QC Tool version 1.0.33.0, where the*.CEL files were uploaded followed by background adjustment (by BC-CG Adjust), normalization (quantile) and finally the generation of summarization file (by median polish).

source_name: DG of the defeated mice

growth_protocol: Age and weight matched C57BL/6-NCrl male mice of 6-8 weeks’ age were used and maintained at 12/12 h light and dark cycle, 25°C ±1°C temperature, 60% relative humidity and standard chow and water ad libitum

treatment_protocol: Mice from the experimental group were subjected to 10 days of social defeat stress. Brain from both the control and experimental mice were dissected after conducting behavioral tests.

value: male

tag: treatment

value: chronic social defeat stress (CSDS)

value: dentate gyrus

value: microRNA


title: Defeated Mice, biological rep3

tag: tissue


title: Defeated Mice, biological rep1


title: Control Mice, biological rep4

source_name: DG of the control mice


title: Control Mice, biological rep3


title: 1022_T


title: Defeated Mice, biological rep4


title: Input_Ctrl_na_1


title: Control Mice, biological rep1


title: Control Mice, biological rep2


title: Proliferating neurospheres, biological rep2

value: hippocampus/dentate gyrus

value: Neurospheres


title: Input_Ctrl_na_2


title: 1011_N


title: nucl_0h_1

city: Kuopio

first: Mikko

middle: P

last: Turunen

address: Yliopistonranta 1 E

department: A. I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalling and demultiplexing were performed using the bcl2fastq Conversion Software from Illumina (service from Exiqon A/S, Vedbaek, Denmark).
Trim FastQ files using Trimmomatic (service from Exiqon A/S, Vedbaek, Denmark)
Align to reference genome Bowtie2 version 2.1.0, parameters  min_length 15, max_length 51, n_ceil “L,0,0.15”, iterations @adapter.length+1, seed mismatch 1 (service from Exiqon A/S, Vedbaek, Denmark)
Differential expression and data normalization was performed using DESeq2
Genome_build: miRBase v20 (GRCm38/mm10)
Supplementary_files_format_and_content: bam files were generated by Exiqon A/S, Vedbaek, Denmark and further processed to xlsx file by authors

source_name: Endothelial cell line

growth_protocol: C166 cells were grown on 150 mm cell culture dish in DMEM containing 10 % FBS and 1 % penicillin-streptomycin. Cells were split for experiments two days prior treatment so that they reach 80% confluency at the time of treatment.

extract_protocol:
Cells were fractionated into nuclear and cytoplasmic fractions and RNA isolated according to a protocol by Gagnon et al. (Gagnon K, Li L, Janowski BA, Corey DR. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nature Protocols 2014, vol. 9, no. 9, p.2045-60).
Library was prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (service from Exiqon A/S, Vedbaek, Denmark).

treatment_protocol: Cells were treated with hypoxia (2h or 24h) or normoxia (control). Hypoxia treatment was done using 1 % oxygen (InvivO2 Baker Ruskinn hypoxia chamber). Normoxia (control) cells were grown in normal humidified incubator (atmospheric oxygen levels, +37 °C, 5 % CO2).

value: Yolk sac -derived endothelial cell line

value: Nuclear RNA


title: cyto_2h_1

value: Cytoplasmic RNA


title: 362_N


title: 988_N


title: nucl_24h_2


title: Defeated Mice, biological rep3

hyb_protocol: Hybridization was done at 45°C for 16 h in the hybridization oven

scan_protocol: The arrays were scanned on the GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Analysis was performed using AltAnalyze v2.0.7 software and raw data were processed with standard RMA and DABG filtering options
the mapping file (that was used to map probe sets or transcript clusters to Ensemble genes) is linked as a Series supplementary file.

label_protocol: 200 ng of total RNA was reverse transcribed to sense strand cDNA by using WT Expression kit (Ambion), as per manufacturer’s instructions. It was then fragmented and labeled, and prepared for hybridization using the GeneChip WT Terminal Labeling and Hybridization kit (Affymetrix).

treatment_protocol: Mice from the experimental group were subjected to 10 days of social defeat stress. Brain from control and experimental mice was dissected after conducting behavioral tests.


title: 941_N


title: Control Mice, biological rep3

value: control


title: Defeated Mice, biological rep1


title: Defeated Mice, biological rep2


title: Late differentiating NSCs/NPCs, biological rep3

hyb_protocol: 1.5 µg purified Biotin-aRNA was mixed with hyb mix buffer and loaded on the BeadChip. Six samples were loaded separately on one BeadChip, which was then fixed in the Hyb chamber and kept in a hybridization oven for 16 h at 58°C with mild shaking

scan_protocol: BeadChips were scanned on the HiScan system (Illumina) using the BeadChip specific *.dmap files

data_processing: Image data files (*.idat) generated from scanner were imported to the GenomeStudio software (Illumina) and analyzed using the Binary Manifest Files (*.bgx) files in the Gene Expression module. Individual samples were assigned to their respective groups and data was exported after the background subtraction in the GeneSpring GX readable format (*.txt). *.txt files were loaded in the GeneSpring 12.0 software (Agilent) for the analysis and visualization of the data.

source_name: Differentiating NSCs/NPCs from late stage (day7)

label_protocol: RNA was labeled by TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip® (Illumina), according to manufacturer’s protocol

treatment_protocol: Cells after dissociation of proliferating neurospheres were passaged and plated on coated dishes and kept in proliferating medium for 2 days. Thereafter proliferating medium was replaced with differentating medium and cells were allowed to differentiate either for 2 or 7 days

value: differentiating NSCs/NPCs (late stage)


title: 380_N

value: LUSC


title: Early differentiating NSCs/NPCs, biological rep3

source_name: Differentiating NSCs/NPCs from early stage (day2)

value: differentiating NSCs/NPCs (early stage)


title: Late differentiating NSCs/NPCs, biological rep2


title: Control Mice, biological rep2


title: Input_PTPN2N1_na_2

value: spleen


title: 253_N


title: 878_N

value: LUAD


title: 687_N


title: Late differentiating NSCs/NPCs, biological rep1


title: Early differentiating NSCs/NPCs, biological rep1


title: Proliferating neurospheres, biological rep3

value: proliferating neurospheres


title: Early differentiating NSCs/NPCs, biological rep2


title: cyto_0h_2


title: Control Mice, biological rep1


title: 1023_N


title: 937_T


title: cyto_0h_1


title: BDE-47 PND120 sample 24

city: Amherst

first: Alexander

last: Suvorov

address: 149A - Goessmann,  686 – N. Pleasant Str.

department: Department of Environmental Health Sciences

institute: University of Massachusetts Amherst

data_processing:
mapping by Bismark (version 0.16.1) and bowtie-2 (version 2.2.9)
PCR-duplicates were removed using nudup.py
Differentially methylated regions (DMRs) were identified using MethPipe
DMR spatial annotations  using closest-features (v. 2.4.25) tool from bedOps package
Genome_build: rn6
Supplementary_files_format_and_content: xlsx files containing for all significant (q<0.05) DMRs the following information: DMRs' coordinates, number of CpGs per DMR, % change in methylation, nearest gene and distance from gene

organism: Rattus norvegicus

source_name: caudal epididimal sperm

growth_protocol: Seven-week-old Wistar rats were purchased from Charles River Laboratories (Kingston, NY, USA) on the sixth day of pregnancy, housed in a temperature- and humidity-controlled room with a 12-h light cycle and maintained at 23±2 °C. All rats were fed ad libitum with a rodent chow (Prolab Isopro RMH 3000, Cat. # 5P75, LabDiet, St. Louis, MO).

extract_protocol:
Upon collection via swim-up procedure, sperm samples were subjected to one-step density gradient centrifugation (40% Isolate, Irvine Scientific, USA) using Eppendorf 5810® centrifuge with bucket rotor A-4-44 and adapter for 15 ml conical tubes to remove somatic cells contamination. DNA was extracted from pellet using the rapid method (Wu H, de Gannes MK, Luchetti G, Pilsner JR. Rapid method for the isolation of mammalian sperm DNA. BioTechniques 2015;58:293-300).
Libraries for RRBS were constructed using 100 ng of epididymal sperm DNA and Ovation RRBS Methyl-Seq System (Cat. # 0353, NuGEN) as per the manufacture’s guidelines. Bisulfte conversion was performed using EpiTect Fast DNA Bisulfite Kit (Cat. # 59824, Qiagen)

treatment_protocol: Between pregnancy day 8 and postnatal day 21 (PND21) dams were fed daily from the tip of a pipette 0.2 µl/gram body weight of vehicle (tocopherol stripped corn oil, MP Biomedicals, Solon, OH) or same volume of 1 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) daily (n=6 per exposure group). In the latter group it resulted in exposure level of 0.2 mg/kg body weight BDE-47 per day.

value: Wistar

value: caudal epididimal sperm

tag: postnatal day

tag: exposure


title: BDE-47 PND120 sample 23


title: nucl_0h_2


title: cyto_24h_2


title: nucl_2h_2


title: BDE-47 PND120 sample 22


title: BDE-47 PND120 sample 19


title: BDE-47 PND120 sample 20


title: nucl_24h_1


title: Control PND120 sample 18

value: Control


title: Control PND120 sample 17


title: Control PND120 sample 16


title: nucl_2h_1


title: Control PND120 sample 15


title: Input_xrn1_2

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

institute: Universitat de Valencia

data_processing:
Read file QC: Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering: Fastx clipper and Fastx collapser were used to remove Illumina adapters, filter reads shorter than 20 bases, and discard the ones with more than 30 Ns.
Genome alignment: Filtered reads were mapped to the yeast genome with Bowtie2 (ChIP-seq) using the yeast R64 (sacCer3) genome as reference
Genome_build: R64 (sacCer3)
Supplementary_files_format_and_content: RPKM-normalised coverage bigWig tracks for the individual ChIP-seq datasets generated with the suite of Python tools deepTools.

organism: Saccharomyces cerevisiae

source_name: xrn1Δ mutant_input

growth_protocol: Strains were grown at 30°C, with liquid cultures growing in an orbital shaking incubator at 180 rpm in YPD medium

extract_protocol:
The ChIP experiments were performed as previously described (Rodríguez-Gil et al., 2010), except that anti-Rpb3 (ab81859; Abcam) or anti-HA (3F10 Roche) antibodies and Sheep anti-Mouse or anti-Rat IgG Dynabeads (Invitrogen) were used.
Samples were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina, following the manufacturer's instructions.

value: xrn1{delta} mutant

value: Input DNA


title: BDE-47 PND120 sample 21


value: hippocampus/dentate gyrus


title: cyto_2h_2


title: 988_T

tag: gender


title: Input_xrn1_1

tag: genotype/variation


title: Control PND120 sample 14


title: IL6 KO TFH (2)

city: Birmingham

first: Andre

last: Ballesteros-Tato

state: Al

address: 1825 University Blvd Shelby building.  Office 413

department: Medicine, Division of Clinical Immunology and Rheumatology

institute: University of Alabama at Birmingham

data_processing:
Basecalling was performed using Illumina's bcl2fastq version 2.18.0.12
ATAC-Seq reads were aligned using Bowtie2 version 2.3.4.1 with parameters -X 2000
Duplicates were removed with Picard tools version 2.9.2
Peaks were called using MACS2 version 2.1.1 with parameters -B, -q 0.05, --call-summits, --nomodel, --nolambda, --keep-dup all
Normalized bedGraph files were created using deepTools version 3.0.1 bamCoverage with parameters -of bedgraph, --normalizeTo1x 2150570000, --ignoreForNormalization chrX chrM, --extendReads, --binSize 10
Genome_build: mm10 UCSC
Supplementary_files_format_and_content: bedGraph files containing location of peaks

source_name: T cell

extract_protocol:
OTII (CD45.1+) cells were adoptively transferred into WT (C57Bl/6) and Il6-/- recipient mice. One day later, recipient mice were infected with PR8-OTII. Seven days after infection, 30,000 donor-derived CD45.1+CXCR5hiSLAMloCD4+CD19- TFH and CD45.1+CXCR5loSLAMhi CD4+CD19- Teff cells were sorted from the mLN of WT and Il6-/- recipient mice.
Nextera primers were used for library amplification.

treatment_protocol: Both Wild-type and IL6 KO mice were infected with influenza.

tag: genotype

value: mediastinal Lymph node

value: CD4+ T cell

tag: cell subset

value: TFH


title: Input_ccr4_2

source_name: ccr4Δ mutant_input

value: ccr4{delta} mutant

tag: molecule subtype


title: BDE-47 PND65 sample 12


title: IL6 KO TFH (1)


title: 380_T


title: IL6 KO TEFF (2)

value: TEFF


title: BDE-47 PND65 sample 11


title: 878_T


title: 1011_T


title: IL6 KO TEFF (1)


title: 362_T


title: BDE-47 PND65 sample 10


title: 253_T


title: 941_T


title: BDE-47 PND65 sample 9


title: B6 TFH (2)

value: wild-type


title: B6 TFH (1)


title: xrn1_2_HA-TFIIS

source_name: xrn1Δ mutant_HA

tag: chip antibody

value: anti-HA (3F10 Roche)

value: IP DNA


title: Input_wt2

value: WT


title: Input_wt1


title: 1023_T

value: LUAD


title: BDE-47 PND65 sample 8


title: 687_T


title: 983_N


title: 965_N


title: xrn1_1_HA-TFIIS


title: Input_ccr4_1


title: Control PND120 sample 13


title: B6 TEFF (2)

tag: cell type


title: BDE-47 PND65 sample 7

tag: strain


title: xrn1_2_Rpb3

source_name: xrn1Δ mutant_Rpb3

value: anti-Rpb3 (ab81859; Abcam)


title: B6 TEFF (1)


title: 851_N

tag: age


title: xrn1_1_Rpb3


title: 835_N

tag: group

value: LUSC


title: Control PND65 sample 5

value: Wistar

value: caudal epididimal sperm


title: Control PND65 sample 6

value: Control


title: Ptpn2-2 sgRNA Sample 2 Rep 2 [T5DP-200_r1_E11]

city: Boston

institute: Harvard Medical School

source_name: Ptpn2-2 sgRNA Sample 2

value: CD8+ T cells; tumor infiltrating T cells

tag: timepoint

value: Day 7


title: Ptpn2-2 sgRNA Sample 3 Rep 1 [T8a19DP_r1_D12]

source_name: Ptpn2-2 sgRNA Sample 3


title: Control PND65 sample 4


title: Control PND65 sample 3


title: ccr4_2_Rpb3

source_name: ccr4Δ mutant_Rpb3


title: Ptpn2-2 sgRNA Sample 2 Rep 1 [T3DP_r1_E12]


title: ccr4_1_HA-TFIIS

source_name: ccr4Δ mutant_HA


title: Control PND65 sample 2


title: Control PND65 sample 1


title: ccr4_1_Rpb3


title: Ptpn2-2 sgRNA Sample 1 Rep 1 [T20DP_r1_C11]

source_name: Ptpn2-2 sgRNA Sample 1


title: wt1_HA-TFIIS


title: Control-1 sgRNA Sample 1 Rep 2 [T19a8SP_r2_F12]

source_name: Control-1 sgRNA Sample 1


title: ccr4_2_HA-TFIIS