title: SKBR3_C1_Cy13_S52

description:
SKBR3_Cy13_S52_S52
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: OVX rep6

status: Public on Mar 30 2020

type: SRA

city: Shizuoka

first: Tomoya

last: Tanaka

address: 632-1 Mifuku, Izunokuni

country: Japan

institute: Asahi Kasei Pharma

library_source: transcriptomic

data_processing:
Sequencing was performed in the paired-end (100 x 2) mode on the HiSeq 2500 (Illumina) using a TruSeq SBS Kit v4-HS (Illumina).
Base call files for each cycle of sequencing were generated by the Real Time Analysis software program v1.18.64 (Illumina) and analyzed primarily and de-multiplexed into a FASTQ file using bcl2fastq v1.8.4 (Illumina).
Sequenced reads data were mapped onto the rn6 using the TopHat software program v2.0.14.
Fragments per kilobase per million (FPKM) values were computed by the Genedata Expressionist software program v9.1.4a (Genedata).
Genome_build: rn6
Supplementary_files_format_and_content: Excel (xlsx) file includes FPKM values and counts for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Dorsal root ganglia

extract_protocol:
The tissue samples were then immersed in RNAlater (Thermo Fisher Scientific) and stored at -80 °C until use. Total RNA was isolated using an RNeasy lipid-tissue mini kit with DNase I (QIAGEN). Sequence libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague-Dawley

tag: tissue

value: dorsal root ganglia (L4-5)

tag: age

value: 20 weeks old

tag: surgery

value: Ovariectomy

tag: treatment

value: Vehicle


title: SKBR3_C1_Cy13_S51

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
SKBR3_Cy13_S51_S51
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

data_processing:
library strategy: GTO sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Map reads to hg19 genome using STAR aligner
Separate aligned reads into exonic and allnonexonic
Realign exonic reads to reference genome hg19 using Kallisto and obtain read count tables
Realign allnonexonic reads to refenrence genome hg19 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
Genome_build: hg19
Supplementary_files_format_and_content: read count tables for RNAseq section of data, Varbin files with bincounts for DNAseq section

organism: Homo sapiens

source_name: SKBR3_Her2 overexpresson breast cancer cell line

growth_protocol: Cells were cultured in respective media at 37C, 5% CO2

extract_protocol:
Cells were trypsinized, diluted to 1000cells/ml and handpicked as single cells in 10x Lysis buffer
Single cells isolated into 10x Lysis Buffer with Rnase inhibitor were processed for mRNA transcription for first strand synthesis and cDNA amplification following SMART-Seq2 protocol. Samples were then treated ionically to fragment gDNA and cDNA to 400-700bp fragments. Later gDNA was amplified using SeqXE kit from Sigma Aldirch using manufacturer instructions. Libraries were made by end repair, Adenylation, Adapter ligation and PCR steps.

treatment_protocol: No treatment

tag: cell line

tag: cell line source

value: Breast

tag: culture type

value: Adherent cell line

tag: media

tag: molecule type

value: genomic DNA and mRNA


title: 59_IL13

type: RNA

city: Chicago

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

department: Human Genetics

institute: The University of Chicago

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scan protocol.

data_processing: All samples had RIN scores >9.6 The probe level raw intensity values across arrays were normalized using quantile normalization and background corrected normalized expression values were obtained for each probe using the R package lumi. Probes that were indistinguishable from background intensity (P<0.01), contained more than one HapMap SNP, or mapped to multiple locations in the genome were excluded. When multiple probes mapped to the same gene, the median probe expression value was used for that gene.

label: biotin

source_name: primary cultured airway smooth muscle cell

label_protocol: not provided

growth_protocol: ASMCs were cultured in 96-well Nusil coated plates in serum free media for 48 hours prior to cytokine exposure.

extract_protocol: RNA for gene expression studies were isolated from cell lysates using the QIAgen AllPrep Kit.

treatment_protocol: ASMCs were exposed to IL-13 (10ng/mL), IL-17 (3 ng/mL), IL-13+IL-17, or vehicle (10% FBS in PBS) for 24 hours prior to RNA and DNA extraction.

tag: cell type

tag: donor

tag: Sex

value: Female

tag: asthma

value: No

tag: race

value: AfricanAmerican


title: SKBR3_C1_Cy13_S38

description:
SKBR3_Cy13_S38_S38
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line


title: 4204_D1

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description: RNA from whole blood

hyb_protocol: 5 micrograms of purified DNA were fragmented into 50-200 bp fragments and were 3-labeled using Encore Biotin Module kit (Nugen). The resulting target was mixed with standard hybridization controls and B2 oligonucleotides following recommendations of manufacturer. The hybridization cocktail was heat-denatured at 99°C for 2 minutes, incubated at 50°C for 5 minutes and centrifuged at 16,000 g for 5 minutes to pellet the residual salts. The HERV-V3 microarrays were prehybridized with 200 µL of hybridization buffer and placed under stirring (60 rpm) in an oven at 50°C for 10 minutes. The hybridization buffer was then replaced by the denatured hybridization cocktail. Hybridization was performed at 50°C for 18 hours in the oven under constant stirring (60 rpm). Washing and staining were carried out according to the protocol supplied by the manufacturer, using a fluidic station: GeneChip fluidic station 450 (Affymetrix).

scan_protocol: The arrays were finally scanned using a fluorometric scanner: GeneChip scanner 3000 7G (Affymetrix)

data_processing: CEL files were transformed into matrix, normalized, adjusted for background noise (RMA normalization) and probes were summarized into probesets  with command apt-probeset-summarize (V 1.18.0)  with rma option . Batch effects were removed using COMBAT. Probesets were filtered when log2 signal was under 5.5 in more than 68% of samples.

source_name: Whole blood

label_protocol: The cDNA synthesis and amplification steps were performed from 16 ng of RNA using the Ovation Pico WTA System V2 kit (Nugen). Briefly, cDNA synthesis was done using a mixture of random and polydT primers, followed by the synthesis of the complementary strand. The Single Primer Isothermal Amplification (SPIA) was then performed with hybrid DNA/RNA primers sensitive to RNAse-H digestion, in the presence of a DNA polymerase with strong strand displacement activity. The resulting amplified cDNA was purified using the QIAquick purification kit (Qiagen), from which, total DNA concentration was measured using the NanoDrop 1000 spectrophotometer (Thermo Scientific) and the product quality was checked on the Bioanalyser 2100 (Agilent).

extract_protocol: Total RNA was extracted from whole blood using PAXgene Blood RNA kit (PreAnalytix) according to the manufacturer’s instructions. No sample with RNA integrity number ≤ 6 (bad RNA quality) was present.

treatment_protocol: Peripheral whole blood from ICU patients or healthy volunteers was collected from ICU patients or healthy volunteers was collected in PAXgeneTM Blood RNA tubes (PreAnalytix). Samples were stabilized at least 4h at room temperature after collection and frozen at -80°C following the manufacturer’s guidelines. For ICU patients, blood was collected at D1, D3 and D6, after ICU admission.

value: Whole blood

value: Patient

tag: diagnosis

value: septic shock


title: OVX rep5


title: OVX rep4


title: 49_Combined

value: primary cultured airway smooth muscle cell

value: Combined


title: SKBR3_C1_Cy13_S35

description:
SKBR3_Cy13_S35_S35
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 49_Vehicle


title: 2110_D6

description: RNA from whole blood


title: 71_IL17

value: Yes


title: 71_Vehicle


title: 49_IL17


title: OVX rep3

value: Sprague-Dawley

value: dorsal root ganglia (L4-5)

value: 20 weeks old


title: 2110_D3

description: RNA from whole blood


title: 49_IL13


title: 2110_D1

description: RNA from whole blood


title: 71_IL13


title: 1072_D6

description: RNA from whole blood


title: SKBR3_C1_Cy13_S33

description:
SKBR3_Cy13_S33_S33
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast


title: 1072_D3

description: RNA from whole blood


title: OVX rep2

value: Ovariectomy

value: Vehicle


title: SKBR3_C1_Cy11_S50

description:
SKBR3_Cy11_S50_S50
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Adherent cell line

value: genomic DNA and mRNA


title: 1072_D1

description: RNA from whole blood


title: SKBR3_C1_Cy13_S34

description:
SKBR3_Cy13_S34_S34
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: Sham rep8

value: Sham


title: Sham rep7


title: SKBR3_C1_Cy11_S48

description:
SKBR3_Cy11_S48_S48
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line


title: OVX rep1


title: Sham rep6


title: SKBR3_C1_Cy11_S47

description:
SKBR3_Cy11_S47_S47
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy11_S49

description:
SKBR3_Cy11_S49_S49
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: 71_Combined

value: Female

value: AfricanAmerican


title: Sham rep5


title: 2066_D1

description: RNA from whole blood

value: Whole blood

value: Patient

value: septic shock


title: MC2

type: genomic

city: Nanjing

first: Feng-Jie

last: Jin

address: 159 Longpan Road

country: China

institute: Nanjing Forestry University

description: Geochip data from triplicate field plots for MC treatment

hyb_protocol: Hybridization was performed with a GeoChip 5.0 array chip on a hybridization station (MAUI, BioMicro Systems, Salt Lake City, UT, USA)  at 42°C for 16 hours.

scan_protocol: Scanning was performed with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Madison, WI, USA),  following their standard operating protocol.

data_processing:
The raw microarray data was processed by GeoChip Microarray Data Manager pipeline (http://ieg.ou.edu/microarray/) as previously described
GeoChip-normalized, averaged gene-level signal intensity

molecule: genomic DNA

organism: uncultured soil microorganism

source_name: Soil sample

label_protocol: Purified DNA was labeled with the fluorescent dye Cy-3 (GE Healthcare, Little Chalfont, UK) using random primers, and the Klenow fragment of DNA polymerase I

growth_protocol: Genomic DNAs were extracted directly from soil samples

extract_protocol: Genomic DNAs were extracted from the soil samples, using the FastDNA Spin Kit for Soil (MP bio., US), according to the manufacturer’s protocol.

treatment_protocol: We applied five treatments:(1) control (CC), (2) biogas slurry applied at the rate of 250 m3 ha-1 (MC), (3) biogas slurry at the rate of 250 m3 ha-1) combined with biochar at the rate of 80 t ha-1 (MM) , (4) biogas slurry at the rate of 375 m3 ha-1 (HC), and (5) biogas slurry at the rate of 375 m3 ha-1 combined with biochar at the rate of 120 t ha-1 (HH).

value: Biogas slurry treatment (250 m3 ha-1)


title: 45_IL17

value: primary cultured airway smooth muscle cell

value: Male

value: Yes


title: 45_IL13


title: SKBR3_C1_Cy11_S45

description:
SKBR3_Cy11_S45_S45
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 45_Vehicle


title: 2066_D6

description: RNA from whole blood


title: Sham rep4

value: Sprague-Dawley

value: dorsal root ganglia (L4-5)

value: 20 weeks old


title: SKBR3_C1_Cy17_S13

description:
SKBR3_Cy17_S13_S53
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast

value: Adherent cell line


title: 2066_D3

description: RNA from whole blood


title: 65_IL13

value: EuropeanAmerican


title: 65_Vehicle

value: Vehicle


title: HV19

description: RNA from whole blood

treatment_protocol: Peripheral whole blood from ICU patients or healthy volunteers was collected from ICU patients or healthy volunteers in PAXgeneTM Blood RNA tubes (PreAnalytix). Samples were stabilized at least 4h at room temperature after collection and frozen at -80°C following the manufacturer’s guidelines. For ICU patients, blood was collected at D1 and D3/4, after ICU admission.

value: HV

value: healthy

tag: mhla-dr expression


title: Sham rep3

tag: strain

value: Sham


title: 65_Combined

value: Combined


title: 87_D3

description: RNA from whole blood

tag: tissue

value: Whole blood

value: Patient

value: septic shock

value: low


title: SKBR3_C1_Cy11_S46

description:
SKBR3_Cy11_S46_S46
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line

value: genomic DNA and mRNA


title: BT549_Cy13_S15

description:
B5549_Cy13_S9
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

source_name: BT549_Triple negative breast cancer cell line

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: 216_D1

description: RNA from whole blood


title: 216_D3

description: RNA from whole blood


title: Sham rep2

value: Sprague-Dawley

value: dorsal root ganglia (L4-5)

tag: age


title: 198_D3

description: RNA from whole blood


title: HV18

description: RNA from whole blood


title: BT549_Cy13_S14

description:
B5549_Cy13_S15
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

value: BT549_Triple negative breast cancer cell line

value: Breast


title: BT549_Cy13_DNA_S16

description:
BT549_DNA_S16
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

value: Adherent cell line


title: 87_D1

description: RNA from whole blood


title: BT549_Cy13_S12

description:
B5549_Cy13_S13
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: 198_D1

description: RNA from whole blood


title: T_3

city: Zhengzhou

first: Gaopeng

last: Yuan

state: Henan

address: Weilai Road Nanduan

institute: CAAS

data_processing:
BGISEQ-500 software used for basecalling.
The original sequencing data contain reads with low quality, joint contamination and high unknown base N content, which should be removed before data analysis to ensure the reliability of the results.
gene expression levels were calculated by FPKM (fragments per kilobase million)
Genome_build: GDDH13
Supplementary_files_format_and_content: FPKM

organism: Malus domestica

source_name: apple callus

growth_protocol: For stable expression, the callus of ‘Orin’ apple was first infiltrated in the resuspending for 15 minutes, then was washed with sterile water for 3 times and placed in a petri dish covered with filter paper for absorbing the water. Then callus was transferred to the subculture medium (MS+2.0 mg L-1 2,4-D+0.5 mg L-1 NAA+2.0 mg L-1 6-BA, pH 5.8) for 22℃ dark culture for 2 days, and then transferred to the subculture medium containing 300 mg L-1 cephalosporin and 30 mg L-1 kanamycin for screening resistant callus.

extract_protocol:
Skins were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.RNA was extracted from 200 mg fruit skin using the RNeasy Plant Mini Kit (Tiangen, China) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISEQ-500

treatment_protocol: The resistant callus was subcultured for several times to obtain stable resistant callus, then the callus was sampled then directly flash-frozen in liquid nitrogen and stored at -80℃ immediately prior to RNA extraction.

value: fruit

tag: developmental stage

value: MdMLP423 transgenic


title: T_2


title: BT549_Cy13_S13

description:
B5549_Cy13_S14
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy13_S11

description:
B5549_Cy13_S12
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: T_1


title: Sham rep1

value: 20 weeks old

tag: surgery

tag: treatment

value: Vehicle


title: CK_3

value: non-transgenic


title: 45_Combined

value: primary cultured airway smooth muscle cell

value: Combined

value: Male

value: Yes

value: AfricanAmerican


title: 42_Vehicle

value: Female

value: No

value: EuropeanAmerican


title: 42_IL17


title: 65_IL17


title: 63_IL13


title: 42_Combined


title: 63_Vehicle


title: CK_2


title: BT549_Cy13_S10

description:
B5549_Cy13_S11
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

tag: cell line

tag: cell line source

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin

value: genomic DNA and mRNA


title: BT549_Cy13_S9

description:
B5549_Cy13_S10
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

value: BT549_Triple negative breast cancer cell line

value: Breast

tag: culture type

tag: media


title: BT549_Cy11_S69

description:
BT549_Cy11_S69_S69
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

value: Adherent cell line

tag: molecule type


title: CK_1

value: fruit


title: 157_D3

description: RNA from whole blood

value: Whole blood

value: Patient

value: septic shock

value: low


title: 81_D3

description: RNA from whole blood


title: 142_D3

description: RNA from whole blood

value: high


title: 157_D1

description: RNA from whole blood


title: 81_D1

description: RNA from whole blood


title: BT549_Cy11_S67

description:
BT549_Cy11_S67_S67
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: 142_D1

description: RNA from whole blood


title: BT549_Cy11_S64

description:
BT549_Cy11_S64_S64
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S66

description:
BT549_Cy11_S66_S66
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S61

description:
BT549_Cy11_S61_S61
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: Stim_Experiment

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

description:
Sample 3
NK and T cells stimulated with PMA/ Ionomycin
Samples labeled as ‘AbSeq’ also have RNA sequencing data

data_processing:
Library strategy: AbSeq + RNAseq
Sample 1 aligned RNA reads using PBMC_Rhapsody_amplicons.fasta and aligned protein reasd using AbSeq_41plex.fasta
Sample 2 aligned RNA reads using PBMC_Rhapsody_amplicons.fasta and aligned protein reasd using AbSeq_38plex.fasta
Sample 3 aligned RNA reads using BD_Rhapsody_T_Cell_Expression_Panel_Hs.fasta and aligned protein reasd using AbSeq_Stim.fasta
FASTQ files were processed with BD Rhapsody Analysis Pipeline hosted by SevenBridges Genomics
FASTQ files were processed with CellRanger software v2.1.1 and Donor 3 sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: Frozen PBMC

extract_protocol:
RNA was extracted using BD Rhapsody or 10x genomics protocols
single-cell RNAseq

treatment_protocol: T and NK cells were stimulated for 1 hour with PMA/ Ionomycin

tag: cell type

value: PBMC

tag: phenotype

value: NK and T cells

tag: individual(s)

value: Donor 5

value: PMA/ Ionomycin


title: BT549_Cy11_S58

description:
BT549_Cy11_S58_S58
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: 69_Vehicle

value: primary cultured airway smooth muscle cell

tag: donor

value: Vehicle

tag: Sex

value: Male

tag: asthma

value: No

tag: race


title: BT549_Cy11_S56

description:
BT549_Cy11_S56_S56
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

value: BT549_Triple negative breast cancer cell line

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin

value: genomic DNA and mRNA


title: 69_IL13

value: EuropeanAmerican


title: 63_IL17

value: Female


title: 69_IL17


title: 124_D1

description: RNA from whole blood

tag: tissue

value: Whole blood

value: Patient

tag: diagnosis

tag: mhla-dr expression


title: 95_D1

description: RNA from whole blood

value: septic shock


title: 95_D3

description: RNA from whole blood

value: high


title: human cancer colon tissue 14

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

state: CA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

institute: UCLA

description: Biological replicate 14 of 11-14

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v4.0 (8 x 60K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: human cancer colon tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: RNA was isolated using  TRIzol (Invitrogen product name) and subsequently the Qiagen  RNeasy mini Kit (cat 74104).  Column based.

treatment_protocol: Immediately after each biopsy the sampled tissue was frozen in liquid nitogen and stored in -800C.

value: colon

tag: disease state

value: cancer


title: BT549_Cy11_S55

description:
BT549_Cy11_S55_S55
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

value: Breast

value: Adherent cell line


title: human cancer colon tissue 12

description: Biological replicate 12 of 11-14


title: human cancer colon tissue 13

description: Biological replicate 13 of 11-14


title: 67_Vehicle

value: primary cultured airway smooth muscle cell

tag: treatment

tag: age


title: 67_IL13


title: 93_D3

description: RNA from whole blood


title: BT549_Cy11_S54

description:
BT549_Cy11_S54_S54
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

tag: cell line

tag: cell line source


title: 93_D1

description: RNA from whole blood


title: human cancer colon tissue 11

description: Biological replicate 11 of 11-14


title: 78_D3

description: RNA from whole blood


title: human normal colon tissue 7

description: Biological replicate 7 of 4-7

source_name: human normal colon tissue

value: normal


title: 69_Combined

value: Combined

value: Male


title: human normal colon tissue 6

description: Biological replicate 6 of 4-7


title: A375_Cy13_DNA

description:
A375_DNA_S33
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

source_name: A375_Melanoma cancer cell line

value: A375_Melanoma cancer cell line

value: Skin

tag: culture type

tag: media

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 78_D1

description: RNA from whole blood


title: HV3

description: RNA from whole blood

value: HV

value: healthy


title: 63_Combined

tag: cell type

value: Female

value: No

value: EuropeanAmerican


title: A375_Cy13_S31

description:
A375_Cy13_S31
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

tag: molecule type

value: genomic DNA and mRNA


title: HV16

description: RNA from whole blood

value: Whole blood


title: A375_Cy13_S30

description:
A375_Cy13_S30
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S29

description:
A375_Cy13_S29
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: 124_D3

description: RNA from whole blood

value: Patient

value: septic shock

value: high


title: A375_Cy13_S28

description:
A375_Cy13_S28
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Adherent cell line


title: A375_Cy13_S27

description:
A375_Cy13_S27
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: 44_IL13

value: primary cultured airway smooth muscle cell

value: Yes


title: 67_Combined

value: Combined


title: A375_Cy13_S26

description:
A375_Cy13_S26
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: A375_Melanoma cancer cell line


title: human normal colon tissue 5

description: Biological replicate 5 of 4-7

value: colon

value: normal


title: 42_IL13


title: 44_IL17


title: 44_Vehicle

value: Vehicle


title: 44_Combined


title: human normal colon tissue 4

description: Biological replicate 4 of 4-7


title: 175_D3

description: RNA from whole blood


title: 175_D1

description: RNA from whole blood


title: 67_IL17


title: 9_Combined


title: 9_IL17


title: 9_IL13


title: A375_Cy13_S25

description:
A375_Cy13_S25
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Skin

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 79_D3

description: RNA from whole blood

value: low


title: 68_D1

description: RNA from whole blood


title: 68_D3

description: RNA from whole blood


title: 9_Vehicle

value: Female

value: No

value: EuropeanAmerican


title: sample_18

city: Wageningen

first: Eiko

middle: E

last: Kuramae

state: Gelderland

address: Droevendaalsesteeg 10

department: Microbial Ecology

country: Netherlands

institute: NIOO-KNAW

data_processing:
Quality of the raw fastq files was checked and filtered with FastQC
Alignment was performed on the genome of WH15 using Bowtie2
Gene expression levels were quantified using software package RNASeq by Expectation Maximization (RSEM)
The matrix of fragment counts from each sample was used for the differential expression analysis via edgeR package
Genome_build: GWH15_04212016
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

organism: Granulicella sp. WH15

growth_protocol: Bacteria were grown in two sugar concentrations, based on solid (1.5% agarose) modified 1/10 TSB medium pH 5.0 (as described above) supplemented with 0.025% and 3% of cellobiose, for low and high sugar conditions, respectively

extract_protocol:
Aurum Total RNA kit (Biorad)
Kapa Biosystems Stranded RNA-Seq kit, using standard Illumina protocols

value: high sugar - 3% cellobiose


title: 34_Vehicle

value: Male


title: 79_D1

description: RNA from whole blood

value: Whole blood

value: Patient

value: septic shock


title: 67_D3

description: RNA from whole blood


title: 67_D1

description: RNA from whole blood


title: A375_Cy11_S47

description:
A375_Cy11_S47_S47
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Adherent cell line

value: genomic DNA and mRNA


title: sample_17

treatment_protocol: 0.025% and 3% of cellobiose, for low and high sugar conditions, respectively


title: sample_16


title: A375_Cy11_S45

description:
A375_Cy11_S45_S45
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: A375_Melanoma cancer cell line


title: sample_15

value: low sugar - 0.025% cellobiose


title: 62_D1

description: RNA from whole blood


title: A375_Cy11_S46

description:
A375_Cy11_S46_S46
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S48

description:
A375_Cy11_S48_S48
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S32

description:
A375_Cy13_S32
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: 62_D3

description: RNA from whole blood


title: A375_Cy11_S44

description:
A375_Cy11_S44_S44
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: sample_14


title: A375_Cy11_S43

description:
A375_Cy11_S43_S43
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: ATAC-seq_TSA_30'_rep2

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

library_source: genomic

data_processing:
[ChIP-seq]  We mapped ChIP-seq reads to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We generated coverage tracks for ChIP-seq samples, which were normalized to spike-in and Input samples.
[Pro-seq]  After trimming the adaptors and removing the reads that mapped to rRNAs, PRO-seq of DMSO, TSA 10 min, and TSA 30 min in two biological replicates were mapped to the Drosophila melanogaster (dm3) genome assembly using BWA with default parameters. To obtain the spike-in reads, we mapped the reads to the human (hg38) genome assembly and counted the reads that only mapped to hg38. We generated PRO-seq coverage tracks, normalized by the spike-ins, with separate strands.
[ATAC-seq]  The ATAC-seq samples of DMSO, TSA 10 min and TSA 30 min in two biological replicates were mapped to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) were used for further analysis.
Genome_build: dm3, hg38
Supplementary_files_format_and_content: bigwig for coverage

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were cultured at 25ºC in Schneider's Drosophila Medium (Gibco # 21720024), supplemented with 10% fetal bovine serum (FBS) and 100 Units/ml Pencillin and 100 µg/ml streptomycin.

extract_protocol:
PRO-seq: Nuclear RUN-on was performed using biotinlated NTPs on nuclei isolated from S2 cells treated with either DMSO or TSA for desired time. Sodium hydroxide was used to hydrolyse the biotynlated nascent RNA synthesised to average fragment size of 100-150. Hydrolysed fragment were isolated using streptavidin coated magnetic beads
ChIP-seq: Chromatin lysates prepared from difffrent treatments were cleared from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ATAC-seq: Crude nuclear extract suitable for ATAC-seq from S2 cells treated with drugs was prepared in ATAC lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2 0.1% IGEPAL), followed by tagmentation using Tn5 Transposase (Illumina, 15027865). Tagmented DNA was purified using Agencourt AMPure XP beads (Beckman coutler, A63880)
PRO-seq: 3' adaptors were ligated to isolated RNA which were decapped prior to 5' adaptor ligation. cDNA was generated from these adaptor ligated RNAs and libraries were generated uning Illumina Tru-seq small-RNA adaptors for sequencing.
ChIP-seq: Libraries from input and immunoprecipitated DNA were prepared with NEBNext® Ultra™ II  DNA Library Prep kit (NEB, E7645) .
ATAC-seq: DNA after Tagmentation were amplified using primers from Nextera Index Kit (Illumina, FC-121-1012).

treatment_protocol: HDAC inhibitor Trichostatin A (TSA) treatment was performed for 10 mins or 30 min on S2 cells resuspended in FBS free media at 400nM final concentration

value: Drosophila S2 cells


title: A375_Cy11_S42

description:
A375_Cy11_S42_S42
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: ATAC-seq_TSA_30'_rep1


title: A375_Cy11_S41

description:
A375_Cy11_S41_S41
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: 34_Combined

value: primary cultured airway smooth muscle cell

value: Combined


title: A375_Cy11_S40

description:
A375_Cy11_S40_S40
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Skin

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 34_IL17


title: A375_Cy11_S39

description:
A375_Cy11_S39_S39
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: 34_IL13


title: 46_D3

description: RNA from whole blood

value: low


title: ATAC-seq_TSA_10'_rep1


title: 46_D1

description: RNA from whole blood


title: 44_D3

description: RNA from whole blood

value: high


title: 44_D1

description: RNA from whole blood


title: sample_13


title: A375_Cy11_S38

description:
A375_Cy11_S38_S38
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: ATAC-seq_DMSO 10'_rep2

description: ATAC-seq_DMSO 10'_rep2

value: DMSO 10'


title: ATAC-seq_TSA_10'_rep2


title: ∆pas N7680 mRNA-seq

city: Eugene

first: Eric

last: Selker

state: Oregon

address: 1370 Franklin Blvd.

department: Biology

institute: University of Oregon

description: TACCGGAT_N7680_NCU04278_polyARNAseq_080818_S228_L007_R1_001

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
RNA-seq processing: Tools available on Galaxy (Afgan et al., 2018) were used to map mRNA-sequencing reads (intron size < 1kb) (Dobin et al, 2012) against the corrected N. crassa OR74A (NC12) genome (Galazka et al., 2016), count the number of reads per gene (Dobin et al., 2012) and determine differentially expressed genes with DESeq2 (Love et al, 2014).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp.
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 previously published replicates of wild type and ∆set-7 strains (both from Klocko et al. 2016; GSE82222). In addition they contain normalized counts for ∆pas replicates and an additional set of wild type replicates (totalling 4 wild type samples). We have also included the pairwise comparisons of wild type to ∆set-7 and wild type to ∆pas from DESeq2 (Love et al., 2014).

molecule: polyA RNA

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNAseI, amplification grade (Thermo Fisher Scientific), cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter), and RNA-seq libraries were prepared (KAPA Stranded mRNA-seq kit, KAPA Biosystems).

value: germinated conidia

tag: genotype

value: mat a; Dpas::nat-1


title: 43_D3

description: RNA from whole blood

value: Whole blood


title: A375_Cy11_S37

description:
A375_Cy11_S37_S37
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: ATAC-seq_DMSO_10'_rep1


title: ∆pas N7617 mRNA-seq

description: AATGACGC_N7617_NCU04278_polyARNAseq_080818_S227_L007_R1_001


title: 33_D3

description: RNA from whole blood

value: Patient


title: 36_D3

description: RNA from whole blood

value: septic shock


title: A375_Cy11_S36

description:
A375_Cy11_S36_S36
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Adherent cell line


title: 43_D1

description: RNA from whole blood


title: LV3_miR375_2

first: huawei

last: ni

state: jiangsu

address: No.24, Tongjiaxiang, Gulou District,

institute: China Pharmaceutical University

description: Expression data from gastric cancer cell line.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Clariom D human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Gastric cancer cell line SGC-7901 was infected with lentivirus overexpressing miR-375, and the cell fluorescence was observed after one week of puromycin selection to obtain gastric cancer cell line stably overexpressing miR-375.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gastric cancer cell line SGC-7901 was infected with lentivirus overexpressing miR-375.

value: Gastric cancer cell line

tag: genotype/variation

value: Stably overexpressing miR375


title: 33_D1

description: RNA from whole blood


title: 36_D1

description: RNA from whole blood


title: PRO-seq_TSA_30'_rep2

description:
Nascent RNA
PRO-seq_TSA_30'_rep2

data_processing:
Library strategy: PRO-seq
[ChIP-seq]  We mapped ChIP-seq reads to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We generated coverage tracks for ChIP-seq samples, which were normalized to spike-in and Input samples.
[Pro-seq]  After trimming the adaptors and removing the reads that mapped to rRNAs, PRO-seq of DMSO, TSA 10 min, and TSA 30 min in two biological replicates were mapped to the Drosophila melanogaster (dm3) genome assembly using BWA with default parameters. To obtain the spike-in reads, we mapped the reads to the human (hg38) genome assembly and counted the reads that only mapped to hg38. We generated PRO-seq coverage tracks, normalized by the spike-ins, with separate strands.
[ATAC-seq]  The ATAC-seq samples of DMSO, TSA 10 min and TSA 30 min in two biological replicates were mapped to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) were used for further analysis.
Genome_build: dm3, hg38
Supplementary_files_format_and_content: bigwig for coverage

tag: spike-in organism

value: Human-HEK-293 cells


title: A375_Cy11_S35

description:
A375_Cy11_S35_S35
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: A375_Melanoma cancer cell line

value: genomic DNA and mRNA


title: PRO-seq_TSA_30'_rep1

description:
Nascent RNA
PRO-seq_TSA_30'_rep1

value: Drosophila S2 cells


title: NC3

value: Control


title: wild type N3752 mRNA-seq

description: GATCAAGG_N3752_WT_polyARNAseq_080818_S222_L007_R1_001

value: mat A; WT


title: A375_Cy11_S34

description:
A375_Cy11_S34_S34
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Skin

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: LV3_miR375_1


title: wild type N3753 mRNA-seq

description: TCTTCGAC_N3753_WT_polyARNAseq_080818_S223_L007_R1_001

value: mat a; WT


title: LV3_miR375_3


title: ATRX_KO_rep3

city: harbin

first: Han

last: Bo

state: heilongjiang

address: nangang district haerbin medical university

institute: HMU

description: Gene expression data from ATRX knockout LN229 cells

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

data_processing: The data were analyzed with Command Console Software 4.0 using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US)/ Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) / Ovation® Pico WTA System V2(Cat#3302， NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200， NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 with 10% fetal bovine serum (Gibco, USA) and at 37°C in a humidified atmosphere with 5% CO2.

treatment_protocol: Briefly, cells were infected with viruses containing the CAS9 gene and selected with 10 mg/ml puromycin for 7 days. The cells were subsequently infected with virus carrying small guide (sg) RNAs designed for ATRX. The infection proceeded for 24 h and ATRX gene expression and KO was confirmed by western blot.

value: GBM cells

value: ATRX knockout


title: PRO-seq_TSA_10'_rep1

description:
Nascent RNA
PRO-seq_TSA_10'_rep1


title: ATRX_KO_rep2


title: ATRX_KO_rep1


title: A375_Cy11_S33

description:
A375_Cy11_S33_S33
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S32

description:
A375_Cy11_S32_S32
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: H24 rep3

city: Hangzhou

first: Yongming

last: Pan

address: No. 548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

description:
4_genes_fpkm_expression.txt
T3_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: abdominal aorta

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Tibetan minipig

tag: tissues

value: abdominal aorta

value: Atherosclerosis

tag: diet

value: High-fat diet for 24wk


title: H24 rep2

description:
4_genes_fpkm_expression.txt
T3_2


title: A375_Cy11_S31

description:
A375_Cy11_S31_S31
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Adherent cell line


title: A375_Cy11_S30

description:
A375_Cy11_S30_S30
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: PRO-seq_DMSO_rep2

description:
Nascent RNA
PRO-seq_DMSO_rep2

value: DMSO


title: NC2

value: Gastric cancer cell line


title: PRO-seq_DMSO_rep1

description:
Nascent RNA
PRO-seq_DMSO_rep1

value: Human-HEK-293 cells


title: ChIPSeq_K27ac_TSA_30'_rep2

tag: chip antibody


title: NC1


title: H8 rep3

description:
4_genes_fpkm_expression.txt
T2_3

value: Hypercholesterolemia

value: High-fat diet for 8wk


title: ChIPSeq_K27ac_TSA_30'_rep1

value: Drosophila S2 cells


title: A375_Cy11_S29

description:
A375_Cy11_S29_S29
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: A375_Melanoma cancer cell line

value: genomic DNA and mRNA


title: H8 rep2

description:
4_genes_fpkm_expression.txt
T2_2


title: H24 rep1

description:
4_genes_fpkm_expression.txt
T3_1


title: ATRX_NC_rep2

description: Gene expression data from ATRX wild type LN229 cells

treatment_protocol: Briefly, cells were infected with viruses containing the CAS9 gene and selected with 10 mg/ml puromycin for 7 days. The cells were subsequently infected with virus carrying  no targeting small guide (sg) RNAs. The infection proceeded for 24 h and ATRX gene expression and KO was confirmed by western blot.

value: ATRX wild type


title: A375_Cy11_S28

description:
A375_Cy11_S28_S28
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Skin

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: H8 rep1

description:
4_genes_fpkm_expression.txt
T2_1


title: ChIPSeq_K14ac_TSA_30'_rep2


title: A375_Cy11_S26

description:
A375_Cy11_S26_S26
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S27

description:
A375_Cy11_S27_S27
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: ChIPSeq_K14ac_TSA_30'_rep1


title: NC rep3

description:
4_genes_fpkm_expression.txt
T1_3

value: Normal control

value: Normal diet for 24wk


title: Input_DNA_TSA_30'_rep1


title: NC rep2

description:
4_genes_fpkm_expression.txt
T1_2

value: Tibetan minipig

value: abdominal aorta


title: NC rep1

description:
4_genes_fpkm_expression.txt
T1_1


title: E315A-DNA-3

description:
single cell whole genome sequencing of 315A DNA
315A-DNA-3_S3

data_processing:
library strategy: bulk DNA sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Reads aligned to refenrence genome hg19 using Bowtie 1.0, remove PCR duplicate reads
The duplicate removed aligned reads were then assigned to variable length bins across the genome based on where they align in the genome
The average bin counts were calculated and used as the diploid 2N average. Bins with higher number are considered as amplified and those with lower are considered deleted. CNV profiles were generated using R.
Genome_build: hg19
Supplementary_files_format_and_content: Varbin files with bincounts for CNV analysis

source_name: 315A Diploid lymphoblastoid cell line

extract_protocol:
Cells were trypsinized and spun down to get a pellet. The cells were processed using Qiagen DNeasy blood and tissue kit.
2ug of DNA was fragmented to 400bp using Covaris sonicator. Following this, libraries for sequencing were prepared by subjecting the resulting DNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

value: 315A Diploid lymphoblastoid cell line

value: Lymphoblastoid

value: Suspension cell line

tag: labelling for flow

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: A375_Cy11_S25

description:
A375_Cy11_S25_S25
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Adherent cell line


title: SKOV-3-PEA-15DD-medium-24h, rep2

city: Bonn

first: Ganna

last: Kalayda

address: An der Immenburg 4

department: Clinical Pharmacy

country: Germany

institute: University of Bonn

hyb_protocol: Labeled samples were hybridized to the arrays overnight in a hybridization oven with rotation at 60 rpm for 16 hr at 45°C.

scan_protocol: Arrays were scanned in Affymetrix FS45U Fluidics Stations according to the Affymetrix automated procedure.

data_processing: The raw data of the array were collected as CEL files and analysed using the Transcriptome Analysis Console (TAC 4.1) software. The gene expression was analysed with the Gene Level SST-RMA (Signal Space Transformation-Robust Multi-Chip Analysis) summarization method. Data obtained from the microarray were normalised by the robust multiarray average method. A probe set was considered expressed if ≥ 50% samples had DABG (Detected Above Background) values below DABG threshold (p < 0.05). Statistical significance of the differences in gene expression was analysed using Limm. Differential expression was assumed at a p values ˂ 0.05 and a fold change in expression ≥ 2 or <= -2.

source_name: SKOV-3 transfected with PEA-15DD, treated with medium for 24 h

label_protocol: The purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: The SKOV-3 cell line (ATCC® HTB77TM) was from American Type Culture Collection (ATCC), Virginia, USA. The SKOV-3 cell line was grown as monolayers in IMDM medium supplemented with 10% foetal calf serum, 100 IU/ml penicillin, 0.1 mg/ml streptomycin in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using my-Budget RNA extraction mini kit following the instructions provided by the manufacturer.

treatment_protocol: Transfected SKOV-3 cells were treated with 15 µM cisplatin for 24 hours.

tag: transfection

value: control

tag: treatment concentration


title: ChIPSeq_K27ac_TSA_10'_rep2

value: Human-HEK-293 cells

tag: treatment


title: SKOV-3-PEA-15DD-medium-24h, rep1

tag: cell line


title: ChIPSeq_K27ac_TSA_10'_rep1

value: Drosophila S2 cells


title: E315A-DNA-1

description:
single cell whole genome sequencing of 315A DNA
315A-DNA-1_S1

tag: cell line source


title: 257015613555_2_4 [R-4-6]

city: Nanning

first: Kaiguo

last: Li

state: Guangxi Zhuang Autonomous Region

address: 71 Hedi Road

department: Department of Radiation Oncology

institute: Guangxi Medical University Cancer Hospital

description: Serum miRNA expression of NPC

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: serum of radioresistant NPC patient

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

growth_protocol: About 5mL of non-coagulant blood was collected from every eligible patient. Serum was isolated by centrifuging at 3000 rpm for 10 min at 4 °C, and stored at −80 °C.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: subject status

value: Nasopharyngeal carcinoma (NPC) patient

tag: subject group

value: radioresistant

tag: age

tag: gender

value: male

tag: tumor stage

value: IV

tag: tissue

value: serum


title: Input_DNA_TSA_30'_rep2

tag: spike-in organism


title: SKOV-3-PEA-15DD-medium-24h, rep3


title: ATRX_NC_rep3

tag: cell type

value: GBM cells

tag: genotype/variation

value: ATRX wild type


title: 257015613555_2_3 [R-4-5]

description: Serum miRNA expression of NPC


title: SKBR3-DNA-3

description:
single cell whole genome sequencing of SKBR3 DNA
SKBR3-DNA-3_S12

source_name: SKBR3 Her2 overexpresson breast cancer cell line

value: Breast

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: ChIPSeq_K14ac_TSA_10'_rep1


title: SKOV-3-PEA-15AA-medium-24h, rep1

source_name: SKOV-3 transfected with PEA-15AA, treated with medium for 24 h


title: SKOV-3-PEA-15AA-medium-24h, rep3


title: 257015613555_2_2 [R-4-4]

description: Serum miRNA expression of NPC

value: female


title: SKOV-3-PEA-15AA-medium-24h, rep2


title: SKOV-3-Vector-Medium-cis-24h, rep2

source_name: SKOV-3 transfected with EV, treated with medium for 24 h

value: EV


title: SKOV-3-Vector-Medium-cis-24h, rep3


title: SKBR3-DNA-1

description:
single cell whole genome sequencing of SKBR3 DNA
SKBR3-DNA-1_S10

value: SKBR3 Her2 overexpresson breast cancer cell line


title: 257015613555_1_1 [R-2-1]

description: Serum miRNA expression of NPC

value: II


title: SKOV-3-Vector-Medium-cis-24h, rep1


title: 257015613555_1_3 [R-4-1]

description: Serum miRNA expression of NPC


title: BT549-DNA-2

description:
single cell whole genome sequencing of BT549 DNA
BT549-DNA-2_S8

source_name: BT549 Triple negative breast cancer cell line

value: Adherent cell line

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: ChIPSeq_K27ac_DMSO_rep2

value: Human-HEK-293 cells

value: DMSO


title: Input_DNA_TSA_10'_rep2

value: Drosophila S2 cells


title: E315A-DNA-2

description:
single cell whole genome sequencing of 315A DNA
315A-DNA-2_S2

value: 315A Diploid lymphoblastoid cell line

value: Lymphoblastoid

value: Suspension cell line


title: SKOV-3-PEA-15DD-15 µM cis-24h, rep2

source_name: SKOV-3 transfected with PEA-15DD, treated with 15 µM cisplatin for 24 h

value: cisplatin


title: SKOV-3-PEA-15DD-15 µM cis-24h, rep1


title: ChIPSeq_K27ac_DMSO_rep1


title: SKOV-3-PEA-15DD-15 µM cis-24h, rep3


title: BT549-DNA-3

description:
single cell whole genome sequencing of BT549 DNA
BT549-DNA-3_S9

value: BT549 Triple negative breast cancer cell line


title: SKBR3-DNA-2

description:
single cell whole genome sequencing of SKBR3 DNA
SKBR3-DNA-2_S11


title: BT549-DNA-1

description:
single cell whole genome sequencing of BT549 DNA
BT549-DNA-1_S7


title: A375-DNA-3

description:
single cell whole genome sequencing of A375 DNA
A375-DNA-3_S6

source_name: A375 Melanoma cancer cell line

value: A375 Melanoma cancer cell line

value: Skin


title: ChIPSeq_K14ac_DMSO_rep1


title: 257015613554_2_3 [S-4-2]

description: Serum miRNA expression of NPC

source_name: serum of radiosensitive NPC patient

value: Nasopharyngeal carcinoma (NPC) patient

value: radiosensitive

value: IV

value: serum


title: Input_DNA_TSA_10'_rep1


title: 257015613554_2_4 [S-4-3]

description: Serum miRNA expression of NPC

value: female


title: A375-DNA-2

description:
single cell whole genome sequencing of A375 DNA
A375-DNA-2_S5

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: 257015613554_2_1 [S-2-5]

description: Serum miRNA expression of NPC

value: male

value: II


title: 257015613554_2_2 [S-4-1]

description: Serum miRNA expression of NPC


title: SKOV-3-Vector-15 µM cis-24h, rep3

source_name: SKOV-3 transfected with EV, treated with 15 µM cisplatin for 24 h

value: EV


title: SKOV-3-PEA-15AA-15 µM cis-24h, rep2

source_name: SKOV-3 transfected with PEA-15AA, treated with 15 µM cisplatin for 24 h


title: 257015613554_1_4 [S-2-4]

description: Serum miRNA expression of NPC


title: SKOV-3-PEA-15AA-15 µM cis-24h, rep1


title: ATAC.TCell.Donor.B.CSF2neg.1

status: Public on Mar 29 2020

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38) (PMID:24695404),  then single-end with min 36-bp reads length were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 (PMID: 22388286) with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools. Then read positions were corrected for transposon insertion offset as described in (PMID:24097267).
Peak calling was performed using pooled samples by conditions and using MACS2 with the “--nomodel”, “--extsize 146”,  “--qvalue 0.05”, "--nolambda" and "--keep-dup all" flags and arguments.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

source_name: primary T lymphocytes derived from human peripheral blood mononuclear cells (PBMC)

extract_protocol:
Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Effector Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7-. TEM cells were then PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-.
Tagmented DNA from GM-CSF- TEM lysed with Buffer1.
50000 cells were pelleted by centrifugation and re-suspended in 50 µl of cold lysis buffer 1 (10mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% Igepal CA-630) or 2 (10mM Tris-HCl pH 7.4, 3mM MgCl2, 10mM NaCl, 0.1% Igepal CA-630). After incubation on ice for three minutes, nuclei were pelleted by centrifugation for 20 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house), 10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), and 39uL of milliQ H2O. The reaction was incubated at 37ºC for 60 minutes with 600 RPM mixing. Then 10 µl of clean up buffer (900mM NaCl, 300mM EDTA), 4ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x) and amplified by PCR. Fragments smaller than 600 bp were isolated using SPRI cleanup and libraries where sequenced on an Illumina NextSeq500 platform.

treatment_protocol: PMA and ionomycin stimulation for 3h for cytokine secretion assay-based separation

value: Effector memory T lymphocytes

tag: label

value: Peneg

tag: antibody


title: ATAC.TCell.Donor.C.CSF2neg.1


title: ATAC.TCell.Donor.A.CSF2neg.1


title: ATAC.TCell.Donor.C.CSF2neg.2

extract_protocol:
Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Effector Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7-. TEM cells were then PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-.
Tagmented DNA from GM-CSF- TEM lysed with Buffer2.
50000 cells were pelleted by centrifugation and re-suspended in 50 µl of cold lysis buffer 1 (10mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% Igepal CA-630) or 2 (10mM Tris-HCl pH 7.4, 3mM MgCl2, 10mM NaCl, 0.1% Igepal CA-630). After incubation on ice for three minutes, nuclei were pelleted by centrifugation for 20 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house), 10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), and 39uL of milliQ H2O. The reaction was incubated at 37ºC for 60 minutes with 600 RPM mixing. Then 10 µl of clean up buffer (900mM NaCl, 300mM EDTA), 4ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x) and amplified by PCR. Fragments smaller than 600 bp were isolated using SPRI cleanup and libraries where sequenced on an Illumina NextSeq500 platform.


title: ATRX_NC_rep1

value: GBM cells

value: ATRX wild type


title: Input_DNA_DMSO_rep2

source_name: S2 cells

value: Drosophila S2 cells

value: Human-HEK-293 cells

value: DMSO

tag: chip antibody


title: ATAC.TCell.Donor.C.CSF2pos.2

extract_protocol:
Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Effector Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7-. TEM cells were then PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-.
Tagmented DNA from GM-CSF+ TEM lysed with Buffer2.
50000 cells were pelleted by centrifugation and re-suspended in 50 µl of cold lysis buffer 1 (10mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% Igepal CA-630) or 2 (10mM Tris-HCl pH 7.4, 3mM MgCl2, 10mM NaCl, 0.1% Igepal CA-630). After incubation on ice for three minutes, nuclei were pelleted by centrifugation for 20 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house), 10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), and 39uL of milliQ H2O. The reaction was incubated at 37ºC for 60 minutes with 600 RPM mixing. Then 10 µl of clean up buffer (900mM NaCl, 300mM EDTA), 4ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x) and amplified by PCR. Fragments smaller than 600 bp were isolated using SPRI cleanup and libraries where sequenced on an Illumina NextSeq500 platform.

value: PEpos


title: SKOV-3-PEA-15AA-15 µM cis-24h, rep3

tag: transfection

value: cisplatin


title: Input_DNA_DMSO_rep1


title: A375-DNA-1

description:
single cell whole genome sequencing of A375 DNA
A375-DNA-1_S4

value: A375 Melanoma cancer cell line

value: Skin

tag: labelling for flow


title: ATAC.TCell.Donor.B.CSF2pos.2


title: ATAC.TCell.Donor.B.CSF2neg.2


title: ChIPSeq_K14ac_DMSO_rep2

tag: treatment


title: 257015613554_1_3 [S-2-3]

description: Serum miRNA expression of NPC

value: Nasopharyngeal carcinoma (NPC) patient

value: radiosensitive

value: female

value: serum


title: 257015613554_1_2 [S-2-2]

description: Serum miRNA expression of NPC

value: male

value: II


title: SKOV-3-Vector-15 µM cis-24h, rep2

tag: cell line

value: EV

tag: treatment concentration


title: Condylar cartilage, fl/fl_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Condylar cartilages dissected under microscope from both control groups

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

organism: Mus musculus

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

value: condylar cartilage

tag: genotype

value: control


title: Condylar cartilage, Mutant_rep2

description: Condylar cartilages dissected under microscope from both mutant groups

value: mutant


title: SKOV-3-Vector-15 µM cis-24h, rep1


title: Condylar cartilage, fl/fl_rep2


title: hESC

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

data_processing:
FASTQ files were re-formatted to add barcode and UMI information from index file (R1) to transcript read headers, using scPipe package v1.0 for R 3.4.1, producing a single FASTQ output ready for alignment.
FASTQ reads were aligned to the reference genome (GRCh38 assembly and ENSEMBL version 86) using Rsubread 1.26.1 with default settings in R version 3.4.1.
The scPipe package v1.0 for R was used to count genes based on UMI profile. Gene expression was normalised using scater v1.6.1 and scran v1.6.6 packages for R.
Cells were removed from further analysis if they fewer than 12500 total counts, or greater than 60000 total counts, or 4500 total genes detected. Genes were filtered out if they failed to achieve 1 count in at least 10% of a particular cell condition group.
Heatmaps were generated on normalised expression values using heatmap2 from the gplots package with row normalisation. Dimensionality reduction was performed on normalised log2-cpm expression values with size factors from computeSumFactors in scran [54].
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_count.txt: tab delimited text file with gene counts
Supplementary_files_format_and_content: gene_count_normalised_log2_CPM.txt: tab delimited text file with abundance measurements
Supplementary_files_format_and_content: sc_barcodes.tsv: tab delimited text file with barcodes for each cell
Supplementary_files_format_and_content: 52056_Index_info_BPA_29723_30106.xlsx: spreadsheet with detailed CEL-Seq read structure

source_name: hESC GCTM2

growth_protocol: hPSC Culture: Human embryonic stem cells (WA09 and FUCCI-G1), were maintained as described previously [43]. The FUCCI cells were a gift from Prof Jonathan S. Draper [21]. Routine maintenance of hPSC was carried out in serum-supplemented medium with fibroblast feeder cell support. For experiments cells were transferred to defined feeder-free conditions (mTeSR conditions) using either mTeSR1 medium or Essential 8TM medium on Matrigel and subculture performed with Dispase according to the manufacturers’ protocols. For dissociation to single cells, cultures were treated with 10 μM of InSolutionTMBlebbistatin (Merck Millipore cat. no. 203389) for 1 hour prior to dissociation to single cells using TrypLETM (Life Tech, cat. no. 12605). Cultures were incubated in media supplement with 10 μM of InSolutionTMBlebbistatin overnight after which Blebbistatin was removed. Routine tests confirmed the absence of mycoplasma contamination and a diploid karyotype (20/20 cells on G-banding) in the cell lines used. Fluourescence activated cell sorting of cell aggregates or single cells and subsequent growth Cells grown for 24 hours in the presence of Y-27632 Rho kinase inhibitor were dissociated using Accutase, harvested, and examined under the microscope to ensure that most of the cells had not completely dissociated into single cells. Immunolabelling was carried out by incubation in a primary antibody cocktail containing TG30 anti-CD9 antibody and GCTM-2 for 20 min at 4° C, followed by incubation in a secondary antibody cocktail containing goat anti-mouse IgG2a AlexaFluor 488 antibody and goat anti-mouse IgM AlexaFluor 647 antibody, diluted in 2% FBS in DMEM-F12 flow cytometry buffer, again at 4° C for 20 min. The cells were resuspended the cells in 1x DAPI in cold mTeSR1before filtering the suspension through a 35 μm cell strainer to remove any larger aggregates and debris. All cell sorting was performed on a BD FACSAria III, using the 100 μm nozzle at 17 psi. A custom cytometer configuration was created that used the 17 psi pressure as opposed to the typical 20 psi pressure. This was performed to minimise aggregates from dissociating into single cells as they were deposited into the 96 well plates. To isolate the GCTM-2 high CD9 high and GCTM-2 mid CD9 mid fractions of aggregates and single cells the gating strategy in Figure 1a was used. The various fractions were deposited into 96 well tissue culture plates coated with Matrigel via the automated cell deposition unit (ACDU) on the Aria III. Subsequent to sorting, tissue culture plates were centrifuged at 200g for 2 minutes at room temperature. The sheath solution and media containing mixture was discarded and replaced with 150 μL of mTeSR1 medium. Single cells from each of two FACS populations (GCTM-2 high CD9 high and GCTM-2 mid CD9 mid ) were plated at a density between 100 to 4000 cells per well of a 96-well matrigel coated plate. Aggregates from each of two FACS populations were placed between 50 to 2000 aggregates per well of a 96-well Matrigel coated plate (Corning, Costar 3603). Cultures were maintained in mTESR1 with medium changed once after 48 hr post-plating. After 72 hours, wells were fixed and stained for colony counting as follows. The culture media was removed from cells and each well rinsed once with PBS prior to fixing with 100% ethanol for 10 minutes at room temperature. Ethanol was removed and wells allowed to air dry for 30 minutes prior to staining with haematoxylin for 10 minutes. Wells were then washed four times with MilliQ water. 0.08% aqueous ammonia solution into each well and incubate at room temperature for 2 minutes. Wash 3 times with MilliQ water and allow to dry overnight. For time lapse video microscopy, cells were imaged during 1-24 hours post-plating in an environmental chamber (Clear State Solutions TCH 885- 9G) to maintain a humid atmosphere with 5%CO 2 in air whilst phase contrast exposures were recorded every fifteen minutes with a Leica SP8 Confocal microscope.

extract_protocol:
Single cells were flow sorted into a chilled 384-well PCR plate containing 1.2μl of primer/lysis mix [20 nM indexed polydT primer, 1:6.000.000 dilution of ERCC RNA spike-in mix (Ambion - 4456740), 1 mM dNTPs, 1.2 units SUPERaseIN Rnase Inhibitor (Thermo Fisher - AM2696), DEPC water (Thermo Fisher - AM9920)] using a BD FACSAria III flow cytometer (BD Biosciences, San Jose, CA, USA) and the protocol described above. Sorted plates were sealed, centrifuged for 1 min at 3000 rpm and immediately frozen upside down at -80C until further processing using an adapted CelSeq2 protocol [51].
Cell sorting and preparation: Single cells were flow sorted into a chilled 384-well PCR plate containing 1.2μl of primer/lysis mix [20 nM indexed polydT primer, 1:6.000.000 dilution of ERCC RNA spike-in mix (Ambion - 4456740), 1 mM dNTPs, 1.2 units SUPERaseIN Rnase Inhibitor (Thermo Fisher - AM2696), DEPC water (Thermo Fisher - AM9920)] using a BD FACSAria III flow cytometer (BD Biosciences, San Jose, CA, USA) and the protocol described above. Sorted plates were sealed, centrifuged for 1 min at 3000 rpm and immediately frozen upside down at -80C until further processing using an adapted CelSeq2 protocol [51]. cDNA synthesis: Sorted plates were thawed on ice and briefly centrifuged. To lyse the cells and anneal the mRNA capture primer the plate was incubated at 65C for 5 min and immediately chilled on ice for at least 2 min before adding 0.8μl reverse transcription reaction mix [in 2μl RT reaction: 1x Fist Strand buffer (Invitrogen - 18064-014), 20 mM DTT (Invitrogen - 18064-014), 4 units RNaseOUT (Invitrogen 10777-019), 10 units SuperScript II (Invitrogen 18064-014)]. The plate was incubated at 42oC for 1 hr, 70C for 10 min and chilled to 4C to generate first strand cDNA. For second strand cDNA synthesis 6μl of second strand reaction mix were added [1x NEBNext Second Strand Synthesis buffer (NEB #E6111S), NEBNext Second Strand Synthesis Enzyme Mix: 2.4 units DNA Polymerase I (E. coli), 2 units RNase H, 10 units E. coli DNA Ligase (NEB #E6111S), DEPC water (Thermo Fisher - AM9920)]. The plate was incubated at 16oC for 2 hrs to generate double stranded cDNA. Pooling and In-vitro-transcription: All samples were pooled and cleaned using a 1.2X NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) according to manufactures instruction. To reduce the amount of beads for each 100μl pooled sample 20μl beads and 100μl bead binding buffer (20% PEG8000, 2.5M Nacl, pH5.5) was added. The cDNA was eluted in 6.4μl DEPC water and kept with beads for the following IVT reaction were 9.6μl of IVT reaction mix [1.6μl of each of the following: A,G,C,U, 10X T7 buffer, T7 enzyme (MEGAscript T7 Transcription Kit – Ambion AM1334)] was added and incubated at 37C for 13 hrs and then chilled and kept at 4 C. To remove leftover primers 6μl ExoSAP-IT For PCR Product Clean-Up (Affymetrix - 78200) was added and the sample was incubated at 37oC for 15 min and then chilled and kept at 4oC. RNA fragmentation and cleanup: Chemical heat fragmentation was performed by adding 5.5μl of 10X Fragmentation buffer (RNA fragmentation reagents - AM8740) to the sample and incubation in pre-heated thermal cycler at 94C for 2.5 min followed by immediately chill on ice and addition of 2.75μl of Fragmentation Stop buffer (RNA fragmentation reagents - AM8740). The fragmented amplified RNA was purified using 1.8X RNAClean XP beads (Beckman coulter - A63987) according to manufactures instruction and eluted in 6 μl DEPC water of which 5μl (no beads) were transferred to a fresh tube for library preparation. 5’-tagged-random-hexamer reverse transcription (ranhexRT): The fragmented RNA was transcribed into cDNA using 5’-tagged random hexamer primers (GCCTTGGCACCCGAGAATTCCANNNNNN) introducing a partial Illumina adapter as also described in [51]. To remove RNA secondary structure and anneal the mRNA capture primer 1μl of tagged random hexamer (100 μM) and 0.5μl of 10mM dNTPs (dNTP solution set NEB - N0446S) were added to the sample and incubated at 65oC for 5 min and immediately chilled on ice for at least 2 min before adding 4μl reverse transcription reaction mix [in 10μl RT reaction: 1x First Strand buffer (Invitrogen - 18064-014), 20 mM DTT (Invitrogen - 18064-014), 4 units RNaseOUT (Invitrogen 10777-019), 10 units SuperScript II (Invitrogen 18064-014)]. Library amplification and cleanup: The PCR primers introduce the full-length adaptor sequence required for Illumina sequencing (for details see Illumina small RNA PCR primers). PCR was performed in 12.5μl using half of the ranhexRT sample as a template [1X KAPA HiFi HotStart ReadyMix (KapaBiosystems KK2602), 400 nM each primer]. The final PCR amplified Library was submitted to two consecutive 1x NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) according to manufactures instruction. The final library was eluted in 20μl of 10 mM Tris-HCl solution (Sigma-Aldrich – T2319-1L).

value: mixed sample (non-demultiplexed)


title: Condylar cartilage, Mutant_rep1


title: ChIPSeq_K14ac_TSA 10'_rep2

description: ChIPSeq_K14ac_TSA 10'_rep2

value: Drosophila S2 cells

value: Human-HEK-293 cells

value: TSA 10'


title: ATAC.TCell.Donor.C.CSF2pos.1

extract_protocol:
Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Effector Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7-. TEM cells were then PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-.
Tagmented DNA from GM-CSF+ TEM lysed with Buffer1.
50000 cells were pelleted by centrifugation and re-suspended in 50 µl of cold lysis buffer 1 (10mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% Igepal CA-630) or 2 (10mM Tris-HCl pH 7.4, 3mM MgCl2, 10mM NaCl, 0.1% Igepal CA-630). After incubation on ice for three minutes, nuclei were pelleted by centrifugation for 20 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house), 10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), and 39uL of milliQ H2O. The reaction was incubated at 37ºC for 60 minutes with 600 RPM mixing. Then 10 µl of clean up buffer (900mM NaCl, 300mM EDTA), 4ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x) and amplified by PCR. Fragments smaller than 600 bp were isolated using SPRI cleanup and libraries where sequenced on an Illumina NextSeq500 platform.

value: Effector memory T lymphocytes

value: PEpos


title: Th17+anti-IL-2, unsorted, biological replicate 3

city: London

first: Leona

last: Gabrysova

address: 1 Midland Road

country: United Kingdom

institute: The Crick Institute

description: 46_Rep3_Th17posaIL2_2_1_Whole_GAGTGG-Reads_aligned_against_transcriptome_and_genome(raw)

data_processing:
Alignment of reads to the mouse transcriptome and genome together with novel splices (GRCm38 / mm10, 2014.10.08) was performed in Strand NGS (Version 2.0) guided by RefSeq annotations (2013.04.01), with minimum 90% identity, max 5% gaps, minimum aligned read length 25 bp, number of matches to output per read 1 ignoring reads with more than 5 matches.
Samples were then filtered on expression where 17,207 transcripts with more than 20 reads in at least 1 out of 24 samples has values within cut-off were retained for downstream analysis.
Raw counts were normalized using DESEQ2 (version 1.10.1) in R (version 3.2.3).
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts in .xlsx format

growth_protocol: Naïve CD4+CD62L+CD44loCD25- T cells were purified to >98% from CD4-enriched spleens by negative selection and further by sorting on a MoFloTM XDP cytometer (Beckman Coulter). Sorted T cells were cultured in IMDM (5% FCS, 1 mM glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin, 0.05 mM b-2-mercaptoethanol) at 5 × 105 per well in flat-bottom 48-well plates in a total volume of 1 ml complete media. For Th17 differentiation, naïve T cells were activated with plate-bound anti-CD3 (2 ug/ml) and anti-CD28 (10 ug/ml) in the presence of recombinant human TGFb1 (2 ng/ml, R&D Systems), human IL-6 (50 ng/ml, R&D Systems) and anti-IFNg, anti-IL-4 and anti-IL-12p40 (all at 10 ug/ml), with added IL-2 (10 ng/ml) or anti-IL-2 (10 ug/ml) for 3 days followed by 4 h restimulation with PDBU and Ionomycin at 500 ng/ml each.

extract_protocol:
Extraction of total RNA was carried out using the FFPE RNeasy Kit (Qiagen) according to manufacturer’s instructions.
Libraries were prepared with TruSeq RNA Sample Preparation Kit V2 (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were stained with CD4 HorizonTM V500 (RM4-5, BD) and LIVE/DEAD Fixable Violet Dead Cell Stain Kit (Molecular Probes), fixed with 4% formaldehyde containing 0.4U/ul RNasin Plus (Promega) for 30mins at 4C and washed with PBS containing 1% FCS and 0.4U/ul RNasin Plus (RNasin wash buffer). Cells were then permeabilized with permeabilization buffer (eBioscience) containing 1.6U/ul RNasin Plus for 15mins and stained for 30mins at 4C with anti-IL17A FITC (eBio17B7, eBioscience) and anti-IL-10 APC (JES5-16E3, eBioscience) diluted in RNasin permeabilization buffer followed by a further wash with RNasin wash buffer. Cells resuspended in PBS containing 0.5% FCS and 1.6U/ul RNasin Plus were then sorted on FACSAria cell sorter (BD Biosecinces) using FACSDiva software, and collected into FACS tubes with 500ul of PBS containing 0.5% FCS and enough RNasin Plus to result in a final concentration of 1U/ul when the tube was filled to 5ml. Live CD4+ T cells were collected first from both Th17+IL-2 and Th17+anti-IL-2 populations, followed by sorting of the different intracellular cytokine producing subpopulations: IL-17-IL-10-, IL-17+IL-10-, IL-17+IL-10+ and IL-17-IL-10+ from Th17+IL-2 cultures and IL-17-IL-10- and IL-17+IL-10- from Th17+anti-IL-2 cultures, each with 3 biological repeat experiments.

tag: strain

value: Unsorted


title: Th17+anti-IL-2, IL-17-IL-10-, biological replicate 3

description: 47_Rep3_Th17posaIL2_2_2_Neg_ACTGAT-Reads_aligned_against_transcriptome_and_genome(raw)


title: ATAC.TCell.Donor.A.CSF2pos.1


title: ATAC.TCell.Donor.B.CSF2pos.1


title: ATAC.TCell.Donor.A.CSF2pos.2


title: Jurkat.BHLHE40 Rep.2

description:
transduced with lv-Bhlhe40-FlagHA
Chromatin IP against Flag

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then single-end reads with minimum of 40-bp  were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.2) with the “--nomodel”, “--extsize 200” and “--qvalue 0.05” flags and arguments. Each replicate was compared to relative empty sample.
GRCh38/hg38
Genome_build: *.narrowPeak, list of the peaks called by MACS2

source_name: Jurkat T cell line

growth_protocol: Jurkat T cells were lentivirally transduced either with a construct harboring Bhlhe40 with an N-terminal Flag-HA tag or an empty vector, in order to stably expressed a tagged version of Bhlhe40. Cells were mycoplasma tested and grown in RPMI medium with 10% FBS and standard supplements and antibiotics.

extract_protocol:
ChIP lysates were generated from 6x10^7 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was sonicated and then immunoprecipitated with 10ug of antibody against FLAG. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads (Dynabeads) in PBS/BSA 0.5%. Beads were then added to lysates and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen).
ChIP DNA was prepared for NextSeq 500 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System. The purified DNA libraries were quantified both with a TapeStation 4200 (Agilent Technologies) and Qubit (LifeTechnologies) and diluted to a working concentration of 2 nM.

treatment_protocol: Two independent Jurkat T cell lines transduced with Bhlhe40 or an empty vector were used to perform chromatin immunoprecipitation with an anti-Flag antibody.

value: Jurkat T lymphocytes

value: GFP

value: Sigma-Aldrich F1804


title: Jurkat.Empty Rep.1

description:
transduced with lv-empty-FlagHA
Chromatin IP against Flag


title: Jurkat.Empty Rep.2


title: Th17+IL-2, unsorted, biological replicate 3

description: 41_Rep3_Th17posIL2_1_1_Whole_GTCCGC-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+anti-IL-2, IL-17-IL-10-, biological replicate 2

description: 39_Rep2_Th17posaIL2_2_2_Neg_ATGTCA-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17-IL-10+, biological replicate 2

description: 37_Rep2_Th17posIL2_1_5_IL17_IL10pos_AGTCAA-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+anti-IL-2, unsorted, biological replicate 2

description: 38_Rep2_Th17posaIL2_2_1_Whole_AGTTCC-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+anti-IL-2, IL-17+IL-10-, biological replicate 3

description: 48_Rep3_Th17posaIL2_2_3_IL17pos_ATTCCT-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17-IL-10-, biological replicate 2

description: 34_Rep2_Th17posIL2_1_2_Neg_TAGCTT-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17+IL-10-, biological replicate 2

description: 35_Rep2_Th17posIL2_1_3_IL17pos_GGCTAC-Reads_aligned_against_transcriptome_and_genome(raw)


title: Jurkat.BHLHE40 Rep.1


title: Th17+anti-IL-2, IL-17+IL-10-, biological replicate 1

description: 32_Rep1_Th17posaIL2_2_3_IL17pos_ACTTGA-Reads_aligned_against_transcriptome_and_genome(raw)


title: Condylar cartilage, fl/fl_rep1


title: Condylar cartilage, Mutant_rep3


title: Th17+IL-2, IL-17+IL-10-, biological replicate 3

description: 43_Rep3_Th17posIL2_1_3_IL17pos_GTGGCC-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17+IL-10+, biological replicate 3

description: 44_Rep3_Th17posIL2_1_4_IL17posIL10pos_GTTTCG-Reads_aligned_against_transcriptome_and_genome(raw)


title: PRO-seq_TSA_10'_rep2

description:
Nascent RNA
PRO-seq_TSA_10'_rep2


title: Th17+IL-2, IL-17-IL-10+, biological replicate 3

description: 45_Rep3_Th17posIL2_1_5_IL17_IL10pos_CGTACG-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17+IL-10+, biological replicate 1

description: 28_Rep1_Th17posIL2_1_4_IL17posIL10pos_TGACCA-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17-IL-10-, biological replicate 1

description: 26_Rep1_Th17posIL2_1_2_Neg_CGATGT-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17-IL-10-, biological replicate 3

description: 42_Rep3_Th17posIL2_1_2_Neg_GTGAAA-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, unsorted, biological replicate 1

description: 25_Rep1_Th17posIL2_1_1_Whole_ATCACG-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17+IL-10+, biological replicate 2

description: 36_Rep2_Th17posIL2_1_4_IL17posIL10pos_CTTGTA-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, unsorted, biological replicate 2

description: 33_Rep2_Th17posIL2_1_1_Whole_GATCAG-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+anti-IL-2, IL-17-IL-10-, biological replicate 1

description: 31_Rep1_Th17posaIL2_2_2_Neg_CAGATC-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+anti-IL-2, unsorted, biological replicate 1

description: 30_Rep1_Th17posaIL2_2_1_Whole_GCCAAT-Reads_aligned_against_transcriptome_and_genome(raw)


title: Donor.A CSF2+

description: Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Effector Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7-.

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to human genome build GRCh38/hg38 using using TopHat v2.1.0 with the option “--b2-very-sensitive”. Only uniquely mapped reads were retained
Gene expression counts were estimated using HTSeq v0.6.1, summarized across all exons as annotated in the GENCODE v25, with option “union” and “no strand-specific assay”.
Differentially expressed genes were identified using EdgeR R-package v3.2.2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.gene.counts.txt files contain raw read counts for each samples. *.edgeR_results.txt files contain differentially expressed genes for each comparison.

growth_protocol: TEM were isolated by magnetic enrichment for CD4 (Miltentyi Biotec) and sorted for CD4+CD25-CD45RA-CCR7- and incubated overnight in complete media

extract_protocol:
PE+/- cells were resuspended in Trizol. Samples of 3 donors were combined and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)
PolyA RNA libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 400ng of total RNA

treatment_protocol: TEM were stimulated for 3h with PMA/ionomycin and labelled for GM-CSF secretion with a GM-CSF cytokine secretion kit (Miltenyi Biotec) before sorting for PE+/- cells with a BD Sorter Aria II


title: Th17+IL-2, IL-17-IL-10+, biological replicate 1

description: 29_Rep1_Th17posIL2_1_5_IL17_IL10pos_ACAGTG-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+IL-2, IL-17+IL-10-, biological replicate 1

description: 27_Rep1_Th17posIL2_1_3_IL17pos_TTAGGC-Reads_aligned_against_transcriptome_and_genome(raw)


title: Th17+anti-IL-2, IL-17+IL-10-, biological replicate 2

description: 40_Rep2_Th17posaIL2_2_3_IL17pos_CCGTCC-Reads_aligned_against_transcriptome_and_genome(raw)


title: Donor.A CSF2-

value: PEneg


title: Donor.C CSF2-


title: Donor.B CSF2+


title: Donor.B CSF2-


title: Donor.C CSF2+


title: 3B

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

description: Gene expression data from IgA CD19+ CD38+CD138+ plasma cells

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: RNA from IgA CD19+ CD38+CD138+ plasma cells

label_protocol: 30ng of total RNA from each sample was processed and labelled according to manuals from GeneChip WT Pico Reagent Kit (P/N 703262, Rev.1 2015)

extract_protocol: RNA was extracted with the RNeasy Micro kit (Qiagen) following the manufacturer's instructions

value: Colon

tag: patient

tag: condition

value: B


title: 5N

description: Gene expression data from naïve B cells

source_name: RNA from naïve B cells

value: N


title: 3A

description: Gene expression data from IgA CD19+ CD38+CD138- plasma cells

source_name: RNA from IgA CD19+ CD38+CD138- plasma cells

value: A


title: 2B


title: 5B


title: 2A


title: 5A


title: 1N

description: Gene expression data from naïve B cells


title: 5D

description: Gene expression data from IgA CD19- CD38+CD138+ plasma cells

source_name: RNA from IgA CD19- CD38+CD138+ plasma cells

value: D


title: 2D


title: 3D


title: R55_CD4_a

description: Gene expression data from total CD4 mononuclear cells

data_processing: Data was analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from total CD4 mononuclear cells

label_protocol: 30ng of total RNA from each sample was processed and labelled according to manuals NuGEN Ovation® Pico WTA  System V2 (M01224 v2) and Encore™ Biotin Module (M01111 v6) (NuGEN, San Carlos, CA,  USA)

extract_protocol: RNA was extracted following the RNeasy Plus Mini Kit protocol (QIAGEN)

value: Peripheral Blood

tag: type

value: CLL

tag: batch

tag: Sex

value: m

tag: age


title: 2N

description: Gene expression data from naïve B cells

tag: tissue


title: 1B


title: R40_CD4_a_P2

value: f


title: R43_CD4_a_P2

value: CTRL


title: R54_CD4_a


title: 3N

description: Gene expression data from naïve B cells


title: 1D


title: R38_CD4_a_P2


title: R45_CD4_a_P2

value: MBL


title: R34_CD4_P


title: R35_CD4_a_P


title: R52_CD4_a_P2


title: R48_CD4_a_P2


title: R53_CD4_a


title: ATAC.TCell.Donor.A.CSF2neg.2

tag: cell type

value: Effector memory T lymphocytes

tag: label

value: Peneg


title: R41_CD4_P


title: R29_CD4_P


title: R30_CD4_a_P


title: R33_CD4_a_P


title: 1A


title: R19_CD4


title: R32_CD4_a_P


title: R25_CD4


title: R37_CD4_a_P


title: R31_CD4_a_P


title: R21_CD4


title: R36_CD4_a


title: R17_CD4


title: R18_CD4


title: R15_CD4


title: Tem_PEpos_E

description:
Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Effector Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7-.
nCounter® Human miRNA Expression Assay

hyb_protocol: Samples were hybridized overnight at 65C

scan_protocol: Samples were run on a Nanostring Sprint Profiler

data_processing: Raw data was processed with nSolver 3.0 Software (Nanostring). Reads were normalized to internal postive & negative controls and to the 25 highest expressed miRNAs. Genes were considered expressed if at least one sample had a read >125 and maximum 1 sample with a read <27

label_protocol: 100 ng of total RNA were labelled with the nCounter® Human miRNA Expression Assay codeset according to the manufacturers protocol

growth_protocol: Effector memory T lymphocytes  were isolated by magnetic enrichment for CD4 (Miltentyi Biotec) and sorted for CD4+CD25-CD45RA-CCR7- and incubated overnight in complete media

extract_protocol: PE+/- cells were resuspended in Trizol. Total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)

treatment_protocol: Tem were stimulated for 3h with PMA/ionomycin and labelled for GM-CSF secretion with a GM-CSF cytokine secretion kit (Miltenyi Biotec) before sorting for PE+/- cells with a BD Sorter Aria II

value: effector memory T lymphocytes

tag: culture condition

value: Effector memory T lymphocytes were stimulated with PMA/Ionomycin, PE-labelled within a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PEpos/neg before total RNA extraction

value: PEpos


title: R10_CD4


title: R39_CD4_a_P3


title: R13_CD4


title: Tem_PEneg_F

value: PEneg


title: R27_CD4


title: R22_CD4_P


title: R3_CD4


title: R11_CD4


title: R8_CD4_P


title: R1_CD4


title: Tcm_PEneg_D


title: Tcm_PEneg_C


title: Tem_PEpos_D


title: R2_CD4