title: 420Input

city: hangzhou

first: ZHANG

last: XUEYOU

address: road 17th,laozheda

institute: Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, China

description: chip-seq.txt

data_processing:
RNA-Seq:index of the reference genome was built and paired-end clean reads were aligned to the reference genome using the software package TopHat2 (v2.0.9) with Bowtie2 (v2.3.4.1). HTSeq (v0.6.1) was used to count the reads numbers mapped to each gene. DESeq2 R package (1.10.1) was used to performe differential expression analysis. Enrichment analysis of differentially expressed genes was performed by KOBAS 3.0 analysis (http://kobas.cbi.pku.edu.cn/index.php).
ATAC-Seq: The resulting libraries were purified and assessed with Qubit 3 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent).
ChIP-Seq:ChIP was performed using Dynabeads Protein G (ThermoFisher Scientific)
Genome_build: mm9
Supplementary_files_format_and_content: SPSS version 13.0 (SPSS Inc., Chicago, IL) was used to complete the statistical analysis. A P value of < 0.05 was considered statistically significant. Quantitative variables were described as the mean ± SD or median (interquartile range) and compared using student t test or Mann-Whitney test. Categorical variables were presented as values (percentages) and compared using Pearson’s χ2 test. Correlation analysis was performed by Pearson linear regression.

source_name: Hepatocellular carcinoma cells

growth_protocol: The PLC-PRF-5 cell line was purchased from the American Type Culture Collection (Manassas, VA, USA) and maintained in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
RNA-Seq:Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Double-stranded complementary DNAs were synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (Invitrogen). The cDNAs were then fragmented.
ATAC-Seq: 50,000 cells for each sample were pelleted by centrifugation and lysed in lysis buffer containing 0.1% NP40, 0.1% Tween 20 and 0.01% Digitonin to obtain nucleic. The nucleic pellets were treated with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to manufacturer’s protocols. Immediately following transposition, DNA fragments were purified with MinElute PCR Purification Kit (QIAGEN) and PCR amplified with primers including barcode for a total of 10-12 cycles. The resulting libraries were purified and assessed with Qubit 3 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent).
CHIP-Seq: cells were harvested and fixed. Chromatin was isolated by adding Lysis Buffer (Active Motif), followed by homogenization with Dounce homogenizer. Soluble chromatin was quantified by Nanodrop 2000 (ThermoFisher Scientific). ChIP was performed using Dynabeads Protein G (ThermoFisher Scientific) and 4 μL antibody against TCF4/TCF7L2 (Catalog number 2569, Cell Signaling Technology) with 20-50 μg soluble chromatins. Rabbit IgG (Catalog number ab172730, Abcam) was used for negative control. The beads-antibody-chromatin complexes were washed using ChIP-IT Express Enzymatic (Active Motif) according to manufacturer’s protocols. The chromatin was reverse cross linked overnight at 65°C, treated with RNase A and proteinase K, respectively. The DNA was cleaned up with QIAGEN MinElute PCR Purification Kit (QIAGEN).
RNA-Seq:using the Illumina paired-end RNA-seq approach according to the standard protocol.
ATAC-Seq:The libraries were sequenced on Illumina Hiseq XTen instrument (Illumina).Briefly, 50,000 cells for each sample were pelleted by centrifugation and lysed in lysis buffer containing 0.1% NP40, 0.1% Tween 20 and 0.01% Digitonin to obtain nucleic. The nucleic pellets were treated with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to manufacturer’s protocols. Immediately following transposition, DNA fragments were purified with MinElute PCR Purification Kit (QIAGEN) and PCR amplified with primers including barcode for a total of 10-12 cycles. The resulting libraries were purified and assessed with Qubit 3 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent).
CHIP-Seq: ChIP-seq libraries were prepared using KAPA Hyper Prep Kit and sequenced on Illumina Hiseq XTen instrument.Briefly, cells were harvested and fixed. Chromatin was isolated by adding Lysis Buffer (Active Motif), followed by homogenization with Dounce homogenizer. Soluble chromatin was quantified by Nanodrop 2000 (ThermoFisher Scientific). ChIP was performed using Dynabeads Protein G (ThermoFisher Scientific) and 4 μL antibody against TCF4/TCF7L2 (Catalog number 2569, Cell Signaling Technology) with 20-50 μg soluble chromatins. Rabbit IgG (Catalog number ab172730, Abcam) was used for negative control. The beads-antibody-chromatin complexes were washed using ChIP-IT Express Enzymatic (Active Motif) according to manufacturer’s protocols. The chromatin was reverse c ross linked overnight at 65°C, treated with RNase A and proteinase K, respectively. The DNA was cleaned up with QIAGEN MinElute PCR Purification Kit (QIAGEN).

value: heterozygote for rs290487 C/C genotype.

tag: antibody


title: 530Input

status: Public on Jul 29 2020

type: SRA

country: China

description: chip-seq.txt

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: genotype

value: heterozygote for rs290488 C/T genotype.


title: TRACE_seq_20ng_replicate_1

city: Beijing

first: Chengqi

last: Yi

address: No.5 YiHeYuan Road

institute: Peking University

library_source: transcriptomic

data_processing:
Raw reads from sequencing were firstly subjected to Trim_galore (v0.6.4_dev) for quality control and adaptor trimming with parameters -q 20 --stringency 3 --length 20
Then trimmed reads were mapped to human (hg19) genome and transcriptome(downloaded from the table browser of UCSC database) using STAR (v2.7.1a) with parameters --runThreadN 20 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterIntronMotifs RemoveNoncanonicalUnannotated
rRNA contamination were determined through directly mapping to the dataset of human rRNA sequence downloaded from NCBI by bowtie2 (v2.2.9) with parameters -N 1 -p 20 -q
Performances related to the processing of sam/bam file were done with the help of Samtools (v1.9)
The FPKM value for annotated genes was calculated by cuffnorm (v2.2.1). Gene body coverage and nucleotide composition for each position of the first 30 bases of each sequence read per library were calculated by QoRTs (v1.1.6). Reads distribution and GC content distribution of mapped reads were calculated by RseQC (v2.6.4), and median coefficient of variation of gene coverage over the 1000 most highly expressed transcripts per library and insert size of library were calculated by Picard Tools (v2.20.6). Library complexity was calculated by Preseq (v2.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample using 293T RNA as input and Tab-delimited text files include counts for each genes in each sample using mESC RNA as input.

molecule: total RNA

source_name: human embryonic kindey cells

growth_protocol: HEK293T cells used in this study were daily maintained in DMEM medium (GIBCO) supplemented with 10% FBS (GIBCO) and 1% penicillin/streptomycin (GIBCO) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells with TRIzol (Invitrogen), according to the manufacturer’s instructions. The resulting total RNA was treated with DNase I (NEB) to avoid genomic DNA contamination. Phenol/chloroform extraction and ethanol precipitation were then performed to purify and concentrate total RNA. For mRNA isolation, two successive rounds of poly(A)+ selection were performed using oligo(dT)25 dynabeads (Invitrogen).
Reverse transcription was carried out using Superscript IV reverse transcriptase (Invitrogen) and then tagmentation reaction was performed with Tn5 transposase (Vazyme). Strand extension reaction was performed by directly adding Bst 3.0 DNA Polymerase and 1X NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB) to tagmentation products and incubating at 72°C for 15 min, followed by Bst 3.0 DNA Polymerase inactivation at 95°C for 5 min. Next, 0.2 μM indexed primers were added to perform enrichment PCR.The library was purified twice using 1X Agencourt AMPure XP beads (Beckman Coulter) and sequenced on the Illumina Hiseq X10 platform which generated 2 x 150 bp of paired-end raw reads.

tag: cell line

value: HEK293T cells

tag: transposase

value: TruePrep Tagment Enzyme (Vazyme, S601-01)


title: 420TCF4_ChIPSeq

description: chip-seq.txt

value: protein

value: TCF4/TCF7L2(Catalog number 2569, Cell Signaling Technology


title: TRACE_seq_200ng_replicate_3


title: TRACE_seq_200ng_replicate_1


title: 530TCF4_ChIPSeq

description: chip-seq.txt


title: TRACE_seq_200ng_replicate_2


title: d8616: rRNA eIF3m kD in vivo replicate 1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
bwa mem version 0.7.12 alignment to Rn45s followed by sorting and depth calculation with samtools version 1.3
Genome_build: NR_046233.2, Mus musculus 45S pre-ribosomal RNA (Rn45s), ribosomal RNA.
Supplementary_files_format_and_content: Rn45s positions and depths of coverage for each sample

organism: Mus musculus

source_name: liver

growth_protocol: Hepa1c1c7 cells were grown in standard DMEM cell culture supplemented with 10%HI-FBS; FVB/N mice, aged 6-8 weeks were purchased from Charles River laboratories and maintained in accordance with the study protocols approved by Committee on Animal Care of MIT

extract_protocol:
Phenol/Chloroform extraction of frozen, ground livers; Sureprep Nuclear RNA purification kit from Fisher Scientific in case of Hepa1c1c7 cells
Clonetech pico without ZapR

treatment_protocol: Hepa1c1c7 cells were treated with the control (scrambled luciferase) or eIF3m siRNA for 3 days at concentration 10uM; in case of in vivo experiment FVB/N mice at 6-8 weeks of age were injected with the control (scrambled luciferase) or eIF3m siRNA LNP formulations at 0.5 mg/kg via tail vein for 13 days.

tag: strain

value: FVB/N

tag: tissue

value: liver

tag: sirna


title: d8617: rRNA eIF3m kD in vivo replicate 2


title: plc-WT atac-seq

description: atac-seq.txt


title: plc-mu rna-seq

description: rna-seq.txt


title: plc-mu atac-seq

description: atac-seq.txt


title: plc-WT rna-seq

description: rna-seq.txt


title: d8618: rRNA eIF3m kD in vivo replicate 3


title: d8613: rRNA control in vivo replicate 1

value: luciferase


title: d8615: rRNA control in vivo replicate 3


title: d4165: rRNA eIF3m kD in vitro replicate 1

source_name: Hepa1c1c7 Liver cells

value: not applicable

value: Hepa1c1c7 Liver cells


title: d4162: rRNA control in vitro replicate 1


title: d4163: rRNA control in vitro replicate 2


title: d8614: rRNA control in vivo replicate 2


title: d4164: rRNA control in vitro replicate 3


title: d4167: rRNA eIF3m kD in vitro replicate 3


title: Untreated/Library coverage

city: Utrecht

first: Niels

last: Geijsen

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Hubrecht institute

data_processing:
Reads were counted by first searchinge in the read file  for the CACCG sequence, located 5′ to all sgRNA inserts. The following 20nt are the gRNA, which was mapped to a reference database. Based on the 8nt barcode included in the P7 primer, the reads were assigned to a condition (e.g. a well on the 96-well PCR plate).
Analysis was conducted using “STARS”, gene-ranking method to generate FDR values developed by Doench et al. that was used to generate p-values and FDR rates
Genome_build: hg19
Supplementary_files_format_and_content: Text files detailing gRNA sequences and their abundance in the screens compared to their untreated counterparts.

source_name: Chronic myeloid leukemia cells

growth_protocol: IMDM basal media with 10% Tet approved FBS, and 100μM 2-ME.

extract_protocol:
Genomic DNA (gDNA) was isolated using NucleoSpin Blood Mini (less than 5 million cells), Midi (L) (5-20 million cells) and Maxi (XL) (more than 20 million cells) kits, depending on the size of cell pellet.
A PCR of the genomic DNA and plasmid DNA was performed to attach sequencing adaptors and barcodes to samples. The PCR amplified products were purified using Agencourt AMPure XP SPRI beads according to manufacturer's instructions.
Genome wide CRIPSR/Cas9 screen

treatment_protocol: 250 ng/ml (low) or 1000ng/ml (high) doxycyline was added to growth media. DIE cells were treated with docycyline for 24 hours. Plates containing DIE cells were washed with DPBS and growth media was subsequently added. Surviving cells were harvested at two timepoints after doxycycline exposure, early (24h) and late (72h).

tag: parental line

value: DIE

value: rtTA

tag: treatment

value: no treatment


title: Early harvest, low doxycyline

value: doxycyline


title: Late harvest, low doxycyline


title: Early harvest, high doxycyline


title: d4166: rRNA eIF3m kD in vitro replicate 2


title: Self Administered Saline Rep 9

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

description: fpkm.csv

data_processing:
Alignment to reference assembly mm10 using Tuxedo bowtie
Mapping results filtering performed using Tuxedo cuffquant
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: FPKM value for each gene in tsv table format

source_name: brain,  ventral tegmental area

extract_protocol:
RNeasy minikit (Qiagen, 74104)
TruSeq RNA Sample Preparation Kit (Illumina)

value: intravenous-self administration of saline


title: Self Administered Saline Rep 7

description: fpkm.csv


title: Self Administered Saline Rep 8

description: fpkm.csv


title: Self Administered Saline Rep 5

description: fpkm.csv


title: Self Administered Saline Rep 6

description: fpkm.csv


title: Self Administered Saline Rep 4

description: fpkm.csv


title: Self Administered Cocaine Rep 12

description: fpkm.csv

value: intravenous-self administration of cocaine


title: Self Administered Saline Rep 2

description: fpkm.csv


title: Self Administered Saline Rep 3

description: fpkm.csv


title: Self Administered Saline Rep 1

description: fpkm.csv


title: Self Administered Cocaine Rep 15

description: fpkm.csv


title: Self Administered Cocaine Rep 14

description: fpkm.csv


title: Late harvest, high doxycyline


title: Self Administered Cocaine Rep 13

description: fpkm.csv


title: Self Administered Cocaine Rep 3

description: fpkm.csv


title: Self Administered Cocaine Rep 11

description: fpkm.csv


title: Self Administered Cocaine Rep 9

description: fpkm.csv


title: Self Administered Cocaine Rep 10

description: fpkm.csv


title: Self Administered Cocaine Rep 8

description: fpkm.csv


title: Self Administered Cocaine Rep 7

description: fpkm.csv


title: Self Administered Cocaine Rep 4

description: fpkm.csv


title: Self Administered Cocaine Rep 5

description: fpkm.csv


title: Self Administered Cocaine Rep 6

description: fpkm.csv


title: Conditioning Saline Rep 6

description: fpkm.csv

value: saline-conditioning


title: Conditioning Saline Rep 4

description: fpkm.csv


title: Conditioning Saline Rep 3

description: fpkm.csv


title: Conditioning Cocaine Rep 6

description: fpkm.csv

value: cocaine-conditioning


title: Conditioning Cocaine Rep 5

description: fpkm.csv


title: Conditioning Cocaine Rep 4

description: fpkm.csv


title: Conditioning Saline Rep 2

description: fpkm.csv


title: Conditioning Saline Rep 5

description: fpkm.csv


title: Conditioning Cocaine Rep 2

description: fpkm.csv


title: Conditioning Cocaine Rep 3

description: fpkm.csv


title: HC: Chronic Saline Rep 5

description: fpkm.csv

value: chronic home cage injections of saline


title: HC: Chronic Saline Rep 2

description: fpkm.csv


title: HC: Chronic Saline Rep 3

description: fpkm.csv


title: HC: Chronic Saline Rep 6

description: fpkm.csv


title: Self Administered Cocaine Rep 2

description: fpkm.csv


title: Self Administered Cocaine Rep 1

description: fpkm.csv


title: HC: Chronic Saline Rep 4

description: fpkm.csv


title: HC: Chronic Saline Rep 1

description: fpkm.csv


title: HC: Chronic Cocaine Rep 6

description: fpkm.csv

value: chronic home cage injections of cocaine


title: Conditioning Saline Rep 1

description: fpkm.csv


title: HC: Chronic Cocaine Rep 4

description: fpkm.csv


title: HC: Chronic Cocaine Rep 3

description: fpkm.csv


title: HC: Chronic Cocaine Rep 5

description: fpkm.csv


title: HC: Chronic Cocaine Rep 2

description: fpkm.csv


title: HC: Acute Saline Rep 6

description: fpkm.csv

value: acute home cage injections of saline


title: HC: Acute Saline Rep 3

description: fpkm.csv


title: HC: Acute Saline Rep 5

description: fpkm.csv


title: HC: Acute Saline Rep 1

description: fpkm.csv


title: HC: Acute Saline Rep 4

description: fpkm.csv


title: Conditioning Cocaine Rep 1

description: fpkm.csv


title: HC: Acute Saline Rep 2

description: fpkm.csv


title: HC: Acute Cocaine Rep 4

description: fpkm.csv

value: acute home cage injections of cocaine


title: HC: Acute Cocaine Rep 5

description: fpkm.csv


title: HC: Acute Cocaine Rep 3

description: fpkm.csv


title: HC: Acute Cocaine Rep 1

description: fpkm.csv


title: UNC-1

city: Buffalo

first: Fengwei

last: Yang

address: 955 Main St

institute: University at Buffalo

data_processing:
Illumina Casava1.7 software used for basecalling.
Strand-specific RNA libraries from  1 μg purified RNA using TruSeq stranded total RNA plus Ribo-zero kits. Single end reads per sample were obtained using the HiSeq 2500 platform from  Illumina.
Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, followed by aligning to mouse RefSeq mRNAs using TopHat2 with default.
Transcript counts were estimated using HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM value for every gene and every sample

source_name: brain prefrontal cortex tissue

extract_protocol:
Trizol extraction method
TruSeq stranded total RNA plus Ribo-zero kits (Illumina)

treatment_protocol: UNC0642 treatment (1 mg/kg, i.p., once per day for 3 days)

value: brain

tag: age

value: post natal week 5-8

value: UNC0642 treatment


title: HC: Chronic Cocaine Rep 1

description: fpkm.csv


title: WT-2

value: wild type

value: saline


title: SAL-3


title: UNC-3


title: SAL-1


title: RNA_LSKder_XL45

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: purified murine bone marrow-derived LSK cells

growth_protocol: MLL-AF9 immortalized LSK or GMP bone marrow cells were expanded in vitro and a minimum of 2x10e5 GFP+ cells were transplanted into lethally irradiated (950 cGy) syngeneic recipient C57BL/6 mice along with 2x10e5 bone marrow support cells from wild-type mice. Murine AML cells were harvested from bone marrow of moribund mice and maintained in culture with IMDM medium containing 15% FBS, 1% penicillin-streptomycin, 2 mM L-glutamine, 20 ng/mL rm-SCF, 10 ng/mL rmIL-3, 10 ng/ml rmIL-6.

extract_protocol:
RNA was isolated by TRIzol extraction
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

tag: cell type

value: retrovirally transduced with MLL-AF9 oncogene


title: WT-1


title: WT-3


title: SAL-2


title: RNA_LSKder_XL46

value: purified murine bone marrow-derived LSK cells


title: RNA_LSKder_XL44


title: RNA_GMPder_XG5

source_name: purified murine bone marrow-derived GMP cells


title: HC: Acute Cocaine Rep 2

description: fpkm.csv


title: RNA_GMPder_XG11

value: purified murine bone marrow-derived GMP cells


title: S10: KO female #1

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then Mouse samples were mapped to NCBI reference GRCm38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package using the NCBI Mus musculus Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCm38
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+0.25) CPM

source_name: intestinal regulatory T cell

growth_protocol: Regulatory T cells (Tregs) were isolated by flow cytometric sorting of singlet, CD4+CD25hiCD127lo T cells from mesenteric lymph nodes of SAMP-WT and SAMP-ERb-KO mice. RNA was isolated immediately after cell isolation.

extract_protocol:
RNA was isolated using the NucleoSpin XS kit.
RNA libraries were prepared for sequencing using the SMART-Seq v4 for CDNA and the Nextera XT kit for library creation

treatment_protocol: no treatment

value: SAMP/YitFC-ERb-KO

tag: gender

value: female

value: intestinal regulatory T cell


title: S9: KO male #3

value: male


title: S8: KO male #2


title: RNA_GMPder_XG19


title: S7: KO male #1


title: UNC-2


title: S11: KO female #2


title: S5: WT female #2

value: SAMP/YitFC-WT


title: S3: WT male #2


title: S2: WT male #2


title: S4: WT female #1


title: S1: WT male #1


title: Prm2-WT2

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

data_processing:
All reads were trimmed with Trim Galore! 0.4.5 (Brabraham Bioinformatics) and mapped to the mouse genome (GRCm38.89) using HISAT2 2.1 (Kim et al.2015).
Transcripts were quantified and annotated using StringTie 1.3.3 (Pertea et al.2015).
Gene annotation information for the mouse genome was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org) (GRCm38.89).
The python script (preDE.py) included in the StringTie package was used to prepare gene-level count matrices for analysis of differential gene expression (DE).
Genome_build: GRCm38.89
Supplementary_files_format_and_content: tab separated text file includes DESeq2 normalized counts for each sample

source_name: testis

extract_protocol:
Total RNA was extracted from testicular tissue after removal of the tunica albuginea using TRIzol™ reagent according to the manufacturer’s protocol (Thermo Fisher Scientific).
RNA sample quality control and library preparation were performed by the University of Bonn Core facility for Next Generation Sequencing (NGS), using the QuantSeq 3´-mRNA Library Prep (Lexogen, Greenland, NH, USA).
RNAseq was performed on the Illumina HiSeq 2500 V4 platform, producing >10 million, 50bp 3’-end reads per sample.

value: testis

value: WT

tag: Sex


title: Prm2-Het3


title: Prm2-WT3


title: Prm2-WT1


title: S12: KO female #3


title: Prm2-Het1


title: Prm2-KO1


title: OE_MI3

city: Rehovot

first: Eldad

last: Tzahor

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were aligned to the mouse genome using Tophat (v2.0.10)
Counting proceeded over genes annotated in Refseq, using htseq-count
Normalization and differential expression was performed using DESeq2 (version 1.6.3)
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: Excel file includes the normalized counts and the differential expression

molecule: polyA RNA

source_name: ERBB2 - OE MI operated heart

growth_protocol: Regular rodent growing conditions

extract_protocol:
RNA was extracted using miRNeasy kit (217004, Qiagen), according to the manufacturer instructions.
Inhouse poly A based RNA seq

treatment_protocol: Mice were sedated with isoflurane (Abbot laboratories) and were artificially ventilated following tracheal intubation. Experimental myocardial infarction was induced by permanent ligation of the left anterior descending coronary artery (LAD ligation) as described before. Following the closure of the thoracic wall, mice were injected s.c with Buprenorphin (0.066mg/Kg) as analgestic and were warmed for several minutes until recovery. RNA was extracted 2 weeks post MI.

value: Heart

value: Adult, aproximatly 3 months old

value: ERBB2 overexpression

value: MI


title: OE_MI2


title: Prm2-KO3


title: OE_MI4


title: Prm2-KO2


title: WT_MI4

source_name: WT MI operated heart


title: OE_MI1


title: WT_MI2


title: S6: WT female #3


title: OE_SHAM4

source_name: ERBB2 - OE Sham operated heart

value: Sham


title: OE_SHAM3


title: WT_MI3


title: WT_SHAM3

source_name: WT Sham operated heart


title: WT_SHAM4


title: TScr2

city: Baltimore

first: Jacquelyn

middle: W

last: Zimmerman

state: Maryland

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

data_processing:
Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files
rsem-1.3.0 was used for running the alignments as well as generating gene and  transcript expression levels.
rsem-1.3.0's EBSeq was used for Differential Expression analysis
Genome_build: RSEM version 1.3.0, aligned to reference genome mm10

source_name: KPC cell line

growth_protocol: Tumor cells, KPC CAFs, and PNAFs were maintained in RPMI 1640 with 10% FBS, 1 mM sodium pyruvate, 2 mM L-glutamine, 1% nonessential amino acids, penicillin (50 U/ml)/streptomycin (50 g/ml) (Life Technologies), and 0.2 U/ml human insulin (NovoLog) in a humidified incubator (37 degrees, 5% CO2)

extract_protocol:
RNA extraction following stable transduction with RNAqueous micro kit
Illumina’s TruSeq Stranded Total RNA Sample Prep Kit

treatment_protocol: miRNA lentiviral particles were purchased from GeneCopoeia with third generation technology for stable transduction

value: scramble miR inhibitor

tag: replicate

value: Tumor


title: WT_SHAM2


title: WT_SHAM1


title: TScr1


title: Prm2-Het2


title: TInhib2

value: miR-21 inhbitor


title: CAFScr2

description: CAFScr_vs_CAFInhib_all_isoforms_sorted.txt

value: CAF


title: CAFScr1


title: CAFInhib1

value: miR-224 inhibitor


title: CAFInhib2


title: muscle_P

first: Gregory

middle: Robert

last: Smith

state: NY

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

data_processing:
Cell Ranger 2.0.1 used for data demultiplexing and alignment to the hg19 genome
Seurat 2.3 used for filtering cells with less than 200 discovered genes and filtering genes expressed in fewer than 3 cells. Cells were further filtered to remove those with high mitochondrial gene counts
Genome_build: mm10
Supplementary_files_format_and_content: csv files of raw UMI counts per sample

source_name: Mouse Peritoneal Macrophage

extract_protocol:
Skeletal muscle single-cell suspension was prepared by collagenase/dispase digestion. Briefly, each tissue was minced in 2.5 ml digestion solution (1 U/ml collagenase B and 1 U/ml dispase II (Roche Diagnostics, Indianapolis, IN, USA) in PBS) and incubated at 37ºC for 1 hour. The reaction was terminated by adding 10 ml PBS containing 10% fetal bovine serum (FBS). The mixture was then filtered through a 70-um cell strainer and centrifuged at 250 g for 5 minutes. The pellet was collected and the supernatant was centrifuged again at 250 g for 5 minutes. The pellet was combined with the pellet from the first centrifugation, washed with PBS, and centrifuged at 670 g for 10 minutes. The pellet was re-suspended in 3 ml PBS and filtered through a 40-um cell strainer. Cell suspension was layered on equal volume of the Lympholyte-M solution (Cedarlane, Burlington, NC, USA) and centrifuged at 2,095 g for 45 minutes. Cells at the interface were collected, centrifuged at 670 g for 10 minutes, and re-suspended in FACS staining buffer. Resident macrophages were sorted as CD45+CD11b+F4/80+CD64+ cells.
Single-cell encapsulation with beads using the 10X Genomics Chromium Single Cell 3’ v2 kit (PN 120235 and PN 120234 Module 1) was performed following manufacturer instructions (User Guide Rev A, 10X Genomics, Pleasanton, CA, USA). Briefly, 4 wells of a 10X microfluidic chip (PN 120236) were loaded each with an individual sample to target 5,000 cells per sample. Single-cell gel beads in emulsion (GEMs) were generated and reverse-transcription was performed in the emulsion prior to 12 cycles of cDNA amplification. Quality control and quantification of the amplified cDNA were assessed by Bioanalyzer. Libraries were constructed according to manufacturer instructions (PN 120234 Module 2). Each library was tagged with a different index for multiplexing (PN 120262) during sequencing. Library quality controls were assessed by Bioanalyzer and quantified by Qubit and quantitative PCR (KAPA Biosystems Quantification for Illumina platforms). Sequencing was performed on an HiSeq 2500 (Illumina, Inc., San Diego, CA) using the following read length: 26 bp Read1 (cell barcode + UMI), 8 bp i7 index (sample index), and 98 bp Read2 (insert).

value: C57 BL/6J

value: Peritoneal

value: Macrophage


title: muscle_Q

source_name: Mouse Quadriceps Muscle Macrophage

value: Quadriceps


title: muscle_D

source_name: Mouse Diaphragm Muscle Macrophage

value: Diaphragm


title: RNA-seq: T_Cell_KO_Memory_rep1

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Mapped reads were counted using htseq-count version 0.9.1 and Ensembl GRCm38.90 gtf files with the following arguments: ‘-m union -s no -f bam’
Genome_build: mm10
Supplementary_files_format_and_content: comma seperated values with one column per sample and one row per gene containing raw counts

source_name: KO Spleen Memory

extract_protocol:
CD8 T cell subsets were flow cytometrically sorted and resuspended in Trizol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of Flow cytometrically purified cells were resuspended in Trizol (Ambion Life Technologies) and total RNA was extracted according to the manufacturer’s protocol. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Only RNA samples having an RNA Integrity Number (RIN) > 8 were subjected to library generation.
Strand-specific cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol. The libraries were analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

value: Spleen memory CD44+ CD62L+


title: RNA-seq: T_Cell_KO_Memory_rep3


title: RNA-seq: T_Cell_Het_Memory_rep3

source_name: Het Spleen Memory


title: RNA-seq: T_Cell_KO_Memory_rep4


title: RNA-seq: T_Cell_KO_Memory_rep2


title: muscle_L

source_name: Mouse Lung Alveolar Macrophage

value: Lung


title: WT_MI1

value: Heart

value: WT


title: OE_SHAM2

value: Adult, aproximatly 3 months old

value: ERBB2 overexpression


title: RNA-seq: T_Cell_Het_Memory_rep4


title: OE_SHAM1

value: Sham


title: RNA-seq: T_Cell_Het_Memory_rep2


title: RNA-seq: T_Cell_WT_Memory_rep2

source_name: WT Spleen Memory


title: RNA-seq: T_Cell_Het_Memory_rep1


title: RNA-seq: T_Cell_WT_Memory_rep1


title: RNA-seq: T_Cell_WT_Memory_rep3


title: RNA-seq: T_Cell_KO_Naive_rep2

source_name: KO Spleen Naïve

value: Spleen naïve CD44- CD62L+


title: RNA-seq: T_Cell_KO_Naive_rep3


title: RNA-seq: T_Cell_Het_Naive_rep4

source_name: Het Spleen Naïve


title: RNA-seq: T_Cell_Het_Naive_rep3


title: RNA-seq: T_Cell_KO_Naive_rep1


title: TInhib1

value: Tumor


title: RNA-seq: T_Cell_Het_Naive_rep2


title: RNA-seq: T_Cell_Het_Naive_rep1


title: RNA-seq: T_Cell_WT_Naive_rep3

source_name: WT Spleen Naïve


title: RNA-seq: T_Cell_WT_Naive_rep4


title: RNA-seq: T_Cell_WT_Memory_rep4


title: RNA-seq: T_Cell_WT_Naive_rep2


title: RNA-seq: T_Cell_WT_Naive_rep1


title: RNA-seq: T_Cell_Het_Thymus_rep4

source_name: Het Thymus

value: Thymus CD8 SP


title: RNA-seq: T_Cell_Het_Thymus_rep3


title: RNA-seq: T_Cell_KO_Naive_rep4


title: ChIP-seq: T_Cell_H3K79me2_WT_Thymus_rep2

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using BWA-MEM version 0.7.15-r1140 with the following argument: ‘-M’
Duplicates were marked with picard’s MarkDuplicates version 2.12 with the following arguments:’VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=false’
Reads with a mapping quality less than 37 or any bits in the flag set to 1804 were excluded with Samtools version 1.3
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage version 3.0.1 from deepTools with the following arguments: ‘-of bigwig --binSize 25 --normalizeUsing RPGC --ignoreForNormalization chrM --effectiveGenomeSize 2652783500’; Scores represents reads per genomic content.

source_name: WT Thymus

extract_protocol:
Flow cytometrically purified cells were cross-linked, and chromatin lysates were prepared. Histone-DNA complexes were isolated with antibodies.
Library preparation was done using KAPA LTP Library preparation kit using the manufacturer’s protocol with slight modifications. Briefly, after end-repair and A-tailing adaptor were ligated followed by SPRI clean-up. Libraries were amplified by PCR and fragments between 250-450 bp were selected using AMPure XP beads (Beckman Coultier). The libraries were analyzed for size and quantity of DNAs on a 2100 Bioanalyzer using a High Sensitivity DNA Kit (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

tag: chip antibody

value: H3K79me2 (Milipore 04-835)


title: RNA-seq: T_Cell_Het_Thymus_rep2


title: RNA-seq: T_Cell_Het_Thymus_rep1


title: ChIP-seq: T_Cell_H3K79me2_WT_Memory_rep2


title: ChIP-seq: T_Cell_H3K79me2_WT_Thymus_rep1


title: Wdr68 KO-NPC-2

city: Hershey

first: Qiang

last: Wang

state: PA

address: 700 HMC Crescent Road

department: Department of Biochemistry & Molecular Biology

institute: Penn State College of Medicine

data_processing:
TopHat, version 2.1.1, default parameters
Cufflinks, version 2.2.1, default parameters
Genome_build: mm9
Supplementary_files_format_and_content: FPKM (relative abundances of the transcripts, output from Cufflinks)

source_name: neural progenitors

growth_protocol: E14 mouse ES cells were cultured in DMEM medium, supplemented with 15% FBS (ES certified, Atlanta Biologicals, Cat# S10250), LIF, non-essential amino acids, b-mercaptoethanol, L-glutamine, penicillin/streptomycin, sodium pyruvate, and two small molecule kinase (Mek and GSK3) inhibitors (PD0325901, Cayman Chemical, Cat# 13034 and CHIR99021, Cayman Chemical, Cat# 13122). E14 cells were either cultured on MEF feeder cells or gelatin coated plates.

extract_protocol:
Total RNA was extracted by Trizol
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. To summarize, polyA RNA was purified from 100 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using the BioAnalyzer High Sensitivity DNA Kit (Agilent). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol.

treatment_protocol: E14 cultured on MEF feeders were transferred onto gelatin-coated plates for two passages before differentiation. Embryonic bodies (EB) were formed in hanging drops (500 cells/drop) in differentiation medium (DMEM medium, 15% FBS, non-essential amino acids, b-mercaptoethanol, L-glutamine, penicillin/streptomycin, sodium pyruvate). After two days, EBs were collected and cultured in ultra-low attachment plates for another two days. Then retinoic acid was added to the medium at 5 mM for four more days.

value: ES-derived neural progenitor cells


title: ChIP-seq: T_Cell_H3K79me2_WT_Naive_rep2


title: ChIP-seq: T_Cell_H3K79me2_WT_Naive_rep1


title: E14-NPC-2


title: Wdr68 KO-ESC-2

source_name: embryonic stem cells

value: embryonic stem cells


title: Wdr68 KO-ESC-1


title: E14-ESC-2


title: E14-ESC-1


title: E14-NPC-1


title: MC B7low HDM 2

city: Boston

first: Daniel

last: Dwyer

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

data_processing:
Transcripts were alligned and quantified using theBroad Technology Labs computational pipeline. Data was separated by barcode and aligned using Tophat version 2.0.10 with default settings (Kim et al., 2013). Transcripts were quantified by the Broad Technology Labs using the Cufflinks suite version 2.2.1 (Trapnell et al., 2012).
Data analysis was conducted using Bioconductor for R. Count normalization and differential was conducted using the DESeq2 software package (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrix

source_name: Sorted MC from lower airway

extract_protocol:
Flow cytometrically identified MCs were sorted into 1.5 mL Eppendorf tubes containing 5 uL of 1xTCL buffer (Qiagen). After sorting, tubes were immediately sealed, subjected to a quick spin on a benchtop microcentriguge, and frozen at -80 C.
SmartSeq2 libraries were prepared according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads. Poly(A)+ mRNA was converted to cDNA which was then amplified. cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Barcoded cDNA fragments were then pooled prior to sequencing. Sequencing was carried out using an Illumina NextSeq500 as paired- end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: Mice were anesthetized via isofluorane inhallation and challenged intranasally with 20 uL saline (PBS) or 20 uL containing 3 ug HDM extract (HDM)

value: Lower Airway

value: mast cells (MCs)

tag: cell markers

value: 5-7 week

value: wild type

value: 3 ug HDM 2x/week for 3 weeks


title: MC B7low HDM 1


title: MC B7hi HDM 2


title: MC B7hi HDM 3


title: MC B7hi HDM 1


title: ChIP-seq: T_Cell_H3K4me3_WT_Memory_rep1

value: Spleen memory CD44+ CD62L+

value: H3K4me3 (Abcam, ab8580)


title: MC B7low PBS 2

value: Saline challenge


title: MC B7hi PBS 2


title: MC B7low PBS 1


title: ChIP-seq: T_Cell_H3K79me2_WT_Memory_rep1


title: Wdr68 KO-NPC-1


title: HSPCs, EGF-2

city: Los Angeles

first: John

middle: P

last: Chute

address: 615 Charles E Young Drive South OHRC 545

institute: University of California, Los Angeles (UCLA)

data_processing:
The data was sequenced onNextSeq500 for a paired-end 75bp read run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were mapped to the latest UCSC transcript set using STAR - 2.7.2a and GRCm38.97 (mm10).
After obtaining gene counts, the counts were normalized by CPM (counts per million).
For all results of differential gene expression analysis, the p-values and fold changes (FC) filters were applied. The filter values were p<.05 and |FC|> 1.5 for all differential gene expression results.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files report CPMs (Ensembl_id, Gene_name, Transcript_type, sample name)

source_name: hematopoietic stem and progenitor cells

growth_protocol: N/A primary cells were used

extract_protocol:
RNA was extracted using Qiagen RNeasy Micro Kit
Libraries for RNA-Seq were prepared with Clontech kit. The workflow consisted of rRNA depletion, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

value: bone marrow

value: hematopoietic stem and progenitor cells

value: 16 weeks

tag: stress

value: 500cGy total body radiation

value: EGF


title: HSPCs, EGF-1


title: HSPCs, EGF-5


title: HSPCs, Saline -2

value: Saline


title: HSPCs, Saline -5


title: HSPCs, EGF-4


title: MC B7low HDM 3


title: d9.RNAseq.cont replicate 2 [d190043.ES34-2]

description:
d190043.ES34-2.RNAseq
This is duplicated sample record of GSM3327720 for the convenient retrieval of the complete raw data from SRA.

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
The sequence GAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGAT was clipped using Cutadapt. The reads were aligned to the RefSeq transcriptome (November 2017) using Bowtie for the ribo-seq and bowtie2 for the paired RNA-seq
Differential expression analysis; The  raw count of riboseq reads aligning to the coding regions was used for genes annotated to be protein coding. For the non-protein coding genes and for the mRNAseq data the number of alignments to the entire transcript were used. The position of each read was taken to be 17 nucleotides downstream from its 5’ end. With the minimum expression level threshold of 2 reads, transcripts were sorted in ascending order and an arranged in bins of size 300. The mean and standard deviation of change in expression of the transcripts within each bin was used to determine a Z-score for each transcripts. For the remaining transcripts, of insufficient number to be binned (<300), the mean and standard deviation was obtained from the previous bin. The distribution of average Z-scores from all the replicates was compared to the average of the absolute Z-scores for genes for which all the replicates did not have the same direction (i.e. all positive or negative). The latter distribution is expected to have similar characteristics as the former in the absence of any differential expression. A FDR of 0.05 was used as a threshold of differential expression.
Genome_build: Refseq release 84
Supplementary_files_format_and_content: esmekal_counts.txt.gz is raw counts assigned to each gene in text format.

growth_protocol: FVB/N mice at 6-8 weeks of age were injected with siRNA in LNP formulations at 0.5 mg/kg via tail vein.

extract_protocol:
KAPA mRNA capture
RNA for sequencing was purified from ground mouse livers with the use of Qiagen RNeasy kit

treatment_protocol: mice were injected with the control (scrambled luciferase) or eIF3m siRNA LNP formulations at 0.5 mg/kg (1 injection in 5 days) via tail vein for 9 or 13 days.

value: FVB/N

tag: day

value: scrambled luciferase

value: liver

tag: library strategy

value: RNA-Seq


title: HSPCs, Saline -1


title: d9.RNAseq.Eif3m replicate 3 [d190047.ES34-6]


title: HSPCs, Saline -3


title: HSPCs, EGF-3


title: d9.RNAseq.Eif3m replicate 1 [d190045.ES34-4]

description:
d190045.ES34-4.RNAseq
This is duplicated sample record of GSM3327722 for the convenient retrieval of the complete raw data from SRA.


title: d9.RNAseq.Eif3m replicate 2 [d190046.ES34-5]

description:
d190046.ES34-5.RNAseq
This is duplicated sample record of GSM3327723 for the convenient retrieval of the complete raw data from SRA.


title: d190044.ES34-3.RNAseq: d9.cont replicate 3

description: d9.cont replicate 3

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads aligned with STAR version 2.5.3a and summarized with rsem version 1.3.0
Genome_build: mm10 with ensemble version 88 annotation
Supplementary_files_format_and_content: integer count data in txt format

source_name: liver

extract_protocol:
RNA for sequencing was purified from ground mouse livers with the use of Qiagen RNeasy kit
KAPA mRNA capture
RNA for sequencing was purified from ground mouse livers with the use of Qiagen RNeasy kit

value: luciferase


title: HSPCs, Saline -4


title: d9.RNAseq.cont replicate 1 [d190042.ES34-1]

description:
d190042.ES34-1.RNAseq
This is duplicated sample record of GSM3327719 for the convenient retrieval of the complete raw data from SRA.


title: d190045.ES34-4.RNAseq: d9.Eif3m replicate 1

description: d9.Eif3m replicate 1


title: MC B7hi PBS 1

value: Lower Airway

value: mast cells (MCs)

value: 5-7 week

tag: genotype


title: d190043.ES34-2.RNAseq: d9.cont replicate 2

description: d9.cont replicate 2


title: d9.RNAseq.cont replicate 3 [d190044.ES34-3]

description:
d190044.ES34-3.RNAseq
This is duplicated sample record of GSM3327721 for the convenient retrieval of the complete raw data from SRA.


title: d190042.ES34-1.RNAseq: d9.cont replicate 1

description: d9.cont replicate 1


title: DIE_4.5h 28

description: Data files 4 techinal replicates

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Differential expression analysis was done using the DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Mapped data files in tekst format containing UMI normalized barcode count, read counts and transcript counts.
Supplementary_files_format_and_content: Supplementary data files as supporting infromation for publication.

source_name: Chronic myeloid leukemia cells

extract_protocol:
Trizol samples were collected of DIE cells that had either an intact DUX4 transgene, or a CRISPR/Cas9 edited DUX4 transgene (DIE_KO), and which were either not induced (0h), 4.5h induced, or 8.5h induced by doxycline. Total RNA samples were subsequently extracted by the addition of chloroform, and isopropanol precipitation
The library prep was performed using CEL-seq1 primers, and were processed using CEL-seq2 protocol.

treatment_protocol: 1000ng/ml doxycyline was added to growth media. DIE cells were treated with docycyline for 4.5 and 8.5 hours before sample collection.

tag: cell line

value: DIE

tag: dux4 transgene

value: intact

value: 4.5h doxycline induction


title: DIE_KO_0h 20

description: Data files 4 techinal replicates

value: knocked-out

value: no treattment


title: DIE_KO_0h 19

description: Data files 4 techinal replicates


title: DIE_4.5h 25

description: Data files 4 techinal replicates


title: DIE_4.5h 26

description: Data files 4 techinal replicates


title: DIE_0h 15

description: Data files 4 techinal replicates

value: no treatment


title: DIE_KO_0h 18

description: Data files 4 techinal replicates


title: d190046.ES34-5.RNAseq: d9.Eif3m replicate 2

description: d9.Eif3m replicate 2

tag: strain

tag: tissue


title: DIE_4.5h 27

description: Data files 4 techinal replicates

tag: parental line


title: DIE_KO_0h 17

description: Data files 4 techinal replicates

tag: treatment


title: DIE_0h 13

description: Data files 4 techinal replicates


title: DIE_KO_8.5h 6

description: Data files 4 techinal replicates

value: 8.5h doxycline induction


title: DIE_8.5h 3

description: Data files 4 techinal replicates


title: DIE_8.5h 4

description: Data files 4 techinal replicates


title: d190047.ES34-6.RNAseq: d9.Eif3m replicate 3

description: d9.Eif3m replicate 3

tag: sirna


title: DIE_KO_8.5h 8

description: Data files 4 techinal replicates


title: DIE_KO_8.5h 5

description: Data files 4 techinal replicates


title: DIE_8.5h 1

description: Data files 4 techinal replicates


title: DIE_KO_8.5h 7

description: Data files 4 techinal replicates


title: RNAseq ISP CD28 thymocytes stimulated with 2.5microliter/100 000 cells ImmunoCult D2

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

data_processing:
RNA sequencing reads were aligned to GRCh38 using STAR (version 2.4.2a)42 and quantified on Gencode v24.
Normalization of counts was done using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: raw and DESeq2 normalized counts

source_name: ISP CD28+ sorted human postnatal thymocytes

growth_protocol: ISP CD28+ (CD28+ CD4+ CD3- CD8-) post-β selection thymocytes were isolated from three independent biological donors, and cultured at the density of 100 000 cells per well in U-bottom 96 well plate in 100 μL of the MEMα medium containing 20% FCS, 10ng/ml SCF (Tebu-bio, 300-07), IL-7 (R&D, 207-IL-005/CF).

extract_protocol:
RNA extraction was performed using the miRNeasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen)

treatment_protocol: Cells were not stimulated or stimulated for 24h with 2.5 μL or 10 μL of ImmunoCult™ (Stemcell technology, 10970 )

tag: cell type

value: 2.5microliter/100 000 cells ImmunoCult

tag: donor


title: RNAseq ISP CD28 thymocytes stimulated with 10microliter/100 000 cells ImmunoCult D1

value: ISP CD28+ sorted human postnatal thymocytes

value: 10microliter/100 000 cells ImmunoCult


title: RNAseq ISP CD28 thymocytes stimulated with 0microliter ImmunoCult D2

value: 0microliter ImmunoCult


title: RNAseq ISP CD28 thymocytes stimulated with 2.5microliter/100 000 cells ImmunoCult D3


title: RNAseq ISP CD28 thymocytes stimulated with 10microliter/100 000 cells ImmunoCult D3


title: RNAseq ISP CD28 thymocytes stimulated with 2.5microliter/100 000 cells ImmunoCult D1


title: RNAseq ISP CD28 thymocytes stimulated with 0microliter ImmunoCult D3


title: RNAseq ISP CD28 thymocytes stimulated with 10microliter/100 000 cells ImmunoCult D2


title: DIE_0h 16

description: Data files 4 techinal replicates


title: DIE_0h 14

description: Data files 4 techinal replicates


title: RNAseq HPC R2

data_processing:
RNA sequencing reads were aligned to GRCh38 using STAR (version 2.4.2a) and quantified on Gencode v24
Normalization of counts was done using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: raw and DESeq2 normalized counts

source_name: Human cord blood CD34+

extract_protocol:
RNA extraction was performed after cell sorting using the miRNeasy Mini Kit (Qiagen).
the True Seq Stranded mRNA Sample Preparation Kit (Illumina) was used, followed by sequencing on the NextSeq 500 (Illumina, SR75)

value: cord blood CD34+

tag: cell population

value: HPC

tag: biological replicate

tag: sort phenotype


title: RNAseq gamma delta CD1+ R2

source_name: Human postnatal thymus

value: postnatal thymus

value: gamma delta CD1+

value: TCRgd+ CD3+ CD1-


title: RNAseq ISP CD28 thymocytes stimulated with 0microliter ImmunoCult D1


title: RNAseq SP CD8+ R2

value: SP CD8+

value: CD8+ CD3+


title: RNAseq gamma delta CD1- R2

value: gamma delta CD1-

value: TCRgd+ CD3+ CD1+


title: RNAseq CD34+ CD4+ R2


title: RNAseq CD34+ CD1- R2


title: RNAseq ISP CD28+ R2

value: ISP CD28+


title: DIE_8.5h 2

description: Data files 4 techinal replicates

value: DIE

value: intact


title: RNAseq gamma delta CD1+ R1


title: RNAseq CD34+ CD1+ R2


title: RNAseq DP CD3- R2

value: DP CD3-

value: CD4+ CD8+ CD3-


title: RNAseq gamma delta CD1- R1


title: RNAseq SP CD8+ R1


title: RNAseq HPC R1


title: RNAseq SP CD4+ R1

value: SP CD4+

value: CD4+ CD3+


title: RNAseq SP CD4+ R2


title: RNAseq DP CD3+ R1

value: DP CD3+

value: CD4+ CD8+ CD3+


title: RNAseq CD34+ CD4+ R1


title: RNAseq ISP CD28+ R1


title: RNAseq CD34+ CD1+ R1


title: RNAseq DP CD3- R1


title: RNAseq CD34+ CD1- R1


title: H3K27ac - γδ CD1+ donor Th2

data_processing:
Reads were trimmed by Trimmomatic and aligned to the reference genome hg38 with Bowtie2.
Peaks were called with MACS2 with the respective input control for each donor pool. Options for MACS2 were set to --extsize 73 –nomodel; the –broad flag was used for H3K27me3.
A matrix containing all significant peaks was made as reference for counting reads from BAM files using the function summarizeOverlaps from the R package GenomicAlignments.
Normalization of counts was done using DESeq2 with donor and subset in the design.
Genome_build: hg38
Supplementary_files_format_and_content: raw and DESeq2 normalized counts

extract_protocol:
50-100 000 sorted, fixed cells were lysed in lysis buffer complemented with 20mM NaBU HDAC inhibitor and sheared on the Bioruptor Pico (Diagenode). Sheared chromatin was magnetically immunoprecipitated and tagmentated using the Auto ChIPmentation Kit for Histones (Diagenode).
Libraries were constructed with the Auto ChIPmentation Kit for histones (Diagenode). Libraries were sequenced with the Nextseq500 (SR75, High Output).

tag: chip antibody

value: H3K27ac (Diagenode, C15410174)


title: H3K27ac - SP CD8+ donor Th2

value: postnatal thymus


title: H3K27ac - γδ CD1- donor Th2


title: H3K27ac - HPC donor CB2

value: cord blood CD34+

value: HPC

value: CB D2


title: H3K27ac - SP CD4+ donor Th2


title: RNAseq DP CD3+ R2


title: H3K27ac - DP CD3- donor Th2


title: H3K27ac - DP CD3+ donor Th2


title: H3K27ac - CD34+ CD1+ donor Th2


title: H3K27ac - CD34+ CD4+ donor Th2


title: H3K27ac - CD34+ CD1- donor Th2


title: H3K27ac - ISP CD28+ donor Th1


title: H3K27ac - γδ CD1- donor Th1


title: H3K27ac - SP CD4+ donor Th1


title: H3K27ac - ISP CD28+ donor Th2


title: H3K4me3 - HPC donor CB2

value: H3K4me3 (Diagenode, C15200152)


title: H3K27ac - γδ CD1+ donor Th1

value: gamma delta CD1+

value: TCRgd+ CD3+ CD1-


title: H3K27ac - DP CD3- donor Th1


title: H3K27ac - SP CD8+ donor Th1

value: SP CD8+

value: CD8+ CD3+


title: H3K27ac - CD34+ CD1+ donor Th1


title: H3K27ac - CD34+ CD1- donor Th1


title: H3K27ac - DP CD3+ donor Th1


title: H3K27ac - CD34+ CD4+ donor Th1


title: H3K4me3 - γδ CD1+ donor Th2


title: H3K4me3 - γδ CD1- donor Th2

value: gamma delta CD1-

value: TCRgd+ CD3+ CD1+


title: H3K4me3 - SP CD4+ donor Th2


title: H3K4me3 - SP CD8+ donor Th2


title: H3K4me3 - DP CD3- donor Th2

value: DP CD3-

value: CD4+ CD8+ CD3-


title: H3K4me3 - HPC donor CB1

value: CB D1


title: H3K4me3 - γδ CD1+ donor Th1


title: H3K4me3 - CD34+ CD4+ donor Th2


title: H3K4me3 - DP CD3+ donor Th2

value: DP CD3+


title: H3K4me3 - ISP CD28+ donor Th2

value: ISP CD28+


title: H3K27ac - HPC donor CB1

value: H3K27ac (Diagenode, C15410174)


title: H3K4me3 - γδ CD1- donor Th1

value: postnatal thymus


title: H3K4me3 - CD34+ CD1+ donor Th2


title: H3K4me3 - SP CD8+ donor Th1


title: H3K4me3 - SP CD4+ donor Th1

value: SP CD4+

value: CD4+ CD3+


title: input control 2

source_name: Human postnatal thymus and human cord blood CD34+

value: postnatal thymus and cord blood CD34+

value: pool of thymic and HPC samples

value: D2+CB D2

value: pool


title: H3K4me3 - DP CD3+ donor Th1

value: H3K4me3 (Diagenode, C15200152)

value: CD4+ CD8+ CD3+


title: H3K4me3 - CD34+ CD1- donor Th1


title: H3K4me3 - CD34+ CD4+ donor Th1


title: H3K4me3 - ISP CD28+ donor Th1


title: H3K27me3 - γδ CD1- donor Th2

value: gamma delta CD1-


title: H3K4me3 - DP CD3- donor Th1


title: H3K27me3 - SP CD8+ donor Th2

value: SP CD8+

value: CD8+ CD3+


title: H3K27me3 - SP CD4+ donor Th2


title: H3K27me3 - HPC donor CB2

value: cord blood CD34+

value: HPC

value: CB D2


title: H3K27me3 - γδ CD1+ donor Th2

value: gamma delta CD1+

value: TCRgd+ CD3+ CD1-


title: H3K4me3 - CD34+ CD1+ donor Th1

value: postnatal thymus


title: H3K27me3 - ISP CD28+ donor Th2

value: ISP CD28+


title: H3K27me3 - DP CD3- donor Th2

value: DP CD3-

value: CD4+ CD8+ CD3-


title: H3K27me3 - CD34+ CD4+ donor Th2


title: H3K27me3 - CD34+ CD1+ donor Th2


title: H3K27me3 - DP CD3+ donor Th2

value: DP CD3+


title: input control 1

value: postnatal thymus and cord blood CD34+

value: pool of thymic and HPC samples

value: D1+CB D1


title: H3K27me3 - CD34+ CD1- donor Th2


title: H3K27me3 - HPC donor CB1

value: CB D1


title: MU03-2427-GS6

type: RNA

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Following labeling, 21.5uL of biotin-labeled samples were hybridized for 16 hr at 48C on GeneChip miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing:
CEL files were analyzed for quality using Affymetrix Transcriptome Analysis Console 4.0 software, and the RMA-DBAG was used for summarization
algorithm-name-0 = rma-bg,pm-only,med-polish
algorithm-name-1 = pm-only,dabg.adjust-dof=1
Q_probeset_summarize-Version = V916
affymetrix-algorithm-name = rma-bg,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: biotin

source_name: Gleason Score 6_urine

label_protocol: Biotinylated miRNA were prepared according to the standard Affymetrix FlashTag HSR protocol from 100 ng total RNA

extract_protocol: Standard urine exosome RNA isolation method by Norgen Biotek Corp.

tag: histopathology

value: Gleason Score 6

value: Urine


title: MU03-2335-GS6


title: MU03-1355-GS6


title: MU03-2350-GS6


title: MU01_0015-Ctrl

value: Control


title: MU03-2589-GS7

source_name: Gleason Score 7_urine

value: Gleason Score 7


title: MU01-1808-Ctrl


title: MU01-1817-Ctrl


title: H3K4me3 - CD34+ CD1- donor Th2

value: H3K4me3 (Diagenode, C15200152)


title: H3K27me3 - γδ CD1- donor Th1

value: gamma delta CD1-

value: TCRgd+ CD3+ CD1+


title: H3K27me3 - γδ CD1+ donor Th1

value: gamma delta CD1+

value: TCRgd+ CD3+ CD1-


title: H3K27me3 - SP CD8+ donor Th1

value: postnatal thymus

value: SP CD8+

value: CD8+ CD3+


title: H3K27me3 - SP CD4+ donor Th1

value: SP CD4+

value: CD4+ CD3+


title: H3K27me3 - DP CD3- donor Th1

value: DP CD3-

value: CD4+ CD8+ CD3-


title: H3K27me3 - DP CD3+ donor Th1

value: DP CD3+

value: CD4+ CD8+ CD3+


title: H3K27me3 - ISP CD28+ donor Th1

value: ISP CD28+


title: H3K27me3 - CD34+ CD1+ donor Th1


title: H3K27me3 - CD34+ CD4+ donor Th1


title: H3K27me3 - CD34+ CD1- donor Th1


title: MU01-1705-GS7

value: Urine


title: MU01-1723-GS6

value: Gleason Score 6


title: MU01-1739-Ctrl

value: Control


title: ATACseq ISP CD28 thymocytes stimulated with 10microliter/100 000 cells ImmunoCult D3

data_processing:
reads were trimmed using Trimmomatic (single end sequencing) or NGmerge (paired end sequencing).
Bowtie2 (version 2.2.6) was used to align ATACseq reads to GRCh38 with option --very-sensitive. SAMTools and BEDTools were used for further data handling, removal of duplicate reads and read shifting (4bp on forward and -5bp on reverse strand).
Significant peaks were called with MACS2 from BED files.
A matrix containing all significant peaks was made as reference for counting reads from BAM files using the function summarizeOverlaps from the R package GenomicAlignments.
Normalization of counts was done using DESeq2 with donor and subset in the design.
Genome_build: hg38
Supplementary_files_format_and_content: raw and DESeq2 normalized counts

extract_protocol:
Sorted cells were incubated with a transposition mix (TDE1 Tagment DNA Enzyme, 1X TD buffer and 0.01 % digitonin). Transposed DNA fragments were purified by using Qiagen MinElute PCR purification kit and amplified by PCR.
Transposed DNA libraries were prepared with the Nextera Index Kit (24 Indices, 96 Samples) and sequenced as single-end or paired-end 75 bp reads on the NextSeq500 Illumina platform.

value: ISP CD28+ sorted human postnatal thymocytes

value: 10microliter/100 000 cells ImmunoCult


title: ATACseq ISP CD28 thymocytes stimulated with 10microliter/100 000 cells ImmunoCult D2


title: ATACseq ISP CD28 thymocytes stimulated with 0microliter ImmunoCult D3

value: 0microliter ImmunoCult


title: MU01-1691-Ctrl


title: ATACseq ISP CD28 thymocytes stimulated with 2.5microliter/100 000 cells ImmunoCult D3

value: 2.5microliter/100 000 cells ImmunoCult


title: MU01-1682-GS7

value: Gleason Score 7


title: MU01-1703-GS7


title: MU01-1713-GS6


title: MU01-1725-GS6


title: MU01-1724-GS6


title: ATACseq ISP CD28 thymocytes stimulated with 0microliter ImmunoCult D2


title: MU01-1657-GS7


title: MU01-1645-GS8

source_name: Gleason Score 8_urine

value: Gleason Score 8


title: MU01-1694-GS6


title: ATACseq ISP CD28 thymocytes stimulated with 10microliter/100 000 cells ImmunoCult D1


title: MU01-1692-GS9

source_name: Gleason Score 9_urine

value: Gleason Score 9


title: ATACseq ISP CD28 thymocytes stimulated with 0microliter ImmunoCult D1


title: MU01-1640-Ctrl


title: MU01-1627-Ctrl


title: Background Lung

city: Southampton

first: Eva

last: Garrido-Martin

address: University Road

country: United Kingdom

institute: University of Southampton

data_processing:
Data was processed as per standard 10x genomics pipeline
The number of reads for each library was normalised to the library with the least number of reads
Samples were then processed in R using the Seurat package
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file include normalised counts for each sample

source_name: Human Background Lung

extract_protocol: RNAseq 10x genomics, completed as per Patil, et al., 2018; Science Immunology

treatment_protocol: Tissue was dispersed and then lymphocytes were sorted by FACS.

tag: cells

value: FACS sorted cells

tag: tissue of origin

value: Background Lung

tag: tumour subtype

value: Paired backround lung

tag: paired

value: Yes

tag: primary / in vitro

value: Primary


title: D2_DLL4 transduced OP9_TCF1

description: D2_DLL4 transduced OP9_TCF1

data_processing:
reads were trimmed using Trimmomatic (single end sequencing) or NGmerge (paired end sequencing).
Bowtie2 (version 2.2.6) was used to align ATACseq reads to GRCh38 with option --very-sensitive. SAMTools and BEDTools were used for further data handling, removal of duplicate reads and read shifting (4bp on forward and -5bp on reverse strand).
Significant peaks were called with MACS2 from BED files.
A matrix containing all significant peaks was made as reference for counting reads from BAM files using the function summarizeOverlaps from the R package GenomicAlignments.
Normalization of counts was done using DESeq2 with donor and subset in the design.
Genome_build: hg38
Supplementary_files_format_and_content: Raw and DESeq2-normalized counts

source_name: ATACseq of HPCs transduced with genomic DNA cultured on TCF1

growth_protocol: Cord blood-derived CD34+ enriched cells, derived from two independent biological donors, were pre-stimulated with stem cell factor (SCF: 100 ng/mL), thrombopoietin (TPO: 20 ng/mL) and FMS-like tyrosine kinase 3 ligand (FLT3-L: 100 ng/mL) for 2 days

treatment_protocol: Cells were transduced with the use of RetroNectin reagent. At day-2 post transduction, CD34+lin-GFP+ cells were sorted and co-cultured with OP9-LIE and OP9-DLL4 stromal cells. Both co-cultures were supplemented with 5 ng/mL of SCF, FLT3-L and interleukin-7. The co-culture medium used was MEMα that contained 20% fetal calf serum. At day-3 post co-culture, CD45+GFP+ cells were sorted.

value: cord blood CD34+

tag: feeder

value: DLL4 transduced OP9

tag: viral transduction


title: MU01-1629-Ctrl

tag: tissue

value: Urine


title: D2_DLL4 transduced OP9_GATA3

description: D2_DLL4 transduced OP9_GATA3

source_name: ATACseq of HPCs transduced with genomic DNA cultured on GATA3


title: MU01-1658-GS7


title: MU01-1660-GS6

value: Gleason Score 6


title: D2_DLL4 transduced OP9_LIE

description: D2_DLL4 transduced OP9_LIE

source_name: ATACseq of HPCs transduced with genomic DNA cultured on LIE

value: LIE


title: NTAM-NSCLC NTAM-228

data_processing:
Single ended 35 bp-length read RNAseq was performed using the HiSeq 2000 Illumina. Briefly, The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC human genome (hg19) using TopHat (v1.4.1) (Trapnell et al, Bioinformatics 2009).
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al, Bioinformatics 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.
The alignment results were parsed via the SAMtools (Li et al, Bioinformatics 2009) to generate SAM files
Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al, Bioinformatics 2014) using the “union” option.
After removing absent features (zero counts in all samples), the raw counts were then imported to R/Bioconductor package DESeq2 (Love et al, Genome Biology 2014) to identify differentially expressed genes among samples. DESeq2 normalizes counts by dividing each column of the count table (samples) by the size factor of this column. The size factor is calculated by dividing the samples by geometric means of the genes. This brings the count values to a common scale suitable for comparison.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file include normalised counts for each sample

source_name: Tumour-free lung tissue from cancer patient (matched)

extract_protocol:
Resected tissue was dissagregated mechanically and enzymatically (liberase DL and DNAseI, 15 min 37C). FACS sorted macrophages (DAPIneg, CD45pos, CD14pos, HLA-DRpos) were stored at -80C in trizol. RNA was extracted using miRNeasy micro kit (QIAGEN) following manufacturer instructions and amplified using SEQR SeqPlex RNA Amplification kit (Sigma)
Amplified dsDNA was subjected to library preparation using TruSeq Nano DNA library prep kit (Illumina). Briefly: Samples were subjected to End-Repair during 30 min at 30C. Size selection was performed using Agencourt AMPure XP beads in two steps: Removal of large DNA fragments (>450 bp) followed by removal of small DNA fragments (<150 bp). 3’ ends of 150-450bp DNA fragments were adenylated using A-Tailing Mix during 30 min at 37C. Then, Illumina adapters were ligated using Ligation Mix 2, Resuspension Buffer and the appropriate barcoded adapter in each case. As a last step, two sets of clean ups were performed using AMPure XP Beads. DNA was eluted and PCR amplified using PCR Primer Cocktail and Enhanced PCR Mix as follows: 3 min at 95C, and 8 cycles of 20 sec at 98C, 15 sec at 60C and 30 sec at 70C. As a final step, the final amplified libraries were cleaned up using Sample Purification Beads. The size of the library was determined by HS-DNA Agilent Bioanalyzer (150-430 bp). The amount of library was determined by Nanodrop and dsDNA Quantifluor.

value: Macrophages

value: lung

value: non-tumor

value: yes

value: primary

tag: fluorescence activated sorting

tag: whole transcriptome amplification

tag: library prep ilumina

value: TruSeq Nano DNA HT

tag: adaptor barcode


title: MU01-1615-GS7

value: Gleason Score 7


title: D2_eGFP transduced OP9_BCL11B

description: D2_eGFP transduced OP9_BCL11B

source_name: ATACseq of HPCs transduced with genomic DNA cultured on BCL11B

tag: donor

value: eGFP transduced OP9


title: NTAM-NSCLC NTAM-227


title: D2_DLL4 transduced OP9_BCL11B

description: D2_DLL4 transduced OP9_BCL11B


title: NTAM-NSCLC NTAM-210


title: MU01-1617-GS6


title: MU01-1581-GS7


title: MU01-1584-GS6


title: D2_eGFP transduced OP9_TCF1

description: D2_eGFP transduced OP9_TCF1


title: MU01-1577-GS7


title: MU01-1592-GS5

source_name: Gleason Score 5_urine

value: Gleason Score 5


title: MU01-1558-GS6


title: MU01-1622-Ctrl

value: Control


title: NTAM-NSCLC NTAM-203

value: Yes


title: Tumour

source_name: Human lung tumour

value: FACS sorted cells

value: Lung Tumor

value: NSCLC

value: Primary


title: MU01-1595-GS9

value: Gleason Score 9

value: Urine


title: MU01-1542-GS6

value: Gleason Score 6


title: MU01-1551-GS7


title: MU01-1536-GS7


title: NTAM-NSCLC NTAM-198

value: Macrophages

value: lung

value: no


title: D2_eGFP transduced OP9_LIE

description: D2_eGFP transduced OP9_LIE

value: cord blood CD34+

value: LIE


title: MU01-1522-Ctrl


title: MU01-1532-GS7

value: Gleason Score 7


title: NTAM-NSCLC NTAM-196

value: non-tumor

value: yes

value: primary

value: TruSeq Nano DNA HT


title: MU01-1552-GS7


title: D1_DLL4 transduced OP9_BCL11B

description: D1_DLL4 transduced OP9_BCL11B

value: DLL4 transduced OP9


title: MU01-1511-GS7


title: MU01-1523-GS6


title: NTAM-NSCLC NTAM-192

value: Yes


title: MU01-1509-GS6


title: D1_DLL4 transduced OP9_GATA3

description: D1_DLL4 transduced OP9_GATA3


title: NTAM-NSCLC NTAM-179


title: D1_DLL4 transduced OP9_LIE

description: D1_DLL4 transduced OP9_LIE


title: NTAM-NSCLC NTAM-186


title: D1_DLL4 transduced OP9_TCF1

description: D1_DLL4 transduced OP9_TCF1


title: D2_eGFP transduced OP9_GATA3

description: D2_eGFP transduced OP9_GATA3

value: eGFP transduced OP9


title: ATACseq ISP CD28 thymocytes stimulated with 2.5microliter/100 000 cells ImmunoCult D2

tag: cell type

value: ISP CD28+ sorted human postnatal thymocytes

tag: treatment

value: 2.5microliter/100 000 cells ImmunoCult


title: MU01-1505-GS6

value: Urine


title: NTAM-NSCLC NTAM-167


title: MU01-1467-Ctrl

value: Control


title: NTAM-NSCLC NTAM-164

value: Macrophages


title: MU01-1402-GS6

value: Gleason Score 6


title: MU01-1434-Ctrl


title: MU01-1395-GS6


title: MU01-1399-GS9

value: Gleason Score 9


title: MU01-1446-Ctrl


title: NTAM-NSCLC NTAM-163

value: lung


title: D1_eGFP transduced OP9_TCF1

description: D1_eGFP transduced OP9_TCF1

value: cord blood CD34+


title: D1_eGFP transduced OP9_GATA3

description: D1_eGFP transduced OP9_GATA3


title: MU01-1393-GS7

value: Gleason Score 7


title: MU01-1388-GS6


title: MU01-1377-GS6


title: NTAM-NSCLC NTAM-161

value: non-tumor


title: MU01-1508-GS6


title: ATAC seq HPC donor CB D3

tag: cell population

value: HPC

value: CB D3

tag: run

tag: sort phenotype


title: D1_eGFP transduced OP9_BCL11B

description: D1_eGFP transduced OP9_BCL11B


title: D1_eGFP transduced OP9_LIE

description: D1_eGFP transduced OP9_LIE

value: LIE


title: NTAM-NSCLC NTAM-156

tag: cells

tag: tissue of origin

value: yes

value: primary

value: TruSeq Nano DNA HT


title: ATAC seq HPC donor CB D2

value: CB D2


title: NTAM-NSCLC NTAM-153

tag: tumour subtype

tag: paired

value: Yes


title: ATAC seq HPC donor CB D1

value: CB D1


title: MU01-1301-GS7

tag: histopathology

value: Urine


title: MU01-1304-GS7


title: MU01-1319-GS6


title: MU01-1295-GS6


title: MU01-1370-GS9


title: MU01-1344-GS8

value: Gleason Score 8


title: MU01-1365-GS9


title: ATAC seq gamma delta CD1- donor D2

value: postnatal thymus

value: gamma delta CD1-

value: TCRgd+ CD3+ CD1-


title: MU01-1290-GS7


title: NTAM-NSCLC NTAM-150

value: Macrophages

value: lung

tag: primary / in vitro


title: ATAC seq gamma delta CD1+ donor D2

tag: tissue

value: gamma delta CD1+

value: TCRgd+ CD3+ CD1+


title: NTAM-NSCLC NTAM-149

value: non-tumor

tag: fluorescence activated sorting


title: NTAM-NSCLC NTAM-159

tag: whole transcriptome amplification


title: NTAM-NSCLC NTAM-137

tag: library prep ilumina

value: TruSeq Nano DNA LT


title: MU01-1289-GS7

value: Gleason Score 7


title: MU01-1243-GS7


title: ATAC seq SP CD8+ donor D2

value: SP CD8+

value: CD8+ CD3+


title: MU01-1235-GS6

value: Gleason Score 6


title: NTAM-NSCLC NTAM-135

value: yes

value: primary

value: Yes

value: TruSeq Nano DNA HT

tag: adaptor barcode


title: MU01-1231-GS6

value: Urine


title: ATAC seq SP CD4+ donor D2

value: postnatal thymus

value: SP CD4+

tag: donor

value: CD4+ CD3+


title: MU01-1213-GS6


title: NTAM-NSCLC NTAM-132

value: Macrophages

value: lung


title: NTAM-NSCLC NTAM-121


title: MU01-1256-GS6


title: NTAM-NSCLC NTAM-117


title: ATAC seq DP CD3+ donor D2

value: DP CD3+

value: CD4+ CD8+ CD3+


title: ATAC seq DP CD3- donor D2

value: DP CD3-

value: CD4+ CD8+ CD3-


title: MU01-1242-GS6


title: MU01-1185-GS6


title: ATAC seq ISP CD28+ donor D2

value: ISP CD28+


title: MU01-1159-GS6


title: MU01-1156-GS6


title: NTAM-NSCLC NTAM-113

value: non-tumor

value: TruSeq Nano DNA LT


title: NTAM-NSCLC NTAM-105

value: yes


title: ATAC seq CD34+ CD4+ donor D2


title: MU01-1148-GS9

value: Gleason Score 9


title: MU01-1154-GS7

value: Gleason Score 7


title: ATAC seq CD34+ CD1+ donor D2


title: MU01-1140-GS6

value: Gleason Score 6


title: ATAC seq CD34+ CD1- donor D2


title: NTAM-NSCLC NTAM-103

value: primary

value: Yes


title: MU01-1139-GS6

value: Urine


title: NTAM-NSCLC NTAM-99


title: MU01-1100-Ctrl

value: Control


title: MU01-1109-GS6


title: MU01-1186-GS6


title: MU01-1092-GS6


title: MU01-1203-GS6


title: NTAM-NSCLC NTAM-96

value: Macrophages

value: TruSeq Nano DNA HT


title: MU01-1145-GS8

value: Gleason Score 8


title: ATAC seq SP CD8+ donor D1

value: postnatal thymus

value: SP CD8+

value: CD8+ CD3+


title: ATAC seq gamma delta CD1+ donor D1

value: gamma delta CD1+

value: TCRgd+ CD3+ CD1+


title: MU01-1073-Ctrl


title: NTAM-NSCLC NTAM-91

value: lung

value: non-tumor

value: TruSeq Nano DNA LT


title: ATACseq ISP CD28 thymocytes stimulated with 2.5microliter/100 000 cells ImmunoCult D1

tag: cell type

value: ISP CD28+ sorted human postnatal thymocytes

value: 2.5microliter/100 000 cells ImmunoCult


title: MU01-1063-GS7

value: Gleason Score 7


title: MU01-1224-GS6

value: Gleason Score 6


title: NTAM-NSCLC NTAM-88

value: yes

value: primary

value: Yes


title: MU01-1059-Ctrl

value: Control

value: Urine


title: NTAM-NSCLC NTAM-80

value: Macrophages


title: ATAC seq DP CD3+ donor D1

value: postnatal thymus

value: DP CD3+

value: CD4+ CD8+ CD3+


title: NTAM-NSCLC NTAM-70

value: TruSeq Nano DNA HT


title: MU01-1045-GS6


title: MU01-1050-GS6


title: ATAC seq ISP CD28+ donor D1

value: ISP CD28+


title: ATAC seq DP CD3- donor D1

value: DP CD3-

value: CD4+ CD8+ CD3-


title: MU01-1048-GS6


title: NTAM-NSCLC NTAM-68

value: lung

value: non-tumor


title: MU01-1078-Ctrl


title: MU01-1033-GS6


title: MU01-1042-GS7

value: Gleason Score 7


title: MU01-1025-GS7


title: MU01-1091-Ctrl


title: ATAC seq gamma delta CD1- donor D1

value: gamma delta CD1-

value: TCRgd+ CD3+ CD1-


title: MU01-1049-GS7


title: ATAC seq CD34+ CD1+ donor D1


title: NTAM-NSCLC NTAM-62

value: yes

value: primary


title: TAM-NSCLC TAM-228-A

source_name: Non-small cell lung carcinoma (NSCLC)

value: Tumour Associated Macrophages

value: Lung Adenocarcinoma

value: Yes


title: ATAC seq SP CD4+ donor D1

value: postnatal thymus

value: SP CD4+

value: CD4+ CD3+


title: MU01-1021-GS6

value: Gleason Score 6

value: Urine


title: MU01-1004-Ctrl

value: Control


title: MU01-0995-Ctrl


title: MU01-1007-GS7


title: TAM-NSCLC TAM-227-S

value: Lung Squamous Cell Carcinoma

value: TruSeq Nano DNA HT


title: MU01-0991-Ctrl


title: TAM-NSCLC TAM-210-A

value: lung


title: ATAC seq CD34+ CD1- donor D1


title: MU01-0981-Ctrl


title: 1x14041_S9

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

country: France

institute: university Lyon1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data demultiplexing performed using CASAVA version 1.8.2
Alignment to reference genome performed using TopHat 2.0.6 including Bowtie 2.0.2
gene expression performed using Cufflinks 2.0.2
Genome_build: Human Genome: hg19 (GRCh37, Fev 2009) from UCSC
Supplementary_files_format_and_content: Cufflinks used gene annotation file to calculate overall normalized gene expression in terms of FPKM (Fragments Per Kilobases of exon per Million mapped reads ).

source_name: Epidermal cell sheets generated by culturing for 12 days human keratinocytes

growth_protocol: Normal human epidermal keratinocyte (NHEK) were isolated from human breast skin. NHEK were grown on a feeder layer of irradiated human fibroblasts pre-seeded at 4000cell/cm², as previously described (37,38) in keratinocyte culture medium (KCM) containing a mix of 3:1 DMEM and HAM’s F12 (Invitrogen, Carlsbad, USA), supplemented with 10% FCS, 10ng/ml epidermal growth factor (EGF; R&D systems, Minneapolis, MN, USA), 0.12 IU/ml insulin (Lilly, Saint-Cloud, France), 0.4 mg/ml hydrocortisone (UpJohn, St Quentin en Yvelelines, France) , 5 mg/ml triiodo-L-thyronine (Sigma, St Quentin Fallavier, France), 24.3 mg/ml adenine (Sigma), isoproterenol (Isuprel, Hospira France, Meudon, France) and antibiotics (20 mg/ml gentamicin (Phanpharma, Fougères, France), 100IU/ml penicillin (Phanpharma), and 1 mg/ml amphotericin B (Phanpharma)).

extract_protocol:
totalRNA were extracted from cultured cells using RNeasy microkit (Qiagen), quantified and qualified using bioanalyzer 2100 (Agilent)
Libraries were prepared from 100 ng totalRNA using the NextFlex Rapid Directional mRNA-seq  preparation (Bioo Scientific)
index list: CGATGT(S1); CCGTTC(S2); GTAGAG(S3); GTCCGC(S4); GTGAAA(S5); GTGGCC(S6); GTTTCG(S7); CGTACG(S8); GAGTGG(S9); GGTAGC(S10)
Sequencing was performed on a NextSeq 500 in single end 75bp on highoutput flow cell (400 miilions reads)

treatment_protocol: Epidermal cell sheets were then treated or not for 24h with 0.25 mM NaHS

tag: treatment


title: TAM-NSCLC TAM-196-A


title: TAM-NSCLC TAM-203-A


title: MU01-0968-Ctrl


title: MU01-0966-GS6


title: MU01-0977-Ctrl


title: MU01-0993-Ctrl


title: MU01-0958-Ctrl


title: 1x14035_S7


title: ATAC seq CD34+ CD4+ donor D1

tag: cell population


title: TAM-NSCLC TAM-186-S


title: TAM-NSCLC TAM-192-A


title: 2x14041_S10

value: 0.25 mM NaHS for 24h


title: MU01-0960-Ctrl


title: MU01-0959-Ctrl


title: MU01-0952-Ctrl


title: 2x14001_S6


title: MU01-0924-Ctrl


title: MU01-0925-Ctrl


title: MU01-0921-Ctrl


title: MU01-0978-Ctrl


title: 2x14035_S8


title: 2x16037_S4


title: MU01-0906-GS7

value: Gleason Score 7


title: TAM-NSCLC TAM-179-A


title: MU01-0905-GS8

value: Gleason Score 8


title: TAM-NSCLC TAM-164-A

value: yes


title: TAM-NSCLC TAM-163-A

value: primary


title: NOD_GFPnegative_3weeks_Replicate_3

city: Toulouse

first: Joost

last: van Meerwijk

state: HG

address: CHU Purpan – BP 3028

institute: INSERM

data_processing:
trimmed with the Trimmomatic tool
quantified, using STAR
Differential expression analysis and normalization of the counts were performed using DESeq2
Genes with an adjusted p-Value < 0.05 (Benjamini & Hochberg), fold change > 2, and mean normalized counts > 100 in at least one strain were selected
Genome_build: mm10
Supplementary_files_format_and_content: Normalyzed counts from DESeq2

source_name: Thymic regulatory T cells

growth_protocol: NA, Sorting

extract_protocol:
Total RNA was extracted with miRNeasy micro kit (Qiagen, USA) and its quality was controlled using an Agilent 2100 BioAnalyzer (Agilent technologies, USA).
Libraries for RNA-sequencing (RNA-seq) were prepared using the TruSeq Standard Total RNA LT protocol (Illumina, USA), using 50-100 ng of high-quality RNA (RIN>8.5).

tag: sorting

value: GFP− CD4+CD8− Thy1.1+

tag: strain

value: NOD

tag: age

value: 3 weeks


title: MU01-0886-GS6


title: 1x16037_S3


title: NOD_GFPnegative_3weeks_Replicate_2


title: TAM-NSCLC TAM-161-A

tag: cells

value: Tumour Associated Macrophages

tag: tissue of origin

value: Lung Adenocarcinoma

value: Yes


title: MU01-0863-GS7


title: 1x14001_S5


title: 2x16003_S2


title: 1x16003_S1


title: TAM-NSCLC TAM-167-A

tag: tumour subtype

tag: paired


title: MU01-0917-GS6

tag: histopathology

value: Gleason Score 6


title: MU01-0862-Ctrl

tag: tissue

value: Urine


title: MU01-0859-GS6


title: NOD_GFPnegative_3weeks_Replicate_1


title: TAM-NSCLC TAM-159-A

tag: primary / in vitro

tag: fluorescence activated sorting


title: LAN5 2D RA input

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: DNA (input control)

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.  Duplicates were allowed
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files (BED coordinates) for each sample.

source_name: Neuroblastoma line LAN5

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation until harvesting for ChIP.

extract_protocol:
harvesting protocol: ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit).  ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen).
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

tag: cell line

value: Neuroblastoma

tag: antibody

tag: enrichment target

value: input

tag: target function

value: ATRA


title: TAM-NSCLC TAM-156-A

value: lung

tag: whole transcriptome amplification

tag: library prep ilumina

value: TruSeq Nano DNA HT

tag: adaptor barcode


title: B6_GFPnegative_3weeks_Replicate_3

tag: sorting

tag: strain


title: LAN5 2D C input

description: DNA (input control)

tag: cell type

tag: treatment

value: Ethanol


title: TAM-NSCLC TAM-153-A

tag: cells

tag: tissue of origin

tag: tumour subtype


title: B6_GFPnegative_3weeks_Replicate_2

tag: age


title: B6_GFPnegative_3weeks_Replicate_1


title: MU01-0850-GS6

tag: histopathology

tag: tissue


title: MU01-0839-Ctrl

value: Control


title: LAN5 8D RA H3K27ac

description: DNA (ChIP-enriched)

tag: cell line

value: H3K27ac (Active Motif, 39133)

value: Active enhancers


title: LAN5 8D C H3K27ac

description: DNA (ChIP-enriched)

tag: antibody


title: TAM-NSCLC TAM-149-S

value: Lung Squamous Cell Carcinoma

tag: paired

value: yes

tag: primary / in vitro

value: primary

tag: fluorescence activated sorting


title: LAN5 4D RA H3K27ac

description: DNA (ChIP-enriched)

tag: enrichment target

tag: target function


title: TAM-NSCLC TAM-137-S

value: Tumour Associated Macrophages

tag: whole transcriptome amplification

tag: library prep ilumina

value: TruSeq Nano DNA LT

tag: adaptor barcode


title: TAM-NSCLC TAM-135-S

value: Yes


title: TAM-NSCLC TAM-132-A

value: Lung Adenocarcinoma


title: MU01-0787-GS6

value: Gleason Score 6

value: Urine


title: TAM-NSCLC TAM-121-A


title: MU01-0780-GS6


title: LAN5 4D C H3K27ac

description: DNA (ChIP-enriched)

tag: cell type

value: Neuroblastoma

tag: treatment


title: MU01-0813-Ctrl


title: LAN5 2D C H3K27ac

description: DNA (ChIP-enriched)


title: MU01-0856-GS7

value: Gleason Score 7


title: TAM-NSCLC TAM-150-A

tag: cells

tag: tissue of origin

value: lung


title: KCNR 8D RA H3K27ac

description: DNA (ChIP-enriched)

source_name: Neuroblastoma line KCNR

value: KCNR

value: ATRA


title: TAM-NSCLC TAM-117-S

tag: tumour subtype

value: TruSeq Nano DNA HT


title: MU01-0828-GS7

tag: histopathology


title: TAM-NSCLC TAM-116-A

value: no


title: KCNR 8D C H3K27ac

description: DNA (ChIP-enriched)

value: H3K27ac (Active Motif, 39133)

value: Active enhancers

value: Ethanol


title: MU01-0754-GS6

source_name: Gleason Score 6_urine

tag: tissue


title: MU01-0749-GS6


title: MU01-0750-GS7

source_name: Gleason Score 7_urine


title: LAN5 2D RA H3K27ac

description: DNA (ChIP-enriched)

tag: cell line


title: KCNR 4D RA H3K27ac

description: DNA (ChIP-enriched)

tag: antibody


title: MU01-0743-Ctrl

value: Control


title: MU01-0765-GS6


city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 3 of 4. Limousin muscle cells_Cy5 vs. Holstein Friesian muscle cells_Cy3_rep3

hyb_protocol: Probe were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and LOWESS normalization.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p≤0.05) and fold change FC≥1.3.

organism: Bos taurus

source_name: Limousin muscle cells_Cy5

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

growth_protocol: Bovine muscle cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/DMEM/AB) was changed every two days. After obtaining 80% of confluence the cells were trypsinized, centrifuged, the supernatant was discarded, and the cell pellet was frozen for further analysis. The muscle cell culture material was subjected to freezing at the proliferation stage, when the cells obtained 80% confluence  for transcriptomic analysis of proliferating satellite cells using the microarray technique. FBS - fetal bovine serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated by using a total RNA kit (A&A BIOTECHNOLOGY, Poland).RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number > 9 were included into the analysis.

treatment_protocol: not applicable

tag: age

value: proliferation - 80% of confluence

tag: satellite cell origin

value: muscle cells isolated from m. semitendinosus

source_name: Holstein Friesian muscle cells_Cy3


title: TAM-NSCLC TAM-113-A

value: Tumour Associated Macrophages

tag: paired

value: yes

tag: primary / in vitro

value: primary

tag: fluorescence activated sorting

value: Yes

value: TruSeq Nano DNA LT


description: Biological replicate 4 of 4. Limousin muscle cells_Cy5 vs. Holstein Friesian muscle cells_Cy3_rep4


description: Biological replicate 2 of 4. Limousin muscle cells_Cy5 vs. Holstein Friesian muscle cells_Cy3_rep2


title: KCNR 4D C H3K27ac

description: DNA (ChIP-enriched)

value: Neuroblastoma

tag: enrichment target

tag: target function


description: Biological replicate 1 of 4. Limousin muscle cells_Cy5 vs. Holstein Friesian muscle cells_Cy3_rep1


description: Biological replicate 3 of 4. Hereford muscle cells_Cy3 vs. Holstein Friesian muscle cells_Cy5_rep3

source_name: Hereford muscle cells_Cy3

source_name: Holstein Friesian muscle cells_Cy5


description: Biological replicate 2 of 4. Hereford muscle cells_Cy3 vs. Holstein Friesian muscle cells_Cy5_rep2


title: TAM-NSCLC TAM-105-A

value: lung

value: Lung Adenocarcinoma

tag: whole transcriptome amplification

tag: library prep ilumina

tag: adaptor barcode


description: Biological replicate 4 of 4. Hereford muscle cells_Cy3 vs. Holstein Friesian muscle cells_Cy5_rep4


title: KCNR 2D RA H3K27ac

description: DNA (ChIP-enriched)

value: KCNR

tag: cell type

tag: treatment

value: ATRA


description: Biological replicate 1 of 4. Hereford muscle cells_Cy3 vs. Holstein Friesian muscle cells_Cy5_rep1


title: TAM-NSCLC TAM-103-A

tag: cells

tag: tissue of origin

tag: tumour subtype


title: KCNR 2D C H3K27ac

description: DNA (ChIP-enriched)

tag: cell line


title: Week 7 sample 1

city: Guangzhou

first: Xiongjun

address: 230 Wai Huan Xi Road

institute: Guangzhou University

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.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.

source_name: liver cell

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.  1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x150 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: a mixed FVB/N and C57BL/14 background mouse line


title: TAM-NSCLC TAM-99-S

value: Lung Squamous Cell Carcinoma


title: KCNR 8D RA input

description: DNA (input control)

tag: antibody

value: input


title: Week 2 sample 2

value: a mixed FVB/N and C57BL/12 background mouse line


title: Week 7 sample 2

value: a mixed FVB/N and C57BL/16 background mouse line


title: MU01-0730-GS7

tag: histopathology

value: Gleason Score 7

tag: tissue

value: Urine


title: MU01-0737-GS6

value: Gleason Score 6


title: Week 2 sample 1

value: a mixed FVB/N and C57BL/10 background mouse line


title: MU01-0738-GS7


title: TAM-NSCLC TAM-97-S

value: Tumour Associated Macrophages

tag: paired

value: no

tag: primary / in vitro

value: primary


title: Week 0 sample 2

value: a mixed FVB/N and C57BL/8 background mouse line


title: TAM-NSCLC TAM-96-A

value: lung

value: yes

tag: fluorescence activated sorting

value: Yes

value: TruSeq Nano DNA HT


title: Week 0 sample 1

value: a mixed FVB/N and C57BL/6 background mouse line


title: MU01-0729-Ctrl

value: Control


title: TAM-NSCLC TAM-91-A

value: Lung Adenocarcinoma

value: TruSeq Nano DNA LT


title: KCNR 8D C input

description: DNA (input control)

value: KCNR

value: Neuroblastoma

tag: enrichment target

value: input

tag: target function

value: Ethanol


title: I2BIMA100_3_intestine

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with I2BIMA100_3 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: All_samples.GeneExpression.FPKM.txt

extract_protocol:
Mouse small intestine samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: ICR

value: Intestine


title: MU01-0713-Ctrl

value: Urine


title: I2BIMA100_2_intestine

description: The group information is prefixed with I2BIMA100_2 in the column of processed data file


title: TAM-NSCLC TAM-81-S

value: Tumour Associated Macrophages

value: Lung Squamous Cell Carcinoma

value: no

value: primary

tag: whole transcriptome amplification

tag: library prep ilumina


title: I2BIMA100_1_intestine

description: The group information is prefixed with I2BIMA100_1 in the column of processed data file


title: MU01-0717-Ctrl


title: TAM-NSCLC TAM-88-S

value: lung

value: yes

value: Yes

tag: adaptor barcode


title: TAM-NSCLC TAM-80-A


title: CS23_12193_RNA-seq

city: Farmington

first: Tara

middle: N

last: Yankee

state: CT

address: 400 Farmington Avenue

department: Genetics and Developmental Biology

institute: University of Connecticut Health Center

data_processing:
Fastq's trimmed with trimmomatic and quality control checked with fastqc and multiqc
Aligned trimmed fastqs to genome using RailRNA 0.2.4b
Generated counts tables from RailRNA output using Recount2 pipeline.
Genome_build: hg38
Supplementary_files_format_and_content: The combined counts table for all samples provided as a .tsv file. The bigWig and bam files are output from RailRNA. The bams were anonymized by having the sequence information removed.

source_name: Embryonic Heart Tissue

growth_protocol: Samples flash frozen immediately after collection by HDBR

extract_protocol:
miRNeasy RNA extraction kit with on-column DNAse treatment (Qiagen protocol)
TruSeq Stranded mRNA kit (Illumina)

tag: developmental stage


title: CS23_12151_RNA-seq


title: MU01-0706-GS6

value: Gleason Score 6


title: MU01-0712-Ctrl

value: Control


title: MU01-0704-Ctrl


title: TAM-NSCLC TAM-74-A

tag: cells

value: Lung Adenocarcinoma

value: TruSeq Nano DNA HT


title: I2WB_IMA10_2_intestine

description: The group information is prefixed with I2WB_IMA10_2 in the column of processed data file

tag: treatment


title: TAM-NSCLC TAM-72-A

tag: tissue of origin

tag: tumour subtype

value: TruSeq Nano DNA LT


title: CS23_12058_RNA-seq


title: CS21_12210_RNA-seq


title: I2WB_IMA10_1_intestine

description: The group information is prefixed with I2WB_IMA10_1 in the column of processed data file

tag: strain


title: I2WB_IMA10_3_intestine

description: The group information is prefixed with I2WB_IMA10_3 in the column of processed data file


title: MU01-0701-Ctrl


title: CS21_12093_RNA-seq


title: TAM-NSCLC TAM-71-A


title: TAM-NSCLC TAM-70-A


title: I2WB_IMC_3_intestine

description: The group information is prefixed with I2WB_IMC_3 in the column of processed data file


title: CS21_11849_RNA-seq


title: MU01-0697-Ctrl


title: I2WB_IMC_2_intestine

description: The group information is prefixed with I2WB_IMC_2 in the column of processed data file


title: TAM-NSCLC TAM-68-A


title: CS20_13068_RNA-seq


title: I2WB_IMC_1_intestine

description: The group information is prefixed with I2WB_IMC_1 in the column of processed data file


title: TAM-NSCLC TAM-62-A


title: MU01-0700-Ctrl


title: MU01-0698-Ctrl


title: MU01-0694-GS6


title: CS20_12451_RNA-seq


title: CS20_12248_RNA-seq


title: I2WB_Sa_3_intestine

description: The group information is prefixed with I2WB_Sa_3 in the column of processed data file


title: TAM-NSCLC TAM-52-A


title: I2WB_Sa_1_intestine

description: The group information is prefixed with I2WB_Sa_1 in the column of processed data file


title: I2WB_Sa_2_intestine

description: The group information is prefixed with I2WB_Sa_2 in the column of processed data file


title: MU01-0693-Ctrl