title: RNA-Seq of parental strain H37Rv rep3

status: Public on Jul 20 2019

city: College Station

first: Thomas

middle: R

last: Ioerger

state: TX

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

data_processing:
Samples were sequenced on an Illumina HiSeq 2500 Rapid in paired-end mode with 125+125bp read length.
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings.
Reads were mapped to the H37Rv genome use BWA 0.7.12.  Read-counts in each ORF were tabulated and converted to RPKMs.
Analysis of differential expression for each knockout strain (compared to parental strain, H37Rv) was performed using DESeq2.
Genome_build: H37RvMA (GCA_000751615.1)
Supplementary_files_format_and_content: Counts files: *.expr files are tab-separated text files that contains abundances for each gene.  6 columns are: ORF id, gene name, length (bp), strain, number of reads mapping to ORF, RPKM.
Supplementary_files_format_and_content: DESeq2 output: tab-delimited files containing log-fold-change and significance (adjusted P-value) for each gene compared to wild-type (H37Rv).

organism: Mycobacterium tuberculosis

source_name: in-vitro

growth_protocol: Cultures were grown to log-phase in-vitro in 7H9 medium.

extract_protocol:
Cells were bead-beat with trizol, and then DNA was extracted by ethanol precipitation.
Illumina RNA-seq sample prep protocol. Depletion of ribosomal RNA using Ribo-Zero kit.

tag: parental-strain

tag: genotype

value: wildtype


title: RNA-Seq of knockout of Rv3916c rep1

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

value: Rv3916c KO


title: RNA-Seq of parental strain H37Rv rep2


title: RNA-Seq of knockout of Rv3684 rep3

value: Rv3684 KO


title: RNA-Seq of knockout of Rv3916c rep3


title: RNA-Seq of parental strain H37Rv rep1


title: RNA-Seq of knockout of Rv3684 rep1


title: RNA-Seq of knockout of Rv3916c rep2


title: RNA-Seq of knockout of Rv3484 rep3

value: Rv3484 KO


title: RNA-Seq of knockout of Rv3484 rep2


title: RNA-Seq of knockout of Rv2680 rep2

value: Rv2680 KO


title: RNA-Seq of knockout of Rv2680 rep1


title: RNA-Seq of knockout of Rv1565c rep2

value: Rv1565c KO


title: RNA-Seq of knockout of Rv2680 rep3


title: RNA-Seq of knockout of Rv1432 rep3

value: Rv1432 KO


title: zr7530-con-rep2

status: Public on Jul 21 2019

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.6.0c
Raw counts were calculated using featureCounts from Subread package v1.6.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

organism: Homo sapiens

source_name: breast cancer cell line

extract_protocol:
Total RNA was extracted using TRIzol reagents. The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 1 ug total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq2500. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer.

tag: tissue

value: mammary gland/breast

tag: cell type

value: epithelial

tag: disease

value: adenocarcinoma

tag: lentivirus

value: control (pLVX)


title: RNA-Seq of knockout of Rv1565c rep1


title: RNA-Seq of knockout of Rv3484 rep1


title: RNA-Seq of knockout of Rv1096 rep2

value: Rv1096 KO


title: RNA-Seq of knockout of Rv1096 rep3


title: RNA-Seq of knockout of Rv1432 rep1


title: RNA-Seq of knockout of Rv1432 rep2


title: RNA-Seq of knockout of Rv0950c rep3

value: Rv0950c KO


title: RNA-Seq of knockout of Rv0950c rep2


title: RNA-Seq of knockout of Rv3684 rep2


title: RNA-Seq of knockout of Rv1096 rep1


title: RNA-Seq of knockout of Rv0950c rep1


title: RNA-Seq of knockout of Rv0307c rep1

value: Rv0307c KO


title: RNA-Seq of knockout of Rv0307c rep2


title: 04_VPC14449_DHT_rep3

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

data_processing:
Base calling was performed using the BGISeq500 platform. The raw reads were pre-filtered by removing adaptor sequences, contamination and low-quality reads.
The high quality of the filtered reads was confirmed using the FastQC (Andrews, 2014) quality control tool.
The reads were mapped and annotated using STAR Aligner (Dobin et al., 2013) (version 2.6.1c).
The reads were counted using featureCounts (Liao, Smyth, & Shi, 2014).
Differential gene expression analysis for different treatments was performed using the DESeq2 (Love, Huber, & Anders, 2014).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: DESeq2 Differential Expression Analysis from RNA seq results of treatment with 3 drugs in comparison to DHT alone, as a Microsoft Excel Spreadsheet.

source_name: LNCaP cells

growth_protocol: LNCaP cells (6 x 10^6) were seeded in RPMI 1640 media containing 10% FBS and 1% penicillin/streptomycin. Following O/N incubation, the media was changed to RPMI 1640 containing 5% CSS and the cells were then grown for 48hrs at 37C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol and the Qiagen RNeasy RNA Extraction Kit. Three biological replicas were collected for each condition.  The concentrations and the qualities of the RNA samples were checked by Nanodrop and tape station. All RIN values were between 9.5 and 10.
Library was constructed by BGI using library construction methods underlying the BGISEQ-500 platform. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. This process was to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer.

treatment_protocol: On the day of treatment, the cells were treated with DHT (10nM) and either DMSO (Control) or compound (MDV3100 (Enzalutamide): 1.5uM, VPC-17005 (Dalal et al., 2018): 6uM, or VPC-14449 (Li et al., 2014): 6uM). Concentration of the compound was selected based on the published IC90. Cells were treated for 6 hours before RNA isolation.

tag: cell line

value: LNCaP


title: 03_VPC17005_DHT_rep2


title: 03_VPC17005_DHT_rep3


title: 04_VPC14449_DHT_rep2


title: RNA-Seq of knockout of Rv1565c rep3


title: 02_Enzalutamide_DHT_rep3


title: 03_VPC17005_DHT_rep1


title: 02_Enzalutamide_DHT_rep2


title: 01_DMSO_DHT_rep1


title: 02_Enzalutamide_DHT_rep1


title: 04_VPC14449_DHT_rep1


title: 01_DMSO_DHT_rep2


title: SR16_SUC_109_a

city: Larissa

first: Sotirios

last: Vasileiadis

email: vasiliad@gmail.com, sovaileiadis@uth.gr

address: Viopolis

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

description: rRNA depleted RNA

data_processing:
Base-calling was performed with the HiSeq Control Software v2.2.58, the RTA v1.18.64.0 and the Consensus Assessment of Sequence And Variation (CASAVA) v1.8.2 software
Sequences were quality controlled with Trimmomatic v0.36 and were mapped against the reference metagenome assembly sequence with STAR v020201. Transcript copy counts were predicted with HTSeq v 0.9.1.
Genome_build: QFCS00000000.1
Supplementary_files_format_and_content: tab delimited text file including the per sample transcript counts

organism: soil metagenome

source_name: soil enrichment metatranscriptome under succinate treatment at 109 hours post inoculation

growth_protocol: A previously enriched consortium from soil was cultivated in minimal salts medium with ammonium as nitrogen source (MSMN) with either 25 µg ml-1 thiabendazole (125 µM) or 37 µg ml-1 of succinate (314 µM) as the sole carbon source (with a carbon concentration of 15 µg ml-1 in each case) retaining also abiotic controls. Samples were retrieved over the thiabendazole degradation course.

extract_protocol:
RNA was extracted from bacterial cell pellets with the NucleoSpin¨ RNA kits (Macherey-Nagel & Co, DŸren, Germany) according to the manufacturerÕs instructions.
KAPA stranded RNA-Seq Library Preparation kit (KAPABiosystems, Wilmington, MA, USA)

tag: treatment


title: 01_DMSO_DHT_rep3


title: SR15_TBZ_109_c

description: rRNA depleted RNA

source_name: soil enrichment metatranscriptome under thiabendazole treatment at 109 hours post inoculation


title: SR18_SUC_109_c

description: rRNA depleted RNA

value: succinate treatment at 109 hours post inoculation


title: iPS-1(p50)

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500/3000 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19

source_name: Fibroblast-derived induced pluripotent stem cells at passage 50

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: iPS cells

tag: gender

value: male

tag: passage


title: SR14_TBZ_109_b

description: rRNA depleted RNA

value: thiabendazole treatment at 109 hours post inoculation


title: RNA-Seq of knockout of Rv0307c rep3


title: SR12_SUC_73_c

description: rRNA depleted RNA

source_name: soil enrichment metatranscriptome under succinate treatment at 73 hours post inoculation


title: SR13_TBZ_109_a

description: rRNA depleted RNA


title: SR11_SUC_73_b

description: rRNA depleted RNA

value: succinate treatment at 73 hours post inoculation


title: SR09_TBZ_73_c

description: rRNA depleted RNA

source_name: soil enrichment metatranscriptome under thiabendazole treatment at 73 hours post inoculation


title: SR08_TBZ_73_b

description: rRNA depleted RNA

value: thiabendazole treatment at 73 hours post inoculation


title: ChIP5-vitD

city: madrid

first: Alba

last: Costales

state: madrid

address: Arturo Duperier, 4

department: cancer genetics

country: Spain

institute: IIB

library_source: genomic

data_processing:
Sequencing reads were aligned to the GRCh37/hg19 genome assembly with Bowtie2 (Langmead and Salzberg 2012).
peaks were called using MACS2 with the following setting: --qvalue=0.15, --nomodel and --extsize 200 using as control concatenated same-patient alignment files from input treated (calcitriol) and untreated (vehicle)
MACS2 bdgdiff function was used to obtain statistically enriched DNA regions using the pileup data obtained from the peak calling.
Genome_build: Hg19
Supplementary_files_format_and_content: Pileups for the input corrected files on .bdg format and enreached VDR binding genomic sites upon calcitriol treatment (*Dpeaks_*) compared to EtOH treatment (*Cpeaks_*) in .bed format

molecule: genomic DNA

source_name: Colonic Stem cell enriched culture

growth_protocol: Human colon organoids from two patients in each starting sample were cultured on 6-well dishes in the presence of 100 nM calcitriol or vehicle for 2 h. The 3D culture media was changed every other day and it was composed of 50% Advanced DMEM/F12, 50% Wnt3a-conditioned medium, 10 mM HEPES, 10 mM Glutamax, 10 mM nicotinamide (Sigma-Aldrich), 1x N2 (Thermo Fisher Scientific), 1x B27 (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:100 Primocin, 0.1 μg/mL Noggin (Peprotech, NJ, USA), 1 μg/mL Gastrin (Tocris, Bristol, UK), 1 μg/mL RSPO1 (Sino Biological, Beijing, China), 50 ng/mL EGF (Peprotech), 0.02 μM PGE2 (Sigma-Aldrich), 1 μM LY-2157299 (Axon Medchem, VA, USA), 10 μM SB-202190 (Sigma-Aldrich) and 10 μM Y-27632 (Tocris).

extract_protocol:
DNA-protein crosslinking was done by incubation with 1% formaldehyde (Thermo Fisher Scientific) for 8 min in rotation at 4ºC. Crosslinking was quenched with 1.25 mM glycine (Bio-Rad) in PBS for 5 min. We transferred the organoid solution to a 50 mL conical tube for centrifugation at 2500 rpm for 5 min at 4ºC. Supernatant was removed and the pellet was washed twice in cold PBS, transferred to a 1.5 mL eppendorf tube and lysed in 1 mL ChIP-lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1 and 1x protease cocktail inhibitors (cOmplete, EDTA-free (Roche, Basel, Switzerland)) for 1 h. We used a 21G syringe to homogenize the solution and force the lysis. Samples were sonicated for 20 min at maximum intensity at 4ºC in a S220 Focused-ultrasonicator (Covaris, MA, USA).
Both ChIP'ed and input DNA samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB, MA, USA). Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a single double-sided SPRI size selection. Cluster generation was performed on an Illumina flow cell and sequenced in the 50 base single-read format on an Illumina HiSeq2500 instrument by following manufacturer's protocols.

treatment_protocol: 1,25(OH)2D3 was added to culture media to a final concntration of 10uM and the treatment lasted 2h.

value: colonic organoids

tag: passages

tag: strain

value: primary culture

tag: chip antibody

value: rabbit-monoclonal VDR antibody (Cell Signalling, custom made 2 mg/mL, MA, USA)

value: calcitriol


title: SR17_SUC_109_b

description: rRNA depleted RNA


title: SR07_TBZ_73_a

description: rRNA depleted RNA


title: ZFN10ug

city: Kenilworth

first: Amit

last: Kumar

state: NJ

address: 2000 Galloping Hill Rd

institute: Merck & Co., Inc.

data_processing:
Illumina MiSeq Control Software version: MCS 2.4.0.4 software used for basecalling.
Prior to CRISPRESSO, BBDuk (http://jgi.doe.gov/data-and-tools/bb-tools/) was utilized for an additional cleanup step. Briefly, right end adapters with a 27-Kmer length were trimmed with a maximum substitution setting of 1. Low quality reads were trimmed from both ends with a minimum quality of 30 and short reads less than 70 base pairs were discarded. Duplicates were removed, and adapters were trimmed based on paired read overhangs with a minimum overlap of 24. CRISPRESSO was utilized to analyze the amplicon sequences. Reads with a phred quality of less than 30 were discarded.
Genome_build: Not provided
Supplementary_files_format_and_content: *_Alleles_frequency_table.txt: Tab-delimited text files include allele frequency for each Sample.

organism: Cricetulus griseus

source_name: CHO Cells

extract_protocol:
Amplicons were purified using Qiagen Purelink PCR Purification Kit.
Illumina TruSeq Nano DNA kit (Illumina, Cat: 20015964).

value: Ovary

tag: genotype/variation

value: Clone

tag: editing

value: ZFN 10ug


title: ZFN3ug

value: ZFN 3ug


title: SR06_SUC_57_c

description: rRNA depleted RNA

source_name: soil enrichment metatranscriptome under succinate treatment at 57 hours post inoculation


title: CRISPRgRNA4

value: CRISPR gRNA4


title: SR05_SUC_57_b

description: rRNA depleted RNA

value: succinate treatment at 57 hours post inoculation


title: CRISPRgRNA2

value: CRISPR gRNA2


title: CRISPRgRNA5

value: CRISPR gRNA5


title: CRISPRgRNA3

value: CRISPR gRNA3


title: CRISPRgRNA1

value: CRISPR gRNA1


title: SR02_TBZ_57_b

description: rRNA depleted RNA

source_name: soil enrichment metatranscriptome under thiabendazole treatment at 57 hours post inoculation


title: SR03_TBZ_57_c

description: rRNA depleted RNA

value: thiabendazole treatment at 57 hours post inoculation


title: SR01_TBZ_57_a

description: rRNA depleted RNA


title: Mock

value: Wild type

value: Mock


title: Cancer1

type: RNA

city: Rochester

first: Fei

last: Gao

address: 200 1st St SW

institute: Mayo Clinic

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Acquired array images were analyzed using the Agilent Feature Extraction Software (v11.0.1.1) and normalized using Agilent GeneSpring GX v12.1
Differentially expressed lncRNAs and mRNAs were identified by setting the cutoff for P values corrected for multiple comparisons by the Benjamini Hochberg false discovery rate method at Q<0.05 and for fold changes at >2 (up- or downregulated).

source_name: human colorectal cancer

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: The total RNA was extracted from normal colorectal tissues and tumor tissues using TRIzol® Reagent (Invitrogen, CA, USA)

tag: disease state

value: colorectal cancer (CRC)

value: colorectal tumor tissue


title: Adjacent3

value: matched, adjacent non-tumoral tissue


title: Adjacent2


title: Adjacent1


title: Cancer2


title: Clone1


title: aerobic

city: nanning

first: jun

last: huang

country: China

institute: guangxi sciences academy

data_processing:
Illumina Casava1.8 software used for basecalling.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Sequences from the JGI for Trire2 (http://genome.jgi-psf.org/Trire2/Trire2.home.html)
Supplementary_files_format_and_content: [.txt] file includes FPKM values for each Sample

organism: Trichoderma reesei

source_name: aerobic, hypha

extract_protocol:
Fungus was collected, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ DNA Library Prep Kit for Illumina® was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: anaerobic fermentation

tag: age

value: 4 days old

value: hypha


title: Cancer3


title: anaerobic

source_name: anaerobic, hypha

value: aerobic fermentation


title: SR04_SUC_57_a

description: rRNA depleted RNA


title: Clone12

value: Ovary

value: Clone


title: ZFN5ug

value: ZFN 5ug


title: Clone13


title: Clone11


title: Clone10


title: Clone9


title: Clone7


title: Clone8


title: T4

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

data_processing:
Reads were filtered based on their length, pairing, and quality using Trimmomatic (v0.32.1)
Cleaned reads were mapped to the Xenopus genome (JGI4.2 assembly) with Ensembl annotations (release 79) using Bowtie-0.12.7 / TopHat 2 (v0.6) software (81) (http://tophat.cbcb.umd.edu) (with a maximum intron size of 250,000 bp to discover novel junctions between exons).
The Cufflinks (v0.0.7) tool was applied to TopHat alignments to enumerate the number of short reads overlapping the Ensembl annotated genes, for each library
Genome_build: (JGI4.2 assembly)
Supplementary_files_format_and_content: GTF file from cufflink including gene ID, gene name and FPKM valuesfor gene expression

organism: Xenopus tropicalis

source_name: Liver

extract_protocol:
For each biological replicate, total RNA was extracted from 15 mg of liver using the RNAqueous®-4PCR Kit (Ambion, USA), according to the manufacturer's instructions. Total RNA quality and quantity were controlled on an Agilent 2100 Bioanalyzer (Agilent, USA). RNA-seq libraries were prepared using the TruSeq Stranded mRNA sample Prep kit (Illumina) and sequenced on an Illumina GAIIx sequencer as 75 bp reads by Hybrigenics-Helixio (Clermont-Ferrand, France).
TruSeq Stranded mRNA sample Prep kit

tag: common name

value: tropical clawed frog

value: exposed to triclosan

tag: Sex

value: female


title: M1

value: exposed to mixture


title: M2


title: Severe Intestinal metaplasia 4

city: Beijing

first: Shao

last: Li

state: Beijing

address: Haidian district

institute: Tsinghua University

data_processing:
We firstly processed 10X genomics raw data by the Cell Ranger Single-Cell Software Suite (release 2.0), including using cellranger mkfastq to demultiplexes raw base call files into FASTQ files and then using cellranger count to preform alignment, filtering, barcode counting, and UMI counting.
The output from different lanes was final aggregated using ‘cellranger aggr’ with default parameter setting.  Then we mapped UMIs to genes, followed by removing low-quality cells.
Cells would be flagged as poor-quality ones if they met one of the following thresholds: 1) the number of expressed genes lower than 400 or larger than 7000; 2) 20% or more of UMIs were mapped to mitochondrial or ribosomal genes.
According to the previous study, we also excluded cells with barcodes appeared in more than one sample with respect to index swapping.
Genome_build: hg19
Supplementary_files_format_and_content: counts

molecule: polyA RNA

source_name: stomach

extract_protocol:
Single-cell RNA-seq using 10X genomics platform was performed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol.  Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol  Libraries were sequenced on Illumina HiSeq X Ten platform to obtain 100 and 32-bp paired end reads using the following read length; read 1, 26 cycles, read 2, 98 cycles and i7 index, 8 cycles.
HiSeq X Ten

value: Male

tag: pathological lesions

value: Gastric Metaplasia (severe)

tag: subject id

tag: agent


title: Early gastric cancer

value: Early gastric caner


title: Wild Intestinal metaplasia 2

value: Female

value: Gastric Metaplasia (wild)


title: Chronic atrophic gastritis 3

value: Chronic atrophic gastritis


title: Severe Intestinal metaplasia 2

value: H. pylori


title: M4


title: Clone6

tag: cell line

tag: cell type


title: T3

tag: treatment


title: 3B-CCN5-2

city: Xi 'an

first: Xia

last: Liao

state: Shaanxi

address: 277# West Yanta Road

institute: Department of nutrition

hyb_protocol: OneArray Plus hybridization program

scan_protocol: Agilent 0.1 XDR program

data_processing: The GPR document is loaded into the Rosetta Resolver ® System (Rosetta Biosoftware) software for data operations.

source_name: hepatoma carcinoma

label_protocol: Total RNA was reverse-transcribed using T7 Oligo (dT), RNase and DNA Polymerase. Five ug  antisense RNA(aRNA) was synthesized and labeled using T7 Promoter, AminoAllyl UTP  and NHS-CyeDye.

extract_protocol: extraction of total RNA from tumor cell

treatment_protocol: Hep3B cells transfected with vector and CCN5

value: Transfected with CCN5


title: Chronic atrophic gastritis 2


title: T2


title: 3B-GFP-1

value: Transfected with vector


title: 3B-CCN5-3


title: 3B-GFP-2


title: M3


title: 3B-GFP-3


title: 3B-CCN5-1


title: Severe Intestinal metaplasia 3


title: SW480 cells, HES1-binding RNAs/LncRNAs

data_processing:
RNA immunoprecipitated by HES1 was extracted
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit v2
Libraries were analyzed by sequencing using Illumina HiSeq 2500 Sequencing Platforms.
RIPSeeker was used to predict RIP peak based on HMM
Genome_build: hg19
Supplementary_files_format_and_content: RIPseeker_lncRNA_HES1_intersect.bed
cross_lnc_peaks_HES1.xls

source_name: human colon cancer SW480 cells

growth_protocol: Human colon cancer SW480 were cultured in RPMI1640 medium (Gibco, CA, USA) supplemented with 10% fetal bovine serum (Hyclone, UT, USA) in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from normal colon tissues and tumor tissues using TRIzol® Reagent (Invitrogen, CA, USA). Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit was used for SW480 cells.
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit v2

value: human colon cancer SW480 cells

value: colorectal cancer (CRC)

tag: rip antibody


title: Clone5

value: Ovary

value: Clone


title: Severe Intestinal metaplasia 1


title: Chronic atrophic gastritis 1


title: Wild Intestinal metaplasia 1


title: T1

value: tropical clawed frog


title: SR10_SUC_73_a

description: rRNA depleted RNA

value: succinate treatment at 73 hours post inoculation


title: Clone4


title: B4

value: exposed to benzo[a]pyrene

value: female


title: Non-atrophic gastritis 3

value: Male

value: Normal


title: Non-atrophic gastritis 2


title: Clone2


title: Non-atrophic gastritis 1


title: Clone3


title: CD57- D [WTCHG_381569_292141]

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

data_processing:
RNA-seq reads were aligned to reference genome sequences using STAR(Dobin et al., 2013) aligner software. Mapped reads were assigned to genomic features using Rsubread(Liao et al., 2013)  R package(Team, 2014).
Genes that were differentially expressed (>2 fold, P<0.01, FDR<0.05) between conditions and their normalised expression values, were generated with EdgeR and limma R packages (Robinson et al., 2010)
Supplementary_files_format_and_content: Raw mapped genes read counts ; Normalized, voom transformed (log cpm) gene expression values.

source_name: Human PBMC_CD57-

extract_protocol:
Trizol extraction was performed on sorted subsets. RNA quality was measured using bioanalyzer chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untouched CD4 T cell kit was used to isolate CD4+ T cells for cell sorting ex vivo.

tag: tissue

value: PBMC

tag: cell subtype

value: CD45RO+CD57- CD4+ T cell subset


title: CD57- E [WTCHG_381569_294165]


title: B2


title: B3


title: siDANCR rep3

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
The libraries were loaded on cBot (Illumina) to generate cluster and sequenced on the Illumina HiSeqXten platform. The RNA-seq reads were mapped to the human reference genome sequence (hg38) assembly by Hisat2 (Version 2.1.0).
Stringtie (version 1.3.3) was used to count the number of fragments of each known gene downloaded from Ensembl (Homo sapiens GRCh38)，NONCDED（v5.0）,lncrnadb（v.2.0）,lncipedia（v.5.0）.
After mapping, we removed genes with fewer than 10 fragments in all of the samples and performed differential expression analysis using R/Bioconductor package edgeR (version 3.0.8).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

growth_protocol: SUNE-1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol:
TRIzol reagent was used to extract total RNA from SUNE-1 cell line.
we constructed Illumina sequencing libraries according to the modified strand-specific RNA sequencing protocol. Briefly, we isolated non-coding RNA and coding RNA from 3 μg of purified total RNA using a ribo-zero kit for rRNA removal. After isolation, we eluted and fragmented the RNA samples at 94°C for 8 min with Elute-Prime-Fragment Mix. Subsequently, we performed first-strand cDNA synthesis using SuperScriptII (Invitrogen, Carlsbad, CA. USA). The product with Second Strand Marking Master Mix were incubated at 16°C for 1 hour to synthesize the second-strand cDNA. After 3’ ends adenylation, we ligated the DNA fragments with TruSeq adapters and the product was amplified using TruSeq PCR primers.

treatment_protocol: SUNE-1 cells were treated with DANCR siRNA or control siRNA using Lipofectamine 3000 reagent. The cells were harvested after transfection at 48h for assays.

value: nasopharyngeal carcinoma

tag: transfection

value: siDANCR


title: CD57+ G [WTCHG_381569_296189]

source_name: Human PBMC_CD57+

value: CD45RO+CD57+ CD4+ T cell subset


title: CD57+ D [WTCHG_381569_291129]


title: CD57- B [WTCHG_381569_290117]


title: B1


title: 4

value: not exposed


title: siDANCR rep1


title: 3


title: CD57+ B [WTCHG_381569_289105]


title: siSCR rep2

value: siSCR


title: H1299 cells ribosome profiling

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

description: ribosome footprints

data_processing:
Adapter sequences were trimmed from the reads.
High quality reads were mapped to human mRNA reference sequence (RefSeq) for GRCh19/hg19 (downloaded from UCSC genome browser on May 21st, 2014) using FANSe2 mapping algorithm with the options -L55 -S10 -I1 -E4 -B1 -U1. The rpkm values were calculated according to the read counts of each gene. The splice variants were merged.
Genome_build: Human mRNA reference sequence (RefSeq) for GRCh19/hg19 (downloaded from UCSC genome browser on May 21st, 2014)
Supplementary_files_format_and_content: read count, rpkm

growth_protocol: HBE, A549 and H1299 cells were cultured in the complete DMEM medium. We detected and analyzed the new proteins with ribosome profiling.

extract_protocol:
We performed ribosome profiling. Ribosome footprints was extracted using Trizol method.
We used Ribo-Zero™ Magnetic Kit (Human/Mouse/Rat) to remove the rRNA. We used NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (1-12) to construct sequencing libraries.

value: Grown under normal condition


title: A549 cells ribosome profiling

description: ribosome footprints


title: Healthy plasma sample2

city: Yantai

first: yeying

last: sun

address: No.346 Guanhai road

institute: Binzhou Medical Univeristy

description:
circular RNA
The expression of circular RNAs in plasma of healthy individual

hyb_protocol: The purified RNAs were hybridized to a microarray (Agilent human circRNA Array V2.0) containing 170,340 human circRNA probes.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan

data_processing: The Agilent Feature Extraction 10.7 software was used to read the values and to obtain the original data. The GeneSpring software V13.0 software was used for quintile normalization and subsequent data processing of the original data. After standardization, the cluster analyses of the six samples were performed with hierarchical and average linkage algorithms of R package. We analyzed the microarray data using GeneSpring software to identify the differentially circRNAs. Threshold values of >2- and   < -2-fold change and a t-test P-value of 0.05 were used.

source_name: plasma

label_protocol: The extracted RNAs were digested, dephosphorylated, denatured, amplified, and labeled with Cy3-dCTP in accordance with the manufacturer’s specifications.

extract_protocol: To extract the circulating RNAs from the plasma samples, we used the miRNeasy Serum/Plasma Kit (Qiagen, Germany) in accordance with the manufacturer’s instruction.

tag: gender

value: male

value: plasma

tag: diagnosis

value: healthy


title: siSCR rep3


title: Healthy plasma sample1


title: Healthy plasma sample3


title: HF plasma sample3

description:
circular RNA
The expression of circular RNAs in plasma of heart failure patient

value: heart failure (HF)


title: CD57+ E [WTCHG_381569_293153]


title: siDANCR rep2


title: 1

value: tropical clawed frog


title: siSCR rep1


title: HF plasma sample2


title: HF plasma sample1


title: cashmere_goats_12month_mRNA

status: Public on Jul 19 2019

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
mRNA
Illumina Casava1.7 software used for basecalling.
All clean reads were obtained by rejecting low quality sequence (more than half of the base qualities less than 5) or reads with more than 10% unknown nucleotides (N), and sequencing adapters. The clean reads were aligned to the Capra hircus genome and gene sequences through Bowtie2, with allowing less than 2 mismatches in the alignment. Unmapped or multi-position matched reads were excluded from further analyses.
The mapped read counts for each gene were normalized for RNA length and for the total read number in the lane according to fragments per kilobaseof exon per million fragments mapped reads (FPKM), which facilitates the comparison of transcript levels between samples
genome build: Capra hircus GCF_001704415.1_ASM170441v1
processed data files format and content: txt format,the expressed genes FPKM & reads of mRNA
mRNA_expressed_gene_reads.txt_symbol.txt: the reads number of genes in each sample of mRNA seq

organism: Capra hircus

source_name: cashmere goat

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For RNA-seq, total RNA was extracted from each embryo, 10 mg of total RNA was used for RNA sequencing (RNA-seq) library preparation. Polyadenylated mRNAs were purified and concentrated with Magnetic Beads Oligo (dT) (Invitrogen, Carlsbad, CA, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and applied to Illumine NextSeq 500 system 151 nt pair-end sequencing by ABlife, Inc. (Wuhan, China).

value: skin

value: 12 month


title: cashmere_goats_6month_mRNA

value: 6 month


title: goat_milk_goat_6m_mRNA

source_name: milk goat


title: goat_milk_goat_3m_mRNA

value: 3 month


title: cashmere_goats_9month_mRNA

value: 9 month


title: cashmere_goats_3month_mRNA


title: 2

value: female


title: goat_milk_goat_9m_mRNA

data_processing:
mRNA
Illumina Casava1.7 software used for basecalling.
All clean reads were obtained by rejecting low quality sequence (more than half of the base qualities less than 5) or reads with more than 10% unknown nucleotides (N), and sequencing adapters. The clean reads were aligned to the Capra hircus genome and gene sequences through Bowtie2, with allowing less than 2 mismatches in the alignment. Unmapped or multi-position matched reads were excluded from further analyses.
The mapped read counts for each gene were normalized for RNA length and for the total read number in the lane according to fragments per kilobaseof exon per million fragments mapped reads (FPKM), which facilitates the comparison of transcript levels between samples
genome build: Capra hircus GCF_001704415.1_ASM170441v1
processed data files format and content: txt format,the expressed genes FPKM & reads of mRNA & reads of mRNA & miRNA
mRNA_expressed_gene_reads.txt_symbol.txt: the reads number of genes in each sample of mRNA seq


title: goat_milk_goat_12m_mRNA


title: LIV_8

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

description: Liver

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were mapped to pig reference mRNA (Sscrofa 10.2) using the SAGE data processiong software
Using R version 3.4.2 software to find differential genes
Clustering analysis was performed by first using K-means clustering method to separate the transcripts to several big groups, and then using Hierarchical clustering to build the internal structure of the transcripts within the groups according to method reported by Gu et al. (Gu et al. 2016).
The CLOVER software (Frith et al. 2004) with JASPAR PWM database (Khan et al. 2018) were used to identify over-represented transcription factor binding motifs for each cluster of genes.
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Reads count (tab deli text)

organism: Sus scrofa

extract_protocol:
Total RNA were extrated by PAXgene RNA kit using the standard protocols.All samples were quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >8.
RNA libraries were prepared for sequencing using Super deepSAGE protocols

value: Liver

tag: replicate


title: LIV_4

description: Liver


title: LIV_5

description: Liver


title: LIV_3

description: Liver


title: LIV_2

description: Liver


title: LIV_1

description: Liver


title: LIV_7

description: Liver


title: MLN_5

description: Mesenteric lymph nodes

source_name: Mesenteric lymph nodes

value: Mesenteric lymph nodes


title: MLN_6

description: Mesenteric lymph nodes


title: MLN_4

description: Mesenteric lymph nodes


title: MLN_3

description: Mesenteric lymph nodes


title: MLN_2

description: Mesenteric lymph nodes


title: MP.ALV_7

description: Porcine alveolar macrophages

source_name: Porcine alveolar macrophages

value: Porcine alveolar macrophages


title: MP.ALV_8

description: Porcine alveolar macrophages


title: MLN_8

description: Mesenteric lymph nodes


title: MP.ALV_6

description: Porcine alveolar macrophages


title: MP.ALV_2

description: Porcine alveolar macrophages


title: MP.ALV_1

description: Porcine alveolar macrophages


title: MP.MD_8

description: Monocyte derived macrophage

source_name: Monocyte derived macrophage

value: Monocyte derived macrophage


title: MP.ALV_5

description: Porcine alveolar macrophages


title: MP.ALV_4

description: Porcine alveolar macrophages


title: MLN_7

description: Mesenteric lymph nodes


title: MP.MD_7

description: Monocyte derived macrophage


title: MLN_1

description: Mesenteric lymph nodes


title: MP.ALV_3

description: Porcine alveolar macrophages


title: HBE cells ribosome profiling

description: ribosome footprints

source_name: HBE

tag: condition

value: HBE


title: MP.MD_3

description: Monocyte derived macrophage


title: MP.MD_6

description: Monocyte derived macrophage


title: MP.MD_5

description: Monocyte derived macrophage


title: MP.MD_4

description: Monocyte derived macrophage


title: MP.MD_1

description: Monocyte derived macrophage


title: CC_8

description: Cerebral cortex

source_name: Cerebral cortex

value: Cerebral cortex


title: CC_6

description: Cerebral cortex


title: CC_7

description: Cerebral cortex


title: LIV_6

description: Liver


title: CC_4

description: Cerebral cortex


title: CC_2

description: Cerebral cortex


title: CC_3

description: Cerebral cortex


title: HT_8

description: Heart

source_name: Heart

value: Heart


title: HT_6

description: Heart


title: HT_7

description: Heart


title: CC_1

description: Cerebral cortex


title: HT_5

description: Heart


title: MP.MD_2

description: Monocyte derived macrophage


title: HT_2

description: Heart


title: PBMC_8

description: Peripheral blood mononuclear cell

source_name: Peripheral blood mononuclear cell

value: Peripheral blood mononuclear cell


title: PBMC_7

description: Peripheral blood mononuclear cell


title: BLD_7

description: Blood

source_name: Blood

value: Blood


title: BLD_4

description: Blood


title: PBMC_1

description: Peripheral blood mononuclear cell


title: BLD_8

description: Blood


title: CC_5

description: Cerebral cortex


title: PBMC_4

description: Peripheral blood mononuclear cell


title: HT_1

description: Heart


title: PBMC_6

description: Peripheral blood mononuclear cell


title: HT_3

description: Heart


title: PBMC_5

description: Peripheral blood mononuclear cell


title: HT_4

description: Heart


title: PBMC_3

description: Peripheral blood mononuclear cell


title: PBMC_2

description: Peripheral blood mononuclear cell


title: BLD_5

description: Blood


title: EDMT_8

description: Endometrium

source_name: Endometrium

value: Endometrium


title: BLD_3

description: Blood


title: EDMT_5

description: Endometrium


title: EDMT_2

description: Endometrium


title: EDMT_7

description: Endometrium


title: EDMT_6

description: Endometrium


title: EDMT_4

description: Endometrium


title: BLD_1

description: Blood


title: EDMT_3

description: Endometrium


title: EDMT_1

description: Endometrium


title: BLD_6

description: Blood


title: BLD_2

description: Blood


title: MS.BF_6

description: Biceps femoris

source_name: Biceps femoris

value: Biceps femoris


title: MS.BF_7

description: Biceps femoris


title: MS.BF_3

description: Biceps femoris


title: MS.BF_8

description: Biceps femoris


title: MS.BF_5

description: Biceps femoris


title: MP.BMD_5

description: Bone-marrow derived macrophage

source_name: Bone-marrow derived macrophage

value: Bone-marrow derived macrophage


title: MP.BMD_2

description: Bone-marrow derived macrophage


title: MS.BF_2

description: Biceps femoris


title: MP.BMD_7

description: Bone-marrow derived macrophage


title: MP.BMD_8

description: Bone-marrow derived macrophage


title: MS.BF_4

description: Biceps femoris


title: MS.BF_1

description: Biceps femoris


title: MP.BMD_1

description: Bone-marrow derived macrophage


title: MP.BMD_6

description: Bone-marrow derived macrophage


title: ADE_8

description: Adenohypophisis

source_name: Adenohypophisis

value: Adenohypophisis


title: ADE_7

description: Adenohypophisis


title: ADE_6

description: Adenohypophisis


title: ADE_4

description: Adenohypophisis


title: ADE_5

description: Adenohypophisis


title: ADE_3

description: Adenohypophisis


title: KID_8

description: Kidney

source_name: Kidney

value: Kidney


title: KID_6

description: Kidney


title: ADE_2

description: Adenohypophisis


title: ADE_1

description: Adenohypophisis


title: KID_7

description: Kidney


title: KID_4

description: Kidney


title: KID_3

description: Kidney


title: KID_2

description: Kidney


title: FT.BF_7

description: Back fat tissue

source_name: Back fat tissue

value: Back fat tissue


title: FT.BF_5

description: Back fat tissue


title: FT.BF_4

description: Back fat tissue


title: KID_1

description: Kidney


title: FT.BF_3

description: Back fat tissue


title: FT.BF_8

description: Back fat tissue


title: MP.BMD_4

description: Bone-marrow derived macrophage


title: MP.BMD_3

description: Bone-marrow derived macrophage


title: VECTOR rep1

city: Shanghai

first: Sheng

last: Yaru

address: Stem Cell Research Center, Ren Ji Hospital, 160 Pujian Road

institute: State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center

data_processing:
Raw reads were cleaned and the TopHat-Cufflinks- Cuffmerge-Cuffdiff pipeline was used to analyze the clean data with default parameters .
The clean reads were mapped to the human GRCh38  reference genome using TopHat v2.0.13 . Cufflinks v2.2.0 was used to construct, identify, and estimate the abundance from TopHat alignment results. The parameter Fragment Per Kilobase of transcript per Million fragments mapped (FPKM) was used to quantify the abundance of assembled transcripts.
Cufflinks results for all samples were used to merge the assemblies by Cuffmerge v1.0.0 . Cuffdiff v2.2.0 was used to re-estimate the abundance of transcripts. Expression levels were measured using the FPKM method, and the distribution of gene expression was analyzed. Statistical comparison of the DEGs between two groups of samples was also performed using Cuffdiff v2.2.0.
To assess the significance of differential gene expression, the threshold of q-value was set at 0.05, and the absolute value of log2 ratios (fold change between two groups of samples) at 1.
Genome_build: ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for all Sample

source_name: CML cell line TF1

growth_protocol: The base medium for this cell line is RPMI-1640 Medium. To make the complete growth medium, add the following components to the base medium: 2 ng/ml recombinant human GM-CSF; fetal bovine serum to a final concentration of 10%.2 uM imatinib was added to culture BAR cells.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, USA)  and treated with RNase-free DNase I (TaKaRa, China) to remove genomic DNA contamination.
Sequencing libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: every 1X10^7 cells for one repilicate

tag: imatinib response

value: imatinib resistant

tag: name in paper


title: FT.BF_2

description: Back fat tissue


title: FT.BF_6

description: Back fat tissue


title: KID_5

description: Kidney


title: SPL_8

description: Spleen

source_name: Spleen

value: Spleen


title: FT.BF_1

description: Back fat tissue


title: SPL_7

description: Spleen


title: BA rep1

value: imatinib sensitive


title: SPL_5

description: Spleen


title: SPL_3

description: Spleen


title: SPL_4

description: Spleen


title: VECTOR rep2


title: SPL_2

description: Spleen


title: BA rep2


title: LNG.DIS_6

description: Lung porcine distal

source_name: Lung porcine distal

value: Lung porcine distal


title: LNG.DIS_7

description: Lung porcine distal


title: LNG.DIS_5

description: Lung porcine distal


title: LNG.DIS_3

description: Lung porcine distal


title: SPL_6

description: Spleen


title: LNG.DIS_1

description: Lung porcine distal


title: LNG.DIS_4

description: Lung porcine distal


title: LNG.DIS_8

description: Lung porcine distal


title: SPL_1

description: Spleen


title: LNG.DIS_2

description: Lung porcine distal


title: LNG.BRO_7

description: Lung porcine bronchus

source_name: Lung porcine bronchus

value: Lung porcine bronchus


title: LNG.BRO_8

description: Lung porcine bronchus


title: HEL 646C Doxo+Cyta+DAC 31

city: Lisboa

first: Francisco

last: Caiado

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

data_processing:
Quality of the reads obtained by HiSeq2000 sequencing was checked with FastQC software (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Preprocessing of the reads was performed with fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.htmL) and aScidea specific perl scripts property of aScidea (http://www.ascidea.com) in order to filter regions of low quality
Raw reads that passed the quality filter threshold were mapped using Bowtie2 2.2.8 to generate read alignments for each sample. The reference genome used was the Homo Sapiens version GRCh38. The transcript isoform level and gene level counts were calculated using FeatureCounts from SubRead Package
Differential transcript expression was then computed using DESeq2. The resulting lists of differentially expressed isoforms were filtered by ln(fold_change) >1 and < -1 and a p-value of 0.05
Genome_build: Homo sapiens version GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing gene read counts (FeatureCounts) per sample

source_name: HEL (Human Erythroleukemia) cell line

growth_protocol: The Human acute myeloid leukemia cell lines HEL (ATCC, TIB-180™) was maintained in Iscove's Modified Dulbecco's Medium GlutaMAX™ Supplement supplemented with 10% (v/v) fetal bovine serum, 1% (v/v) Sodium Pyruvate (Gibco®, NY, USA), 1% (v/v) penincillin-streptomycin and 0.1% (v/v) Gentamycin (Gibco®, NY, USA) at 37ºC with 5% CO2. Cells were seeded at 0,2x106 cells/mL and maintained between 0,2x106 cells/mL and 0,6x106 cells/mL.

extract_protocol:
Total RNA was extracted from frozen cells pellets using the High Pure RNA Isolation Kit (Roche, Basileia, Swiss). According to manufacturers instructions, manual V12:  https://lifescience.roche.com/en_ch/products/high-pure-rna-isolation-kit.html#documents
ASCIDEA Computational Biology Solutions, Barcelona, performed the sequencing. One microgram of high-purity total RNA (defined as having an RNA integrity number greater than 7.0) was used as input for the Illumina TruSeq RNA Sample Prep Kit, Sets A/B (48Rxn) (Illumina). The gel-free protocol was employed for the TruSeq RNA Sample Prep Kit per the manufacturer’s specifications and performed on the Beckman Coulter Biomek FXp robotics platform. The standard RNA-fragmentation profile was used as recommended by Illumina (94 °C for 8 min). The PCR-amplified RNA-seq library products were then quantified using the Fragment Analyzer Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies). The samples were diluted to 10 nM in EB Buffer (Qiagen), denatured, and loaded at 2.75 pM on an Illumina HiSeq2000 in Rapid Run Mode using TruSeq Rapid PE Cluster Kit–HS and TruSeq Rapid SBS Kit–HS (200 cycle) reagents (Illumina). The RNA-seq libraries were sequenced at 100 bp paired-end with a 7-bp index using the standard Illumina primers.

treatment_protocol: All the in vitro treatment regimens were optimized using the mainstream drugs used in clinical management of AML. The different treatment regimens consisted in using only the anthracycline doxorubicin (1.8 uM, doxorubicin chlorohydrate, 2mg/mL, medac), cytarabine (6 uM, Citaloxan, 20 mg/mL, Hospira Portugal Lda) or hypomethylating agent decitabine (0.1 uM, 5-Aza-2′-deoxycytidine, 5 mg, Sigma) and using conjugations of this drugs with or without the hypomethylating agent (namely, doxorubicin plus cytarabine and doxorubicin plus cytarabine combined with decitabine). Non-treated cells were cultured in IMDM with 0.1 μM of dimethyl sulfoxide (DMSO), as control. The drugs were always added to the cells at time T0h (beginning of each experiment) and each treatment condition was always performed at least in three biological replicates per experiment. Barcoded HEL cells were counted by Trypan blue exclusion method (> 75 % of viability was ensured), and 6 million cells were seeded at the concentration of 2x105cells/mL in the presence or absence of each treatment regimen and incubated for 72-74 hours at 37 ºC, 5% CO2. After incubation, cells were thoroughly washed and enriched for live cells through Ficoll-Paque (Histopaque®-1077, sigma) gradient exclusion of dead cells. The recovered live cells were washed three time and reseeded at the concentration of 2x105 cells/mL in fresh IMDM complete medium. Culture cells were kept growing at 37 ºC, 5% CO2 during approximately 30 days until the number of live cells reached the initially seeded number (6 million cells). Every 3 or 4 days 1% of each cell culture was stained with 10 uL/mL of 7AAD (Biolegend, USA) and 2.5 uL/mL of AnnexinV-APC (InvitrogenTM, NY, USA) and analyzed for the total cell numbers and the live/dead cells by flow cytometry on an LSR FortessaII Cell Analyzer (BD Biosciences). Pellets of live cells (1x106) were collected and frozen for RNA extraction.

value: Doxorubicin + Cytarabine + Decitabine (Doxo+Cyta+DAC)

value: AML cell line - HEL (Human Erythroleukemia)


title: HEL 646C Doxo+Cyta+DAC 33


title: LNG.BRO_6

description: Lung porcine bronchus


title: HEL 646C Doxo+Cyta+DAC 32


title: LNG.BRO_5

description: Lung porcine bronchus


title: HEL 646C Doxo+Cyta+DAC 30


title: HEL 646C Doxo+Cyta 20

value: Doxorubicin + Cytarabine (Doxo+Cyta)


title: HEL 646C Doxo+Cyta 22


title: 8week_Src(p53-)_DIO

city: Hsinchu

first: Yong Chun

last: Luo

address: Boai Street

country: Taiwan

institute: National Chiao Tung University

description:
8wSRCDIO11
Treatment of overfed in 8week Src(p53-) fish.

hyb_protocol: An automated Hyb-Wash-Scan workflow with ZebGene1.1ST Array Plate was performed with the GeneTitan™ Multi-Channel (MC) Instrument (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 702933 Rev. 2).

scan_protocol: Hybridized arrays were washed and the signal intensity of the chip was scanned using a GeneChip Scanner.

data_processing: Data were processed using R, BioConductor package oligo, and normalized using the Robust Multichip Average (RMA) method at the probe level. The probe mapping to core transcripts using package pd.zebgene.1.1.st.

label: Biotin

organism: Danio rerio

label_protocol: Target cRNA and ss-cDNA samples were prepared stepwise from 100 ng of total RNA diluted into 3 ul of volume using GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 703147 Rev. 3). The resulting purified ss-cDNA samples were fragmented and labelled with terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin (Thermo Fisher Scientific, US).

growth_protocol: The AB zebrafish strain (Danio rerio), Tg(fabp10a:src,p53-), Tg(fabp10a:HBx,p53-), and Tg(fabp10a:HBx,src,p53-), were used and growth for 8 weeks.

extract_protocol: Total RNA was isolated by NucleoSpin® RNA kit (MACHEREY-NAGEL, US) following the manufacturer manual, and RNA samples was eluted in 40 μl RNase-free water. RNA quantity and purity were assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7.

treatment_protocol: The three months old of four types of fish were fed using three different feeding methods: normal diet, overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily, and high-fat diet fish food (one spoon, about 0.22g) three times daily. For 8 weeks, the zebrafishes were sacrificed and liver specimens were collected.

tag: strain/background

value: AB

tag: genotype/variation

value: Liver

tag: diet

value: Overfed


title: 8week_HBx,Src(p53-)_DIO_sample 1

description:
8wTRIDIO7
Treatment of overfed in 8week HBx,Src(p53-) fish, sample 1.


title: LNG.BRO_4

description: Lung porcine bronchus


title: 8week_HBx,Src(p53-)_NOR_sample 1

description:
8wTRINOR3
Treatment of normal diet in 8week HBx,Src(p53-) fish, sample 1.

source_name: 8week_HBx,Src(p53-)_Normal diet

value: Normal diet


title: 8week_Src(p53-)_FAT

description:
8wSRCFAT4
Treatment of high fat diet in 8week Src(p53-) fish.

source_name: 8week_Src(p53-)_High fat diet

value: High fat diet


title: 8week_Src(p53-)_NOR

description:
8wSRCNOR5
Treatment of normal diet in 8week Src(p53-) fish.

source_name: 8week_Src(p53-)_Normal diet


title: 8week_WT_NOR_sample 2

description:
8wWTNOR20
Treatment of normal diet in 8week WT fish, sample 2.

source_name: 8week_WT_Normal diet

value: WT


title: HEL 646C Doxo6

value: Doxorubicin (Doxo)


title: 8week_WT_DIO

description:
8wWTDIO16
Treatment of overfed in 8week WT fish.


title: LNG.BRO_3

description: Lung porcine bronchus


title: LNG.BRO_1

description: Lung porcine bronchus


title: 8week_HBx,Src(p53-)_DIO_sample 2

description:
8wTRIDIO11
Treatment of overfed in 8week HBx,Src(p53-) fish, sample 2.


title: 8week_WT_FAT

description:
8wWTFAT12
Treatment of high fat diet in 8week WT fish.

source_name: 8week_WT_High fat diet


title: PLACT_8

description: Placenta

source_name: Placenta

value: Placenta


title: 8week_HBx(p53-)_NOR

description:
8wHBxNOR15
Treatment of normal diet in 8week HBx(p53-) fish.

source_name: 8week_HBx(p53-)_Normal diet


title: 8week_WT_NOR_sample 1

description:
8wWTNOR2
Treatment of normal diet in 8week WT fish, sample 1.


title: HEL 646C Doxo4


title: PLACT_7

description: Placenta


title: PLACT_6

description: Placenta


title: HEL 646C Doxo+Cyta 19


title: HEL 646C NT2

value: No treatment (NT)


title: 8week_HBx,Src(p53-)_NOR_sample 2

description:
8wTRINOR11
Treatment of normal diet in 8week HBx,Src(p53-) fish, sample 2.


title: PLACT_5

description: Placenta


title: V1SSV2_24M_off2

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
quality and adapter trimming with cutadapt v1.9.1
filter mapping to tRNA and rRNA (RepBase) with bwa mem 0.7.14-r1136
trimming and filtering with fqtrim v0.9.5
alignment to Ensembl GRCm38.85 using STAR v2.5.2
feature counting with subread v1.5.3
differential expression analysis using DESeq2 v1.16.1
Genome_build: Ensembl GRCm38.85
Supplementary_files_format_and_content: tab-delimited text with rlog normalized count data

organism: Mus musculus

source_name: Brain

extract_protocol:
Qiagen miRNeasy Mini (Qiazol)
Qiagen RNase-Free DNase Set (on-column  digestion 15min)
Illumina TruSeq Stranded mRNA Library Prep Kit

tag: phenotype

value: DT Venus Dox 24 Months


title: V1SSV2_24M_on4

value: DT Venus Glucose 24 Months


title: PLACT_4

description: Placenta


title: V1SSV2_24M_on3


title: PLACT_2

description: Placenta


title: PLACT_1

description: Placenta


title: PLACT_3

description: Placenta


title: HEL 646C Doxo5


title: V1SSV2_24M_on1


title: 8week_HBx(p53-)_FAT

description:
8wHBxFAT12
Treatment of high fat diet in 8week HBx(p53-) fish.

source_name: 8week_HBx(p53-)_High fat diet


title: LNG.TRA_8

description: Lung porcine trachea

source_name: Lung porcine trachea

value: Lung porcine trachea


title: 8week_HBx(p53-)_DIO

description:
8wHBxDIO13
Treatment of overfed in 8week HBx(p53-) fish.


title: LNG.TRA_6

description: Lung porcine trachea


title: LNG.TRA_7

description: Lung porcine trachea


title: LNG.TRA_5

description: Lung porcine trachea


title: LNG.TRA_4

description: Lung porcine trachea


title: LNG.TRA_3

description: Lung porcine trachea


title: LNG.TRA_1

description: Lung porcine trachea


title: LNG.TRA_2

description: Lung porcine trachea


title: 103_HiC_KO_rep3

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description:
sample56_HiC8
lab data ID: 171212_SN7001365_0423_AHW2FLBCXY/3_KO_Th1_103_HiC_4_ACTTGA_R1(or R2).fastq.gz

data_processing:
V: CASAVA1.8.2/bcl2fastq1.8.4
preprocess and normalization: juicer.sh using default parameter
5 kb resolution matrices extraction: juicebox dump obsevered NONE .hic BP 5000
R and custom script: generate genome wide contact matrix as in Sanborn et al. PNAS 2015
estimation of number on in silico spike-ins: median of the genome-wide per-bin coverage of the HiC matrix at the targeted region
reconstruct HiC matrix: combine the targeted region local HiC with the global CH12 wt matrix which matched to spike-ins
re-normalization : Knight-Ruiz balancing algorithm with the juicebox pre -r 5000
Genome build: mm9
Processed data files format and content: Hic files

source_name: mouse in-vitro activated Th1 cells

growth_protocol: CD4+ T cells were purified from splenocytes and lymph nodes of untreated 6- to 14-week-old mice by negative selection and magnetic separation (Miltenyi Biotec). To obtain naïve T cells, CD4+ T cells were sorted into CD4+CD62L+CD44−CD25− T cells by fluorescence activated cell sorting (FACS) using FACSAria Illu or FACSAria Fusion (BD). Naive CD4+ T cells were activated on a 24-well-plate at a density of 4 x 10^5 cells/ml by plate-bound anti-CD3 (10 μg/ml, clone: 145-2C11) and anti-CD28 (10 μg/ml, clone: 37.51) in cRPMI (RPMI with 10% (vol/vol) FCS, 2 mM glutamine, 100 IU/ml of penicillin, 0.1 mg/ml of streptomycin and 20 mM HEPES buffer, pH 7.2–7.5, 1 mM sodium pyruvate, nonessential amino acids (all Thermo Fisher), and 2 μM β-mercaptoethanol (Sigma-Aldrich)) for 3 days with IL-12 (10 ng/ml, R&D Systems) and anti-IL-4 (10 µg/ml, 11B11) for Th1 cells or IL-4 (20 ng/ml, R&D Systems) and anti-IFN-γ (10 µg/ml, XMG1.2) for Th2. After 3 days, cells are split onto uncoated plates with fresh media and cytokines added along with IL-2 (100 U/ml, R&D Systems).

extract_protocol:
A detailed protocol to generate HiC libraries including sequence alignment can be obtained at PMID:25497547 and PMID:26499245.
Libraries were sequenced for 50 cycles (paired-end reads) on a Illumina HiSeq 2500 (rapid mode).

tag: strain

tag: culture condition

value: 6 days in vitro culture

tag: genotype

value: Ifng-as1 KO

value: mouse in-vitro activated Th1 cells


title: 102_HiC_KI_rep1

description:
sample58_HiC9
lab data ID: 170907_SN7001365_0403_AHVFCHBCXY/3_KI_Th1_102_HiC_3_CTTGTA_R1(or R2).fastq.gz

value: Ifng-as1 PolyA_KI


title: OC-0_day

first: Cui

address: No. 37 Xueyuan Road

institute: Buaa

data_processing:
Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA(rRNA) database. The rRNA mapped reads were then removed.
The rRNA removed reads of each samples were then mapped to reference genome mm10 by Tophat2. After aligned with Bowtie2, the enriched unmapped reads (or mapped very poorly) were then re-aligned with Bowtie
The reconstruction of transcripts was carried out withsoftware Cufflinks, which together with Tophat2, allow biologists to identify new genes and new splice variants.
Transcripts abundances were quantified by software RSEM.
The transcript expression level was normalized by using FPKM(Fragments Per Kilobase of transcript per Million fragments mapped) method
The edgeR package was used to identify differentially expressed transcripts across samples or  groups. We identified  transcripts with a fold change ≥1 and a false discovery rate (FDR) <0.05 in comparison as significant DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow-derived macrophages (BMMs)

growth_protocol: Mouse primary osteoclasts were differentiated from bone marrow-derived macrophages (BMMs) with the stimulation of M-CSF (Peprotech, #315-02) and RANKL (Peprotech, #315-11C). Briefly, collect long bones from eight to twelve weeks old C57BL/6J mice, then flush out bone marrow using 1-ml syringe with serum-free α-MEM medium (Gibco, #12571-500). The bone marrow cells were suspended in growth medium (α-MEM + 10% FBS (Gibco, #10100-147) and culture for 1 day. Then unattached cells were collected and adjust to 3 × 106 cells/ml with α-MEM growth medium contain 50 ng/ml M-CSF and seeded in cell culture dish for 1 day. Subsequently, exchanged to differentiation medium (α-MEM + 10% FBS + 50 ng/ml M-CSF + 100 ng/ml RANKL) and renewal medium every 2 days for a total 6 days.

extract_protocol:
The TRIzol Reagent (Invitrogen, # 15596-018) was used for total RNA isolation from cultured cells according to the manufacturer’s instructions.
After total RNA was extracted, rRNAs were removed to retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: C35_HiC_KI_rep3

description:
sample58_HiC11
lab data ID: 180619_SN7001365_0483_BHJH3MBCX5/3_KI_Th1_CAJ_35_HiC_7_CTTGTA_R1(or R2).fastq.gz


title: OC-6_day

source_name: BMMs-derived osteoclasts (OCs)


title: 97_HiC_KO_rep1

description:
sample54_HiC6
lab data ID: 170526_SN7001365_0389_AHHKVVBCXY/r170717______3_KO_Th1_99_HiC_2_R1.fastq.gz


title: 99_HiC_KO_rep2

description:
sample55_HiC7
lab data ID: 170717_SN7001365_0398_BHMYHTBCXY/r170717______3_KO_Th1_99_HiC_2_R1(or R2).fastq.gz


title: MS.LD_6

description: Longissimus dorsi

source_name: Longissimus dorsi

value: Longissimus dorsi


title: V1SSV2_24M_on2


title: 103_HiC_KI_rep2

description:
sample58_HiC10
lab data ID: 171212_SN7001365_0423_AHW2FLBCXY/5_KI_Th1_103_HiC_4_TAGCTT_R1(or R2).fastq.gz


title: C35_HiC_WT_rep5

description:
sample53_HiC5
lab data ID: 180619_SN7001365_0483_BHJH3MBCX5/1_WT_Th1_CAJ_35_HiC_7_GCCAAT_R1(or R2).fastq.gz


title: MS.LD_8

description: Longissimus dorsi


title: MS.LD_7

description: Longissimus dorsi


title: 102_HiC_WT_rep3

description:
sample51_HiC3
lab data ID: 170907_SN7001365_0403_AHVFCHBCXY/1_WT_Th1_102_HiC_3_GCCAAT_L001_R2.fastq.gz


title: 103_HiC_WT_rep4

description:
sample52_HiC4
lab data ID: 171212_SN7001365_0423_AHW2FLBCXY/1_WT_Th1_103_HiC_4_ATCACG_R1(or R2).fastq.gz


title: MS.LD_5

description: Longissimus dorsi


title: MS.LD_4

description: Longissimus dorsi


title: HEL 646C NT1

tag: treatment

tag: cell type

value: AML cell line - HEL (Human Erythroleukemia)


title: 99_HiC_WT_rep2

description:
sample50_HiC2
lab data ID: 170717_SN7001365_0398_BHMYHTBCXY/r170717______1_WT_Th1_99_HiC_2_R1.fastq.gz

tag: tissue


title: MS.LD_3

description: Longissimus dorsi


title: MS.LD_2

description: Longissimus dorsi


title: 97_HiC_WT_rep1

description:
sample49_HiC1
lab data ID: 170526_SN7001365_0389_AHHKVVBCXY/r170526______WT_Th1_local_Ifng_R1.fastq.gz


title: MS.LD_1

description: Longissimus dorsi


title: 85_ATAC_KO_Th1_rep2

description:
sample47_ATAC15
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s459

data_processing:
V: CASAVA1.8.2/bcl2fastq1.8.4
alignment: PE reads were mapped to the mouse genome (mm9 assembly) using Bowtie 1.1.1.
peak calling: Redundant reads were removed using Fastquniq. Uniquely mapped reads from fragments less than 175 bp were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
Genome build: mm9
Processed data files format and content: Peak bw files

extract_protocol:
ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013) with minor modification. Fifty thousand cells were pelleted and washed with 50 μl 1× PBS, followed by treatment with 50 μl lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After pelleting the nuclei by centrifuging at 500 × g for 10 min, the pellets were re-suspended in a 40-μl transposition reaction with 2 μl Tn5 transposase (FC-121-1030; Illumina) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37°C with shaking at 300 rpm for 30 min. The fragmentalized DNAs were then purified using a QIAGEN MinElute kit and amplified with 10 or 11 cycles of PCR based on the amplification curve. Libraries were purified using a QIAGEN PCR cleanup kit.
Libraries were sequenced for 75 cycles (paired-end reads) on a Illumina HiSeq 2500.


title: CPT.FIL_8

description: Conceptus filamentous

source_name: Conceptus filamentous

value: Conceptus filamentous


title: 85_ATAC_KO_Th2_rep2

description:
sample48_ATAC16
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s460

source_name: mouse in-vitro activated Th2 cells

value: mouse in-vitro activated Th2 cells


title: 85_ATAC_WT_Th2_rep2

description:
sample46_ATAC14
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s458


title: CPT.FIL_6

description: Conceptus filamentous


title: 85_ATAC_KO_Th1_rep1

description:
sample43_ATAC11
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s455


title: CPT.FIL_4

description: Conceptus filamentous


title: 85_ATAC_WT_Th1_rep2

description:
sample45_ATAC13
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s457


title: CPT.FIL_3

description: Conceptus filamentous


title: 85_ATAC_WT_Th2_rep1

description:
sample42_ATAC10
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s454


title: 85_ATAC_KO_Th2_rep1

description:
sample44_ATAC12
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s456


title: 117_ATAC_KI_Th2_rep2

description:
sample40_ATAC8
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s588


title: CPT.FIL_2

description: Conceptus filamentous


title: 117_ATAC_KI_Th1_rep2

description:
sample38_ATAC6
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s586


title: CPT.FIL_1

description: Conceptus filamentous


title: 117_ATAC_WT_Th2_rep2

description:
sample39_ATAC7
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s587


title: CPT.FIL_5

description: Conceptus filamentous


title: 120_CTCF_ChIP_KI_Th2_CTCF_rep2

description:
sample32_CTCF_ChIP24
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s12_2

data_processing:
V: CASAVA1.8.2/bcl2fastq1.8.4
alignment: SE reads were aligned to the mouse genome build mm9 with Bowtie 1.1.1
peak calling: Non-redundant and Uniquely mapped reads were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
Genome build: mm9
Processed data files format and content: Raw bw files

extract_protocol:
For ChIP-seq, 10 million Th1 and Th2 cells cultured as indicated above were cross-linked for 10 min with 1% formaldehyde and harvested. Cells were lysed by sonication (Sonifier S-450 Digital Ultrasonic Cell Disruptor/Homogenizer, Branson Ultrasonics) in shearing buffer (50mM Tris-HCl pH 7.6, 0.2% Triton X) and immuno-precipitated using a polyclonal rabbit anti-mouse anti-CTCF antiserum (07-729, Millipore Sigma, 8 µl per assay). ChIP was performed overnight at 4 ˚C using Protein A Dynabeads (Thermo Fisher). Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE buffer (pH 8.0) containing 0.2% Triton X-100, and once with TE buffer (pH 8.0). DNA was released by incubating the beads at 65°C for 4 hrs in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by a DNA clean and concentrator column (Zymo research). 80 ng of ChIPed DNA was subsequently used to prepare ChIP-Seq libraries using Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol.
Libraries were sequenced for 50 single read cycles on HiSeq 3000 following the manufacturer's protocols.


title: 117_ATAC_KI_Th2_rep1

description:
sample36_ATAC4
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s584


title: 117_ATAC_WT_Th1_rep2

description:
sample37_ATAC5
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s585


title: STOM_8

description: Stomach

source_name: Stomach

value: Stomach


title: CPT.FIL_7

description: Conceptus filamentous


title: 120_CTCF_ChIP_KO_Th2_CTCF_rep2

description:
sample30_CTCF_ChIP22
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s10_2


title: STOM_7

description: Stomach


title: 117_ATAC_KI_Th1_rep1

description:
sample34_ATAC2
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s582


title: 117_ATAC_WT_Th1_rep1

description:
sample33_ATAC1
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s581


title: 85_ATAC_WT_Th1_rep1

description:
sample41_ATAC9
lab data ID: 170717_SN7001365_0397_BHMVN5BCXY/s453


title: STOM_5

description: Stomach


title: STOM_6

description: Stomach


title: D16-1578_Old RF pan (GGCAAC

city: Cambridge

first: Chia-Wei

last: Cheng

state: MA

address: 500 Main St

institute: Koch Institute at MIT

data_processing:
Base-calling was performed using the Illumina HiSeq Control Software v 2.2.58 / RTA 1.18.64 in standalone mode.
Quality control: Reads from each sequencing run were aligned against mm9 using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against mm9 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
Reads from the three sequencing runs merged and aligned against the mm10 murine genome assembly, with ENSEMBL 88 annotation, using  STAR v.2.5.3a, with flags --runThreadN 8 --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM pointing to a 75nt-junction STAR genome suffix array [Dobin2013]. Quantification was performed using RSEM with flags --forward-prob 0 --calc-pme --alignments -p 8 [Li&Dewey2011].
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with posterior mean estimates of genes counts for each samples, as reported by RSEM.

extract_protocol:
As previously reported and briefly summarized here, small intestines were removed, washed with cold PBS, opened longitudinally and then incubated on ice with PBS−/− EDTA (10 mM) for 30-45 min. Tissues were then moved to PBS. Crypts were then mechanically separated from the connective tis-sue by shaking, and then filtered through a 70-μm mesh into a 50-ml conical tube to remove villus material and tissue fragments. Crypts were removed from this step and dissociated into single cells and sorted by flowcytometry.
PolyA+  RNA extraction (Spri beads), followed by RNA fragmentation, reverse transcription, end-repair and adjunction of Illumina adapters by PCR (TruSeq protocol, Spri size selection 200-400 bps).

tag: age

value: Old

value: Re-fed

value: Intestinal crypt cells

tag: cell subtype

value: CD24+C-kit+ Paneth (PA) cells


title: D16-1577_Old RF low (CTACTG)

value: Lgr5-GFP low progenitors (Low)


title: 120_CTCF_ChIP_WT_Th1_CTCF_rep2

description:
sample27_CTCF_ChIP19
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s07_2

value: WT


title: 120_CTCF_ChIP_WT_Th2_CTCF_rep2

description:
sample28_CTCF_ChIP20
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s08_2


title: LNG.BRO_2

description: Lung porcine bronchus

source_name: Lung porcine bronchus

value: Lung porcine bronchus


title: STOM_4

description: Stomach


title: 120_Input_KI_Th2_rep2

description:
sample26_CTCF_ChIP18
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s06_2


title: D16-1575_Old fast pan (ACTTGA)

value: Fasted


title: 120_CTCF_ChIP_KI_Th1_CTCF_rep2

description:
sample31_CTCF_ChIP23
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s11_2

value: 6 days in vitro culture


title: D16-1572_Old AL pan (GTCCAG)

value: Fed


title: 117_ATAC_WT_Th2_rep1

description:
sample35_ATAC3
lab data ID: 180326_SN7001365_0463_AHGG3CBCX2_lane2/s583


title: STOM_3

description: Stomach


title: 120_Input_KI_Th1_rep2

description:
sample25_CTCF_ChIP17
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s05_2

value: mouse in-vitro activated Th1 cells


title: D16-1573_Old fast hi (TCGTCA)

value: Lgr5-GFP high intestinal stem cells (High)


title: D16-1570_Old AL hi (ATGATA)


title: D16-1571_Old AL low (CAAGTT)


title: D16-1569_Yng RF pan (TACCGC)

value: Young


title: D16-1521_Yng RF low (GCAGCG)


title: 120_Input_KO_Th2_rep2

description:
sample24_CTCF_ChIP16
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s04_2

value: Ifng-as1 KO


title: STOM_1

description: Stomach


title: D16-1520_Yng  RF hi (CGTTAT)


title: 120_Input_KO_Th1_rep2

description:
sample23_CTCF_ChIP15
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s03_2


title: D16-1574_Old fast low (TGGACC)


title: D16-1519_yng fast pan (CTTAAA)


title: MS.DI_8

description: Diaphragm muscle

source_name: Diaphragm muscle

value: Diaphragm muscle


title: 120_Input_WT_Th2_rep2

description:
sample22_CTCF_ChIP14
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s02_2

value: mouse in-vitro activated Th2 cells


title: D16-1517_yng fast hi (TCCGGG)


title: D16-1515_yng AL low (GTAACA)


title: MS.DI_6

description: Diaphragm muscle


title: D16-1514_yng AL hi (CATCAC)


title: MS.DI_7

description: Diaphragm muscle


title: 119_CTCF_ChIP_KI_Th2_CTCF_rep1

description:
sample20_CTCF_ChIP12
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s12

value: Ifng-as1 PolyA_KI


title: STOM_2

description: Stomach

value: Stomach


title: MS.DI_5

description: Diaphragm muscle


title: 119_CTCF_ChIP_KI_Th1_CTCF_rep1

description:
sample19_CTCF_ChIP11
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s11


title: OMPCre mediated SMAD4cKO VNO at P21, biological rep1

city: Albany

first: Paolo

middle: E

last: Forni

state: New York

address: 1400 Washington Avenue

institute: University at Albany

data_processing:
Raw FASTQ files were processed using salmon (v 0.14.0) in quant mode to the ensmbl mm10.GRCm38 cDNA assembly with the --validateMappings flag
Raw count values per gene were extracted from salmon output files and imported into DESeq2 (v 1.22.2) for calculation of differential gene expression.
Genome_build: mm10.GRCm38.ensmbl
Supplementary_files_format_and_content: Raw count values per gene

source_name: Vomeronasal Organ

growth_protocol: Mice were raised in a normal 12hr light/dark cycle until collection.

extract_protocol:
Mice were euthanized by CO2 at P21 and immediately put on ice for immediate VNO isolation. Extraction of total RNA was performed according to manufacturer instructions of the PureLink™ RNA Mini Kit
RNA libraries were prepared from 1ug of RNA according to the NEXTflex Rapid directional mRNA-seq Bundle, cat# 5138-10
polyA+ RNA-Seq, single-end, 75bp

value: post natal day 21

value: OMPCre +/- SMAD4 Flox

tag: Sex

value: F

value: mature Apical and Basal VSNs


title: OMPCre mediated SMAD4cKO VNO at P21, biological rep3


title: OMPCre mediated SMAD4cKO VNO at P21, biological rep2


title: OMP Het VNO at P21, biological rep3

value: OMPCre +/-


title: 119_CTCF_ChIP_KO_Th2_CTCF_rep1

description:
sample18_CTCF_ChIP10
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s10


title: MS.DI_3

description: Diaphragm muscle

tag: replicate


title: MS.DI_4

description: Diaphragm muscle


title: 120_CTCF_ChIP_KO_Th1_CTCF_rep2

description:
sample29_CTCF_ChIP21
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s09_2


title: OMP Wild-type VNO at P21, biological rep3

value: Wild Type


title: MS.DI_2

description: Diaphragm muscle


title: D16-1516_yng fast hi (TCCGGG)

value: Fasted

value: Intestinal crypt cells


title: D16-1518_yng fast low (AAGCTC)

value: Progenitor cells


title: 120_Input_WT_Th1_rep2

description:
sample21_CTCF_ChIP13
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s01_2

value: 6 days in vitro culture

value: WT

value: mouse in-vitro activated Th1 cells


title: OMP Wild-type VNO at P21, biological rep2


title: 119_CTCF_ChIP_WT_Th2_CTCF_rep1

description:
sample16_CTCF_ChIP8
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s08


title: 119_CTCF_ChIP_KO_Th1_CTCF_rep1

description:
sample17_CTCF_ChIP9
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s09

value: Ifng-as1 KO


title: AP2eCre mediated SMAD4cKO VNO at P21, biological rep3

value: AP2eCre +/- SMAD4 Flox

value: immature Basal VSNs


title: 119_CTCF_ChIP_WT_Th1_CTCF_rep1

description:
sample15_CTCF_ChIP7
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s07


title: AP2eCre mediated SMAD4cKO VNO at P21, biological rep2


title: FT.AB_8

description: Abdominal fat tissue

source_name: Abdominal fat tissue

value: Abdominal fat tissue


title: OMP Wild-type VNO at P21, biological rep1


title: AP2eCre mediated SMAD4cKO VNO at P21, biological rep1


title: 119_Input_KI_Th2_rep1

description:
sample14_CTCF_ChIP6
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s06

value: Ifng-as1 PolyA_KI

value: mouse in-vitro activated Th2 cells


title: AP2e Het VNO at P21, biological rep3

value: post natal day 21

value: AP2eCre +/-


title: OMP Het VNO at P21, biological rep2

value: F

value: mature Apical and Basal VSNs


title: 119_Input_KI_Th1_rep1

description:
sample13_CTCF_ChIP5
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s05


title: OMP Het VNO at P21, biological rep1

value: OMPCre +/-


title: AP2e Het VNO at P21, biological rep4


title: FT.AB_7

description: Abdominal fat tissue


title: AP2e Het VNO at P21, biological rep2


title: AP2e Het VNO at P21, biological rep1


title: 119_Input_KO_Th2_rep1

description:
sample12_CTCF_ChIP4
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s04


title: AP2e Wild-type VNO at P21, biological rep3

value: Wild Type


title: FT.AB_5

description: Abdominal fat tissue


title: 119_Input_KO_Th1_rep1

description:
sample11_CTCF_ChIP3
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s03


title: AP2e Wild-type VNO at P21, biological rep2


title: MS.DI_1

description: Diaphragm muscle

value: Diaphragm muscle


title: FT.AB_6

description: Abdominal fat tissue


title: FT.AB_4

description: Abdominal fat tissue


title: Socs1-/- 3 hr LPS rep2

city: Glasgow

first: Jennifer

last: Mitchell

address: Sir Graeme Davies Building, 120 University Avenue

department: Insitute of Infection, Immunity and Inflammation

institute: University of Glasgow

data_processing:
Read quality was checked for each sample using FastQC
Reads were aligned to human reference sequence iGenome NCBI GRCh38 using HISAT
Aligned reads were assembled into transcripts using Stringtie
Aligned reads were counted using htseq-count
Differential gene expression was determined using DESeq2
Genome_build: iGenome NCBI GRCh38
Supplementary_files_format_and_content: Reads counts generated using htseq-count; DESeq2 differential gene expression testing

growth_protocol: RAW 264.7 cells were cultured in high glucose Dulbecco’s Modified Eagle Medium (DMEM), supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM L-glutamine, and 100 units/ml of streptomycin and penicillin. Cells were sub-cultured by mechanical detachment. Cells were maintained at 37ºC in a humidified environment with 5% CO2.

extract_protocol:
Qiashredders and Rneasy (Qiagen) kit used
1 μg of total RNA was used for library construction. For PolyA selection, the TruSeq stranded mRNA sample prep kit was used. Illumina NextSeq™500 platform was used to sequence single-end 75bp reads to a depth of 20 million.

treatment_protocol: HEK293T cells were either left untreated or were treated with 100 ng/ml LPS for 3 hours prior to RNA extraction.

tag: cell line


title: Socs1-/- 3 hr LPS rep1


title: 119_Input_WT_Th2_rep1

description:
sample10_CTCF_ChIP2
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s02


title: FT.AB_3

description: Abdominal fat tissue


title: Socs1-/- untreated rep2


title: FT.AB_2

description: Abdominal fat tissue


title: Socs1-/- untreated rep1


title: AP2e Wild-type VNO at P21, biological rep1


title: Ing4-/- 3 hr LPS rep2


title: V1SSV2_24M_off1

value: DT Venus Dox 24 Months


title: Ing4-/- 3 hr LPS rep1


title: FT.AB_1

description: Abdominal fat tissue


title: 70_RNA_KO_Th2_rep2

description:
sample7_RNA7
lab data ID: 170504_0049/s07

data_processing:
V: CASAVA1.8.2/bcl2fastq1.8.4
alignment: SE reads were mapped to the mouse genome mm9 using TopHat 2.1.0
RPKM calculation : RPKMs were calculated using Partek6.6
Genome build: mm9
Processed data files format and content: RPKM files

extract_protocol:
For RNA-seq, total RNA was isolated using the RNeasy kit (Quiagen), 500 ng of RNA were subsequently used to prepare (polyA-)RNA-seq libraries by a combination of NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol.
Libraries were sequenced for 50 single read cycles on HiSeq 2500 following the manufacturer's protocols.

value: 6 days in vitro culture


title: CPT.TUB_8

description: Conceptus tubular

source_name: Conceptus tubular

value: Conceptus tubular


title: 119_Input_WT_Th1_rep1

description:
sample9_CTCF_ChIP1
lab data ID: 180629_JOO177_0146_AHVLT5BBXX/s01

value: WT

value: mouse in-vitro activated Th1 cells


title: Ing4-/- untreated rep2


title: 70_RNA_KO_Th1_rep2

description:
sample6_RNA6
lab data ID: 170504_0049/s06

value: Ifng-as1 KO


title: WT 3 hr LPS rep2

value: Wild type


title: Ing4-/- untreated rep1


title: WT 3 hr LPS rep1


title: CPT.TUB_7

description: Conceptus tubular


title: WT untreated rep2


title: 70_RNA_WT_Th1_rep2

description:
sample5_RNA5
lab data ID: 170504_0049/s05


title: CPT.TUB_6

description: Conceptus tubular


title: ChIP-seq-230-238-ChIP-input-3

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

description:
Peaks-230-238-a-FLI1-vs-Input
Annotated-230-238-FLI1-15-norm-tag-peaks

data_processing:
RNA-Sequencing and data analysis: Libraries  were single-end sequenced on a NextSeq500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A etal. 2012),) with single read, standard settings. If not indicated, further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, followed by the getDiffExpression.pl  command using edgeR(3.12.0).
ChIP-sequencing and data analysis: For ChIP-Seq samples, Libraries were single-end sequenced on a NextSeq500, reads were aligned to the mm10 genome using default single end parameters for Bowtie2 (2.3.4.2) (Langmead, B. etal. 209 and 2012).  Aligned read files from ChIP seq experiments were analyzed with HOMER (v4.8, v4.10) (Heinz et al. 2010) to find peaks,  perform motif-enrichment, and  other analyses in the study.
Genome_build: mm10
Supplementary_files_format_and_content: peak-files, annotated peak-files and expressionmatrices in txt format

source_name: 230-238 murine PreB celline

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations. For ChIP-seq: Cells for transcription factor ChIP were fixed at room temperature with DSG for 30 min followed by 1% formaldehyde/PBS for 10 minutes. Reaction was then quenched by adding glycine to 0.125 M. Cells were washed  pelleted and snap-frozen and stored at -80°C until ready for ChIP or used immediately for ChIP.   Nuclei for ChIP were isolated  by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8))+ PIC and sonicated on a Bioruptor (Diagenode) max power for 30s followed by 30 s rest. Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted 5X in Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8) + PIC). Anti-bodies were hybridized to ProteinA or G Dynabeads®  (LifeTechnologies)  and added to the diluted chromatin. ChIP was performed over night at 4°C. and subsequently washed (1 time with 500 μl Low Salt Immune Complex Wash Buffer, 1 time with 200 μl High Salt Immune Complex Wash Buffer, 1 time with 200 μl LiCl Immune Complex Wash Buffer, 2 times with 200 μl TE buffer) and eluted for 4 h at 65°C ( 20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, 100 μg RNase A and 50 μg proteinase K) treated and finally cleaned up using Zymo ChIP DNA Clean & Concentrator before ChIP-seq libary preparation.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA). ChIP-Seq: Libraries were constructed using Illumina Truseq Nano DNA library preparation kit or by addition of Bioo-scientiffic Nextflex barcodes following standard procedures. Libraries were run on the Illumina NextSeq500.

treatment_protocol:
Cell culture:  Fetal liver cells were purified from wild-type, Ebf1 deficient, or Pax5 deficient fetus, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol.    Infection: Retronectin coated 24-well plates were pre-inkubated with 500ul viral supernatant. Cells were harvested,  resuspended 500ul media and added to 500μl of virus supernatant. Polybrene was added to supernatant at concentration of 0.5μg/ml. Spin-infection was performed at 1800xg, for 90min at 32°C.
230-238-cells were cultured in RPMI1640 with UltraGlutamine (Lonza, Basel, Swiss) supplemented with 10% heat-inactivated FCS, 20mM HEPES, 50mg/ml Gentamicin and 50mM β-ME.

tag: celline

value: 230-238 murine PreB celline

tag: celline background

value: Abelson transformed PreB cell-line

tag: genotype / variation

value: PreB

tag: cuture protocol

value: Cultured in RPMI1640 + UltraGlutamine +10% FBS, 20mM HEPES, 50ug/ml Gentamicin and 50uM β-ME.

tag: antibody


title: 68_RNA_KO Th2_rep1

description:
sample4_RNA4
lab data ID: 170504_0049/s04

value: mouse in-vitro activated Th2 cells


title: WT untreated rep1


title: CPT.TUB_5

description: Conceptus tubular


title: ChIP-seq-230-238-a-FLI1-ChIP

value: Rabbit anti-FLI1 polyclonal IgG (ab15289, Abcam)


title: 68_RNA_KO_Th1_rep1

description:
sample3_RNA3
lab data ID: 170504_0049/s03


title: ChIP-seq-FL-Ebf1-KO-a-RUNX1-ChIP

data_processing:
RNA-Sequencing and data analysis: Libraries  were single-end sequenced on a NexSeq500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A etal. 2012),) with single read, standard settings. If not indicated, further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, followed by the getDiffExpression.pl  command using edgeR(3.12.0).
ChIP-sequencing and data analysis: For ChIP-Seq samples, Libraries were single-end sequenced on a NexSeq500, reads were aligned to the mm10 genome using default single end parameters for Bowtie2 (2.3.4.2) (Langmead, B. etal. 209 and 2012).  Aligned read files from ChIP seq experiments were analyzed with HOMER (v4.8, v4.10) (Heinz et al. 2010) to find peaks,  perform motif-enrichment, and  other analyses in the study.
Genome_build: mm10
Supplementary_files_format_and_content: peak-files, annotated peak-files and expressionmatrices in txt format

source_name: Ebf1-/- FL

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations. For ChIP-seq: Cells for transcription factor ChIP were fixed at room temperature with DSG for 30 min followed by 1percent formaldehyde/PBS for 10 minutes. Reaction was then quenched by adding glycine to 0.125 M. Cells were washed  pelleted and snap-frozen and stored at -80°C until ready for ChIP or used immediately for ChIP.   Nuclei for ChIP were isolated  by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5percent NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5percent SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8))+ PIC and sonicated on a Bioruptor (Diagenode) max power for 30s followed by 30 s rest. Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted 5X in Dilution Buffer (1percent Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8) + PIC). Anti-bodies were hybridized to ProteinA or G Dynabeads®  (LifeTechnologies)  and added to the diluted chromatin. ChIP was performed over night at 4°C. and subsequently washed (1 time with 500 μl Low Salt Immune Complex Wash Buffer, 1 time with 200 μl High Salt Immune Complex Wash Buffer, 1 time with 200 μl LiCl Immune Complex Wash Buffer, 2 times with 200 μl TE buffer) and eluted for 4 h at 65°C ( 20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1percent SDS, 100 μg RNase A and 50 μg proteinase K) treated and finally cleaned up using Zymo ChIP DNA Clean & Concentrator before ChIP-seq libary preparation.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA). ChIP-Seq: Libraries were constructed using Illumina Truseq Nano DNA library preparation kit or by addition of Bioo-scientiffic Nextflex barcodes following standard procedures. Libraries were run on the Illumina NexSeq500.

treatment_protocol:
Cell culture:  Fetal liver cells were purified from wild-type, Ebf1 deficient, or Pax5 deficient fetus, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10percent heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10percent heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol.    Infection: Retronectin coated 24-well plates were pre-inkubated with 500ul viral supernatant. Cells were harvested,  resuspended 500ul media and added to 500μl of virus supernatant. Polybrene was added to supernatant at concentration of 0.5μg/ml. Spin-infection was performed at 1800xg, for 90min at 32°C.
230-238-cells were cultured in RPMI1640 with UltraGlutamine (Lonza, Basel, Swiss) supplemented with 10percent heat-inactivated FCS, 20mM HEPES, 50mg/ml Gentamicin and 50mM β-ME.

tag: strain background

tag: genotype/variation

value: Ebf1 knock out

value: ProB

value: Cultured in Optimem +10percent FBS, 25mM HEPES, 50microg/ml Gentamicin, 50microM beta-mercaptoethanol FL, KL, IL7 on OP9

value: Rabbit polyclonal anti-RUNX1 [ab23980, Abcam]


title: 68_RNA_WT_Th2_rep1

description:
sample2_RNA2
lab data ID: 170504_0049/s02

tag: strain

tag: culture condition


title: 70_RNA_WT_Th2_rep2

description:
sample8_RNA8
lab data ID: 170504_0049/fp14

tag: genotype


title: ChIP-seq-FL-Ebf1-KO-ChIP-Input-2

tag: cell type


title: CPT.TUB_4

description: Conceptus tubular

tag: tissue


title: ChIP-seq1-FL-Ebf1-KO-a-IKZF1-ChIP

value: Rabbit anti-Ikzf1 polyclonal IgG [ab26083, Abcam]


title: ChIP-seq1-FL-Ebf1-KO-ChIP-Input-1


title: CPT.TUB_3

description: Conceptus tubular


title: CPT.TUB_2

description: Conceptus tubular


title: ChIP-seq-FL-Pax5-KO-ChIP-Input-2

source_name: Pax5-/- FL

value: Pax5 knock out


title: ChIP-seq-FL-Pax5-KO-a-RUNX1-ChIP


title: 68_RNA_WT_Th1_rep1

description:
sample1_RNA1
lab data ID: 170504_0049/s01

value: 6 days in vitro culture


title: V1SSV2_24M_off3

source_name: Brain

tag: phenotype

value: DT Venus Dox 24 Months


title: ChIP-seq-FL-Pax5-KO-ChIP-Input-1


title: CPT.TUB_1

description: Conceptus tubular

value: Conceptus tubular


title: ChIP-seq-FL-WT-ChIP-Input-2

description:
Peaks-FL-WT-a-Pax5-vs-input
Peaks-FL-WT-a-RUNX1-vs-input

source_name: Wt FL


title: CPT.SPH_8

description: Conceptus spherical

source_name: Conceptus spherical

value: Conceptus spherical


title: ChIP-seq-FL-WT-a-Pax5-ChIP

description:
Peaks-FL-WT-a-Pax5-vs-input
Annotated-FL-WT-Pax5-15-norm-tag-Peaks

value: Wild type

value: Rabbit polyclonal anti-Pax5 [ab183575, Abcam]


title: ChIP-seq-FL-WT-a-RUNX1-ChIP

description:
Peaks-FL-WT-a-RUNX1-vs-input
Annotated-FL-WT-RUNX1-15-norm-tag-Peaks


title: ChIP-seq-FL-WT-ChIP-Input-1


title: CPT.SPH_7

description: Conceptus spherical


title: D16-1576_Old RF hi (AATGGT)

tag: age

value: Old

tag: treatment

value: Re-fed

value: Intestinal crypt cells

tag: cell subtype

value: Lgr5-GFP high intestinal stem cells (High)


title: ChIP-seq-FL-Pax5-KO-a-IKZF1-ChIP


title: ChIP-seq-FL-Wt-a-IKZF1-ChIP

description:
Peaks-FL-WT-a-IKZF1-vs-input
Annotated-FL-WT-IKZF1-10-norm-tag-Peaks


title: CPT.SPH_5

description: Conceptus spherical

tag: replicate


title: ChIP-seq-230-238-a-PAX5-ChIP

description:
Peaks-230-238-a-Pax5-vs-Input
Annotated-230-238-Pax5-15-norm-tag-peaks

tag: cell line background

value: Abelson transformed PreB cell-line

value: PreB

value: Cultured in RPMI1640 + UltraGlutamine +10percent FBS, 20mM HEPES, 50ug/ml Gentamicin and 50uM beta-ME.


title: ChIP-seq-230-238-a-RUNX1-ChIP

description:
Peaks-230-238-a-RUNX1-vs-Input
Annotated-230-238-RUNX1-15-norm-tag-peaks


title: ChIP-seq-230-238-ChIP-input-1


title: RNA-seq-FL-WT-TEL-AML-3

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-TEL-AML-3

value: ProB

value: Cultured in Optimem +10percent FBS, 25mM HEPES, 50microg/ml Gentamicin, 50microM beta-mercaptoethanol FL, KL, IL7 on OP9


title: CPT.SPH_3

description: Conceptus spherical