title: RTK17.1_RNAseq C819

city: Christchurch

first: Carlo

middle: Robert

last: Carere

address: University of Canterbury, Private Bag 4800,, Deliver to Carlo Carere, Link Building, room A311

department: Chemical and Process Engineering

country: New Zealand

institute: University of Canterbury

data_processing:
From this, an average of 7809886 raw untrimmed reads were obtained for each of the conditions sampled (Methanol exponential, Methanol Steady-state, Formate steady-state). These reads were then analyzed using the Artificial Intelligence RNA-Seq pipeline (Sequentia Biotech, Barcelona, Spain), as described elsewhere  , which were reduced following quality filtering and trimming. Retained paired-end reads (100 bp) were then mapped to the genome of Methylacidiphilum infernorum .
Differential gene expression profiles and accompanying statistical analysis was performed to investigate transcriptional regulation using edgeR (Robinson et al., 2009). Synonomous conditions (methanol exponential, methanol steady state) were grouped as replicates for differential gene expression analysis and compared to formate grown.
Genome_build: Methylacidiphilum infernorum strain V4 (GCA_000019665.1)
Supplementary_files_format_and_content: tab-delimited text files include values for each sample

organism: Candidatus Methylacidiphilum infernorum

source_name: Microbial biomass, chemostat (steady-state)

growth_protocol: Chemostat cultivation was performed to investigate growth of Methylacidiphilum sp. RTK17.1 cells on methanol and formate. For these experiments, cells were cultivated in a bioreactor with a working volume of 2 L (LABFORS 3; max volume 3.6 L) at pH 2.5, 45 °C and with continuous agitation at 450 rpm. A gas headspace composition of 2% O2, 2% CO2 (v/v; balance N2) was supplied continuously at 150 mL min-1 via mass flow control. Initially, cells were grown on methanol (10.2 mM) in a fed-batch mode; such that exhaustion of methanol (as determined spectrophotometrically via cessation of cell growth) prompted repeated dosing of additional methanol to a concentration of 10.2 mM. Once cell density exceeded OD600nm 0.5, the bioreactor was switched to chemostat operation for continuous growth experiments. During chemostat growth experiments, V4 mineral media was supplemented with either 12 mM methanol or 12 mM formate and supplied at a constant flow rate of 10.4 mL h-1 (D = 0.0052 h-1). After achieving a steady-state, cultures were monitored over a period of several days in order to determine biomass productivity data. During this time, biomass samples of Methylacidiphilum sp. RTK17.1 were harvested directly from the bioreactor for transcriptome sequencing and high performance liquid chromatography (HPLC) analysis. Steady state methanol and formate concentrations (from feed medium and bioreactor samples) were quantified using a Thermo UltiMate 3000 HPLC (Dionex) equipped with an Aminex HPX-87H column (300 x 7.8 mm) and refractive index and UV vis (wavelength = 210 nm) detectors. A 5 mM H2SO4 mobile phase was provided at a constant flowrate of 0.5 mL min-1. Resultant chromatogram profiles were integrated using tools embedded within the Chromeleon 7.2 SR5 software. Effluent biomass (500 mL) was collected over this period for cell dry weight determinations. For this analysis, cell pellets were collected by centrifugation (10,000 rpm, 10 min, 25C; Eppendorf Centrifuge 5810 R) and then dried to constant weight using Labconco FreeZone 2.5 freeze dryer.

extract_protocol:
Total RNA was extracted using the Mo Bio PowerBiofilm RNA Isolation kit following the manufacturers recommended protocol, eluted into 100 ml ddH2O and quantified using the Qubit HS assay kit (Thermo Fisher Scientific). Following this, 2mg RNA was transferred into RNAstable preservation medium (Sigma Aldrich) and dehydrated at room temperature before transport for transcriptome sequencing (Custom Science; China). Upon receipt of samples, RNA integrity was confirmed using an Agilent 2100 Bioanalyser. Following total RNA extraction, ribosomal RNAs were removed using the Ribo-Zero rRNA removal kit (bacteria) and the quality of the remaining RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent). Library construction was performed using the TruSeq Stranded Total RNA Sample Prep (microbe) Kit (Illumina) and sequencing was performed using an Illumina HiSeq2500 platform.
Ribo-Zero User Guide, TruSeq Stranded Total RNA prep

treatment_protocol: Samples for transcriptome sequencing were harvested (10 ml) from exponential (methanol) and steady-state (methanol, formate) phases of chemostat experiments. Methylacidiphilum sp. RTK17.1 cells were pelleted by centrifugation at 5,000 x g (15 min, 4 °C), suspended in 300 ml RNAlater Stabilisation solution (ThermoFisher Scientific) and then stored at -20 °C until required for further analysis (as per the manufacturer’s recommended protocols).

tag: oxygen

tag: nitrogen

value: N-sufficient (NH4+)

tag: carbon source

value: Formate


title: RTK17.1_RNAseq C818

status: Public on Oct 31 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

value: Methanol


title: Vein_T1_Drought_3

city: pasco

first: aaron

last: ogden

state: wa

address: 902 battelle boulevard

department: integrative omics

country: USA

institute: Pacific Northwest National Lab

data_processing:
Quality control, FastQC v0.11.5
Alignment, HISAT2 v2.1.0
Transcript Assembly, StringTie v1.3.3b
Normalization, DESeq2 v1.20.0
Differential Expression, DESeq2 v1.20.0
Genome_build: Solanum lycopersicum (SL3.0)
Supplementary_files_format_and_content: DESeq2 normalized gene count estimate and DESeq2 differential expression matrix for VT1D vs VT1W and IVT1D vs IVT1W, file named Gene_count_matrix.xlsx

organism: Solanum lycopersicum

source_name: Vein Enriched Tomato Leaf section

growth_protocol: Tomato (Solanum lycopersicum) plants were grown and subjected to drought as described in Ogden et al. 20203. Briefly, plants were grown in 4 inch pots containing 300 g soil within a Percival growth chamber under ~400 PAR light at 16/8 hours light/dark cycle. Plants were selected at random and subjected to drought stress by withholding watering for 6 days, at which point timepoint 1 (T1) samples were collected. Timepoint 2 (T2) leaves were collected 3 days after a return to normal watering. In all cases, the 4th true leaf was excised and dissected to enrich for vasculature and non-vasculature tissue (Figure 1A). Vein and inter-vein tissues were immediately flash frozen in liquid nitrogen and stored at -80° C until protein and RNA extraction.

extract_protocol:
Rneasy Plant Mini Kit, Qiagen Cat#74904, according to manufacturers instructions.
The libraries were made by the Penn State Genomics Core Facility at University Park using the Illumina TruSeq Stranded mRNA kit following the manufacturer's protocol (Illumina Inc.). Library concentration was determined by qPCR using the KAPA Library Quantification Kit Illumina platforms (KAPABiosystems) and used to make an equimolar pool of the libraries. The library pool was sequenced on two NextSeq High Output 75 nt single read sequencing runs."

treatment_protocol: At 25 days post sowing (DPS), timepoint 0 (T0) was collected, and 6 biological replicates of plants selected at random were subjected to drought stress by withholding water for an additional 4 days, while 6 control plants continued to receive 150 mL H2O every other day. After skipping 3 alternate day waterings (totaling 6 days since the last watering), vein and intervein tissue was captured from half of the drought-stressed plants, and half of the control plants at 29 DPS as the initial comparative drought condition, constituting Timepoint 1 (T1, i.e. T1D vs T1W, 3 plants each, 2 tissues). Drought-recovered plants were watered 150 mL H2O on 29 and 30 DPS after which both vein and intervein tissues were collected, and the same was also done for plants that constantly received water throughout the experiment (T2, i.e. T2D vs T2W, 3 plants each, 2 tissues).

tag: tissue

value: Vein

tag: stress

value: drought

tag: timepoint


title: D5_pos

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalization with BeadStudio software

label: biotin

organism: Homo sapiens

source_name: Activated Treg isolated from PBMC of healty donor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted with Agencourt RNA advance cell V2 system (Beckman Coulte). Quality control was performed with Agilent Bioanalyser.

tag: donor

tag: lag-3 (positive or negative)

value: positive


title: ASC1_3

city: South San Francisco

first: Rebecca

middle: Y

last: Wang

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Science LLC

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ASC1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

data_processing:
RNAseq: Samples were demultiplexed using bcl2fastq, then fastq files were processed using Salmon and aligned using STAR
BARseq: Samples were demultiplexed using Barcas
Whole Genome Sequencing: Samples were demultiplexed using bcl2fastq and then BowTie2 was used to align the samples
Genome_build: SacCer3
Supplementary_files_format_and_content: 20190909_rawTPMtable.csv: csv file with raw TPMs from RNAseq
Supplementary_files_format_and_content: zev_wgs_processeddata.csv: csv file with sequencing information, rDNA coverage, copy number and gc content
Supplementary_files_format_and_content: ZEV_TOF_all_merge.txt: text file with normalized BARseq results (normalized to wild type, time 0, and read depth)

organism: Saccharomyces cerevisiae

growth_protocol: All BARseq, WGS, and RNAseq samples were grown using glutamate as a nitrogen source

extract_protocol:
BARSeq: pooled cultures were propagated at low density (OD < 0.05) and > 2 x 106 cells were collected at each time point. Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research) and 5 ng of DNA were used to PCR amplify the uptag barcode region with custom primers
Whole Genome Sequencing: Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research)
RNAseq:  cells were frozen in lysis mastermix, then reverse transcription was done to obtain cDNA, which was then amplified and cleaned up with RNAClean Ampure XP beads
Libraries were constructed using the Nextera DNA Flex kit (Whole Genome Sequencing) and Nextera XT kit (RNAseq)

tag: background strain

tag: time point

tag: media

value: SC+ClonNAT+estradiol

tag: genotype

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ASC1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: N702_SL236980

city: Charlottesville

first: Maria

middle: Florencia

last: Martinez

address: 409 Lane Rd. Rm 2006

institute: University of Virginia

library_source: genomic

data_processing:
Peaks identified using the MACS2 peak caller with a q value threshold of 0.01, were merged with DiffBind. Coverage values were calculated using bedtools multicov. In short, the coverage values were normalized using the estimate SizeFactors function from the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: wig files

molecule: genomic DNA

organism: Mus musculus

source_name: As4.1 cells

growth_protocol: The renin-expressing As4.1 cell line, harboring a Ren-2 5′-flanking sequence/SV40 T antigen hybrid transgene, was cultured in high glucose DMEM (Gibco #11965-092), 10% FBS at 37C in a humidified incubator containing 5% of CO2

extract_protocol:
Native Renin cells were isolated from the kidney cortex of adult animals using FACS sorting, utilizing our Ren1c-YFP reporter mice. Ren1c-YFP and Ren1c-/-; Ren1c-YFP mice were anesthetized with tribromoethanol and the kidneys were excised, decapsulated, demedullated. The kidney cortices from each animal were dissected and minced to a smooth consistency, and transferred into a 15 ml Falcon tube with 5 ml of enzymatic solution [0.3% collagenase A (Roche, Indianapolis, IN), 0.25% trypsin (Sigma- Aldrich, St. Louis, MO), and 0.0021% DNase I (Roche Applied Science)]. The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37℃. Then, the solution was pipetted up/down ten times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected with a plastic pipette and transferred to a fresh 15 ml tube on ice. The supernatants collected from the three digestions round were pooled and centrifuged in a Sorvall RT 6000 Refrigerated Centrifuge at 1,200 g for 4 minutes at 4°C. The cell pellet was resuspended with 25 ml of fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352360) and washed with an additional 3–5 ml of buffer 1. The flow-through was poured through a sterile 40 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352340) and washed with 3–5 ml of buffer 1. The flow-through was centrifuged at 1,200 g for 4 min at 4°C. After the centrifugation, the cell pellet was resuspended in 1ml of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Roche Applied Science)] and analyzed using a fluorescent-activated cell sorter (Influx Cell Sorter).
We collected 50,000 cells for As4.1 and from chronically recruited mice, and 17,000 juxtaglomerular cells and cells from acutely recruited mice. Cells were washed with PBS and treated with Lysis Buffer. Then, cells were re-suspended in a transposition reaction mix (Illumina, cat # FC-121-1030) followed by DNA purification, before PCR amplification with 12-16 cycles with barcode primers (Illumina, cat # FC-121-1011). PCR products were purified with AmpureXP beads (Beckman Coulter, cat # A63881)

tag: cell line

value: As4.1 Tumoral cell


title: Vein_T1_Drought_2


title: RTK17.1_RNAseq C817


title: Vein_T1_Drought_1


title: AS4-1


title: D1_pos


title: D4_neg

value: negative


title: ASC1_2


title: D4_pos


title: 8_RA4

city: Geneva

first: Laurent

last: Brodier

state: Geneva

address: 30 Quai Ernest-Ansermet

department: Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Mapping raw reads to reference genome was performed using STAR aligner v.2.5.3a to the UCSC Gallus gallus Galgal5 reference.
The table of counts with the number of reads mapping to each gene feature of the UCSC Gallus gallus Galgal5 reference was prepared with HTSeq v0.6p1.
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v.3.18.1. Briefly, the counts were normalized according to the library size and filtered. The genes having a count above 1 count per million reads (cpm) in at least 3 samples were kept for the analysis.
The differentially expressed genes tests were done with paired data GLM (general linearized model) using a negative binomial distribution.
Genome_build: UCSC Gallus gallus Galgal5
Supplementary_files_format_and_content: Processed data files are in .csv format and contain raw counts and normalized counts for each sample.

organism: Gallus gallus

source_name: Hes5.3+ cells from E5 retina

growth_protocol: Chicken eggs were kept at 37°C in an incubator. Retinas were removed and cultured in 800 μl of culture medium (DMEM, 10% FBS, 1% penicillin/streptomycin) containing either 2.5 μM RA or DMSO, and placed in a 37°C incubter with 5% CO2 for 8 hours.

extract_protocol:
RNA from FACS sorted cells was extracted using TRIzol reagent according to manufacturer's protocol. The SMARTer™ Ultra Low RNA kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 1 ng of total RNA as input.
200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled and loaded at 2 nM for clustering on a Single-read Illumina Flow cell. Reads of 100 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

treatment_protocol: Retinas were removed and incubated for 8h in culture medium (DMEM, 10% FBS, 1% penicillin/streptomycin) containing 2.5 μM RA or DMSO. Retineas were dissociated with Trypsin 0.05% for 20 minutes, and Hes5.3+ cells were sorted by FACS.

tag: treatment

value: 2.5 microM Retinoic Acid

tag: total rna ng

tag: nb of cells


title: Intervein_T0_Watered_3

source_name: Intervein Enriched Tomato Leaf section

value: Intervein

value: watered


title: D1_neg


title: D2_neg


title: D3_neg


title: D2_pos


title: ASC1_1


title: 7_CT4

value: DMSO


title: N703_SL273947

source_name: renin cells

tag: strain


title: 6_RA3


title: ARO1_8

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 5_CT3


title: Intervein_T0_Watered_1


title: ARO1_9


title: Intervein_T0_Watered_2


title: N702_SL273946


title: 2_RA1


title: Vein_T0_Watered_3


title: ARO1_7


title: Vein_T0_Watered_2


title: siRev-erb-β + Dex rep 3

city: New York

first: Ivana

last: Grbesa

address: 413 E 69th St

department: Urology

institute: Weill Cornell Medicine

data_processing:
Reads were aligned to the mouse genome using STAR, and were counted on genes using HTseq
Enrichment analysis between each combination was done using edgeR that assigns to each gene a FDR value and calculates the logFC between the two conditions. Genes with FDR <0.05 and logFC greater than |0.5| were considered differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each sample

molecule: polyA RNA

source_name: 3134 cells

growth_protocol: 3134 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Biological Industries) supplemented with 10% fetal bovine serum (FBS, Biological Industries), 2 mM L-glutamine, 0.5 mg/mL penicillin-streptomycin and 1 mM sodium pyruvate (Biological Industries) in a humidified 37°C incubator with 5% CO2.

extract_protocol:
RNA was extracted and on-column treated with DNase I with Quick-RNA Mini Prep kit (Zymo).
Messenger RNA (mRNA) was enriched from 1 μg of total RNA by Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. cDNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocol

treatment_protocol: Before treatment (EtOH or 100 nM Dexamethasone for 1 h, Sigma), cells were cultured in media containing 10% charcoal-stripped serum (CSS) (Sigma, USA).

tag: cell type

value: epithelial

value: breast adenocarcinoma

value: RIII


title: ASC1_10


title: Vein_T0_Watered_1


title: ARO1_6


title: siRev-erb-β + Dex rep 2


title: 1_CT1


title: siRev-erb-β + Dex rep 1


title: Normal-conditioned_4

city: Merelbeke

first: Osvaldo

last: Bogado Pascottini

state: Flanders

address: Salisburylaan 133

country: Belgium

institute: Ghent University

description:
9-A8-O_S43_R1_001
CountTable.csv

data_processing:
Concentration and quality of the extracted RNA was double-checked by using the 'Quant-it ribogreen RNA assay' (Life Technologies, Grand Island, NY, USA) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, USA), respectively. The RIN value was between 5.2 and 7.8 for all samples. Subsequently, 500 ng of RNA was used to perform an Illumina sequencing library preparation employing the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to the manufacturer’s protocol using 14 enrichment PCR cycles. Libraries were quantified by qPCR, according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A high sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US) was used to control the library’s size distribution and quality. Libraries were equimolarly pooled and sequenced on an Illumina Nextseq 500 flow cell, generating 75 bp single-end reads.
Per sample, on average 8.5 x 106 ± 1.2 x 106 reads were generated. First, these reads were trimmed using cutadapt (Martin, 2011) version 1.18 to remove the “QuantSEQ FWD” adaptor sequence and bases not passing the phred score threshold of 20, and at the same time removing reads containing ambiguities, and removing reads shorter than 15 after trimming. For all samples, the reads were mapped on the Bos Taurus ARS-UCD1.2 genome (bosTau9) using the splice-aware STAR (v2.6.0c) mapper. Features were counted at the gene and transcript isoform level as defined by the Bos_taurus.ARS-UCD1.2.99 Gene transfer format file (GTF) using rsem_calc_expression (RSEM v1.3.1; Li and Dewey, 2011). Both the genome and the annotated data were downloaded from Ensembl.

organism: Bos taurus

source_name: Liver

extract_protocol:
Frozen-thawed liver samples (20 mg) were finely chopped with scalpel blades (RNA away sprayed) and homogenized in 1 mL of Purezol (Qiagen, Antwerp, Belgium). Total RNA was isolated using the Aurum Total RNA Mini Kit (BioRad Laboratories Inc., Hercules, CA) according to the manufacturer’s instructions. After RNA isolation, a DNase treatment with 6 μL of RQ1 RNase-Free DNase (1 U/μL, Promega, Leiden, the Netherlands) and 3 μL of RQ1 DNase 10x Reaction Buffer (Promega) was performed for 15 min at room temperature. Then, RNA was purified by spin-column centrifugation (purification step: 2 times for 7 min at 16,100 × g at 20°C, concentration step: 1 time for 3 min at 1,000 × g at 20°C; Amicon Ultra-0.5 centrifugal filters, Merck Millipore, Billerica, MA). Quantity and purity of RNA were evaluated with the Nanodrop ND-1000 spectrophotometer (Nanodrop Products, Thermo Fisher Scientific, Wilmington, DE). Additionally, RNA integrity was verified by visualization of the ribosomal bands on a 2% agarose gel. Genomic DNA contamination was verified by a minus reverse transcriptase control PCR with LRP10 primers. All RNA samples had a purity between 1.91 and 2.16 (optical density 260/280 ratio), clear ribosomal RNA bands on gel, and were free of genomic DNA.
Total RNA was prepared and sent to NXTGNT. The sequencing library was constructed using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen and was sequenced as SE75 on an Illumina Nextseq 500

tag: breed

value: Holstein cow

value: Collected 2 weeks before expected calving

tag: condition

value: normal


title: Normal-conditioned_5

description:
10-B8-O_S15_R1_001
CountTable.csv


title: ARO1_4


title: siRev-erb-β rep 3

tag: tissue


title: Normal-conditioned_3

description:
8-H7-O_S16_R1_001
CountTable.csv


title: ARO1_5


title: N703_SL236979

value: Ren1c-/-; Ren1c-YFP


title: ARO1_3


title: ARO1_2


title: Normal-conditioned_2

description:
7-G7-O_S46_R1_001
CountTable.csv


title: siRev-erb-β rep 2


title: ARO1_1


title: Normal-conditioned_1

description:
5-E7-O_S22_R1_001
CountTable.csv


title: ARO1_10


title: siROR-β+γ + Dex rep 2


title: siROR-β+γ + Dex rep 3


title: siRev-erb-β rep 1


title: Over-conditioned_5

description:
6-F7-O_S28_R1_001
CountTable.csv

value: over-conditioned


title: ANY1_9

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ANY1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: SC+ClonNAT+estradiol

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ANY1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: siROR-β+γ + Dex rep 1


title: MDA mixed

city: San Diego

first: Stephanie

middle: I

last: Fraley

address: 9500 Gilman Drive MC 0412

institute: UCSD

data_processing:
Count matrix for each sample was generated using cellRanger (10x Genomics)
Depth normalization was performed using cellRanger (10x Genomics)
Differential gene expression analysis was performed using Seurat (Stuart et al., 2019)
Genome_build: hg38, mm10
Supplementary_files_format_and_content: RDS files contain Seurat objects with raw and processed counts for each sample

extract_protocol:
Cells were collected using flow cytometry (FACS), and the Chromium Single Cell 3’ v3 kit (10x genomics, Pleasanton, CA) was used to extract the RNA
Chromium Single Cell 3’ v3 kit (10x genomics, Pleasanton, CA) was used for library construction

tag: phenotypic supervision status

value: no

tag: phenotype

value: mixed


title: Over-conditioned_4

description:
4-D7-O_S27_R1_001
CountTable.csv


title: ANY1_8


title: Over-conditioned_3

description:
3-C7-O_S17_R1_001
CountTable.csv


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 4 Technical Replicate B

city: Boulder

first: Dylan

last: Taatjes

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

description:
steady-state RNA (RNA-seq) from HL60 cells
OldSY351_4_S96.rcc.tdf

data_processing:
The Dowell group performed metagene and termination defect analysis data using their RNA-seq processing pipeline
The Bentley group performed splicing analysis using Star mapper v2.5.2a to map reads and MAJIQ v1.1.3a to perform splicing analysis on highly correlated mapped reads
Genome_build: GRCh38
Supplementary_files_format_and_content: Genome track and DESeq2 counts tables for metagene and termination defect analysis
Supplementary_files_format_and_content: MAJIQ output LSV file for splicing analysis

source_name: wild type HL60 cells

growth_protocol: HL60 cells were grown in Iscove's culter medium with 20% fetal bovine serum added at 37C in 5% CO2

extract_protocol:
RNA was TRIzol exracted and polyA enriched
Libraries were constructed with the Illumina TruSeq RNA Library Prep kit

treatment_protocol: HL60 cells were treated with 50nM SY-351 or DMSO for 5 hours

value: wild type HL60 cells

value: Acute promyelocytic leukemia cells

value: SY351 CDK7 Inhibition


title: siROR-β+γ rep 3


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 4 Technical Replicate A


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 3 Technical Replicate B

description:
steady-state RNA (RNA-seq) from HL60 cells
OldSY351_3_S95.rcc.tdf


title: Over-conditioned_1

description:
1-A7-O_S35_R1_001
CountTable.csv


title: siROR-β+γ rep 2


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 3 Technical Replicate A


title: ANY1_6


title: siROR-β+γ rep 1


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 2 Technical Replicate B

description:
steady-state RNA (RNA-seq) from HL60 cells
OldSY351_2_S94.rcc.tdf


title: siKlf4 + Dex rep 3


title: ANY1_5


title: ANY1_4


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 2 Technical Replicate A


title: siKlf4 + Dex rep 2


title: ANY1_3


title: E. coli MG1655 Culture C Replicate 3

city: Leipzig

first: Jens

middle: Olaf

last: Kroemer

address: Permoserstr. 15

department: Solar Materials

country: Germany

institute: Helmholtz-Zentrum für Umweltforschung GmbH - UFZ

description:
C-3
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_CvsWT.csv

data_processing:
Sequencing data was demultiplexed using Illumina bcl2fastq 2.17.1.14.
Adapters were clipped from the reads and rRNA was filtered using RiboPicker 0.4.3.
Sequences were aligned using STAR 2.4 and rRNA or tRNA reads were filtered. TopHat-aligned reads were counted using htseq-count.
Differential expression was determined using edgeR 3.2.3, DESeq 1.12.0 and cuffdiff 2.1.1.
Raw p-values from statistical test were adjusted for multiple testing by the Benjamini-Hochberg false discovery rate method.
Genome_build: NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome
Supplementary_files_format_and_content: Semicolon-separated files with gene locus transcribed_length Read_count_replicates edgeR_log2FC edgeR_p-value edgeR_FDR edgeR_DE_call DESeq_log2FC DESeq_p-value DESeq_FDR DESeq_DE_call cuffdiff_count_mean_6_G1 cuffdiff_count_mean_6_G2 cuffdiff_FPKM_6_G1 cuffdiff_FPKM_6_G2 cuffdiff_log2FC cuffdiff_p-value cuffdiff_FDR cuffdiff_DE_call

source_name: Isoprenol Adaptation

growth_protocol: Cells were grown in biological triplicates with 50 mM isoprenol until an OD of 1.0 in 25 mL M9 medium with 5 g/L glucose at 37°C and 200 rpm in baffled sealed flasks.

extract_protocol:
10 mL of cell-culture was vacuum filtered using a Supor ® 800 Grid filter (Pall, NY, USA) with 0.8 µM pore size. The filter containing the cells was put in a 15 mL falcon tube containing 700 µL PGTX solution and immediately frozen in liquid nitrogen. The samples were stored at -80°C until further processing.
RNA quality was determined using Bioanalyzer (Agilent, CA, USA). Ribo-Zero rRNA Removal Kit for Bacteria (Illumina, CA, USA) was used to deplete rRNA. First strand cDNA synthesis and second strand synthesis was carried out using NEBNext RNA First Stand and Second Strand Synthesis Module (New England Biolabs, MA, USA). cDNA was then purified and concentrated using MiniElute Columns (Qiagen, Netherlands) and the Encore Rapid DR Multiplex system (Tecan, Switzerland) was used for library preparation. Libraries were amplified for 12 cycles using MyTaq (Bioline, UK) and standard Illumina primers. Size selection was done using a preparative Agarose Gel selecting fragments between 300 and 500 bp and quality control of libraries was performed with Bioanalyzer and Qubit.

tag: genotype/phenotype

value: Isoprenol adapted


title: E. coli MG1655 Culture C Replicate 2

description:
C-2
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_CvsWT.csv

organism: Escherichia coli str. K-12 substr. MG1655


title: E. coli MG1655 Culture C Replicate 1

description:
C-1
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_CvsWT.csv


title: siKlf4 + Dex rep 1


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 1 Technical Replicate B

description:
steady-state RNA (RNA-seq) from HL60 cells
OldSY351_1_S93.rcc.tdf


title: E. coli MG1655 Culture B Replicate 3

description:
B-3
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_BvsWT.csv


title: siKlf4 rep 3


title: ANY1_7


title: Over-conditioned_2

description:
2-B7-O_S4_R1_001
CountTable.csv


title: ANY1_2


title: E. coli MG1655 Culture B Replicate 2

description:
B-2
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_BvsWT.csv


title: ANY1_1


title: wild-type HL60, SY351 CDK7 inhibition, Replicate 1 Technical Replicate A


title: wild-type HL60 Replicate 4 Technical Replicate B

description:
steady-state RNA (RNA-seq) from HL60 cells
OldDMSO_4_S100.rcc.tdf

value: DMSO control


title: E. coli MG1655 Culture B Replicate 1

description:
B-1
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_BvsWT.csv


title: siKlf4 rep 2

value: epithelial


title: E. coli MG1655 Culture A Replicate 3

description:
A-3
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_AvsWT.csv


title: siNeg.C. + Dex rep 4

value: breast adenocarcinoma


title: wild-type HL60 Replicate 4 Technical Replicate A


title: Thymus GEN3

city: nanjing

first: zengpeng

last: lv

address: weigang

country: China

institute: nanjing agricultural 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 Gallus_gallus.GRCg6a.96  whole genome using featureCounts v1.5.0-p3
Expected number of Fragments Per Kilo base of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Gallus_gallus.GRCg6a.96
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Thymus

extract_protocol:
Thymus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ROSS 308

value: Thymus

tag: age

value: post natal day 21

value: lipopolysaccharide+genistein treated


title: ANY1_10

tag: background strain


title: siKlf4 rep 1

value: RIII


title: Thymus GEN2


title: wild-type HL60 Replicate 3 Technical Replicate B

description:
steady-state RNA (RNA-seq) from HL60 cells
OldDMSO_3_S99.rcc.tdf


title: siNeg.C. + Dex rep 3


title: wild-type HL60 Replicate 3 Technical Replicate A


title: wild-type HL60 Replicate 2 Technical Replicate B

description:
steady-state RNA (RNA-seq) from HL60 cells
OldDMSO_2_S98.rcc.tdf


title: Thymus GEN1


title: Thymus LPS3

value: lipopolysaccharide-treated


title: E. coli MG1655 WT Replicate 3

description:
WT-3
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_AvsWT.csv
All_genes_edgeR-DESeq-cuffdiff_BvsWT.csv
All_genes_edgeR-DESeq-cuffdiff_CvsWT.csv

source_name: Strain collection CGSC6300

value: Wild-type


title: siNeg.C. + Dex rep 2


title: E. coli MG1655 Culture A Replicate 1

description:
A-1
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_AvsWT.csv


title: wild-type HL60 Replicate 2 Technical Replicate A


title: E. coli MG1655 WT Replicate 2

description:
WT-2
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_AvsWT.csv
All_genes_edgeR-DESeq-cuffdiff_BvsWT.csv
All_genes_edgeR-DESeq-cuffdiff_CvsWT.csv


title: E. coli MG1655 WT Replicate 1

description:
WT-1
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_AvsWT.csv
All_genes_edgeR-DESeq-cuffdiff_BvsWT.csv
All_genes_edgeR-DESeq-cuffdiff_CvsWT.csv


title: Thymus LPS1


title: Thymus LPS2


title: siNeg.C. rep 4


title: wild-type HL60 Replicate 1 Technical Replicate A

description:
steady-state RNA (RNA-seq) from HL60 cells
OldDMSO_1_S97.rcc.tdf


title: Thymus CON3

value: basic diet-treated


title: E. coli MG1655 Culture A Replicate 2

description:
A-2
Escherichia coli MG1655
All_genes_edgeR-DESeq-cuffdiff_AvsWT.csv


title: Thymus CON1


title: SUP (B-ALL/Niche/B-ALL-Niche)

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
SUP-B15 alone control/Niche alone control/SUP-B15 bone marrow niche model
processed data file: counts.raw.csv.gz
processed data file: counts.normalized.csv.gz

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software.
Hashtag oligo (HTO) counts were quantified using CITE-seq-count.
HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells and demultiplexed using the HTODemux function in Seurat.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content:
Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.
barcodes.tsv.gz: raw barcodes
features.tsv.gz: raw genes
*.matrix.mtx.gz: raw gene-barcode matrix
*.dense_umis.tsv.gz: hashtag count matrix
counts.raw.csv.gz: combined raw counts matrix
counts.normalized.csv.gz: combined normalized counts matrix

source_name: ex vivo human bone marrow niche models

growth_protocol: The leukemia BM niche samples (designated as B-ALL-Niche) were prepared in parallel with control groups of leukemia culture alone (designated as B-ALL alone) and niche cells (HUVEC, hMSCs, and hFOB)culture without leukemia (designated as Niche alone). The microfluidic devices were cultured for 7 days in the media of a mixture (2:1:1:1) of HUVEC medium (EGMTM-2, Lonza), hMSCs medium (MSCGMTM, Lonza), hFOB medium (DMEM/F12) and Human B-ALL cell medium (RPMI1640 or IMDM, GIBCO).

extract_protocol:
The leukemia BM niche samples (designated as B-ALL-Niche) were prepared in parallel with control groups of leukemia culture alone (designated as B-ALL alone) and niche cells (HUVEC, hMSCs, and hFOB) culture without leukemia (designated as Niche alone). The prepared leukemia models were cultured for 7 days in the media of a mixture (2:1:1:1) of HUVEC medium (EGMTM-2, Lonza), hMSCs medium (MSCGMTM, Lonza), hFOB medium (DMEM/F12) and Human B-ALL cell medium (RPMI1640 or IMDM, GIBCO). Single-cell suspensions of B-ALL samples were prepared by treating the ex vivo BM niche model devices with nattokinase (50 Fu/ml) for 45 min at 37 °C to release cells from the fibrin hydrogel, followed by centrifuging at 400×g at 4°C for 5 min. The cell pellets were re-suspended in PBS with 2% FCS and Human TruStain FcX Blocking Solution (BioLegend) and incubated on ice for 10 min. Cell suspensions were centrifuged at 400×g at 4°C for 5 min, and supernatant discarded. For cell hashing 6, cells retrieved from groups of B-ALL alone, Niche alone, and B-ALL-Niche were respectively labelled with three hashtag antibodies (TotalSeqTM, BioLegend), according to manufacturer’s instructions. The mixed into two samples, REH and SUP samples.
Single Cell 3’ Reagent Kits: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000075; Single Cell 3’ Chip Kit v3 PN-1000073 and i7 Multiplex Kit PN-120262 (10x Genomics). Samples were tagged with cell hashing oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions.

tag: experimental groups

value: B-ALL alone/Niche alone/B-ALL-Niche

tag: source

value: primary and immortal cell lines

value: SUP-B15/HUVEC, Osteoblast, hMSCs/SUP-B15, HUVEC, Osteoblast, hMSCs

tag: source institute

value: SUP-B15 (ATCC,CRL-1929)/HUVEC (Lonza, C2519A), hMSC (Lonza, PT2501), hFOB 1.19 (ATCC, CRL-11372)/SUP-B15 (ATCC,CRL-1929), HUVEC (Lonza, C2519A), hMSC (Lonza, PT2501), hFOB 1.19 (ATCC, CRL-11372)


title: REH (B-ALL/Niche/B-ALL-Niche)

description:
REH alone control/Niche alone control/REH bone marrow niche model
processed data file: counts.raw.csv.gz
processed data file: counts.normalized.csv.gz

value: REH/HUVEC, Osteoblast, hMSCs/REH, HUVEC, Osteoblast, hMSCs

value: REH (ATCC, CRL-8286)/HUVEC (Lonza, C2519A), hMSC (Lonza, PT2501),hFOB 1.19 (ATCC, CRL-11372)/REH (ATCC, CRL-8286), HUVEC (Lonza, C2519A), hMSC (Lonza, PT2501),hFOB 1.19 (ATCC, CRL-11372)


title: siNeg.C. + Dex rep 1

tag: cell line


title: wild-type HL60 Replicate 1 Technical Replicate B

value: wild type HL60 cells

value: Acute promyelocytic leukemia cells

tag: treatment

value: DMSO control


title: Seabass_PostStress_T4_R10

status: Public on Oct 30 2020

city: Montpellier

first: Selim

last: Ben Chehida

address: 1093-1317 Route de Mende

country: France

institute: Institut des Sciences de l'Evolution de Montpellier

data_processing:
Raw sequencing data were trimmed of low quality reads and adapter residues using Trim Galore!. The trimmed reads were then demultiplexed with STACKS.The option disable_rad_check was applied to avoid reads with bisulfite-modified restriction sites to be discarded. The demultiplexed reads were trimmed a second time on both 5’ and 3’ ends with the options --clip_R1 --clip_R2 and --three_prime_clip_R1 --three_prime_clip_R2 to remove introduced methylated cytosines during adapter ligation.
Using the bismark_genome_preparation function of the program bismark (Krieger and Andrews 2011, Bioinformatics, doi: 10.1093/bioinformatics/btr167), a bisulfite converted version of the European sea bass genome was prepared against which the demultiplexed and trimmed reads were mapped
The R package MethylKit was used to determine differential methylation between pre- and post-stress fish. Coverage was normalized across samples. Using Methylkit, differentially methylated CpG sites were determined between pre- and post-stress individuals using logistic regression (30X read depth; nominal q-value: 0.001; 15% methylation threshold)
Genome_build: GCA_000689215.1
Supplementary_files_format_and_content: Fastq files containing demultiplexed and one round trimmed reads
Supplementary_files_format_and_content: Txt files providing chromosomes, posotions, strand, percentages cytosine and thymine for each methylated sites

organism: Dicentrarchus labrax

source_name: blood red cells

growth_protocol: 20 sea bass families were reared separately in open circulation tanks at Nireus S.A. research facilities (Greece). Fish were tagged at ~280 days post-hatch and distributed in 20 tanks; each tank receiving 1 fish from each family (i.e., 20 fish per tank). Throughout the experimental period, the photoperiod was set at 12L:12D, the water temperature and the salinity held constant (18.1 ± 0.2°C and 28 ppt, respectively). Fish were submitted to one acute challenge test per month for three consecutive months, from July to October 2018.

extract_protocol:
Blood from the caudal vessel was collected. Plasma and red blood celles were separated by centrifugation at 2,000g for 10 min. Careful separation of the plasma and RBCs was performed using 200 µl pipettes. RBC extracts were heparinized (heparin sodium; Sigma-Aldrich), transferred in microtubes and conserved at -20°C in 1 ml of RNA later. Genomic DNA was extracted using the Macherey Nagel Nucleo Spin Tissue DNA kit and quantified using a Qubit fluorometer (Qubit dsDNA BR Assay Kit, Q32853, Invitrogen).
EpiGBS approach adapted from van Gurp et al. (2016, Nature Methods doi: 10.1038/nmeth.3763), with main addition of a second restriction enzyme in the protocol. The couple of enzymes retained: MspI/ SfbI. A single libray was prepared: 200 ng of DNA of each sample were digested in a 40 µl reaction, using 0.25 µl MspI (NEB, 20,000 U/ml R0106S), 0.25 µl SbfI-HiFi (NEB 20,000 U/ml R3642L) and 4 µl of 10X cutsmart buffer. The reaction was run overnight at 37°C. Unique forward and reverse adapter combinations allow multiplexing samples in the library. We added forward and reverse adapters in unique combinations (1 µl of adapter, 2.5 µM), 0.5 µl T4 Ligase (NEB, 400,000 U/ml m0202L), 6 µl of 10X T4 ligase buffer and 11.5µl water were added directly to the digested DNA. Adapters were ligated for 3 h at 23°C followed by 10 min of enzyme inactivation at 65°C. After ligation, all samples were pooled and one third of the total volume was used in the following step. The mixture volume was reduced using a Qiaquick PCR purification kit (28104 Qiagen). The resulting product was cleaned a second time to ensure the removal of small fragments and adapter remnants using CleanPCR paramagnetic beads (Proteigene, CPCR-0050) with a ratio of 0.8X [sample : beads]. a nick translation was performed to repair the nick of the DNA at the restriction site and to fully methylate the hemi-methylated adapters. To do so, 19.25 µl of the concentrated and purified ligation pool were used in a 25 µl reaction, including 0.75 µl DNA Polymerase I (E. coli, 10,000 U/ml M0209S), 2.5 µl of 10 mM 5-Methylcytosine dNTP mix (Zymo Research, D1030), and incubated at 15 °C for one hour. The library was then treated with sodium bisulfite using the EZ DNA Methylation Gold Kit (D5005, Zymo Research) following manufacturer instructions to convert unmethylated cytosines to uracil, paying attention to the optimal DNA amount per reaction. After bisulfite conversion, 14 cycles of PCR (95°C for 1 min, 91°C for 10s, 65°C for 15s, 72°C for 10s and a final elongation step at 72°C for 5 min) were performed, followed by a paramagnetic bead clean up with a 0.8X ratio. The library quality was verified on an Agilent 5300 Fragment Analyzer (Santa Clara, USA). It was sequenced (paired-end, 150 bp) on one lane of a SP flow cell on an ILLUMINA NovaSeq 6000.

treatment_protocol: Fish were exposed to high density stress by lowering water levels in the tank to 1/3 of the original volume, followed by chasing of the fish with a net for five minutes and a 30 min waiting period before sampling. This protocol took place in each tank then for each fish individual entering the experiment. It was repeated for 3 consecutive times at 20-21 day intervals (period long enough for fish to recover). An initial blood sampling occurred two weeks prior to the implementation of the stress challenge (T0 label, July 19th, 2018, pre-stress/control group) then at the end of the challenge test (T4 label, October 5th, 2018).

tag: developmental stage

value: juvenile

value: 9 months

value: post-stress

tag: family

value: R


title: siNeg.C. rep 3

value: epithelial

value: breast adenocarcinoma

tag: strain

value: RIII


title: Seabass_PostStress_T4_R11


title: Seabass_PostStress_T4_P11

value: P


title: Seabass_PostStress_T4_R15


title: Seabass_PostStress_T4_P9


title: Seabass_PostStress_T4_D18

value: D


title: Seabass_PostStress_T4_R8


title: siNeg.C. rep 2

tag: cell type


title: Seabass_PostStress_T4_G8

value: G


title: Seabass_PostStress_T4_T19

value: T


title: YFP

tag: genotype

value: Ren1c-/-; Ren1c-YFP


title: Thymus CON2

tag: breed

value: ROSS 308

value: Thymus

value: post natal day 21

value: basic diet-treated


title: Seabass_PostStress_T4_S2

value: S


title: Seabass_PostStress_T4_P3

value: juvenile


title: Seabass_PostStress_T4_K18

value: 9 months

value: K


title: Seabass_PostStress_T4_G16

value: post-stress


title: siNeg.C. rep 1

value: epithelial

tag: tissue


title: Seabass_PostStress_T4_P5


title: Seabass_PreStress_T0_S19

value: 6 months

value: pre-stress


title: Seabass_PostStress_T4_H3

value: H


title: Seabass_PostStress_T4_G14


title: Seabass_PreStress_T0_M17

value: M


title: Seabass_PreStress_T0_M19


title: Seabass_PreStress_T0_R14

value: R


title: Seabass_PostStress_T4_F13

value: F


title: Seabass_PreStress_T0_S14


title: Seabass_PostStress_T4_F10


title: Seabass_PreStress_T0_M13


title: Seabass_PreStress_T0_G12

value: G


title: Seabass_PreStress_T0_G7


title: Seabass_PreStress_T0_M18


title: Seabass_PreStress_T0_F2


title: Seabass_PreStress_T0_G9


title: Seabass_PreStress_T0_G5


title: Seabass_PreStress_T0_T18

value: T


title: Seabass_PostStress_T4_R19


title: Seabass_PreStress_T0_G16


title: Seabass_PostStress_T4_H16


title: Seabass_PostStress_T4_K16


title: Seabass_PostStress_T4_L15

value: L


title: Seabass_PostStress_T4_T16


title: Seabass_PostStress_T4_I16

value: I


title: Seabass_PreStress_T0_R15


title: Seabass_PreStress_T0_R2


title: Seabass_PreStress_T0_P2

value: P


title: Seabass_PostStress_T4_A17

value: A


title: Seabass_PostStress_T4_O13

value: juvenile

value: O


title: Seabass_PostStress_T4_J14

value: 9 months

value: J


title: Seabass_PostStress_T4_B19

value: post-stress

value: B


title: Seabass_PostStress_T4_J12


title: Seabass_PostStress_T4_E14

value: E


title: Seabass_PostStress_T4_P7


title: Seabass_PostStress_T4_T5


title: Seabass_PreStress_T0_G10

value: 6 months

value: pre-stress


title: Seabass_PreStress_T0_R3

value: R


title: Seabass_PostStress_T4_L7


title: Seabass_PostStress_T4_H18

value: H


title: Seabass_PreStress_T0_O17


title: Seabass_PostStress_T4_E8


title: Seabass_PreStress_T0_J9


title: Seabass_PreStress_T0_N18

value: N


title: Seabass_PreStress_T0_H17


title: Seabass_PreStress_T0_H19


title: Seabass_PostStress_T4_O10


title: Seabass_PreStress_T0_E13


title: Seabass_PreStress_T0_O8


title: Seabass_PostStress_T4_C1

value: C


title: Seabass_PreStress_T0_K10

value: K


title: Seabass_PostStress_T4_D1

value: D


title: Seabass_PreStress_T0_C19


title: Seabass_PostStress_T4_R18


title: Seabass_PostStress_T4_H2


title: Seabass_PostStress_T4_H5


title: Seabass_PreStress_T0_L6

value: L


title: Seabass_PreStress_T0_O6


title: Seabass_PostStress_T4_D15


title: Seabass_PostStress_T4_I19

value: I


title: Seabass_PreStress_T0_I16

value: juvenile


title: Seabass_PreStress_T0_R18


title: Seabass_PreStress_T0_D15


title: Seabass_PreStress_T0_H9


title: Seabass_PostStress_T4_C12


title: Seabass_PreStress_T0_K4


title: Seabass_PreStress_T0_E6


title: Seabass_PreStress_T0_I17


title: Seabass_PreStress_T0_E2


title: Seabass_PreStress_T0_T16

value: T


title: Seabass_PreStress_T0_C12


title: Seabass_PreStress_T0_C1


title: Seabass_PreStress_T0_H2


title: Seabass_PreStress_T0_D11


title: Wt 8 d30 Tcf7-

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

description:
sample name:
36

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3) (Martin et al., 2011) and filtered for low complexity with seq crumbs (v. 0.1.8).
Reads were aligned against Mus musculus (version GRCm38) genome using STAR (v. 2.4.2a) (Dobin et al., 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) (Anders et al., 2015) using M. musculus (Ensembl v. GRCm38.82) gene annotation.
Genome_build: Mus musculus Ensembl vGRCm38.82
Supplementary_files_format_and_content: A tab-delimited text file include htseq gene raw counts for all samples

source_name: Wt Tcf7GFP- P14 cells at d30 of LCMV Arm infection

extract_protocol:
Cells were lysed and stored in Trizol before extraction of total cellular RNA using the Direct-zol™ RNA MiniPrep kit (Zymo Research).
RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA reagents (# 634888, Clontech) according to the protocol provided with the reagents beginning with 5ng of total RNA and using 9 cycles of PCR.  150 pg of the resulting cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (# 15032354, Illumina).

treatment_protocol: Splenocytes  were enriched for CD8 T-cells using the EasySep Mouse CD8+ T Cell Isolation Kit (StemCell Technologies). Naive Tcf7GFP P14 cells were flow sortedbased Tcf7GFPhi and CD62L+ (Naive). Tcf7GFPhi and Tcf7-GFP- CD8+ CD45.2+ CD45.1- (P14) cells were flow sorted from the spleen of infected mice..

value: CD8 T cells expressing a P14 TCR and a Tcf7GFP reporter

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ   B6-Tg(Tcf7GFP)WHe


title: Wt 8 d30 Tcf7hi

description:
sample name:
35

source_name: Wt Tcf7GFPhi P14 cells at d30 of LCMV Arm infection


title: SLX18580_WT_LK

city: Cambridge

first: Sam

last: Watcham

address: Jeffery Cheah Biomedical Centre

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
Reads aligned to mm10 and processed using Cell Ranger v1.3.
Counts extracted using Scanpy in python
Each sample was filtered for potential doublets by simulating synthetic doublets from pairs of scRNAseq profiles and assigning scores based on a k nearest-neighbour classifier on principle component analysis (PCA) transformed data. The top 4.5% of cells with the highest doublet scores from each sample were removed from further analysis. Cells with >10% of unique molecular identifier (UMI) counts mapping to mitochondrial genes, expressing fewer than 500 genes, or with the total number of UMI counts further than 3 standard deviations from the mean for all cells were excluded. The remaining cells were used for all analyses in the manuscript.
Genome_build: mm10
Supplementary_files_format_and_content: Counts: Normalised UMI counts per gene, per cell

source_name: LK blood progenitors from WT, experiment 2

extract_protocol:
Bones were crushed in PBS with 2% fetal bovine serum (2% FBS) and the cells filtered through a 40µm strainer, depleted of red blood cells and stained with relevant antibodies.
Cells were washed in PBS with 0.04% BSA and re-suspended before loading 10,000 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584). Quantification of library construction was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584).

value: Blood (Lin-c-Kit+)

value: WT


title: SLX18580_CALR_LSK

source_name: LSK blood progenitors from CALR mutant, experiment 2

value: Blood (Lin-Sca1+c-Kit+)

value: CALR mutant


title: SLX18580_WT_LSK

source_name: LSK blood progenitors from WT, experiment 2


title: SLX14832_WT_LK

source_name: LK blood progenitors from WT, experiment 1


title: SLX18580_CALR_LK

source_name: LK blood progenitors from CALR mutant, experiment 2


title: SLX14832_CALR_LK

source_name: LK blood progenitors from CALR mutant, experiment 1


title: Ko 6 d8 Tcf7hi

description:
sample name:
29

source_name: Ko Tcf7GFPhi P14 cells at d8 of LCMV Arm infection

value: CD8 T cells expressing a P14 TCR, a Tcf7GFP reporter and lacking the Tcf7 gene

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ   B6-Tg(Tcf7GFP)Whe  B6; 129-(Tcf7tm1Cle)


title: SLX14832_CALR_LSK

source_name: LSK blood progenitors from CALR mutant, experiment 1


title: Wt 7 d30 Tcf7-

description:
sample name:
34


title: Ko 4 d8 Tcf7-

description:
sample name:
26

source_name: Ko Tcf7GFP- P14 cells at d8 of LCMV Arm infection


title: Wt 6 d30 Tcf7hi

description:
sample name:
31


title: Ko 6 d8 Tcf7-

description:
sample name:
30


title: Wt 6 d30 Tcf7-

description:
sample name:
32


title: epidermis, Large_2

city: St Louis

first: Cristina

last: de Guzman Strong

state: MO

address: 660 South Euclid

department: Dermatology

institute: Washington University in St Louis

data_processing:
ENCODE ATAC-Seq processing pipeline used
Reads mapped with Bowtie2
Unmapped reads, duplicates, and reads mapping to chrM were filtered out.
Peaks were called using MACS2
Biological replicates were included if both the rescue and self-consistency IDR values per genotype were below (or very near) 2
Differential accessibility was assessed using EdgeR within the DiffBind R package
Genome_build: mm10
Supplementary_files_format_and_content: zipped narrow peaks files

source_name: epidermis

extract_protocol:
Whole skin tissue was isolated from newborn mice and epidermal keratinocytes were speperated after treatment with HBSS:Dispase (1:1)
Lysed cells were treated with Illumina Nextera TD enzyme to cut and insert sequencing adapters. Libraries were amplified and treated with AMPure XP beaks to size select,

value: newborn

value: epidermal keratinocytes


title: epidermis, Large_1


title: Ko 3 d8 Tcf7-

description:
sample name:
24


title: SLX14832_WT_LSK

source_name: LSK blood progenitors from WT, experiment 1


title: Wt 6 d8 Tcf7-

description:
sample name:
22

source_name: Wt Tcf7GFP- P14 cells at d8 of LCMV Arm infection


title: Wt 7 d30 Tcf7hi

description:
sample name:
33


title: Wt 5 d8 Tcf7-

description:
sample name:
20


title: Wt 6 d8 Tcf7hi

description:
sample name:
21

source_name: Wt Tcf7GFPhi P14 cells at d8 of LCMV Arm infection


title: Seabass_PreStress_T0_H55

value: 6 months

value: pre-stress

value: H


title: Wt 5 d8 Tcf7hi

description:
sample name:
19


title: Ko 3 d8 Tcf7hi

description:
sample name:
23


title: Wt 3 d8 Tcf7-

description:
sample name:
16


title: Wt 3 d8 Tcf7hi

description:
sample name:
15


title: Naïve Wt 5

description:
sample name:
05

source_name: Naïve Wt Tcf7GFP P14 cells


title: Naïve Wt 6

description:
sample name:
06


title: DAY14_1

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited gene counts per cell

source_name: injured mouse kidneys_day14

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: 4 weeks

tag: time point

value: Kidney Cortex


title: DAY14_2


title: Naïve Wt 3

description:
sample name:
03


title: DAY7_2

source_name: injured mouse kidneys_day7


title: CONTROL

source_name: normal mouse kidneys


title: DAY7_1


title: DAY2

source_name: injured mouse kidneys_day2


title: DAY4

source_name: injured mouse kidneys_day4


title: Ko 4 d8 Tcf7hi

description:
sample name:
25


title: DAY11_1

source_name: injured mouse kidneys_day11


title: DAY1

source_name: injured mouse kidneys_day1


title: AGS-EBF1-WT and Q196P-OE-batch2019

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

description: RNA-Seq in AGS

data_processing:
For ChIP-Seq, sequencing reads were mapped to the human reference genome (hg19) using BWA-MEM. Reads with MAPQ<10 and potential PCR duplication were filtered using SAMTools. Peaks were predicted using MACS2 or CCAT with default parameters. For RNA-Seq,  sequencing was performed using paired-end 101bp reads. RNA-seq reads were aligned to the human genome (hg19) using TopHat2 (version 2.0.12) using default parameters. Transcript abundances in units of FPKM at the gene level were estimated using Cufflinks. Gene expression values from primary samples showing variation sgreater than zero was corrected for potential batch effects using ComBat.
Genome_build: hg19

source_name: gastric cancer cell line

extract_protocol:
For ChIP-Seq, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and reactions were stopped by adding glycine to a final concentration of 0.2 M. Chromatin was extracted and sonicated to 500 bp. EBF1 (H00001879-M01, Abnova), H3K27me3 (#07-449, Millipore), h3k27AC (ab4729, Abcam), or H3K4me1 (ab8895, Abcam) antibodies were used for chromatin immunoprecipitation (ChIP). Input DNA from cells prior to immunoprecipitation were used to normalize ChIP-seq peak calling.
ChIPed DNA (10-30 ng) was used for ChIP with DNA sequencing (ChIP-seq) library construction following manufacturer protocols (New England Biolabs). For RNA-Seq, sequencing libraries were constructed from total RNA of GC cell lines with 300-400 bp insert lengths
ChIP-seq, RNA-Seq

value: AGS

tag: antibody

value: not applicable


title: AGS-vector-batch2019

description: RNA-Seq in AGS


title: ALL07

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: nascent RNA

data_processing:
Libraries were sequenced for 51 cycles (single-end) on an Illumina HiSeq 2000, according to the manufacturer’s instructions.
GRO-Seq reads were trimmed to remove A-stretches originating from the library preparation using the Homer software (homerTools trim) and from resulting sequences those shorter than 25 bp were discarded.  Sequence reads were further quality filtered with the FASTX software (-q 10 -p 97)
GRO-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 (-v 2 -k 3 -m 1 --best)
bigWig files were generated using the HOMER software http://biowhat.ucsd.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bigWig GRO-seq signal files, separately for plus and minus strand

source_name: freshly isolated primary bone marrow cells

growth_protocol: Cells were freshly isolated from bone marrow samples collected at diagnosis using Ficoll separation of mononuclear cells.

extract_protocol:
GRO-seq: Mononuclear cells (MNC) were extracted from fresh BM at diagnosis using Ficoll-Paque Plus (GE Healthcare, #17-1440-02). Nuclei were extracted from 20 million cells and frozen in -80C.
GRO-seq: Nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. Trizol was added RNA was extracted , DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP ab  using magnetic bead separation and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified. The recovered cDNA was circularized, linearized, amplified for 13-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.
GRO-seq

tag: disease state

value: acute lymphoblastic leukemia

tag: subtype

value: ALL cells


title: AGS-EBF1-Q196P-OE-batch2019

description: RNA-Seq in AGS


title: ALL13

description: nascent RNA

value: freshly isolated primary bone marrow cells


title: AGS-EBF1-WT-OE-batch2019

description: RNA-Seq in AGS


title: YCC11-Input-(control for H3K4me1,H3K27ac)

description: Input (background)


title: YCC10-Input-(control for H3K4me1)

description: Input (background)


title: SNU719-Input-(control for H3K4me1)

description: Input (background)


title: YCC10-H3K4me1

description: H3K4me1 ChIP-seq in YCC10

value: ab8895, Abcam


title: KATO-III-Input-(control for H3K4me1)

description: Input (background)

value: KATO-III


title: YCC11-H3K4me1

description: H3K4me1 ChIP-seq in YCC11


title: SNU16-Input-(control for H3K4me1,H3K27ac)

description: Input (background)


title: SNU719-H3K4me1

description: H3K4me1 ChIP-seq in SNU719


title: KATO-III-H3K4me1

description: H3K4me1 ChIP-seq in KATO-III


title: DAY11_2

tag: age


title: YCC11-H3K27ac

description: H3K27ac ChIP-seq in YCC11

value: ab4729, Abcam


title: SNU16-H3K27ac

description: H3K27ac ChIP-seq in SNU16


title: SNU484_Input [histone]

description: Input (background) for SNU484

data_processing:
DNA sequencing reads were aligned to the human reference genome, hg19. Processing was performed as described in Ooi et al., 2016 (PMID: 27677335). Mapped reads were de-duplicated using Samtools. Genomic regions associated with histone modifications (H3K27ac) were predicted by CCAT using default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.significant.region.txt: Tab-delimited text files; Interval format for UCSC genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR".

extract_protocol:
For primary tissues, fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized piece for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer. For cell lines, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min). Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode).
ChIP was performed using antibodies to: H3K27ac (ab4729, Abcam). After recovery of ChIP and input DNA, whole-genome-amplification was performed using the WGA4 kit (Sigma-Aldrich) and BpmI-WGA primers. Amplified DNAs were purified using PCR purification columns (QIAGEN) and digested with BpmI (New England Biolabs) to remove WGA adapters. 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs).

value: gastric cancer cell line

tag: chip antibody


title: T980097_H3K27ac [histone]

description: H3K27ac ChIP-seq in T980097

source_name: primary gastric tumor

value: primary gastric tumor

value: H3K27ac (Abcam, ab4729)


title: T980097_Input [histone]

description: Input (background) for T980097


title: N980097_H3K27ac [histone]

description: H3K27ac ChIP-seq in N980097

source_name: primary normal gastric

value: primary normal gastric


title: N980097_Input [histone]

description: Input (background) for N980097


title: LMSU_H3K27ac [histone]

description: H3K27ac ChIP-seq in LMSU

value: LMSU


title: LMSU_Input [histone]

description: Input (background) for LMSU


title: IM95_Input [histone]

description: Input (background) for IM95


title: IM95_H3K27ac [histone]

description: H3K27ac ChIP-seq in IM95


title: SNU719_H3K27ac [histone]

description: H3K27ac ChIP-seq in SNU719


title: YCC11_EBF1

description: EBF1 ChIP-seq in YCC11

data_processing:
Sequencing reads were mapped to the human reference genome (hg19) using BWA-MEM. Reads with MAPQ<10 and potential PCR duplication were filtered using SAMTools. Peaks were predicted using MACS2 with default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.txt: Please refer to the website: https://github.com/taoliu/MACS for details.

extract_protocol:
30 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and reactions were stopped by adding glycine to a final concentration of 0.2 M. Chromatin was extracted and sonicated to 500 bp. EBF1 (sc-137065, Santa Cruz Biotechnology; H00001879-M01, Abnova) and EZH2 (#5246, Cell Signaling) antibodies were used for chromatin immunoprecipitation (ChIP). Input DNA from cells prior to immunoprecipitation were used to normalize ChIP-seq peak calling.
ChIPed DNA (10 ng) was used for ChIP with DNA sequencing (ChIP-seq) library construction following manufacturer protocols (New England Biolabs).

treatment_protocol: EBF1 cDNAs were cloned into MIGR1 vector (#27490, Addgene) between the HpaI and Bgl 2 sites. Retrovirus packaging was performed using Platinum-A (Plat-A) retroviral packaging cell lines by transfection using Lipofectamin 2000 (Thermo Fisher Scientific). GC cells were infected with retrovirus packaged with EBF1 genes for 48 hours and sorted for GFP.

value: EBF1 (Santa Cruz Biotechnology, sc-137065)


title: SNU719_Input [histone]

description: Input (background) for SNU719


title: YCC10_H3K27ac [histone]

description: H3K27ac ChIP-seq in YCC10


title: KATOIII_H3K27ac [histone]

description: H3K27ac ChIP-seq in KATOIII

value: KATOIII


title: KATOIII_Input [histone]

description: Input (background) for KATOIII


title: HS746T_Input

description: Input (background) for HS746T EBF1 ChIP-seq


title: OCUM1 Input

description: Input (background) for OCUM1 CapStarr-seq.

data_processing:
Library strategy: CapStarr-seq
CapStarr-seq consists of two parts of data with different types of readouts. The input library represents the insert fragments in original plasmid pool, while the output library measures the abundance of self-transcribed mRNA from insert fragments of the transfected plasmid pool.
Paired-end sequencing reads (2 × 100 bp) from Illumina Hiseq2000 were aligned to human genome hg19 by BWA using default parameters. Only reads that mapped in proper pairs were used for downstream analysis. To exclude potential PCR amplification bias, fragments (inferred from paired-end reads) that have the same start and end positions were collapsed into distinct fragments by Picard (http://broadinstitute.github.io/picard/). Uniquely mapped distinct fragments from the 160 different indexing libraries were pooled and all included for downstream analysis, since duplicated fragments coming from different indexing libraries are considered as biological duplicates.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: OCUM1_enhancerseq_R1_peaks.narrowPeak: Tab-delimited text file. Please refer to the website https://github.com/taoliu/MACS for details.

extract_protocol:
Generation of plasmid libraries was based on the method described by Vanhille et al. Briefly, SNU16 genomic DNA was extracted using the PerfectPure DNA Cultured Cell kit (5 Prime). The DNA was sheared by sonication (Covaris S2) and size-selected on 1% agarose gels (350–650 bp). Size-selected DNA fragments were ligated to adaptors (Adaptor 1: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; adaptor 2: 5’-GATCGGAAGAGCACACGTCT-3’) after end repair and A-tailing (NEBNext Ultra End Repair/dA- Tailing and Ultra Ligation Module, New England Biolabs) and subjected to capture (NimbleGen SeqCap EZ, Roche). Post-capture DNA was PCR amplified using Q5 High-Fidelity DNA polymerase (NEB) to add homology arms for subsequent cloning (forward primer: 5’-GTAATAATTCTAGAGTCGGGGCGGGAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; reverse primer: 5’- TATCATGTCTGCTCGAAGCGGCATAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; PCR program: 98 °C for 30 s; 17 cycles of 98 °C for 10 s, 65 °C for 30 s, and 72 °C for 30 s). The vector backbone was modified from pGL4.23[luc2/minP] (Promega). Briefly, the minP promoter was replaced with the SCP1 promoter and a CmR-ccdB cassette was cloned between luc2 ORF and SV40 poly (A). The PCR product was cloned into the vector backbone (linearized by SphI and NdeI restriction enzymes) through Gibson Assembly (Gibson Assembly Master Mix, New England Biolabs) and transformed into MegaX DH10B™ T1R electrocompetent cells (ThermoFisher Scientific). A total of 8 Gibson Assembly and transformations were performed. All transformed E. coli cells were pooled and cultured in 4 L LB medium and harvested at OD600 1.0. The input plasmid library was extracted using Plasmid Mega Kit (Qiagen) and drop dialyzed before transfection. Sequencing libraries were prepared from the input plasmid libraries by amplifying inserts from the plasmid DNA. 10 PCR reactions were set up, using Q5 High-Fidelity DNA polymerase (New England Biolabs), each with 1 ng plasmid as template (PCR program: 98 °C for 30 s; 12 cycles of 98 °C for 10 s, 65 °C for 30 s, and 72 °C for 30 s). Reactions were pooled, cleaned up and submitted for sequencing.
Total RNA was extracted from transfected cells using PerfectPure RNA Cultured Cell Kit (5 Prime), followed by mRNA isolation using Dynabeads® Oligo (dT) kit (ThermoFisher Scientific) and treatment with TURBO DNase (ThermoFisher Scientific). Then target-specific first strand cDNA synthesis was performed with SuperScript III (ThermoFisher Scientific) to specifically reverse transcribe mRNA from the transfected plasmid library (RT primers: 5’-CAGTGACTGGAGTTCAGACG-3’, 5’-GCAGCTTATAATGGTTACAAATAAAGC-3’, 5’-ACATTTGTAGAGGTTTTACTTGCT-3’, 5’-TCAATGTATCTTATCATGTCTGCTCGAAG-3’). After reverse transcription, reactions were treated with RNase A + H. Finally, the cDNA was PCR amplified using 5 μL cDNA reaction as template in every 50 μL PCR reaction. Q5 High-Fidelity DNA polymerase (New England Biolabs) was used, and the following PCR program: 98 °C for 30s; 20 cycles of 98 °C for 10 secs, 65 °C for 30 secs and 72 °C for 30 secs. Illumina HiSeq platform compatible primers were used (forward: 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; reverse: 5’-CAAGCAGAAGACGGCATACGAGAT-index-GTGACTGGAGTTCAGACGTG-3’). For each replicate, we set up separate final PCR reactions using 160 different indexing primers. PCR products for every 10 indexes were pooled and cleaned up by AmPure XP beads (Beckman Coulter; beads/reaction ratio = 0.8) and submitted for Illumina sequencing.


title: HS746T_EBF1

description: EBF1 ChIP-seq in HS746T


title: YCC11-Input

description: Input (background) for YCC11 H3K27me3

data_processing:
DNA sequencing reads were aligned to the human reference genome, hg19. Processing was performed as described in Ooi et. al., 2016 (PMID: 27677335). Mapped reads were de-duplicated using Samtools. Genomic regions associated with histone modifications were predicted by CCAT using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: interval format for ucsc genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR"

extract_protocol:
ChIP was performed using antibodies: H3K27ac (ab4729, Abcam), H3K4me1 (ab8895, Abcam). After recovery of ChIP and input DNA, whole-genome-amplification was performed using the WGA4 kit (Sigma-Aldrich) and BpmI-WGA primers. Amplified DNAs were purified using PCR purification columns (QIAGEN) and digested with BpmI (New England Biolabs) to remove WGA adapters. 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs). H3K27me3 ChIP was performed by Zymo Research (ab6002, Abcam).
ChIP-seq libraries were prepared following manufacturer protocols (New England Biolabs).

value: input


title: SNU16-H3K4me1

description: H3K4me1 ChIP-seq in SNU16


title: YCC11_Input

description: Input (background) for YCC11 EBF1 ChIP-seq


title: OCUM1 CapStarr-seq

description: CapStarr-seq in OCUM1.


title: SNU484-Input

description: Input (background) for SNU484 H3K27me3


title: YCC11-H3K27me3

description: H3K27me3 ChIP-seq in YCC11


title: SNU484-H3K27me3

description: H3K27me3 ChIP-seq in SNU484


title: IM95-Input

description: Input (background) for IM95 H3K27me3


title: IM95-H3K27me3

description: H3K27me3 ChIP-seq in IM95


title: YCC10_Input [histone]

description: Input (background) for YCC10


title: AGS-Input

description: Input (background) for AGS H3K27me3

source_name: AGS


title: AGS-H3K27me3

description: H3K27me3 ChIP-seq in AGS


title: SNU484_H3K27ac [histone]

description: H3K27ac ChIP-seq in SNU484


title: BT53M OE Contrl

city: Calgary

first: Hena

middle: Rehman

last: Ramay

state: AB

address: 6 Erlton Terrace SW

department: International microbiome centre

country: Canada

institute: University of Calgary

data_processing:
Primers were removed
Quality filtering was done
Kallisto software was used
Txiimport
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: BTI cells

growth_protocol: BTICs were cultured in serum-free medium suplemented with fibroblast and epidermal growth factors.

extract_protocol:
RNA was extracted by RNeasy Mini Ki (Qiagen)
Total RNA samples were verified for integrity using RNA assays on an Agilent TapeStation instrument. Satisfactory samples (RIN scores were > 9.3) were then subjected to poly-A mRNA enrichment, cDNA synthesis and Illumina compatible library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module, the NEBNext Ultra II Directional RNA  Library Prep Kit for Illumina and NEBNext Multiplex Index Primers, all according to the New England Biolabs recommended protocols. Libraries were then quantitated by both Agilent TapeStation High Sensitivity assays and a Kapa qPCR Library quantitation assay before pooling. Sequencing was performed on an Illumina NextSeq 500 sequencer with 75 cycle high-output sequencing kits, as per standard Illumina methods, to yield an average of 70 million reads per sample.

treatment_protocol: Cells were incubated for 3 hours in 37c CO2 5% incubatotor without treatment.

value: Brain tumor-initiating cells

tag: origin

value: Glioblastoma patient

tag: transfection

value: vector control


title: GBM5 OE


title: BT53M OE


title: MM6 5LO-KO + LPS - rep 3

city: Frankfurt am Main

first: Marius

last: Kreiss

address: Max-von-Laue-Str. 9

department: Pharmaceutical Chemistry

institute: Goethe-University

description:
small RNA
smallRNA_WTvsKO_LPS.txt

data_processing:
Base calling was automatically performed by RTA 2.4.11
FASTQ generation was automatically performed by FASTQ generator v 1.0.0 via BaseSpace (Illumina)
Trimming, annotiation and differential expression analysis were performed with the web tool omiRas (http://tools.genxpro.net/omiras/)
Genome_build: hg19
Supplementary_files_format_and_content: Differential expression table containing normalized expression values and the comparison of WT and 5-LO KO samples with or without LPS treatment.

source_name: Mono Mac 6

growth_protocol: MM6 cells were grown in glutamine containing RPMI 1640 medium (supplemented with 10% (v/v) heat inactivated FCS, 10 µg/mL insulin, 1 x MEM non-essential amino acids, 1 mM sodium pyruvate, 1 mM oxaloacetate, 100 U/mL penicillin, and 100 µg/mL streptomycin) at 37°C and 5% CO2. The seeding density for experiments is about 0.25 mio. cells /mL

extract_protocol:
Total RNA was extracted with TriZol (Invitrogen).
1 µg total RNA was used for the small RNA-Seq Library Prep Kit (Lexogen) according to the manufacturer's protocol. Libraries were mixed equimolarly and size selected for pre- and mature miRNA (130 - 260 bp including 126 bp linkers) by agarose gel electrophoresis

treatment_protocol: All samples were differentiated with 1 ng/mL TGF-beta (Peprotech) and 50 nM Calcitriol (Cayman) for 72 h at 6% CO2 and stimulated with or without 1 µg/mL LPS for 6 h.

tag: cell line

value: Mono Mac 6

tag: treatment 1

value: TGF-b + Calcitriol for 72 h

tag: treatment 2

value: LPS for 6 h


title: BT073 OE


title: hpGSC

city: Gwangjin-gu

first: junghwa

last: Moon

state: Seoul

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: human parotid tissue

growth_protocol: low glucose-Dulbecco's modified Eagle’s medium (low-DMEM) supplemented with 10% FBS and 1% antibiotics at 37°C in an incubator with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Single clonal glandular stem cells derived from human parotid glands


title: MSC

source_name: human adipose tissue

value: adipose mesenchymal stem cell


title: MM6 5LO-KO - rep 2

description:
small RNA
smallRNA_WTvsKO.txt

value: untreated


title: MM6 5LO-KO - rep 3

description:
small RNA
smallRNA_WTvsKO.txt


title: MM6 5LO-KO - rep 1

description:
small RNA
smallRNA_WTvsKO.txt


title: MM6 5LO-KO + LPS - rep 1

description:
small RNA
smallRNA_WTvsKO_LPS.txt


title: MM6 5LO-KO + LPS - rep 2

description:
small RNA
smallRNA_WTvsKO_LPS.txt


title: MM6 WT + LPS - rep2

description:
small RNA
smallRNA_WTvsKO_LPS.txt

value: wild type


title: GBM5 OE Contrl


title: BT073 OE Contrl


title: MM6 WT + LPS - rep3

description:
small RNA
smallRNA_WTvsKO_LPS.txt


title: MM6 WT + LPS - rep1

description:
small RNA
smallRNA_WTvsKO_LPS.txt


title: MM6 WT - rep 3

description:
small RNA
smallRNA_WTvsKO.txt


title: MM6 WT - rep 2

description:
small RNA
smallRNA_WTvsKO.txt


title: MM6 WT - rep 1

description:
small RNA
smallRNA_WTvsKO.txt

treatment_protocol: All samples were differentiated with 1 ng/mL TGF-beta (Peprotech) and 50 nM Calcitriol (Cayman) for 72 h at 6% CO2 and stimulated with or without 1 µg/mL LPS for 6 h."


title: patient_TEF 19

city: Rotterdam

first: Erwin

last: Brosens

state: - If in U.S, Select a State -

address: Dr molewaterplein 50

department: Clinical genetics

country: Netherlands

institute: ErasmusMC

description: patient

hyb_protocol: Fragmented biotinylated cRNA was subsequently hybridised onto Affymetrix Human Genome U133 Plus 2.0 microarray chips, which were scanned with the Affymetrix GeneChip Scanner.

scan_protocol: The measured intensity values were analyzed using GeneChip Operating Software (GCOS). The percentage of present calls, background, and ratio of actin and GAPDH 3’ to 5’ all indicated a high quality of samples and an overall comparability. Probe sets that were not present (according to Affymetrix MAS5.0 software) in any of the Genechips were omitted from further analysis. Raw intensities of the remaining probe sets of each chip were log2 transformed and raw expression values were Quantile normalized. Then, the data were transformed back to normal intensity values.

data_processing: Data analysis was carried out using BRB-array tools version 4.6.0 (October 2018) in combination with R version 3.5.1 (July 2018).

source_name: tracheoesophageal fistula

label_protocol: Depending on the availability and/or quality of purified total RNA, cDNA was synthesized from 0.8-15 μg RNA using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA, USA). Biotin-labelled cRNA synthesis, purification and fragmentation were performed according to standard protocols.

extract_protocol: total RNA was isolated following the manufacturer’s instructions, but the phase separation was repeated by adding 200µl of 0.1% DEPC water to increase RNA yield.  RNA was purified using the Rneasy MinElute Cleanup kit (Qiagen, Valencia, CA, USA) and stored at –80°C until further processing.

value: tracheoesophageal fistula


title: patient_TEF 13

description: patient


title: patient_TEF 17

description: patient


title: patient_TEF 18

description: patient


title: RS4.11 AZD1775 input 10h ChIP-seq 2

description: Mnase digested input

data_processing:
Single-end sequencing (75 bp) was performed with Illumina NextSeq 500/550 High Output Kit v2.5, according to the manufacturer instructions.
Sequencing reads were quality controlled using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bases with poor quality scores were trimmed (min 97% of positions have a min phred quality score of 10) using the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Duplicate reads were collapsed from ChIP-seq files using fastx (collapse)
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version bowtie/1.2.3 (-v 2 -k 3 -m 1 --best)
bigWig signal files were generated using HOMER software http://biowhat.ucsd.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bigWig ChIP-seq signal files

source_name: RS4;11 mixed lineage leukemia t(4;11) rearranged (MLLr) cells

growth_protocol: Cells were cultured in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM  L-glutamine (Gibco, Thermo Fisher), penicillin (100 U/ml), streptomycin (100 mg/ml) (Sigma-Aldrich), and 10 mM HEPES (Lonza).

extract_protocol:
Cells were crosslinked with 1/10 of volume of 11% formaldehyde solution (37% formaldehyde (Sigma-Aldrich), 5 M NaCl, 0.5 M EDTA pH 8.0, 0.5 M EGTA, 1 M HEPES) for 10 min gently rotating at 1 million/ml cell concentration in media. The reactions were quenched by adding glycine to a final concentration of 120 mM, and cells were washed twice with ice-cold PBS. Crosslinked lysate was flash frozen with liquid nitrogen and stored at - 80°C. Lysates were thawed, nuclei were extracted, and MNase  treated. 5 U of MNase (Thermo Fisher Scientific) was used and supernatant was diluted with dilution buffer 2.5 times. Samples were pre-cleared with 25 μl per sample Protein G Dynabeads (Thermo Fisher Scientific) for 1h at 4°C on a rotating platform. Subsequently,  input samples were collected. Next, 5 μg of the RUNX1 antibody (cat# ab23980, Abcam) for 10-16 million cells or 2.5 μg of H3K27ac antibody (cat# ab4729, Abcam) for 5-9 million cells were added. Bound chromatin fragments were collected by adding 25 μl of Dynabeads Protein G (Thermo Fisher Scientific) for 1 hour at 4°C rotating. Beads were washed with 1ml of cold wash buffers for 3 minutes.
Beads were eluted twice in elution buffer (1% SDS, 100 mM NaHCO3). Immunoprecipitated chromatin was reverse crosslinked by adding NaCl to a final concentration of 0.2 M. Next, 2,65 mg/ml of RNAse A (Invitrogen) was added to each sample and crosslinks were reversed overnight at 65°C. Proteinase K treatment was performed by adding 31 μl of buffer containing 161 mM EDTA, 645 mM Tris pH 7.4, Proteinase K 0.65 mg/ml (Thermo Fisher Scientific) for 1 h at 50°C. For DNA purification, ChIP DNA Clean & Concentrator (Zymo Research, Irvine, CA, USA) was used according to manufacture´s protocol. ChIP-Seq libraries were prepared  Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adaptor ligation using barcoded adapters (NextFlex, Bioo Scientific) with 13-14 cycles in PCR amplification and size selected for 225 bp-350 bp fragments by gel extraction.

treatment_protocol: Cells were treated with DMSO control or 1 μM AZD1775 (MK-1775 / Adavosertib)  for  4 h, 10 h, or 24 h.

tag: time

tag: treatment

value: AZD1775 1 μM

tag: replicate


title: RS4.11 DMSO input 10h ChIP-seq 2

description: Mnase digested input

value: DMSO


title: patient_TEF 15

description: patient


title: RS4.11 AZD1775 RUNX1 10h ChIP-seq 2

description: Immunoprecipitated DNA

value: RUNX1 (Abcam, ab23980)


title: patient_TEF 21

description: patient


title: patient_TEF 12

description: patient


title: patient_TEF 14

description: patient


title: RS4.11 AZD1775 H3K27ac 10h ChIP-seq 2

description: Immunoprecipitated DNA

value: H3K27ac (Abcam, ab4729)


title: RS4.11 DMSO H3K27ac 10h ChIP-seq 2

description: Immunoprecipitated DNA


title: RS4.11 DMSO RUNX1 10h ChIP-seq 2

description: Immunoprecipitated DNA


title: patient_TEF 11

description: patient


title: RS4.11 AZD1775 input 24h ChIP-seq 1

description: Mnase digested input


title: RS4.11 AZD1775 input 10h ChIP-seq 1

description: Mnase digested input


title: RS4.11 AZD1775 input 4h ChIP-seq 1

description: Mnase digested input


title: patient_TEF 9

description: patient


title: patient_TEF 5

description: patient


title: patient_TEF 7

description: patient


title: patient_TEF 2

description: patient


title: patient_TEF 1

description: patient


title: RS4.11 DMSO input NA ChIP-seq 1

description: Mnase digested input


title: patient_TEF 8

description: patient


title: RS4.11 AZD1775 H3K27ac 24h ChIP-seq 1

description: Immunoprecipitated DNA


title: RS4.11 DMSO H3K27ac 24h ChIP-seq 1

description: Immunoprecipitated DNA


title: RS4.11 AZD1775 H3K27ac 10h ChIP-seq 1

description: Immunoprecipitated DNA


title: RS4.11 AZD1775 H3K27ac 4h ChIP-seq 1

description: Immunoprecipitated DNA


title: RS4.11 DMSO H3K27ac 10h ChIP-seq 1

description: Immunoprecipitated DNA


title: patient_TEF 4

description: patient


title: patient_TEF 3

description: patient


title: RS4.11 DMSO H3K27ac 4h ChIP-seq 1

description: Immunoprecipitated DNA


title: Nalm6-RUNX1 H3K27ac ChIP-seq 1

description: Immunoprecipitated DNA

data_processing:
Single-end sequencing (75 bp) was performed with Illumina NextSeq 500/550 High Output Kit v2.5, according to the manufacturer’s instructions.
Sequencing reads were quality controlled using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bases with poor quality scores were trimmed (min 97% of positions have a min phred quality score of 10) using the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Duplicate reads were collapsed from ChIP-seq files using fastx (collapse)
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version bowtie/1.2.3 (-v 2 -k 3 -m 1 --best)
bigWig signal files were generated using HOMER software http://biowhat.ucsd.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bigWig ChIP-seq signal files

source_name: Nalm-6 pre-B-ALL cell line with inducible RUNX1 construct

growth_protocol: Cells were cultured in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM  L-glutamine (Gibco, Thermo Fisher), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich).

treatment_protocol: Nalm-6 RUNX1 and Nalm-6 Empty vector constructs were induced for 48h before crosslinking cells for ChIP-seq using 500 ng/ml doxycycline (Sigma-Aldrich).

tag: construct


title: patient_TEF 6

description: patient


title: control_lung 1

description: control

source_name: lung

value: lung


title: control_lung 3

description: control


title: Nalm6-RUNX1 input ChIP-seq 1

description: Mnase digested input


title: Nalm6-RUNX1 RUNX1 ChIP-seq 2

description: Immunoprecipitated DNA

value: RUNX1(Abcam,catalog #ab23980)


title: control_esophagus 1

description: control

source_name: esophagus

value: esophagus


title: control_esophagus 3

description: control


title: control_lung 2

description: control


title: Nalm6-EV input ChIP-seq 1

description: Mnase digested input

source_name: Nalm-6 pre-B-ALL cell line with inducible EV (empty vector) construct

value: Empty vector ctrl


title: Nalm6-EV RUNX1 ChIP-seq 2

description: Immunoprecipitated DNA


title: control_trachea 1

description: control

source_name: trachea

value: trachea


title: control_trachea 2

description: control


title: control_trachea 3

description: control


title: Nalm6-RUNX1 H3K27ac ChIP-seq 2

description: Immunoprecipitated DNA


title: control_lung 4

description: control


title: SU8686

city: Heidelberg

first: Matthias

last: Neulinger Munoz

address: INF 133

institute: Universitätsklinikum Heidelberg

data_processing:
Quality control performed with FastQC v0.11.8
obtained reads were pseudoaligned using the hg38 reference genome and quantified by Salmon v1.2 with standard parameters
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Pancreatic cancer cell lines

growth_protocol: The cells were routinely grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 µg/mL streptomycin. All cell lines were routinely tested for mycoplasma by PCR. PBMCs from healthy donors were isolated from whole blood using Histopaque-1077 (Sigma-Aldrich, St. Louis, MO 63103 USA). The blood was mixed with an equal amount of PBS and gently layered over Histopaque-1077 in a Falcon tube, resulting in volume ratios of blood to PBS to Histopaque-1077 of 1:1:1. After centrifugation at 800g for 20 minutes at room temperature, PBMCs were recovered from their corresponding layer and resuspended in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol:
mRNA was isolated from the cell culture using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. After isolation, the mRNA was treated with Turbo DNAfree Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions to decrease the amount of contaminating genomic DNA. The RNA concentration and quality were evaluated by Nanodrop and by using the Agilent2000 Bioanalyzer.
RNAseq libraries were prepared using the TruSeq stranded mRNA kit. The RNAseq libraries were sequenced using an Illumina HiSeq 4000 platform, resulting in 150bp single end reads

treatment_protocol: No treatment. Basal expression of cell lines


title: MiaPaca2


title: Panc1


title: T3M4


title: patient_TEF 10

description: patient


title: Nalm6-EV H3K27ac ChIP-seq 2

description: Immunoprecipitated DNA


title: Colo357


title: Capan1


title: Nalm6-RUNX1 input ChIP-seq 2

description: Mnase digested input


title: control_esophagus 2

description: control


title: BxPC3


title: Nalm6-EV H3K27ac ChIP-seq 1

description: Immunoprecipitated DNA


title: Prenatal Isocaloric exposure vs Prenatal ethanol exposure

city: Guadalajara

first: Pedro

last: Juárez Rodríguez

state: Jalisco

address: Sierra Mojada #950

department: Biología Molecular y Genómica

country: Mexico

institute: Universidad de Guadalajara

hyb_protocol: Equal quantities of labeled cDNA were hybridized for 14 hr at 42°C to the 22,000 Mus musculus oligo arrays in UniHyb hybridization solution (TeleChem International, Inc).

scan_protocol: ScanArray 4000 apparatus using the accompanying ScanArray 4000 software (Packard BioChips; PerkinElmer, MN, USA)

data_processing: Data processing was performed using the GenArise free software. GenArise performs a number of transformations: background correction, Lowess normalization, intensity filter, replicate analysis, and selection of differentially expressed genes

organism: Rattus norvegicus

source_name: ISO Nucleus accumbens

label_protocol: 10 µg of total RNA was used as the template, incorporating dUTP-Cy3 or dUTP-Cy5 employing the CyScribe First-Strand cDNA labeling kit (Amersham)

extract_protocol: Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions

treatment_protocol: Pregnant Wistar rats weighting 250-300 g at treatment onset were treated with ethanol (EtOH) (20% w/v in a 0.9% saline solution) by intragastric gavage between gestational days (GD) 8–20. The daily dose was 6.0 g/kg divided into two 3.0 g/kg doses administered 5–6 h apart during weekdays. A single daily dose of 4 g/kg ethanol was given during weekends. The control group received a solution of sucrose (ISO) 10.5 g/kg (in 0.9% saline) divided into two 5.25 g/kg doses to substitute for ethanol isocalorically during weekdays. A single daily dose of 7.0 g/kg were administered on weekends.

tag: strain

value: Wistar

value: PND 38

value: Nucleus accumbens

source_name: EtOH Nucleus accumbens

tag: gender

value: Male

tag: sample type

value: Total RNA from 7 pooled rat nucleus accumbens PND38


title: patient_TEF 16

description: patient

tag: tissue


title: AsPC1


title: 41-Tn-CD226-PLUS

city: Toulouse

first: ludovic

last: Martinet

address: 2 av Hubert Curien

department: CRCT

institute: INSERM U1037

description:
Freshly FACS purified
41-Tn-CD226-PLUS

data_processing:
Fastq files were aligned to the Ensembl GRCh38 human reference genome using STAR (version 2.3.0, (Dobin et al., 2013))
Gene expression summary was obtained using the Subread featurecount algorithm (version 1.4.6, (Liao et al., 2014)).
Patient gene expression was then normalized using standard procedure from the limma R package(Ritchie et al., 2015), retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.
Supplementary_files_format_and_content: tab-delimited text files include normalized gene xepression values retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.

source_name: Tn CD226+

extract_protocol:
RNeasy mini kit (Qiagen)
The RNA-Seq library preparation was performed using TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, Calif) according to the manufacturer’s instructions (High Sample Protocol). The RNA-Seq libraries were checked on the 2200 Tapestation System (Agilent) using the High-Sensitivity DNA 1000 ScreenTape assay. The average fragment size of the final libraries was found to be 230 to 327 bps. Libraries were quantified by qPCR on a LightCycler 480 System (Roche Molecular Diagnostics, Pleasanton, Calif) using KAPA Library Quantification Kit for Illumina platforms (Kapa Biosystems, Boston, Massachusetts). Libraries were then pooled in equal quantities, checked and quantified using same techniques (2200 Tapestation and LightCycler 480).
Paired-end sequencing (2 x 75 bps) of these libraries was performed on a NextSeq 500 Illumina sequencing platform (Illumina) by 5 successive runs using NextSeq 500 High Output kit v2 (Illumina) generating in average 20 million pairs of reads per sample.

value: male

tag: sampling date

value: peripheral blood

tag: cell type

value: Tn CD226+


title: 13-Tn-CD226-PLUS

description:
Freshly FACS purified
13-Tn-CD226-PLUS


title: 1-Tn-CD226-PLUS

description:
Freshly FACS purified
1-Tn-CD226-PLUS


title: ASAN

value: ASAN


title: 48-Tn-CD226-MOINS

description:
Freshly FACS purified
48-Tn-CD226-MOINS

source_name: Tn CD226-

value: female

value: Tn CD226-


title: 3 prime HS1 deleted HUDEP2 clone B6 CTCF Cut&Run

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

description: CTCF Cut&Run

data_processing:
Reads were aligned to the human genome (hg19) using Bowtie2 (version 2.3.5).
The resulting alignments bam files were indexed, sorted with SAMtools and marked for duplicates with Picard "MarkDuplicates" function.
Reads were then normalized using deeptools bamCoverage with RPGC parameter :bamCoverage --bam SA73051_unique_picard.bam --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2827437033 --extendReads -o dTag_H3K4m3_norm1x.bw
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Erythroid progenitor

growth_protocol: HUDEP clone 2 (HUDEP-2) cells were cultured as previously described [3]. Cells were expanded in StemSpan serum-free expansion medium supplemented with 1μM dexamethasone (D2915, Sigma), 1μg/mL doxycycline (D9891, Sigma), 50 ng/mL human SCF (300-07, Peprotech), 3 units/mL EPO (Amgen), and 1% penicillin/streptomycin. HUDEP-2 cells were differentiated in a two-phase differentiation protocol consisting of IMDM supplemented with 5% human AB serum (H6914, Sigma), 10μg/mL recombinant human insulin (91077C, Sigma), 330μg/mL holo-transferrin (T4132, Sigma), 3 units/mL EPO (Amgen), 1μg/mL doxycycline (D9891, Sigma), 2 units/mL heparin (H3149, Sigma), and 1% penicillin/streptomycin. 50 ng/mL human SCF (300-07, Peprotech) was included in the phase one of the culture (day 1-3) and withdrawn in the phase two of the culture (day 4 and beyond).

extract_protocol:
CTCF Cut&Run was performed according to published protocol 5. Briefly, 500,000 of HUDEP2 cells upon 5 days of differentiation were immobilized with BioMag Plus Concanavalin A (BangsLabs, Inc). Cells were permeabilized and incubated with CTCF antibody (ab70303, Abcam) for overnight. pA-MNase (a gift from Dr. Steven Henikoff) was then added to the cells and incubated for 30 min in metal block on ice. MNase reaction was stopped, chromatin was released, and DNA was extracted.
Accel-NGS 2S Plus DNA library kit (21096, Swift Bioscience) was used to construct the library followed by 2S combinatorial dual indexing kit (28096, Swift Bioscience).
Cut&Run

treatment_protocol: Cas9 nuclease (1081058, IDT) were mixed with synthetically modified sgRNAs (synthesized by Synthego) at a 1:3 molar ratio in resuspension buffer T and incubated at 37oC for 10 minutes to form ribonucleoprotein complexes (RNPs). For the CTCF inversion clones, homology-directed repair (HDR) approach was used by adding 2μg of dsDNA homology repair template (synthesized by Gene Universal) to the RNP complexes. dsDNA repair templates were designed to have 90-130 bp of homology arms distal and proximal to the PAM sequence.

value: erythoid


title: 3 prime HS1 inverted HUDEP2 clone A2 CTCF Cut&Run

description: CTCF Cut&Run