title: RUNX1_ChIP_S00XUNH1

source_name: AML samples carrying RUNX1 mutation

tag: gender

value: male

tag: subject status

value: Acute myeloid leukemia

value: Venous blood

value: Myeloid cell

value: RUNX1 antibody (Abcam:ab23980)


title: RUNX1_ChIP_d34_DOX_iPSC

status: Public on Feb 06 2019

type: SRA

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

library_source: genomic

data_processing:
Sequenced reads were aligned against the UCSC human reference genome (GRCh37/hg19) with Burrows-Wheeler Aligner (BWA) program with default parameters. The resultant BAM files were subjected to removal of potential PCR and optical duplicates using Picard MarkDuplicates option. The peak calling algorithm MACS2 was used to detect the RUNX1 binding sites at p-value of 10e-6. Peaks overlapping with the consensus excludable ENCODE blacklist and on sex chromosomes were discarded to avoid confounding by repetitive regions and gender-specific bias. All alignment files were extended to the estimated fragment length and scaled to RPKM-normalized read coverage files using deepTools for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deepTools by scaling read depth to RPKM-normalized coverage

molecule: genomic DNA

organism: Homo sapiens

source_name: iPSC

extract_protocol:
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x10 minutes (30 seconds on; 30 seconds off). 67µl of chromatin (1 million cells) was incubated with 229µl dilution buffer, 3µl protease inhibitor cocktail and 0.5-1µg of RUNX1 antibody (Abcam: ab23980) and incubated overnight at 4ºC with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 minutes at 4°C. Beads were washed with 400µl buffer for 5 minutes at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 minutes. Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C.Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C. Subsequently adapters were ligated by adding 30µl ligation buffer, 10 Kapa l DNA ligase, 5µl diluted adaptor in a total volume of 110µl and incubated for 15 minutes at 15°C. Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis. Sequencing was performed using Illumina NextSeq 500 machines and generated 43bp paired-end reads.

tag: mutation status

value: DOX-induced RUNX1mut

tag: harvest time

value: day 34

tag: cell type

value: iPSC


title: RNASeq_RMCO3

library_source: transcriptomic

data_processing:
For expression analyses, the hg19 reference genome index was first generated using STAR aligner with UCSC gene annotation. Paired-end reads were mapped to the indexed genome in two-pass mode with default parameters, to increase alignment accuracy and sensitivity. Stranded gene-level read counts were enumerated at the same time. Expression quantification for each RefSeq gene was performed by Cuffnorm function in Cufflinks, to estimate Fragments Per Kilobase per Million aligned reads value (FPKM). All alignment files were  scaled to RPKM-normalized read coverage files using deepTools for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: Gene-level read counts were enumerated by STAR tool. bigWig files were generated using deepTools by scaling read depth to RPKM-normalized coverage

molecule: total RNA

source_name: Cord blood CD34 cells

extract_protocol:
Total RNA was extracted from 1x10e6 iPSC control and RUNX1mut cells using the RNeasy mini kit (Qiagen) and performing on-column DNaseI treatment. Ribosomal RNA was depleted by using the ribo-zero rRNA removal kit (Illumina). RNA was fragmented in 300 bp fragments by incubation for 7.5 minutes in fragmentation buffer (200 mM Tris-acetate, 500 mM Potassium Acetate, 150 mM Magnesium Acetate (pH 8.2)). First strand cDNA synthesis was performed using superscript III (Life Technologies), followed by synthesis of the second cDNA strand. Libraries were generated using the Kapa hyper prep kit (KAPA Biosystems).
Libraries were generated using the Kapa hyper prep kit. End repair and A-tailing was performed on the double strand DNA using end repair and A-tailing buffer. Subsequently, the adapters were ligated and a post-ligation cleanup was performed using Agencourt AMPure XP reagent. The libraries were amplified by PCR using the Kapa Hifi hotstart readymix and primer mix, 10 cycles. Samples were purified using the Qiaquick MinElute PCR purification kit and 300 bp fragments were selected from E-gel and the size was checked on the agilent bioanalyzer. Samples were sequenced on the Illumina NextSeq 500.

value: RUNX1mut transduced

value: Cord blood CD34 cells


title: RUNX1_ChIP_d34_CTR_iPSC

value: control


title: RNASeq_RMCO2


title: RUNX1_ChIP_d31_CTR_iPSC

value: day 31


title: RUNX1_ChIP_d31_DOX_iPSC


title: RUNX1_ChIP_CTR_CB


title: RUNX1_ChIP_MT_CB


title: RUNX1_ChIP_S00D55H1

tag: age

tag: tissue

tag: chip antibody


title: RUNX1_ChIP_S00D47H1


title: DN3 population, sample 2

status: Public on Feb 04 2019

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.5.3a), and read counting on Ensembl 84 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R (v3.4.0). The UMI matrix was filtered to included only cells with a count of at least 100 genes detected, giving a total of 22,862 cells (18,274 genes).
Further quality controls and analyses were performed using the scran (1.4.5) and scatter (1.4.0) Bioconductor packages, and following the Bioconductor workflow (for Bioconductor version 3.5). Expression values of 11,448 genes for 18,128 cells were obtained after stringent quality filtering and normalization.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 84 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-DN3_1")

organism: Mus musculus

source_name: Double-negative developing thymocytes from the DN3 population

extract_protocol:
Single cells were extracted from suspensions of thymus of six pooled C57BL/6 female mice
DN2, DN3, and DN4 cells were sorted by flow cytometry (using a FACSAria IIu, BD Biosciences). Double-negative cells were gated for CD4-, CD8-, CD3- and B220- expression. DN2 cells were additonally gated for CD25high, CD44high and CD177high expression, while DN3 cells were gated for CD25high, CD44low and CD117low expression, and DN4 cells were gated for CD25-, CD44-, CD117- and CD28+ expression.
Around 5,000 cells from the DN2 and DN4 populations were loaded on one well each, along with around 10,000 cells from the DN3 population loaded on two wells of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

tag: strain

tag: Sex

value: female

value: double-negative developing thymocyte

tag: population


title: DN3-4 population from mouse overexpressing Duxbl, replicate 1

data_processing:
Reads were aligned to the mouse genome (mm10) using the spliced read aligner STAR (version 2.5.2a) with default parameters, except reporting only one hit in the final alignment for multimappers (outSAMmultNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Sequencing and mapping quality was assessed by the qQCReport function of the R package QuasR (version 1.18).
Gene expression was quantified by the qCount function of QuasR using an exon-union model of Ensembl 84 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. ENSEMBL ID, 2. gene length (exon union model), 3.-10. read counts per gene and sample

molecule: polyA RNA

source_name: Double-negative developing thymocytes gated for CD4-, CD8-, CD3-, B220-, CD25int, CD44low and CD117low expression

growth_protocol: Cells were flushed from the thymus of a single Duxbl[ind] x pTα[Cre] mouse

extract_protocol:
Double-negative developing thymocytes from the DN3-4 populations were isolated from WT and transgenic mice by flow cytometry, gating for CD4-, CD8-, CD3-, B220-, CD25int, CD44low and CD117low expression, and were pooled for bulk RNA-sequencing.
Total RNA was isolated from 100,000-200,000 cells with an Ambion RNAqueous Micro Kit (Invitrogen). RNA quality was assessed with a Fragment Analyzer (Advanced Analytical).
50 ng of RNA were used for library preparation (Illumina Truseq stranded kit)

treatment_protocol:
Duxbl[ind] mice were generated at the Center for Transgenic Models in Basel by random integration into C57BL/6 zygotes of a construct composed of a CAG promoter, followed by an mCherry STOP-cassette flanked by lox-P sites, followed by the Duxbl1 cDNA coupled via an internal-ribosomal-entry-site (IRES) to the enhanced green fluorescent protein (eGFP) gene, and ending with the bovine growth hormone polyadenylation site (bpA).
To induce the expression of Duxbl1 sequence in the contruct, the Duxbl[ind] mice were crossed to mice expressing the Cre recombinase under the control of the pTα (Ptcra) promoter (Luche et al. 2013, https://www.ncbi.nlm.nih.gov/pubmed/23509324). The resulting Duxbl[ind] x pTα[Cre] mice lost their mCherry STOP-cassette by cre-mediated recombination, leading to induction of Duxbl expression together with eGFP.

tag: genotype/variation

value: Duxbl[ind] x pTa[Cre]

value: 5-7 weeks


title: DN3 population, sample 1


title: DN2 population

source_name: Double-negative developing thymocytes from the DN2 population


title: DN3-4 population from mouse overexpressing Duxbl, replicate 2


title: DN3-4 population from mouse overexpressing Duxbl, replicate 4


title: DN4 population

source_name: Double-negative developing thymocytes from the DN4 population


title: DN3-4 population from wild-type mouse, replicate 3

growth_protocol: Cells were flushed from the thymus of a single WT C57BL/6 mouse

value: wild type


title: DN3-4 population from wild-type mouse, replicate 4


title: DN3-4 population from mouse overexpressing Duxbl, replicate 3


title: DN3a CD27high population, replicate 4

data_processing:
Reads were aligned to the mouse genome (mm10) using the spliced read aligner STAR (version 2.5.2a) with default parameters, except reporting only one hit in the final alignment for multimappers (outSAMmultNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Sequencing and mapping quality was assessed by the qQCReport function of the R package QuasR (version 1.18).
Gene expression was quantified by the qCount function of QuasR using an exon-union model of Ensembl 84 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. ENSEMBL ID, 2. gene length (exon union model), 3.-14. read counts per gene and sample

source_name: Double-negative developing thymocytes gated for CD4-, CD8-, CD3-, B220-, CD25high, CD44low, CD117low, CD27low, CD28low expression

growth_protocol: Cells were flushed from thymuses of a pool of 5 WT mice (1 female and 4 males pooled).

extract_protocol:
Double-negative developing thymocytes from the DN3 subpopulation were isolated by flow cytometry, gating for CD4-, CD8-, CD3-, B220-, CD25high, CD44low, CD117low expression.
DN3 cells were separated in 3 groups based on their CD27 and CD28 expression (DN3a CD27low CD28low, DN3a CD27high CD28low, and DN3b CD27high CD28high) that were pooled for bulk RNA-sequencing
Total RNA was isolated from 100,000-200,000 cells with an Ambion RNAqueous Micro Kit (Invitrogen). RNA quality was assessed with a Fragment Analyzer (Advanced Analytical).
50 ng of RNA were used for library preparation (Illumina Truseq stranded kit)

tag: cell population

value: DN3a CD27high

tag: facs run

value: pooled male and female


title: DN3-4 population from wild-type mouse, replicate 1

extract_protocol:
Double-negative developing thymocytes from the DN3-4 populations were isolated from WT and transgenic mice by flow cytometry, gating for CD4-, CD8-, CD3-, B220-, CD25int, CD44low and CD117low expression, and were pooled for bulk RNA-sequencing
Total RNA was isolated from 100,000-200,000 cells with an Ambion RNAqueous Micro Kit (Invitrogen). RNA quality was assessed with a Fragment Analyzer (Advanced Analytical).
50 ng of RNA were used for library preparation (Illumina Truseq stranded kit)

value: male


title: DN3b population, replicate 4

source_name: Double-negative developing thymocytes gated for CD4-, CD8-, CD3-, B220-, CD25high, CD44low, CD117low, CD27high, CD28high expression


title: DN3a CD27low population, replicate 4

source_name: Double-negative developing thymocytes gated for CD4-, CD8-, CD3-, B220-, CD25high, CD44low, CD117low, CD27high, CD28low expression

value: DN3a CD27low


title: RUNX1_ChIP_S00D63H1

value: Acute myeloid leukemia

value: Bone marrow

value: Myeloid cell

value: RUNX1 antibody (Abcam:ab23980)


title: DN3-4 population from wild-type mouse, replicate 2


title: DN3b population, replicate 1


title: DN3a CD27low population, replicate 1


title: DN3a CD27high population, replicate 1


title: DN3a CD27high population, replicate 2


title: DN3b population, replicate 5


title: DN3a CD27low population, replicate 5


title: DN3b population, replicate 2


title: Dln_d7_rep1

status: Public on Jan 23 2019

description: Sample 9

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

source_name: mesenchymal breast cancer cells (MTΔECad)

growth_protocol: Cells were seeded at density of 20,000 cells/cm2 and incubated overnight at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated from cells of 2 independent experiments using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction.
200 ng of RNA was utilized for library preparation with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina). Poly-A+ RNA was sequenced by HiSeq SBS kit v4 (Illumina) on an Illumina HiSeq 2500 using protocols defined by the manufacturer.

treatment_protocol: To induce differentiation of 3T3-L1, the growth medium was replaced with medium containing 5μg/ml insulin, 1μM Dexamethasone (dissolved in ethanol), 2μM Rosiglitazone (dissolved in DMSO) for 48 hours, then in medium containing 5μg/ml insulin for 48h, then in medium containing 1μM Rosiglitazone. To induce differentiation in cancer cells, cells were seeded and incubated overnight, incubated with 200ng/ml human recombinant BMP2 (Sigma) for 3 days with 200ng/ml BMP2 and 2μM Rosiglitazone (Rosi) for 4 days, and with medium containing 2μM Rosiglitazone for another 3 days. The addition of other growth factors or inhibitors is indicated in the figures, usually from day 0 to day 7 such as human recombinant TGF1 at 2ng/ml, the MEK inhibitor PD98059 at 40μM and the TGFR1 inhibitor SB431542 at 10μM. Control cells were treated with medium containing DMSO.

tag: time

value: 7 days


title: Dln_d10_rep2

description: Sample 12

value: 10 days


title: Dln_d10_rep1

description: Sample 11


title: Dln_d7_rep2

description: Sample 10


title: Dln_d3_rep2

description: Sample 6

value: 3 days


title: Dln_d5_rep1

description: Sample 7

value: 5 days


title: DN3a CD27high population, replicate 5


title: DN3a CD27low population, replicate 2


title: Dln_0h_rep1

description: Sample 1


title: Dln_6h_rep2

description: Sample 4


title: Dln_6h_rep1

description: Sample 3


title: Dln_d3_rep1

description: Sample 5


title: Dln_d5_rep2

description: Sample 8


title: Dln_0h_rep2

description: Sample 2


title: A549, Control, 0 Hours, Rep 3

status: Public on Nov 21 2018

type: RNA

city: London

first: William

last: Cookson

address: Dovehouse Street

country: United Kingdom

institute: Imperial College London

hyb_protocol: Samples were hybridized to the AffymetrixTM Human Gene 1.1 ST Array Plate (Affymetrix) for 16 hours on the Affymetrix GeneTitanTM.

scan_protocol: Arrays were scanned on the Affymetrix GeneTitanTM.

data_processing: Data quality was assessed using Array Quality Metrics (Version 3.22.1). Raw signal intensity data were normalized and summarized into transcript clusters (TC) using the Affymetrix Power Tools implementation of the RMA algorithm (APT, 1.16.1). TC classified as part of the main design were retained. Cross-hybridizing (Affymetrix release 35, hg19 annotation) and universally low expressed TC were removed. Universal low expression was defined as expression less than or equal to the dataset median across all samples in the study.  Differential expression was assessed using Limma (3.22.7). A baseline shift in transcription between ORMDL3 knockdown and control cells at time point 0 was assessed via group-means parametrization. P-values were adjusted for multiple testing by the Benjamini and Hochberg method, controlling the expected FDR below 0.05. A change in the temporal transcriptional profile during IL1B stimulation was assessed by specifying TC that respond differently between any two sequential time-points in ORMDL3 knockdown and control cells. Again P-values were adjusted for multiple testing by the Benjamini and Hochberg method, controlling the expected FDR below 0.05.

label: Biotin

source_name: A549, Control, 0 Hours

label_protocol: For each sample, 1µg of total RNA was converted to labelled cDNA using the AmbionTM WT Expression Kit (Ambion). The single-stranded DNA was fragmented and labelled using Affymetrix GeneChipTM WT Terminal Labelling Kit (Affymetrix).

growth_protocol: A549 human lung epithelial cells (American Type Culture Collection (ATCC)) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% (vol/vol) FCS and 2mM L-Glutamine and were used at passage numbers 90-110. Cells were maintained in 150 cm2 (T150) flasks with 5% CO2 at 37°C. Medium was replaced every second day, and cells were passaged when >85% confluent by washing with Dulbecco’s Phosphate Buffered Saline (DPBS) and dislodging with 0.5% trypsin.

extract_protocol: Cells were collected at 0, 2, 4, 6,8, 10 and 24 hours.  RNA was extracted using the Qiagen RNeasy mini kit (Qiagen, Crawley, UK). RNA quality was assessed using the RNA 6000 Nano AssayTM kit with the Agilent 2100 BioanalyserTM. Only samples with a RNA integrity number (RIN) score of > 9 above underwent subsequent processing.

treatment_protocol: ORMDL3 siRNAs (ON-TARGETplus SMARTpool) were obtained from Dharmacon Research Inc (Dharmacon Research Inc., Lafayette, CO). Cells were seeded into 24-well plates (Corning Costar Corp.) at 4x104 cells/well to reach 40–60% confluence on the day of transfection. siRNAs and transfection reagents were mixed according to supplier protocols, then added to a single well before the cells were placed in a CO2 incubator at 37°C for 48 hours. Forty-eight hours after induction of ORMDL3 gene silencing, cells were starved in serum free medium for 24 hours before stimulation with 1 ng/ml of IL1B (R&D).

tag: cell line

tag: genotype

value: Control

tag: treatment

value: untreated

tag: hours


title: A549, Control, 2 Hours, Rep 3

source_name: A549, Control, 2 Hours

value: IL1B stimulation


title: A549, Control, 8 Hours, Rep 3

source_name: A549, Control, 8 Hours


title: A549, Control, 4 Hours, Rep 3

source_name: A549, Control, 4 Hours


title: A549, ORMDL3 knockdown, 4 Hours, Rep 2

source_name: A549, ORMDL3 knockdown, 4 Hours

value: ORMDL3 knockdown


title: A549, ORMDL3 knockdown, 4 Hours, Rep 1


title: A549, ORMDL3 knockdown, 8 Hours, Rep 1

source_name: A549, ORMDL3 knockdown, 8 Hours


title: A549, ORMDL3 knockdown, 10 Hours, Rep 3

source_name: A549, ORMDL3 knockdown, 10 Hours


title: A549, ORMDL3 knockdown, 2 Hours, Rep 1

source_name: A549, ORMDL3 knockdown, 2 Hours


title: A549, ORMDL3 knockdown, 10 Hours, Rep 2


title: A549, ORMDL3 knockdown, 8 Hours, Rep 3


title: A549, Control, 8 Hours, Rep 2


title: A549, Control, 0 Hours, Rep 2


title: A549, Control, 2 Hours, Rep 2


title: A549, Control, 10 Hours, Rep 2

source_name: A549, Control, 10 Hours


title: A549, ORMDL3 knockdown, 2 Hours, Rep 2


title: A549, ORMDL3 knockdown, 0 Hours, Rep 2

source_name: A549, ORMDL3 knockdown, 0 Hours


title: A549, ORMDL3 knockdown, 4 Hours, Rep 3


title: A549, ORMDL3 knockdown, 2 Hours, Rep 3


title: A549, Control, 4 Hours, Rep 2


title: A549, ORMDL3 knockdown, 8 Hours, Rep 4


title: A549, Control, 10 Hours, Rep 3


title: A549, ORMDL3 knockdown, 2 Hours, Rep 4


title: A549, ORMDL3 knockdown, 4 Hours, Rep 4


title: A549, ORMDL3 knockdown, 10 Hours, Rep 4


title: A549, ORMDL3 knockdown, 10 Hours, Rep 1


title: A549, Control, 4 Hours, Rep 4


title: A549, ORMDL3 knockdown, 8 Hours, Rep 2


title: HD17C_CD44

status: Public on Nov 10 2018

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

country: USA

institute: University of Rochester Medical Center

data_processing:
Trimming of adapter sequences and low-quality bases with Trimmomatic (version 0.32), parameters: "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Single-end read alignment to human genome build GRCh38 with Subread (version 1.5.1), parameters: "-t 0 -I 5 -m 3 -M 3 -T 1"
Paired-end read alignment to human genome build GRCh38 with Subread (version 1.5.1), parameters: "-t 0 -I 5 -m 3 -M 3 -T 1 -S fr"
Single-end read feature counting with featureCounts (version 1.5.1) with grouping exons into genes, parameters: "-g gene -F GTF -Q 0 -s 0 -t exon"
Paired-end read feature counting with featureCounts (version 1.5.1) with grouping exons into genes, parameters: "-g gene -F GTF -Q 0 -s 0 -t exon -B -p"
Genome_build: GRCh38

source_name: Astrocyte Progenitor Cell

extract_protocol: Human emryonic stem cell lines (hESC) were obtained from Genea Biocell (http://geneabiocells.com/services/shelf-products/human-embryonic-stem-cells/). The hESCs were then differentiated into Glial Progenitor Cells (GPCs) and Astrocyte Progenitor Cells (APCs) by previously described methods. The differentiated GPC and APC populations were further purified by FACS targeting CD140a and CD44 cell surface markers, respectively. The FACS-purified cell populations were used in mRNA isolation and sequencing.

value: Brain

tag: facs marker

tag: subject

value: Huntington's Patient

tag: subject gender

value: Male

tag: source

value: hESC

value: APC


title: HD20B_CD44

tag: tissue

value: Female

tag: cell type


title: HD20A_CD44


title: HD17D_CD44


title: HD20D_CD44


title: HD17E_CD44


title: HD17B_CD44


title: HD18A_CD44


title: A549, Control, 2 Hours, Rep 4


title: A549, Control, 0 Hours, Rep 1


title: A549, Control, 0 Hours, Rep 4


title: A549, ORMDL3 knockdown, 0 Hours, Rep 4


title: CTR02C_CD44


title: CTR19C_CD44


title: CTR19B_CD44


title: CTR19A_CD44


title: A549, Control, 8 Hours, Rep 1


title: A549, Control, 10 Hours, Rep 1


title: A549, ORMDL3 knockdown, 0 Hours, Rep 1


title: A549, Control, 10 Hours, Rep 4


title: CTR19D_CD44


title: A549, Control, 2 Hours, Rep 1


title: HD17A_CD44


title: A549, Control, 4 Hours, Rep 1


title: HD20G_CD140a

data_processing:
mRNA sequencing on Illumina HiSeq 2500 platform
Trimming of adapter sequences and low-quality bases with Trimmomatic (version 0.32), parameters: "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Single-end read alignment to human genome build GRCh38 with Subread (version 1.5.1), parameters: "-t 0 -I 5 -m 3 -M 3 -T 1"
Paired-end read alignment to human genome build GRCh38 with Subread (version 1.5.1), parameters: "-t 0 -I 5 -m 3 -M 3 -T 1 -S fr"
Single-end read feature counting with featureCounts (version 1.5.1) with grouping exons into genes, parameters: "-g gene -F GTF -Q 0 -s 0 -t exon"
Paired-end read feature counting with featureCounts (version 1.5.1) with grouping exons into genes, parameters: "-g gene -F GTF -Q 0 -s 0 -t exon -B -p"
Genome_build: GRCh38

source_name: Glial Progenitor Cell

growth_protocol: The GPC differentiation from hESCs is published in Wang et al. "Human iPSC-Derived Oligodendrocyte Progenitor Cells Can Myelinate and Rescue a Mouse Model of Congenital Hypomyelination" in Cell Stem Cell Volume 12, Issue 2, 2013

value: hPDGFRa

value: GPC


title: HD20A_CD140a


title: HD18D_CD140a


title: HD18B_CD140a


title: HD18F_CD140a


title: HD20E_CD140a


title: HD20C_CD140a


title: HD17C_CD140a


title: CTR19F_CD140a


title: CTR19B_CD140a


title: HD20D_CD140a


title: HD20F_CD140a


title: HD17A_CD140a


title: HD18C_CD140a


title: CTR02D_CD140a


title: HD17B_CD140a


title: HD17F_CD140a


title: CTR19D_CD140a


title: CTR19H_CD140a


title: CTR19A_CD140a


title: CTR02F_CD140a


title: CTR02C_CD140a


title: CTR19C_CD140a


title: CTR02E_CD140a


title: CTR02B_CD140a


title: AngII

status: Public on Nov 01 2018

city: New York

first: Michele

last: Silvestro

address: 550 1st Avenue

department: Surgery

institute: New York University Langone Medical Center

description: Single cell

data_processing:
The Cell Ranger Single Cell Software Suite, version 1.3 was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at:  https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cloupe file was generated using the Cell Ranger 1.3 version. A description of the pipeline and instructions can be found at:  https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/cellranger
Cell types were identified by their expression levels of gene provided that at least two copies of the transcript were found in the cell (cutoff: log2 fold-increased copies = 1 vs 1 copy only per cell). Loupe Cell Browser version 1.0.1 was then used to compare the transcriptome of each identified cluster corrected for False Discovery Rates, as applied in RNA sequencing. Excel files were exported from Loupe Cell Browser 1.0.1 analyses.
For the fastq files, they are as follow for each lane (S5 to S8) Biological is Read 1: each R1 file (length of read 150) Technical reads are as follow:   Read 2 for UMI: each R2 file (length of read 10)   Index 1 for the barcodes: each I1 file (length of read 14)
Genome_build: mm10
Supplementary_files_format_and_content: Cloupe file content K-mean clustering and t-SNE representation of 2440 cells with 217,547 mean reads per cell and a median 1,875 genes per cell
Supplementary_files_format_and_content: Excel files extracted from Loupe Cell Browser: Supplemental table 1 immune cell clustering and analysis of Netrin1 expression. Contains Ensemble ID, gene name, Log2 Fold change and p value in the distinct cell types, macrophages, B cells, T cells, Dendritic cells and neutrophils for 118 distinct genes
Supplementary_files_format_and_content: Excel files extracted from Loupe Cell Browser: Supplemental Table 2. Gene expression in Netrin-1 high and low Macrophages. Contains Ensemble ID, gene name, Log2 Fold change and p value in Netrin Low vs Netrin High Macrophages for 60 distinct genes

source_name: Aortic cells

extract_protocol:
Aortas were collected and digested for 1 hour at 37°C in an enzymatic mix (10 mg/ml Collagenase type II (C6885, Sigma Aldrich) and 1mg/ml Elastase (LS002292, Worthington Biochemistry). Digested aortas were mechanically disrupted and immediately processed for single-cell RNA-sequencing. The cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single cell gel beads in emulsion (GEMs)
Libraries were prepared using the following kits: Chromium Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262, 10x Genomics)
Sequencing was performed on an Illumina HiSeq 4000 as 2 x 150 paired-end reads, one full lane per sample, for approximately >90% sequencing saturation. For alignment, barcode assignment and unique molecular identifiers (UMI) counting, the Cell Ranger Single Cell Software Suite, version 1.3 was used to perform sample de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting (https://support.10xgenomics.com/single-cell-gene)

tag: disease

value: Abdominal aortic aneurysm

value: Apolipoprotein E deficient (ApoE-/-)

value: Angiotensin II perfusion 28 days


title: CTR02A_CD140a


title: Sample20_60h rep2

status: Public on Oct 03 2018

description: BSSE_QGF_13528_130710_SN792_0245_BD2BGDACXX_6_CTTGTA_L006

extract_protocol: Total RNA was extracted using miRNeasy kit (Qiagen).

treatment_protocol: One day after plating, NMuMG/E9 cells were treated with 2ng/ml TGFbeta1 for 0-10d. TGFbeta containing medium was renewed every three days.

value: NMuMG

value: normal mammary gland cells

tag: subclone

value: subclone 9

tag: tgfbeta treatment

tag: replicate


title: Sample23_168h rep2

description: BSSE_QGF_13531_130626_SN792_0239_BD264BACXX_2_ACTTGA_L002


title: Sample16_12h rep2

description: BSSE_QGF_13524_130710_SN792_0245_BD2BGDACXX_4_CTTGTA_L004


title: Sample22_96h rep2

description: BSSE_QGF_13530_130626_SN792_0239_BD264BACXX_2_TGACCA_L002


title: Sample18_36h rep2

description: BSSE_QGF_13526_130710_SN792_0245_BD2BGDACXX_6_TGACCA_L006


title: Sample17_24h rep2

description: BSSE_QGF_13525_130710_SN792_0245_BD2BGDACXX_6_ATCACG_L006


title: Sample21_72h rep2

description: BSSE_QGF_13529_130626_SN792_0239_BD264BACXX_2_ATCACG_L002


title: Sample24_240h rep2

description: BSSE_QGF_13532_130626_SN792_0239_BD264BACXX_2_CTTGTA_L002


title: Sample19_48h rep2

description: BSSE_QGF_13527_130710_SN792_0245_BD2BGDACXX_6_ACTTGA_L006


title: 4d siCtrl rep2

status: Public on Oct 09 2018

source_name: NMUMG cells, clone E9_siCtrl_4d

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen).
200ng RNA was used to generate sequencing libraries with the TruSeq Stranded mRNA LT Sample Prep kit (Illumina). Sequencing was performed on an Illumina HiSeq 2500 with the HiSeq SBS kit v4 from Illumina.

treatment_protocol: NMuMG/E9 cells were transfected with 20nM siRNA. After two days, TGFbeta was added and one day later, cells were retransfected in the presence of TGFbeta to ensure proper downregulation until the end of the experiment (4d TGFb). 0d TGFbeta cells were transfected for three days in the absence of TGFbeta.

tag: cell line/clone

tag: sirna transfected

value: siCtrl

tag: tgfb treatment


title: 0d siCtrl rep2

source_name: NMUMG cells, clone E9_siCtrl_0d


title: 4d siCtrl rep1


title: 0d siCtrl rep1


title: 4d siFoxf2 rep2

source_name: NMUMG cells, clone E9_siFoxf2_4d


title: 4d siFoxf2 rep1


title: Sample15_6h rep2

description: BSSE_QGF_13523_130710_SN792_0245_BD2BGDACXX_4_ACTTGA_L004

tag: cell line


title: Sample12_240h rep1

description: BSSE_QGF_13520_130710_SN792_0245_BD2BGDACXX_3_CTTGTA_L003


title: Sample14_2h rep2

description: BSSE_QGF_13522_130710_SN792_0245_BD2BGDACXX_4_TGACCA_L004


title: Sample11_168h rep1

description: BSSE_QGF_13519_130710_SN792_0245_BD2BGDACXX_3_ACTTGA_L003


title: Sample10_96h rep1

description: BSSE_QGF_13518_130710_SN792_0245_BD2BGDACXX_3_TGACCA_L003


title: Sample9_72h rep1

description: BSSE_QGF_13517_130710_SN792_0245_BD2BGDACXX_3_ATCACG_L003


title: Sample8_60h rep1

description: BSSE_QGF_13516_130710_SN792_0245_BD2BGDACXX_2_CTTGTA_L002


title: Sample7_48h rep1

description: BSSE_QGF_13515_130710_SN792_0245_BD2BGDACXX_2_ACTTGA_L002


title: Sample6_36h rep1

description: BSSE_QGF_13514_130710_SN792_0245_BD2BGDACXX_2_TGACCA_L002


title: Sample5_24h rep1

description: BSSE_QGF_13513_130710_SN792_0245_BD2BGDACXX_2_ATCACG_L002


title: Sample4_12h rep1

description: BSSE_QGF_13512_130710_SN792_0245_BD2BGDACXX_1_CTTGTA_L001


title: Sample3_6h rep1

description: BSSE_QGF_13511_130710_SN792_0245_BD2BGDACXX_1_ACTTGA_L001


title: Sample2_2h rep1

description: BSSE_QGF_13510_130710_SN792_0245_BD2BGDACXX_1_TGACCA_L001


title: Sample13_0h rep2

description: BSSE_QGF_13521_130710_SN792_0245_BD2BGDACXX_4_ATCACG_L004


title: Sample1_0h rep1

description: 5ug of RNA was subjected to rRNA depletion (epicentre ribozero kit) and concentrated (Qiagen min Elute kit) followed by library preparation with the Scriptseq v2 kit form Epicentre/Illumina. All libraries were barcoded and 4-6 plex were used for sequencing.


title: Quadriceps-Healthy-PH11

status: Public on Aug 16 2018

hyb_protocol: Samples were hybridised to Affymetrix HuGene 1.1 ST 16- or 24-PEG array plates for 16 hours using the GeneTitan platform (Affymetrix Ltd.).

scan_protocol: GeneChips were  scanned using the  GeneTitan platform (Affymetrix Ltd.).

data_processing: Raw signal intensity data were RMA-treated, summarizing at the level of Transcript Clusters (TC) using Affymetrix Power Tools (APT, version 1.16.1). Technical batch effects were identified via Principal Variance Component Analysis (PVCA 1.6.0), and the data adjusted accordingly using ComBat (SVA 3.12.0). TC not forming part of the main array design, and universally low expressed TC were removed.

label: biotin*

source_name: Human quadriceps

label_protocol: For each sample, 200ng of total RNA was converted to cDNA using the Ambion Whole Transcript (WT) expression kit.  The Affymetrix GeneChip WT Terminal Labelling Kit* was used to fragment and label 5.5µg of the prepared single-stranded cDNA.

extract_protocol: Total RNA was extracted from quadriceps biopsies using the RNeasy fibrous tissue mini kit (Qiagen). RNA quality was determined by Bioanalyzer (Agilent), and samples with a RIN (RNA Integrity Number) <6 were excluded. RNA was prepared for whole transcriptome microarray analysis using the WT expression kit (Ambion).

tag: disease state

value: Healthy


title: Quadriceps-Healthy-PH13


title: Quadriceps-Healthy-PH1


title: Quadriceps-Healthy-PH21


title: Quadriceps-Healthy-PH5


title: Quadriceps-Healthy-PH16


title: Quadriceps-Healthy-PH19


title: Quadriceps-Healthy-PH17


title: Quadriceps-Healthy-PH8


title: Quadriceps-Healthy-PH20


title: Quadriceps-Healthy-PH15


title: Quadriceps-Healthy-PH10


title: Quadriceps-COPD-PC85

value: COPD


title: Quadriceps-Healthy-PH12


title: Quadriceps-Healthy-PH9


title: Quadriceps-COPD-PC87


title: Quadriceps-COPD-PC86


title: Quadriceps-Healthy-PH14


title: Quadriceps-COPD-PC80


title: Quadriceps-COPD-PC81


title: Quadriceps-COPD-PC89


title: Quadriceps-COPD-PC79


title: Quadriceps-COPD-PC78


title: Quadriceps-COPD-PC77


title: Quadriceps-COPD-PC83


title: Quadriceps-COPD-PC75


title: Quadriceps-COPD-PC73


title: HD18B_CD44

value: Brain


title: Quadriceps-COPD-PC70


title: Quadriceps-COPD-PC72


title: Quadriceps-COPD-PC71


title: Quadriceps-COPD-PC60


title: Quadriceps-COPD-PC67


title: Quadriceps-COPD-PC59


title: Quadriceps-COPD-PC63


title: Quadriceps-COPD-PC62


title: Quadriceps-COPD-PC66


title: Quadriceps-COPD-PC53


title: Quadriceps-COPD-PC52


title: Quadriceps-COPD-PC57


title: Quadriceps-COPD-PC56


title: Quadriceps-COPD-PC5


title: Quadriceps-COPD-PC58


title: Quadriceps-COPD-PC54


title: Quadriceps-COPD-PC55


title: Quadriceps-COPD-PC49


title: Quadriceps-COPD-PC50


title: Quadriceps-COPD-PC61


title: Quadriceps-COPD-PC48


title: Quadriceps-COPD-PC45


title: Quadriceps-COPD-PC9


title: Quadriceps-COPD-PC47


title: Quadriceps-COPD-PC51


title: Quadriceps-COPD-PC43


title: Quadriceps-COPD-PC37


title: Quadriceps-COPD-PC36


title: Quadriceps-COPD-PC39


title: Quadriceps-COPD-PC42


title: Quadriceps-COPD-PC41


title: Quadriceps-COPD-PC34


title: Quadriceps-COPD-PC40


title: Quadriceps-COPD-PC4


title: Quadriceps-COPD-PC32


title: Quadriceps-COPD-PC44


title: Quadriceps-COPD-PC31


title: Quadriceps-COPD-PC3


title: Quadriceps-COPD-PC28


title: Quadriceps-COPD-PC29


title: Quadriceps-COPD-PC25


title: Quadriceps-COPD-PC2


title: Quadriceps-COPD-PC21


title: HD18A_CD140a

value: Huntington's Patient


title: Quadriceps-COPD-PC20


title: Quadriceps-COPD-PC14


title: HD17E_CD140a

value: Male


title: Quadriceps-COPD-PC15


title: Quadriceps-COPD-PC19


title: Quadriceps-COPD-PC38


title: Quadriceps-COPD-PC23


title: Quadriceps-COPD-PC17


title: Quadriceps-COPD-PC10


title: Quadriceps-Healthy-H12


title: Quadriceps-COPD-PC11


title: Quadriceps-COPD-C31


title: Gfi1_WT_132_Spleen

status: Public on Jul 13 2018

description: chromatin IP against AML1-ETO

data_processing:
Bases were called using the Illumina CASAVA 1.8.2
ChIP-seq: Tags were mapped using bwa.
Reads (42 bp) were aligned to the Human (Homo Sapiens) reference genome HG19 or to mouse reference genome mm9.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 10 bp window.

source_name: mouse spleen

growth_protocol: Leukemic cells were cultured in normal cell culture containing 10% serum, spleen cells were isolated from sacrificed wt and KO Gfi1 mice

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: genotype

value: Gfi1 WT

tag: chip antibody

value: antibody AML1-ETO (Diagenode, A706, polyclonal)


title: Quadriceps-COPD-PC13


title: Quadriceps-COPD-PC1


title: Quadriceps-COPD-PC12


title: Quadriceps-COPD-C32


title: Quadriceps-COPD-C30


title: Quadriceps-COPD-C26


title: Quadriceps-COPD-C23


title: 9_SP

status: Public on Jun 22 2018

description: Sample 13

source_name: Hematopoietic cells

extract_protocol:
Total RNA was isolated from cells using the Ambion RNAqueous-Micro kit.
cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).
RNA libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina).

value: IL7R+ SP progenitor

tag: strain


title: 2_BM

description: Sample 15

value: mature BM pDC


title: Quadriceps-COPD-C29


title: Quadriceps-COPD-C34


title: Quadriceps-COPD-C28


title: 8_SP

description: Sample 10


title: 5_DN

description: Sample 4

value: IL7R+ DN progenitor


title: Quadriceps-COPD-C14


title: 2_DP

description: Sample 2

value: IL7R+ DP progenitor


title: 8_DN

description: Sample 8


title: 5_DP

description: Sample 5


title: Quadriceps-COPD-C16


title: Quadriceps-COPD-C15


title: Gfi1_KO_KP66_Spleen

description: chromatin IP against AML1-ETO

value: Gfi1 KO


title: 9_DN

description: Sample 16


title: BSSE_QGF_66850_BM_3_SI-GA-F3

description: Sample 6

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.0.0) to perform quality control, sample de-multiplexing, barcode processing, and single-cell 3′gene counting (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Samples were first demultiplexed and then aligned to the UCSC mouse (mm10) transcriptome and genome using “cellranger mkfastq” with default parameters for all 6 samples.
UMI were counted using “cellranger count”. Samples were merged using “cellranger aggregate” procedure without downscaling.
Further analysis was performed in R (v3.4.0) using the scran (1.4.5) and scatter (1.4.0) packages and following the Bioconductor workflow (for version 3.5).
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl Genes , 1.column is EntrezGeneID, 2. and remaining columns contain UMI counts

extract_protocol: Single cell capture, cDNA and library preparations were performed with the Single Cell 3’ v2 Reagent Kit (10x Genomics)

value: BM pDCs


title: BSSE_QGF_66848_BM_1_SI-GA-D3

description: Sample 4


title: 9_BM

description: Sample 14


title: BSSE_QGF_66849_BM_2_SI-GA-E3

description: Sample 5


title: 8_DP

description: Sample 9


title: BSSE_QGF_66845_SP_1_SI-GA-A3

description: Sample 1

value: splenic pDCs


title: 5_BM

description: Sample 7


title: 9_DP

description: Sample 12


title: IL7R_pDCs_3

description: Sample 11

source_name: Hematopoietic cell

growth_protocol: Progenitors were cultured under FLT3L (100ng/ml) for 4 days and generated mature BST2+ SiglecH+ pDCs were sorted.

value: IL7R progenitor derived pDCs


title: 2_SP

description: Sample 3


title: 5_SP

description: Sample 6


title: Quadriceps-COPD-C22


title: CDP_pDCs_1

description: Sample 4

value: CDP derived pDCs


title: 2_DN

description: Sample 1


title: IL7R_pDCs_1

description: Sample 3


title: Splenic_pDCs_1

description: Sample 2

value: Mature splenic pDCs


title: BSSE_QGF_66846_SP_2_SI-GA-B3

description: Sample 2


title: BM_pDCs_3

description: Sample 9

value: Mature BM pDCs


title: Splenic_pDCs_3

description: Sample 10


title: CDP_pDCs_3

description: Sample 12


title: BSSE_QGF_66847_SP_3_SI-GA-C3

description: Sample 3


title: CDP_pDCs_2

description: Sample 8


title: 8_BM

description: Sample 11


title: IL7R_pDCs_2

description: Sample 7


title: BM_pDCs_2

description: Sample 5


title: Splenic_pDCs_2

description: Sample 6


title: YMB10290_c

status: Public on Jun 20 2018

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

description: liquid culture

data_processing:
basecalling Illumina RTA 1.18.64
demultiplexing Bcl2fastq v2.17
adapter/quality trimming Trimmomatic 0.36 -phred33 ILLUMINACLIP:TruSeq_and_nextera_adapters.fa:3:50:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MAXINFO:50:0.8 MINLEN:25
alignment STAR 2.5.1
quantitation rsem-calculate-expression (RSEM 1.2.22)
Genome_build: Saccharomyces S288C annotation Ensembl_EF4
Supplementary_files_format_and_content: rsem-calculate-expression gene level expression estimates; tab-delimited text

organism: Saccharomyces cerevisiae

source_name: NLS-Htt103Q with SLX5/CEN

growth_protocol: Cells were grown in a 2% raffinose synthetic complete medium at 25°C until reaching mid-log phase. Then, galactose was added to the media to a final concentration of 2% to induce NLS-Htt25Q-GFP or NLS-Htt103Q-GFP expression from the GAL promoter for 4 hrs at 25°C.

extract_protocol:
Total RNAs were isolated from 3 OD600 equivalent cells using MasterPure Yeast RNA purification kit with Dnase I treatment as indicated by the manufacturer (Epicentre).
TruSeq mRNA Prep Kit RS-122-2101; stranded

tag: plasmid

value: BOK372 (SLX5, CEN, HIS)

tag: clone

value: c


title: Kasumi_GFI1

description: chromatin IP against GFI1

data_processing:
Bases were called using the Illumina CASAVA 1.8.2
ChIP-seq: Tags were mapped using bwa.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 10 bp window.

growth_protocol: Leukemic cells were cultured in normal cell culture containing 10% serum.

value: Acute Myeloid Leukemia

value: antibody GFI1 (Santa Cruz, N-20, polyclonal, Lot H3012 )


title: YMB10290_a

description: liquid culture

value: a


title: YMB10289_b

description: liquid culture

source_name: NLS-Htt103Q with empty vector

value: BOK333 (empty vector, CEN, HIS)

value: b


title: YMB10289_a

description: liquid culture


title: YMB10289_c

description: liquid culture


title: YMB10544_b

description: liquid culture

source_name: NLS-Htt25Q with empty vector


title: YMB10545_c

description: liquid culture

source_name: NLS-Htt25Q with SLX5/CEN


title: YMB10545_b

description: liquid culture


title: YMB10544_a

description: liquid culture


title: YMB10545_a

description: liquid culture


title: BM_pDCs_1

description: Sample 1


title: 01-077_At Dx

status: Public on Apr 03 2018

type: genomic

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

hyb_protocol: HumanMethylationEPIC BeadChip

scan_protocol: BeadStudio

data_processing: non-normalized, background subtracted

label: biotin

source_name: Peripheral Blood

label_protocol: standard illumina

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)

tag: gender

value: Male

tag: age

tag: diagnosis

value: Crohn's disease

tag: baseline vs follow-up

value: BL

tag: disease stage at diagnosis

value: B2 stricturing

tag: disease stage at at follow up


title: 01-077_24M

value: FU


title: 05-054_At Dx

value: Female

value: B1 inflammatory


title: 03-009_At Dx


title: 05-054_12M


title: 03-009_24M


title: 06-087

value: non-IBD control


title: 08-016_24M


title: miRNA_240h_rep2

status: Public on Apr 05 2018

data_processing:
Sequencing adapters were removed from obtained single-end miRNA-seq reads (51-mers).
Preprocessed reads were mapped to mouse genome assembly, version mm10, with Bowtie (included in R/Bioconductor package QuasR, version 1.0.9.) allowing up 50 hits in the genome.
miRNA coordinates from miRBase (http://www.mirbase.org/, version 21) were extented by 3bp on each side and miRNA expression levels were quantified as the number of reads that started within any extended mature miRNA.
The differentially expressed miRNAs were identified using the edgeR package (version 3.2.4).
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for miRNAs, 1.column is miRNA id, 2. and remaining columns contain raw counts

source_name: normal mammary gland cells

growth_protocol: NMuMG cells were cultured in normal DMEM medium supplemented with glutamine (2 mM), penicillin (100 U), streptomycin (0.2 mg/l) and fetal calf serum (10%).

extract_protocol:
Total RNA was isolated from NMuMG/E9 cells undergoing TGFβ-induced EMT by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction.
Illumina TruSeq Small RNA Sample Prep was used  to create small RNA libraries as described by the manufacturer. cDNA libraries were size fractionated on a 6 % TBE gel and fragments of 140-160 nt were extracted.

treatment_protocol: NMuMG cells were cultured in the absence and presence of human recombinant TGFbeta for 2, 6, 12, 24, 36, 48, 60, 72 and 96 hours.

value: NMuMG cells

tag: subclone

value: subclone 9

tag: time

tag: replicate


title: miRNA_168h_rep1


title: miRNA_168h_rep2


title: 06-092_36M


title: 03-049_12M


title: SP-49_H3K27ac

status: Public on Jun 03 2018

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

data_processing:
ChIP-Seq: Reads were aligned to the hg19 genome assembly using bwa-aln and bwa-sampe (bwa version 0.7.12).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq: Data were filtered to remove PCR duplicates and reads mapping to >2 genomic sites. Then .tdf display files were generated with igvtools count.

source_name: SP-49 cell line

growth_protocol: Cell lines were grown in RPMI medium 1640 (Invitrogen) supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1mM sodium pyruvate and 5μM 2-mercaptoethanol.

extract_protocol:
ChIP-Seq: Cells were crosslinked by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a Branson sonifier in a 1% SDS-containing lysis buffer. Samples were diluted 1:10 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples, 1:10 diluted sonicated chromatin (whole cell extract; wce) was added directly to the reverse crosslinking step without immunoprecipitation.
ChIP-Seq: Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced (38 bp x 2) on Illumina NextSeq.

tag: cell type

value: Mantle cell lymphoma cell line

value: H3K27ac (Active Motif, catalog #39133)


title: miRNA_240h_rep1

tag: cell line


title: 08-016_At Dx


title: 03-049_At Dx


title: 03-106_At Dx


title: 03-106_36M


title: 07-051


title: 04-006_36M


title: 01-038_24M


title: 04-006_At Dx


title: 01-044_At Dx


title: 01-044_36M


title: 13-126_At Dx


title: 13-126_36M


title: 06-092_At Dx


title: 20-005_At Dx


title: 20-005_36M


title: 04-135_At Dx


title: 04-097_At Dx


title: 02-015_At Dx


title: 04-097_24M


title: 03-043


title: 02-015_36M


title: 03-187


title: 13-185


title: 04-080_At Dx


title: 04-080_36M


title: 22-002


title: 03-103_At Dx


title: 01-038_At Dx


title: 11-023_12M


title: 16-008_36M


title: 18-008_At Dx


title: 06-053_24M


title: 03-099_36M


title: 01-088


title: 18-008_24M


title: 04-135_36M


title: 06-053_At Dx


title: 09-015_At Dx


title: 03-103_36M


title: 04-117


title: 09-015_36M


title: 09-035_At Dx


title: 22-012


title: 03-155


title: 09-035_24M


title: 17-002_At Dx


title: 17-002_24M


title: 10-034_At Dx


title: 10-034_36M


title: 12-013_At Dx


title: 06-010_36M


title: 11-023_At Dx


title: 18-009_At Dx


title: 06-010_At Dx


title: 16-008_At Dx


title: 18-009_36M


title: 05-124_At Dx


title: 18-001_At Dx


title: 03-099_At Dx


title: 05-124_36M


title: 03-127_At Dx


title: 03-127_36M


title: 17-026_At Dx


title: 17-026_36M


title: 17-005_36M


title: 06-045_12M


title: 21-029


title: 07-007_12M


title: 17-005_At Dx


title: 06-045_At Dx


title: 03-121


title: 07-007_At Dx


title: 18-001_24M


title: 04-132_36M


title: 22-001_At Dx


title: 22-001_24M


title: 04-132_At Dx


title: 14-003_At Dx


title: 03-120_At Dx


title: 14-003_36M


title: 03-120_12M


title: 22-021_12M


title: 04-085_At Dx


title: 22-021_At Dx


title: 04-116_At Dx


title: 22-010_At Dx


title: 04-116_36M


title: 08-043


title: 01-042


title: 07-056_At Dx


title: 04-085_36M


title: 20-013_At Dx


title: 05-119_At Dx


title: 07-026_At Dx


title: 07-026_36M


title: 13-070_24M


title: 13-070_At Dx


title: YMB10290_b

description: liquid culture

value: BOK372 (SLX5, CEN, HIS)


title: 03-191_At Dx


title: 07-056_24M


title: 05-119_36M


title: 06-059_At Dx


title: 04-077


title: 06-059_12M


title: 22-024


title: 14-013_36M


title: 22-010_36M


title: 04-017_36M


title: 14-013_At Dx


title: 09-025_24M


title: 04-017_At Dx


title: 22-008_24M


title: 22-008_At Dx


title: 20-013_36M


title: 04-120_36M


title: 04-120_At Dx


title: 15-013


title: 09-048


title: 14-037_12M


title: 03-145_At Dx


title: 09-063_24M


title: 03-144


title: 19-029_36M


title: 27-016_36M


title: 07-066


title: 26-006_12M


title: 18-012_12M


title: 20-012_36M


title: 26-006_At Dx


title: 18-012_At Dx


title: 20-012_At Dx


title: 01-065_36M


title: 01-034_At Dx


title: 18-021_At Dx


title: 03-145_36M


title: 18-021_12M


title: 01-034_36M


title: 14-037_At Dx


title: 03-064_36M


title: 14-027_24M


title: 03-064_At Dx


title: 09-025_At Dx


title: 03-191_36M


title: 27-016_At Dx


title: 16-009_36M


title: 01-065_At Dx


title: 09-063_At Dx


title: 03-112


title: 04-123_12M


title: 16-009_At Dx


title: 04-123_At Dx


title: 13-011_At Dx


title: 06-104


title: 12-013_24M


title: 04-096


title: 13-011_36M


title: 12-036_At Dx


title: 14-027_At Dx


title: 09-008


title: 19-029_At Dx


title: 12-036_36M


title: 04-103_At Dx


title: 01-110_At Dx


title: 04-103_36M


title: 03-168


title: 05-151


title: 03-189


title: 01-110_12M


title: 13-092_At Dx


title: 03-178


title: 13-092_36M


title: 04-129


title: 10-030_At Dx


title: 09-068_At Dx


title: 14-028_At Dx


title: 14-010_36M


title: 01-019_At Dx


title: 14-010_At Dx


title: 14-028_24M


title: 09-068_12M


title: 01-019_36M


title: 01-097


title: 12-018_36M


title: 12-018_At Dx


title: 19-023_At Dx


title: 04-128_At Dx


title: 13-049_At Dx


title: 04-128_24M


title: 03-070


title: 04-034_At Dx


title: 19-023_12M


title: 13-049_36M


title: 19-015_12M


title: 04-034_24M


title: 03-163_36M


title: 03-163_At Dx


title: 13-111


title: 19-015_At Dx


title: 14-036


title: 10-036_24M


title: 01-031_At Dx


title: 10-036_At Dx


title: 01-103


title: 15-014_36M


title: 18-038_At Dx


title: 15-014_At Dx


title: 10-042


title: 10-030_24M


title: 01-031_24M


title: 18-026_12M


title: 21-016_36M


title: 18-026_At Dx


title: 21-016_At Dx


title: 03-152


title: 27-043_36M


title: 07-057_12M


title: 03-060


title: 27-043_At Dx


title: 09-022_At Dx


title: 07-057_At Dx


title: 07-004_36M


title: 09-022_24M


title: 05-127


title: 18-038_24M


title: 13-159_24M


title: 22-036_At Dx


title: 21-013_12M


title: 21-013_At Dx


title: 13-073


title: 05-105_At Dx


title: 05-105_36M


title: 03-182


title: 01-023_At Dx


title: 01-023_36M


title: 13-027_At Dx


title: 20-003


title: 13-027_36M


title: 05-059_36M


title: 07-037


title: 19-038_36M


title: 19-038_At Dx


title: 09-057


title: 03-171


title: 13-006_36M


title: 13-006_At Dx


title: 13-123_At Dx


title: 07-029_At Dx


title: 22-036_24M


title: 06-067


title: 13-123_24M


title: 05-059_At Dx


title: 04-025_At Dx


title: 04-054_36M


title: 14-017


title: 04-054_At Dx


title: 04-025_36M


title: 18-029_24M


title: 18-029_At Dx


title: 06-099_12M


title: 12-014_At Dx


title: 12-014_36M


title: 06-099_At Dx


title: 17-006_At Dx


title: 18-034_At Dx


title: 06-028


title: 03-004_At Dx


title: 03-004_36M


title: 10-023


title: 16-013_12M


title: 16-013_At Dx


title: 09-044_At Dx


title: 07-029_24M


title: 01-079


title: 17-006_36M


title: 08-048_36M


title: 14-006_36M


title: 03-056


title: 18-034_36M


title: 07-004_At Dx


title: 14-006_At Dx


title: 26-001_24M


title: 26-001_At Dx


title: 27-038


title: 02-053


title: 22-013


title: 04-056_At Dx


title: 05-079_At Dx


title: 05-079_36M


title: 09-044_36M


title: 10-039_12M


title: 04-056_36M


title: 14-038_At Dx


title: 02-021_At Dx


title: 05-135


title: 14-038_36M


title: 21-025


title: 08-048_At Dx


title: 03-165_At Dx


title: 02-021_36M


title: 12-029_36M


title: 10-039_At Dx


title: 03-165_36M


title: 27-046


title: 13-159_At Dx


title: 04-073


title: 14-048_36M


title: 14-048_At Dx


title: 10-027_24M


title: 14-021_At Dx


title: 10-027_At Dx


title: 05-104


title: 11-052


title: 21-014_At Dx


title: 21-014_24M


title: 14-021_36M


title: 08-045_At Dx


title: 08-045_24M


title: 12-009_36M


title: 12-009_At Dx


title: 22-039_12M


title: 05-015_At Dx


title: 06-055_12M


title: 21-003_At Dx


title: 21-003_36M


title: 13-174_At Dx


title: 04-044


title: 11-013_At Dx


title: 03-118_24M


title: 13-145_At Dx


title: 05-015_36M


title: 03-032


title: 06-085


title: 13-145_36M


title: 02-019_At Dx


title: 02-019_24M


title: 05-081_At Dx


title: 06-055_At Dx


title: 09-055_At Dx


title: 03-118_At Dx


title: 05-097_At Dx


title: 03-095


title: 01-021_At Dx


title: 13-174_24M


title: 12-029_At Dx


title: 18-017_At Dx


title: 06-052_36M


title: 11-013_12M


title: 19-024_At Dx


title: 05-097_12M


title: 09-055_24M


title: 01-021_24M


title: 22-039_At Dx


title: 14-008


title: 19-018_At Dx


title: 19-024_24M


title: 05-081_36M


title: 06-090


title: 01-014_36M


title: 06-094_12M


title: 03-119


title: 06-094_At Dx


title: 05-028_At Dx


title: 13-028_At Dx


title: 06-076


title: 13-074_At Dx


title: 06-052_At Dx


title: 18-017_24M


title: 13-028_36M


title: 19-018_36M


title: 10-010_36M


title: 10-010_At Dx


title: 01-014_At Dx


title: 14-012_36M


title: 05-028_36M


title: 13-074_36M


title: 14-012_At Dx


title: 09-061_36M


title: 27-007


title: 09-061_At Dx


title: 13-139_At Dx


title: 13-139_36M


title: 18-022_At Dx


title: 18-022_24M


title: 03-076


title: 27-013_36M


title: 13-137


title: 27-013_At Dx


title: 03-170


title: 01-093


title: 13-040_At Dx


title: 03-094


title: 13-040_24M


title: 11-038


title: Sample 41_To_1a

status: Public on Jan 09 2018

data_processing:
Adapter sequence (AAGCAGTGGTATCAACGCAGAGT) was trimmed from obtained single-end RNA-seq reads (51-mers) using the preprocessReads function from QuasR package (Gaidatzis et al., Bioinformatics 2015).
Pre-processed reads were mapped to the human genome assembly, version hg19, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for reporting for multi-mappers only one hit in the final alignment files (outSAMmultNmax=1) and filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR.
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in February 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: hg19
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes, 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts.

source_name: NKp44+ innate lymphoid cells from huNSG tonsils (not cultured)

growth_protocol: NKp44+ innate lymphoid cells were seeded with irradiated feeders (allogeneic human peripheral blood mononuclear cells (20 Gy) (150 000 cells per well) and the B-lymphoblastoid cell line 721.221 (60 Gy) (15 000 cells per well)) in the presence of phytohemagglutinin (PHA-L) (2.5 μg/ml, EMD Millipore) and either IL-2 (600 U/ml) plus IL-7 (10 ng/ml) or IL-12 (50 ng/ml) plus IL-15 (20 ng/ml) (Peprotech). Cytokines were replenished every 3-4 days starting at day 5 and after 3 weeks of culture expanded cells were harvested for RNA-seq. Cultures were maintained in RPMI + 10% human serum AB (Bioconcept) + L-glutamine (2 mM, Gibco) + gentamicin (20 μg/ml) at 37°C under 5% CO2.

extract_protocol:
Total RNA was isolated using PicoPure RNA isolation kit (ThermoFisher). 2 000 – 15 000 freshly isolated splenic ILC3s, 900 – 9 000 tonsillar ILC3s and 10 000 expanded cells were used for RNA isolation.
Non-stranded libraries were prepared according to the Smart-Seq2 protocol (Picelli et al., Nature Protocols 2014) and sequenced on an Illumina HiSeq 2500 using protocols defined by the manufacturer.

tag: tissue

value: tonsil

tag: cultured with

value: none; not cultured


title: Sample 45_To_2a

value: NKp44+ innate lymphoid cells from huNSG tonsils


title: Sample 40_To_17b

source_name: NKp44+ innate lymphoid cells from huNSG tonsils (cultured with IL2 and IL7)

value: IL-2 and IL-7


title: Sample 35_To_13a


title: Sample 53_To_5b


title: Sample 46_To_2b


title: Sample 49_To_3b


title: Sample 51_To_4a


title: Sample 38_To_16b


title: Sample 36_To_13c

source_name: NKp44+ innate lymphoid cells from huNSG tonsils (cultured with IL-12 and IL-15)

value: IL-12 and IL-15


title: Sample 37_To_16a


title: Sample 44_To_20c


title: Sample 34_To_11c


title: Sample 54_To_5c


title: Sample 32_To_10b


title: Sample 33_To_11a


title: Sample 43_To_20b


title: Sample 52_To_5a


title: Sample 42_To_20a


title: Sample 47_To_2c


title: Sample 50_To_3c


title: Sample 39_To_17a


title: Sample 31_To_10a


title: Sample 30_Sp_9c

source_name: NKp44+ innate lymphoid cells from huNSG spleens (cultured with IL-12 and IL-15)

value: spleen


title: Sample 48_To_3a


title: Sample 26_Sp_8b

source_name: NKp44+ innate lymphoid cells from huNSG spleens (cultured with IL2 and IL7)


title: Sample 25_Sp_8a

source_name: NKp44+ innate lymphoid cells from huNSG spleens (not cultured)


title: Sample 29_Sp_9b

value: NKp44+ innate lymphoid cells from huNSG spleens


title: Sample 28_Sp_9a


title: Sample 27_Sp_8c


title: Sample 24_Sp_7c


title: Sample 22_Sp_7a


title: Sample 16_Sp_5a


title: Sample 21_Sp_6c


title: Sample 23_Sp_7b


title: Sample 1_Fe_b

source_name: mixture of irradiated human peripheral blood mononuclear cells (PBMCs) and the B-lymphoblastoid cell line (LCL) 721.221


title: Sample 3_Sp_10a


title: Sample 9_Sp_13a


title: Sample 14_Sp_4b


title: Sample 8_Sp_12c


title: Sample 4_Sp_10c


title: Sample 6_Sp_11c


title: Sample 12_Sp_3a


title: Sample 19_Sp_6a


title: Sample 15_Sp_4c


title: Sample 7_Sp_12a


title: Sample 17_Sp_5b


title: Sample 13_Sp_4a


title: Sample 10_Sp_1a


title: Sample 20_Sp_6b


title: Sample 18_Sp_5c


title: Sample 2_Fe_c

value: mixture of irradiated human peripheral blood mononuclear cells (PBMCs) and the B-lymphoblastoid cell line (LCL) 721.221


title: Sample 5_Sp_11a


title: P6.H3K4me3

status: Public on Dec 20 2017

description: antibody: H3K4me3 (pAb-003-050, A5051-001P, Diagenode)

data_processing:
Bases were called using the Illumina CASAVA 1.8.2
ChIP-seq: Tags were mapped using the Burrows-Wheeler Alignment Tool (BWA).
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 10 bp window.

source_name: Bone marrow mononuclear cells

extract_protocol:
Chromatin was harvested and ChIPs were performed as described (Mandoli A, GDATA, 2014).
ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the HiSeq 2000 (Illumina).

value: AML blast cells

tag: translocation


title: P5.MLL

description: antibody: MLL (AT71-Ab1542, Diagenode)


title: P7.H3K4me3


title: P9.H3K4me3


title: Sample 11_Sp_2a


title: P5.H3K27ac

description: antibody: H3K27ac (A1723-0041d, Diagenode)


title: P4.H3K4me3


title: P3.H3K4me3


title: P5.H3K4me3


title: Usc

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the hg19 genome assembly (see characteristics) BWA
Peaks were called using the hotspot pipeline (Neph et al. 2012)
Genome_build: All ChIP-seq tracks were mapped to genome build HG19
Supplementary_files_format_and_content: wig files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps

growth_protocol: U937 cells were cultured in RPMI 1640 supplemented with 10% FCS and 1% pen/strep at 37 °C.

extract_protocol:
DNA was prepared by isolating nuclei and incubating them with DNaseI before DNA isolation.
DNaseI-seq libraries were prepared according to  Illumina's standard protocol.

value: acute myeloid leukemia (AML) cells

tag: transduced with

value: constructs expressing scrambled (sc) control


title: Umir-194-5p

value: constructs expressing mir-194-5p


title: True memory CD8 T cells sample 2

status: Public on Nov 09 2017

description: Sample 10

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm9, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in July 2013) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm9
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

source_name: lymph nodes, spleen

growth_protocol: Naïve and virtual memory CD8+ T cells were isolated from germ-free mice. True memory T cells were isolated from SPF mice.

extract_protocol:
Trizol extraction followed by RNA clean-up&concentrator (Zymoresearch) with in-column DNAse treatment
200 ng of RNA was utilized for library preparation with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina). Poly-A+ RNA was sequenced by HiSeq SBS kit v4 (Illumina) on an Illumina HiSeq 2500 using protocols defined by the manufacturer.

treatment_protocol: True memory T cells were induced by the immunization with Listeria monocytogenes expressing ovalbumin.

tag: strain (genetic background), hygienic status

value: C57Bl/6, SPF

tag: strain (mutation)

tag: sorted population

value: CD8b+ CD4- CD44+ CD62L+ OVA-4mer+ CD49d+ viable


title: Virtual memory CD8 T cells sample 3

description: Sample 6

value: C57Bl/6, germ-free

value: CD8b+ CD44+ CD62L+ CD49d- viable


title: Naïve CD8 T cells sample 4

description: Sample 7

value: CD8b+ CD44- CD62L+  viable


title: True memory CD8 T cells sample 3

description: Sample 11


title: P8.H3K4me3


title: Virtual memory CD8 T cells sample 1

description: Sample 2


title: miRNA_60h_rep2

value: NMuMG cells

value: subclone 9


title: miRNA_48h_rep2


title: miRNA_24h_rep2


title: miRNA_72h_rep2


title: miRNA_12h_rep2


title: miRNA_96h_rep1


title: miRNA_2h_rep2


title: miRNA_36h_rep2


title: miRNA_0h_rep2


title: True memory CD8 T cells sample 1

description: Sample 9


title: miRNA_6h_rep2


title: miRNA_72h_rep1


title: Virtual memory CD8 T cells sample 4

description: Sample 8


title: miRNA_60h_rep1


title: Virtual memory CD8 T cells sample 2

description: Sample 4


title: Naïve CD8 T cells sample 2

description: Sample 3


title: Naïve CD8 T cells sample 1

description: Sample 1


title: miRNA_48h_rep1


title: Naïve CD8 T cells sample 3

description: Sample 5


title: miRNA_24h_rep1


title: miRNA_36h_rep1


title: miRNA_96h_rep2


title: miRNA_12h_rep1


title: miRNA_6h_rep1


title: miRNA_0h_rep1


title: mmu-miR-429-3p_rep2

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

growth_protocol: NMuMG cells were cultured in normal DMEM medium supplemented with glutamine (2 mM), penicillin (100 U), streptomycin (0.2 mg/l) and fetal calf serum (10%). Cells were cultured in the absence or presence of human recombinant TGFbeta1 (2 ng/ml) for 4 days

extract_protocol:
Total RNA was isolated  using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction.
200 ng of RNA was utilized for library preparation with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina). Poly-A+ RNA was sequenced by HiSeq SBS kit v4 (Illumina) on an Illumina HiSeq 2500 using protocols defined by the manufacturer.

treatment_protocol: NMuMG cells were transfected with 20 nM of pre-miR miRNA precursors (Ambion) using Lipofectamine RNAiMax (Invitrogen). A random sequence has been used as negative control. To maintain an overexpression of miR-1199-5p, miR-200b-3p and miR-429-3p the transfection was repeated every 3rd days.


title: miRNA_2h_rep1


title: mmu-miR-200b-3p_rep1


title: mmu-miR-200b-3p_rep2


title: mmu-miR-Ctr_1_0d_rep2


title: mmu-miR-429-3p_rep1


title: mmu-miR-1199-5p_rep2


title: mmu-miR-Ctr_1_0d_rep1


title: mmu-miR-Ctr_1_4d_rep1


title: mmu-miR-Ctr_1_4d_rep2


title: mmu-miR-1199-5p_rep1


title: no_coating_rep3

status: Public on Oct 26 2017

data_processing:
Obtained single-end RNA-seq reads (51-mers) were mapped to the rat genome assembly, version rn4, with SpliceMap (Au et al., NAR, 2010), included in the R/Bioconductor package QuasR (Gaidatzis et al. Bioinformatics, 2015, version 1.8.4) using the command ‘qAlign("samples.txt", "BSgenome.Rnorvegicus.UCSC.rn4", splicedAlignment=TRUE)’.
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in June 2014) and the qCount function, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample, wig files representing scaled counts in 100 bins

organism: Rattus norvegicus

source_name: cardiac progenitor cells

growth_protocol: Rat CPCs (derived from a clone described in: Beltrami et al., Cell 2003) were cultured in F12 medium (Gibco #21127) containing 10% fetal bovine serum (FBS), 10µg/L leukemia inhibitory factor (LIF; Millipore #ILF2050), 10ng/mL basic fibroblast growthfactor (bFGF; PeproTech #100-18B), 5U/L erythropoietin (Sigma #E5627) and 0.2mM glutathione (Sigma #G6013) at 37℃ with 5% CO2.

extract_protocol:
Cells were washed with PBS and collected with TRIzol (Sigma). Total RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer’s protocol.
TruSeq Stranded Total RNA LT (Illumina) kit were used to generate libraries.

treatment_protocol: Experiments were performed on culture dishes coated with Laminin (Sigma #L2020, ready-made in solution) and Fibronectin (Sigma #F4759, diluted in water). Cells were seeded at low density to avoid cell-cell contact and cultured for 2 hours with 0.1% FBS.

tag: culture conditions

value: no coating

tag: batch


title: no_coating_rep2


title: laminin_rep3

value: laminin


title: fibronectin_rep1

value: fibronectin


title: suspension_rep2

value: suspension


title: fibronectin_rep3


title: no_coating_rep1


title: suspension_rep3


title: laminin_rep2


title: laminin_rep1


title: suspension_rep1


title: tdT positive replicate 4

status: Public on Aug 07 2017

description:
biological replicate 4
BSSE_QGF_55839

data_processing:
Reads were aligned to the mouse genome (mm10) using the spliced read aligner STAR. Sequencing and mapping quality was assessed by the qQCReport function of the R package QuasR. Gene expression was quantified by the qCount function of QuasR using an exon-union model of mm10 RefSeq genes (downloaded from UCSC 2015-12-18).
Genome_build: mm10
Supplementary_files_format_and_content: count table with columns: ENTREZID; SYMBOL; GENENAME; LENGTH; Number of reads overlapping with gene (exon union model) per sample

source_name: Bone-marrow derived macrophages - Il19-tdT positive

growth_protocol: Macrophages were derived from murine bone marrow cells in the presence of 20 ng recombinant murine M-CSF for 7 days

extract_protocol:
Cells were lysed in TRI-reagent (Zymo Research) and RNA was subsequently isolated using the DirectZol RNA Microprep Kit (Zymo Research) according to manufacturers instructions.
Library preparation was performed with 220ng total RNA using the TruSeq Stranded mRNA LT Sample Prep Kit (Cat# RS-122-2101, Illumina, San Diego, CA, USA). Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical). Samples were pooled to equal molarity. Each pool was quantified by PicoGreen Fluorometric measurement in order to be adjusted to 1.5pM and used for clustering on the NextSeq 500 instrument (Illumina).

treatment_protocol: 1 µg/ml LPS (from Escherichia coli O111:B4 (Sigma-Aldrich))

tag: strain

value: Bone-marrow derived macrophages


title: tdT positive replicate 2

description:
biological replicate 2
BSSE_QGF_55835


title: tdT negative replicate 3

description:
biological replicate 3
BSSE_QGF_55838

source_name: Bone-marrow derived macrophages - Il19-tdT negative


title: tdT negative replicate 4

description:
biological replicate 4
BSSE_QGF_55840


title: tdT positive replicate 3

description:
biological replicate 3
BSSE_QGF_55837


title: tdT negative replicate 1

description:
biological replicate 1
BSSE_QGF_55834


title: tdT negative replicate 2

description:
biological replicate 2
BSSE_QGF_55836


title: tdT positive replicate 1

description:
biological replicate 1
BSSE_QGF_55833


title: fibronectin_rep2


title: phenotypically normal siblings of uhrf1-hi272 mutants-1

status: Public on Jul 21 2017

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

description: RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol with Ribo-Zero Gold (Catalog #: RS-122-2501)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed read were mapped to GRCz10 whole genome using bowtie2 v2.1.0 with parameters -q
Accepted bam files were transformed to .sam format for counting repeats read numbers with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes and repeats

organism: Danio rerio

source_name: larvae

extract_protocol: 10 embryos were pooled per sample and extracted with Trizol as manufacturer's instructions.

tag: genotype

value: mix of +/+ and +/-


title: uhrf1-hi272 mutant-1

extract_protocol: 10 embryos were pooled per sample and extracted with Trizol as manufacturer's instructions


title: uhrf1-hi272 mutant-2


title: SCZ164F

status: Public on Jul 20 2017

data_processing:
mRNA sequencing in Illumina HiSeq 2500 platform for approximately 45 million 1x100 bp reads per sample
Trimming of adapter sequences and low-quality bases with Trimmomatic (version 0.32), parameters: "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Read alignment to human genome build GRCh38 with Subread (version 1.4.6-p3), parameters: "-T 12 --gzFASTQinput --BAMoutput -H"
Feature counting with featureCounts (version 1.4.6-p3) with grouping exons into genes, parameters: "-t exon -g gene"
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: Glial Progenitor Cell

growth_protocol: The GPC differentiation from human iPS cells is published in Wang et al. "Human iPSC-Derived Oligodendrocyte Progenitor Cells Can Myelinate and Rescue a Mouse Model of Congenital Hypomyelination" in Cell Stem Cell Volume 12, Issue 2, 2013

extract_protocol:
Human iPS cells were derived from fibroblasts obtained from schizophrenic patients and controls. The iPS cells were then differentiated into Glial Progenitor Cells (GPCs) which were than purified by FACS with PDGFRa (aka CD140a) as cell surface marker. The PDGFRa-positive GPC population was used in RNA isolation and sequencing.
RNA libraries were prepared for sequencing using Illumina's TruSeq RNA V2 library preparation kit.

value: Brain

tag: facs marker

value: hPDGFRa

tag: subject

value: Schizophrenic Patient

tag: subject age

tag: subject ethnicity

value: African American

tag: subject gender

value: Female

tag: source

value: hiPSC

value: GPC


title: SCZ164B

tag: tissue

tag: cell type


title: SCZ164C


title: SCZ164H


title: SCZ164D


title: SCZ164A


title: SCZ164E


title: Desmoplastic small round cell tumor 5

status: Public on Aug 15 2017

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 normalisation with BeadStudio software v3.8

source_name: Desmoplastic small round cell tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: gender

value: M

tag: age (at disease onset)

tag: ct regiment/courses(weeks)

value: epirubicin/ifosfamide/ etoposide/CDDP/3

tag: administration stop befor surgery (weeks)

tag: fu (mons)

value: AWD, 48 , lost

tag: studyid (supplementary table 5)

tag: site of disease

value: diffuse abdominopelvic


title: Desmoplastic small round cell tumor 4

value: epirubicin/ifosfamide/ etoposide/CDDP/6

value: AWD, 20, lost


title: Desmoplastic small round cell tumor 2

value: epirubicin/ifosfamide/ etoposide/CDDP3

value: AWD, 8, lost


title: Desmoplastic small round cell tumor 1

value: DOD, 11


title: Desmoplastic small round cell tumor 6

value: DOD, 60


title: SCZ8D

data_processing:
mRNA sequencing in Illumina HiSeq 2500 platform for approximately 45 million 1x100 bp reads per sample
Trimming of adapter sequences and low-quality bases with Trimmomatic (version 0.32), parameters: "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Read alignment to human genome build GRCh38 with Subread (version 1.4.6-p3), parameters: "-T 12 --gzFASTQinput --BAMoutput -H"
Feature counting with featureCounts (version 1.4.6-p3) with grouping exons into genes, parameters: "-t exon -g gene"
Genome_build: GRCh38

value: Brain

value: Caucasian


title: Desmoplastic small round cell tumor 7

value: epirubicin/ifosfamide/ etoposide/CDDP/4

value: DOD, 36


title: SCZ8A

value: hPDGFRa

value: Schizophrenic Patient

value: Female


title: SCZ51C

value: Male

value: hiPSC

value: GPC


title: SCZ8B


title: phenotypically normal siblings of uhrf1-hi272 mutants-2

description:
" RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol with Ribo-Zero Gold (Catalog #: RS-122-2501)
 	"

value: mix of +/+ and +/-


title: SCZ51E


title: SCZ51B


title: SCZ51A


title: SCZ51F


title: CTR37D

value: Control

value: African American


title: SCZ164G


title: CTR37C


title: SCZ29B


title: CTR37B


title: Desmoplastic small round cell tumor 3

value: M

value: lost

value: diffuse abdominopelvic


title: SCZ8C


title: CTR37A


title: CTR205D


title: CTR205A


title: SCZ51G


title: CTR205F


title: CTR205G


title: CTR205E


title: CTR205B


title: CTR22C


title: CTR22B


title: CTR22A


title: Input_heart_rep2

status: Public on May 24 2017

data_processing:
2007 M. musculus genome assembly (NCBI37/mm9) was used as a basis for all analyses.
Reads were mapped to the mouse genome using the qAlign function from QuasR package with default parameters,  except for allowing up to 10 hits in the genome.
The sample specific fragment sizes were estimated from cross correlation profiles of read density on both chromosomal strands using the Chipcor software.
Reads were shifted by half of the fragment size (100bp) towards the middle of the fragment.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using qExportWig fucntion from QuasR package; Scores represent number of reads in 100bp window scaled to the average library size

source_name: heart

growth_protocol: Dissected cardiac embryonic tissues

extract_protocol:
A modified ChIP protocol was used based on the protocols described in Kim et al. 2007 (PMID: 18265397) and Visel et al. 2009 (PMID: 19212405)
DNA library Prep Kit from New England Biolabs

treatment_protocol: No treatment

tag: developmental stage

tag: strain

value: Hand2 3xFlag mice (Osterwalder et al., Dev Cell, 2014)

tag: chip antibody


title: ChIP_Hand2_heart_rep2

value: mouse monoclonal anti-FLAG , M2 (Sigma, Cat.-No.:F1804)


title: ChIP_Hand2_heart_rep1


title: Input_heart_rep1


title: CTR205C

value: Brain

tag: facs marker

tag: subject

value: Caucasian


title: yeasts under NR, biological rep1

status: Public on Jun 30 2017

city: Seoul

first: Kyung-Mi

last: Choi

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

hyb_protocol: Fragmented and labeled 5 ug of cRNA were hybridized for 16 hr at 45 degree Celsius on GeneChip Yeast 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The microarray data were normalized by Robust Multiarray Average (RMA) using Transcriptome Analysis Console 2.0 (TAC 2.0; Affymetrix). We calculated fold-change between two conditions out of three conditions. We applied one-way analysis of variance (ANOVA) followed by pairwise comparison to obtain p-value between two conditions.

source_name: yeasts under NR at day 5

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneChip Yeast 2.0 array protocol from 100 ng total RNA.

growth_protocol: Yeast cells were grown in YPD media containing 2% glucose (NR), 0.5% glucose (CR) or 2% glucose + 100 nM rapamycin (RM) at 30 degree Celsius.

extract_protocol: We used TRIzol reagent for RNA extraction and treated with DNase1 to reduce genomic DNA contamination. The total RNA was purified using RNeasy Mini kit before microarry experiment.

value: BY4741 background

tag: age

value: five days after inoculation


title: yeasts under NR, biological rep2


title: tumor-artLCMV-OVA-rep3

status: Public on Mar 08 2017

description: treated

hyb_protocol: 100 ng of total RNA were hybridized overnight at 65°C with the nanostring Mm v2 Inflammation codeset according to manufacturer specification. Target-probe complexes were purified on the nCounter Prep Station

scan_protocol: Cartridges were scaned on the Gen1 nCounter Digital Analyzer asking for 1155 FOV

data_processing: Raw counts as provided by the nCounter assay were scale-normalized using the TMM method implemented in the calcNormFactors function of the R package edgeR (McCarthy et al. 2012). The transformed counts (log-CPM values) were subsequently used for linear modelling.

source_name: EG7-OVA tumor subcutanous, 9 days after treatment

label_protocol: not applicable

extract_protocol: Tumor tissue was collected in 1ml QIAzol (QIAGEN) and homogenized using a metal bead and the QIAGEN Tissue Lyser. RNA was extracted with a standard isopropanol precipitation method according to the manufacturer's instructions.

treatment_protocol: EG7-OVA tumor cells were implanted subcutaneously into the flank of C57BL/6 mice. When tumors became palpable (d7), they were treated with artLCMV-OVA or left  untreated. Tumor tissue was analyzed on d9 after treatment.

value: tumor EG7-OVA cells

tag: sample collection time

value: 9 days post treatment


title: tumor-untreated-rep2

description: untreated


title: tumor-untreated-rep4

description: untreated


title: tumor-untreated-rep1

description: untreated


title: yeasts under CR, biological rep1

source_name: yeasts under CR at day 5


title: tumor-artLCMV-OVA-rep2

description: treated


title: yeasts under RM, biological rep2

source_name: yeasts under RM at day 5


title: tumor-artLCMV-OVA-rep1

description: treated


title: yeasts under RM, biological rep1


title: tumor-artLCMV-OVA-rep5

description: treated


title: yeasts under CR, biological rep2


title: yeasts under CR, biological rep3


title: tumor-untreated-rep3

description: untreated


title: yeasts under NR, biological rep3


title: yeasts under RM, biological rep3


title: THP-1_RUNX1

status: Public on Jan 24 2017

data_processing:
Bases were called using the Illumina CASAVA 1.8.2
ChIP-seq: Tags were mapped using the Burrows-Wheeler Alignment Tool (BWA).
RNA-seq: Tags were mapped using TopHat2 (Bowtie2).
4C-seq: A reduced genome was generated by extracting the sequences flanking DpnII sites (30bp on each strand from the DpnII sites to downstream). Only uniquely mapped DpnII sites were considered for downstream analysis.  Reads from each library were parsed based on the bait-specific primer sequence and mapped to the reduced genome using bwa (version 0.6.2) with the default parameters. 4C signal was calculated using a sliding window of 10Kb (±5Kb of a given DpnII site) and normalized to the total number uniquely mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 10 bp window. BedGraph files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 50 bp window

growth_protocol: Cell lines were routinely cultured in RPMI 1640 supplemented with 10% FCS and 1% pen/strep at 37 °C.

extract_protocol:
Chromatin from cell lines was harvested and ChIPs were performed as described (Mandoli A, GDATA, 2014). Total RNA was extracted with TRIzol (Invitrogen) or RNAsol (GenDepot), treated with DNAse on column (Qiagen) and analyzed by strand specific sequencing.
ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, AF9, AF4, and RUNX1, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the Genome Analyzer (Illumina) or HiSeq 2000 (Illumina). For RNA-seq 250 ng of RNA was used for ribosomal RNA depletion with RiboZero (Illumina) and subsequent strand specific (USER) library preparation. 4C-seq libraries were prepared as previously described (Van de Werken, Nat. Meth., 2012)

value: AML cell line

tag: translocation


title: MV4-11_RUNX1


title: THP-1_PHLPP1_Bait_2


title: THP-1_MLL


title: THP-1_H3K27ac


title: THP-1_RNA


title: THP-1_RNA_PE


title: THP-1_BCL2_Bait_2


title: THP-1_H3K79me2


title: THP-1_PHLPP1_Bait_1


title: THP-1_H3K4me3


title: AML_MLLAF9_1_RNA

value: AML blast cells


title: THP-1_BCL2_Bait_1


title: AML_MLLAF9_4.2_RNA_PE


title: MV4-11_H3K27ac


title: AML_MLLAF9_2_RNA


title: MV4-11_RNA


title: AML_MLLAF9_4.1_RNA


title: MV4-11_H3K4me3


title: MV4-11_AF4


title: ChIP P300

status: Public on Nov 15 2016

data_processing:
Basecalls performed using CASAVA for both ChIP-seq and RNA-seq
Reads were aligned to the hg19 genome assembly (see characteristics) BWA for both ChIP-seq and RNA-seq
Peaks were called using MACS2 on settings: q 0.01
Genome_build: All ChIP-seq and RNA-seq tracks were mapped to genome build HG19
Supplementary_files_format_and_content: wig files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps

growth_protocol: Kasumi-1 cells was cultured in RPMI 1640 supplemented with 10% FCS and 1% pen/strep at 37 °C and shRNA cell lines were culture in tet free FCS.

extract_protocol:
Chromatin was sonicated and used for ChIP seq using specific antibodies (avialable on suplementry table). RNA was extracted using qiagen rneasy and treated with ribozero kit.
ChIP seq libraries were preapared according to  Illumina's standard protocol. For RNA-seq cDNA was prepared according to strand specific and libraries were preapared according to  Illumina's standard protocol

treatment_protocol: shRNA was induced for 72hr for knockdown by adding 600ng/ml doxycyclin.

tag: cell line

value: human acute myeloid leukemia cell line

tag: antibody target

tag: chip antibody vendor

value: Santa cruz

tag: chip antibody cat. #


title: ChIP HDAC1

tag: cell type

value: Abcam


title: RNA seq ERG Knockdown

value: Kasumi -1

tag: genotype/variation

value: ERG Knockdown


title: ChIP HDAC2


title: ChIP H3K9K14ac (MS275_24h)

value: Diagenode


title: ChIP FLI1


title: ChIP AML1-ETO


title: ChIP LYL

value: LYL


title: AML_MLLAF9_3_RNA


title: ChIP ERG

value: ERG


title: THP-1_AF9


title: MV4-11_H3K79me2


title: RNA seq ERG control


title: ChIP_RUNX1


title: ChIP GATA 2


title: NB4_RUNX1

status: Public on Nov 22 2016

description:
chromatin IP against RUNX1
NB4_RUNX1_4649

data_processing:
Reads (42 bp) were aligned to the Human (Homo Sapiens) reference genome HG19. Peaks were called using MACS.
Bases were called using the Illumina CASAVA 1.8.2
ChIP-seq: Tags were mapped using bwa.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 10 bp window.

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

value: leukemic cells

value: antibody RUNX1 (Abcam ab23980)


title: MV4-11_MLL


title: ChIP TAL1


title: ChIP H3K9K14ac (MS275_4h)


title: ChIP H3K9K14ac

value: Upstate


title: Spleen_Isotype_9

status: Public on Sep 19 2016

description: tissue: Spleen, treatment: Isotype, annimal id: 9, batch: 20160107

data_processing: The read.markup.RCC function the R package NanoStringNorm (Waggott, D.M., 2015) was used to read the raw count data. Raw counts were scale-normalized using the TMM method implemented in the calcNormFactors function of the R package edgeR (McCarthy et al. 2012). The transformed counts (log-CPM values) were subsequently used for linear modelling.

source_name: spleen

extract_protocol: Samples were harvested directly in Trizol, after homogeneization of the tissue, phase separation was performed with chloroform and RNA was precipitated with Isopropanol and washed with ethanol according to standard procedures.

treatment_protocol: αIFNAR and isotype control antibody were administred i.p. one day prior to infection at a dose of 1mg per mouse. αGR-1 antibody was administered 2 days and half a day prior to infection at a dose of 500ug ip

tag: tissue

value: spleen

tag: gender

value: male

value: 8 weeks old


title: Spleen_anti-IFNAR_6

description: tissue: Spleen, treatment: anti-IFNAR, annimal id: 6, batch: 20160107


title: Spleen_anti-IFNAR_8

description: tissue: Spleen, treatment: anti-IFNAR, annimal id: 8, batch: 20160107


title: Spleen_anti-IFNAR_5

description: tissue: Spleen, treatment: anti-IFNAR, annimal id: 5, batch: 20160107


title: Spleen_anti-Gr1_3

description: tissue: Spleen, treatment: anti-Gr1, annimal id: 3, batch: 20160107


title: ChIP H4ac

value: millipore


title: Spleen_anti-Gr1_2

description: tissue: Spleen, treatment: anti-Gr1, annimal id: 2, batch: 20160107


title: Spleen_Isotype_12

description: tissue: Spleen, treatment: Isotype, annimal id: 12, batch: 20160107


title: BM_Isotype_9

description: tissue: BM, treatment: Isotype, annimal id: 9, batch: 20160107

source_name: Bone Marrow

value: Bone Marrow


title: Spleen_anti-Gr1_1

description: tissue: Spleen, treatment: anti-Gr1, annimal id: 1, batch: 20160107


title: Spleen_Isotype_10

description: tissue: Spleen, treatment: Isotype, annimal id: 10, batch: 20160107


title: BM_anti-IFNAR_8

description: tissue: BM, treatment: anti-IFNAR, annimal id: 8, batch: 20160107


title: BM_anti-IFNAR_6

description: tissue: BM, treatment: anti-IFNAR, annimal id: 6, batch: 20160107


title: Spleen_Isotype_11

description: tissue: Spleen, treatment: Isotype, annimal id: 11, batch: 20160107


title: BM_anti-IFNAR_5

description: tissue: BM, treatment: anti-IFNAR, annimal id: 5, batch: 20160107


title: BM_anti-Gr1_3

description: tissue: BM, treatment: anti-Gr1, annimal id: 3, batch: 20160107


title: Isotype_5

description:
treatment: Isotype, annimal id: 5, batch: 1
processed data: counts.tsv, column C_1

data_processing:
Sequenced reads were mapped to mm9 whole genome using STAR version 020201 (Dobin et al., Bioinformatics 2013) with parameters --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within
Raw reads and mapping quality was assessed by the qQCReport function from the R package QuasR (Gaidatzis et al., 2015).
Expression of RefSeq genes (UCSC version downloaded 2013-07-25) was quantified by counting reads mapping into exons using the qCount function of QuasR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with EntrezId (1st column), gene symbol (2nd column), gene name (3rd column), total length of exons in bp (4th column) and followed by raw counts for each sample (columns 5-12)

extract_protocol:
Cells were FACS-sorted directly ex-vivo into Trizol and RNA was extracted using Direct-zolTM RNA MicroPrep kit (Zymo research)
Library preparation was performed with a TruSeq kit (Illumina) according to the provider’s protocol.

treatment_protocol: αIFNAR and isotype control antibody were administred i.p. one day prior to infection at a dose of 1mg per mouse.

value: 10 weeks old

value: KL25HL B cell

tag: cell markers


title: Isotype_6

description:
treatment: Isotype, annimal id: 6, batch: 1
processed data: counts.tsv, column C_2


title: aIFNAR_8

description:
treatment: aIFNAR, annimal id: 8, batch: 2
processed data: counts.tsv, column A_3


title: aIFNAR_2

description:
treatment: aIFNAR, annimal id: 2, batch: 1
processed data: counts.tsv, column A_2


title: BM_uninfected_13

description: tissue: BM, treatment: uninfected, annimal id: 13, batch: 20151217


title: Spleen_uninfected_13

description: tissue: Spleen, treatment: uninfected, annimal id: 13, batch: 20151217


title: BM_Isotype_10

description: tissue: BM, treatment: Isotype, annimal id: 10, batch: 20160107


title: Spleen_uninfected_15

description: tissue: Spleen, treatment: uninfected, annimal id: 15, batch: 20151217


title: aIFNAR_1

description:
treatment: aIFNAR, annimal id: 1, batch: 1
processed data: counts.tsv, column A_1


title: BM_anti-Gr1_2

description: tissue: BM, treatment: anti-Gr1, annimal id: 2, batch: 20160107


title: Isotype_11

description:
treatment: Isotype, annimal id: 11, batch: 2
processed data: counts.tsv, column C_3