title: lungcancer4-Input

first: Shuibin

last: Lin

address: 1 Blackfan Circle

institute: Boston Childrens Hospital

description:
Input
m6A_gene_list.txt

data_processing:
To analyze the global profiling of mRNA lifetime and translation efficiency, the clean reads were aligned to human reference genome (hg19) using Tophat2 (Kim et al., 2013) after trimming the adapters and filtering low quality sequences from the raw data. The reads mapped to each genes were counted using HTSeq (Harrow et al., 2012) based on the GENCODE gene model (v19) (Anders et al., 2015). The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM). ERCC RNA Spike-In Control Mixes (Ambion) were added into each sample before constructing the library to normalize the reads.
For m6A MeRIP-Seq, reads were aligned to hg19 using tophat, peak calling was done with MACS2
To identify the alternative splicing events, all the clean RNA-Seq reads of control and METTL3 knockdown samples were firstly trimmed to same length with 72 bp, which were then alighted against the human hg19 (GRCh37) reference genome using Tophat263. rMATS v3.2.564 was used to detect the splicing events and significant splicing differences between METTL3 knockdown and control samples.
Genome_build: hg19

source_name: Patient sample

growth_protocol: HeLa cells were cultured with DMEM plus 10% FBS and antibiotics. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
For mRNA half life and translation efficiency, total RNA samples were isolated with Trizol following the manufacturer’s instructions. For m6A MeRIP-Seq, portions of fresh tumor tissue approximately 0.5 x 0.5 x 0.5cm were snap frozen and preserved at -80C, pulverized in liquid nitrogen and stabilized in Trizol for total RNA isolation. Then the mRNA purification from total RNA was performed using PolyATtract mRNA Isolation Systems (Promega). 2g of the purified mRNA was fragmented and immunoprecipitated with α-m6A antibody (Synaptic Systems, 202003). The purified RNA fragments from m6A MeRIP were used for library construction using the TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101) and sequenced with Illumina NextSeq 500.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit.

treatment_protocol: METTL3 expression were knockdown using shRNA.

value: lung cancer

value: Tumor sample


title: lungcancer4-m6A-IP2

status: Public on Sep 21 2018

type: SRA

city: Boston

country: USA

description:
m6A-IP
m6A_gene_list.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

tag: experiment


title: lungcancer3-m6A-IP1

description:
m6A-IP
m6A_gene_list.txt


title: lungcancer3-m6A-IP2

description:
m6A-IP
m6A_gene_list.txt


title: lungcancer2-m6A-IP2

description:
m6A-IP
m6A_gene_list.txt


title: 02212018-A07-NA19098

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description:
eset.rds
scqtl-counts.txt.gz
scqtl-annotation.txt
scqtl-annotation-description.txt
quality-single-cells.txt
genes-pass-filter.txt

data_processing:
We used `umi_tools extract` (UMI-tools 0.5.3) to extract the 6 base pair unique molecular identifier (UMI) from the 5’ end of each read.
We used `subjunc` (Subread 1.5.3) to map reads to the human genome (Ensembl GRCh37.75; chromosomes 1-22, X, Y, MT) and ERCC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa). Some samples included spike-in RNA from Drosophila melanogaster or Caenorhabditis elegans, so we also included the Ensembl genomes BDGP5.75 and WBcel235.75.
We used `featureCounts` (Subread 1.5.3) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 75) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
We used `umi_tools dedup` (UMI-tools 0.5.3) to deduplicate reads with the same UMI and start position to molecules.
We used `verifyBamID` (1.1.3) to identify the individual of origin for each sample based on the overlap of the RNA-seq reads with the known genotypes.
Genome_build: GRCh37
Supplementary_files_format_and_content: The file eset.rds is a serialized R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS(“eset.rds”)`. It contains the gene counts, sample metadata, and feature metadata for 54,616 genes (H. sapiens, C. elegans, D. melanogaster, ERCC) and 7,584 single cells. The file scqtl-counts.txt.gz is a gzipped tab-delimited plain text file that contains the counts for 20,151 human genes for 7,584 single cells. The file scqtl-annotation.txt is a tab-delimited plain text file that contains 40 metadata columns for the 7,584 single cells.  The file scqtl-annotation-description.txt is a tab-delimited plain text file that contains descriptions of the 40 metadata columns in scqtl-annotation.txt. The file quality-single-cells.txt is a tab-delimited plain text file (no header row) that contains a logical vector denoting whether each single cell was determined to be a high-quality cell and used in the study (TRUE) or a low-quality cell that was discarded (FALSE). The file genes-pass-filter.txt is a tab-delimited plain text file (no header row) that contains a logical vector denoting whether each human gene (total of 20,151) was determined to be expressed and included in the study (TRUE) or discarded (FALSE).

source_name: LCL-derived iPSC

growth_protocol: We cultured Yoruba iPSCs (Banovich et al., 2018) in feeder-free conditions for at least ten passages in E8 medium (Life Technologies) (Chen et al., 2011).

extract_protocol:
We collected cells using the C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm).
We performed single cell capture and library preparation as previously described using 6 bp Unique Molecular Identifiers (Tung et al., 2017). We pooled the 96 samples on each C1 chip and sequenced them on an Illumina HiSeq 2500 using the TruSeq SBS Kit v3-HS (FC-401-3002).

tag: well

tag: individual

tag: batch


title: lungcancer2-m6A-IP1

description:
m6A-IP
m6A_gene_list.txt


title: Mock 3h replicate 1

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
Mock_3h_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv

data_processing:
Constructed libraries were sequenced on a NextSeq 500 Illumina platform, producing 2x100nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Sequencing and cell quality control of the primary sequencing data were performed using Illumina's SureCell scRNA-seq application in Basespace.
Alignments to the hg38 genome and subsequent counts were generated using Illumina's SureCell scRNA-seq application.
Following count generation, all processing steps (batch correction, normalization, differential expression) were performed using Seurat v2.3.4.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: All_counts_passfilter_all_merged.csv: Comma-separated text file includes counts.

molecule: total RNA

source_name: A549 cells

extract_protocol:
Single cells were individually partitioned into subnanoliter droplets on a cartridge using a one-touch ddSEQ Single-Cell Isolator. Cell lysis and cell barcoding occur inside individual droplets, and single-cell-barcoded RNA-Seq libraries are subsequently prepared using Nextera technology.
SureCell WTA 3′ Library Prep Kit for the ddSEQ System.

treatment_protocol: A549 cells were treated with IL-1β for 3h, 6h, or 12h.

tag: cell line

value: alveolar basal epithelial cells

tag: treatment

value: Mock 3h


title: 02212018-A06-NA18505


title: lungcancer2-Input

description:
Input
m6A_gene_list.txt


title: lungcancer1-m6A-IP2

description:
m6A-IP
m6A_gene_list.txt


title: 02212018-A05-NA18913


title: lungcancer1-m6A-IP1

description:
m6A-IP
m6A_gene_list.txt


title: 02212018-A04-NA18505


title: 02212018-A03-NA18913


title: lungcancer1-Input

description:
Input
m6A_gene_list.txt


title: 02212018-B06-NA18913


title: HMEC-CT2 DMSO rep 1

first: Jean

last: Zhao

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
FASTX to filter for read quality, remove adaptor sequences, remove short reads, and trim the 5' most nucleotide
Bowtie2 to remove rRNA, tRNA and mtRNA sequences
For ribosomal footprint samples, awk to filter for reads of footprint lengths
STAR to align reads
GenomicAlignments to filter for reads compatible with known splice variants
Replace alignments with nucleotide at central most position
Bedtools to count reads aligning to CDS regions of each gene (across only common regions between all isoforms, and excluding short regions spanning from -2 to +15 codons of each start codon, and -8 to +2 codons of each end codon)
Calculate RPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene in each sample, columns are arranged by sample name, i.e. CT2_RF1, CT2_RF2, and so on.

source_name: Cell line

growth_protocol: HMEC-CT2 and MCF10A (Er-Src) cells were cultured under standard conditions. MCF10A cells were treated with 4HT to induce nuclear translocation of Er-Src and oncogenic transformation.

extract_protocol:
Cells were processed for ribosomal profiling using the protocol by Ingolia et al.
Libraries were constructed using the protocol by Ingolia et al.

treatment_protocol: HMEC-CT2 cells were treated with DMSO or Torin-1 for 1 h. MCF10A (Er-Src) cells were treated with vehicle control, glucose limitation, or cysteine/cystine limitation, for 30 min.

value: DMSO

tag: replicate number

tag: molecule

value: Ribosomal footprint RNA


title: ShML3-3-B6h

description:
stability
Stability.txt

source_name: HeLa cells

tag: actd treatment

tag: shRNA knockdown

value: HeLa

value: cervical cancer cells

value: HeLa ShMETTL3 shRNA-3


title: ShML3-2-B6h

description:
stability
Stability.txt

value: HeLa ShMETTL3 shRNA-2


title: ShGFP-B6h

description:
stability
Stability.txt

value: ShGFP

value: HeLa ShGFP control


title: 02202018-H12-NA19203


title: 02212018-A02-NA18913


title: ShML3-3-B4h

description:
stability
Stability.txt


title: 02212018-A08-NA18913


title: HeLa-B6h

description:
stability
Stability.txt

value: control

value: HeLa parental cells


title: 02202018-H11-NA19159


title: ShGFP-B4h

description:
stability
Stability.txt


title: 02202018-H09-NA19204


title: HeLa-B4h

description:
stability
Stability.txt


title: ShML3-3-B2h

description:
stability
Stability.txt


title: ShML3-2-B2h

description:
stability
Stability.txt


title: 02202018-H06-NA19159


title: 02202018-H05-NA19159


title: lungcancer4-m6A-IP1

description:
m6A-IP
m6A_gene_list.txt


title: 02202018-H07-NA19159


title: ShGFP-B2h

description:
stability
Stability.txt


title: ShML3-2-B4h

description:
stability
Stability.txt


title: ShML3-3-B0h

description:
stability
Stability.txt


title: 02202018-H04-NA19159


title: ShML3-2-B0h

description:
stability
Stability.txt


title: 02212018-A01-NA19143


title: 02202018-H02-NA19159


title: lungcancer3-Input

description:
Input
m6A_gene_list.txt


title: HeLa-B2h

description:
stability
Stability.txt


title: 02202018-H03-NA19159


title: 02202018-H01-NA19159


title: ShGFP-B0h

description:
stability
Stability.txt


title: 02202018-G12-NA18913


title: HeLa-B0h

description:
stability
Stability.txt


title: 02202018-H10-NA19204


title: 02202018-G10-NA18913


title: 02202018-H08-NA19159


title: 02202018-G11-NA19159


title: ShML3-3-A6h

description:
stability
Stability.txt


title: 02202018-G07-NA19203


title: ShGFP-A6h

description:
stability
Stability.txt


title: 02202018-G08-NA18913


title: 02202018-G06-NA18913


title: ShML3-3-A4h

description:
stability
Stability.txt


title: ShML3-2-A4h

description:
stability
Stability.txt


title: ShGFP-A4h

description:
stability
Stability.txt


title: HeLa-A6h

description:
stability
Stability.txt


title: HeLa-A4h

description:
stability
Stability.txt


title: 02202018-G04-NA19159


title: 02202018-G03-NA19159


title: ShML3-3-A2h

description:
stability
Stability.txt


title: ShML3-2-A2h

description:
stability
Stability.txt


title: 02202018-G02-NA19159


title: 02202018-F12-NA19159


title: 02202018-G01-NA19159


title: HeLa-A2h

description:
stability
Stability.txt


title: ShGFP-A2h

description:
stability
Stability.txt


title: 02202018-F10-NA19204


title: 02202018-F11-NA19159


title: ShML3-3-A0h

description:
stability
Stability.txt


title: ShML3-2-A0h

description:
stability
Stability.txt


title: 02202018-F09-NA19159


title: ShGFP-A0h

description:
stability
Stability.txt


title: 02202018-G09-NA18913


title: 02202018-F07-NA19159


title: ShML3-2-A6h

description:
stability
Stability.txt


title: 02202018-F08-NA19159


title: HeLa-A0h

description:
stability
Stability.txt


title: 02202018-F06-NA19204


title: ShML3-3_Mono

description:
monosome
Polysome_profiling.txt


title: ShML3-3_Poly

description:
polysome
Polysome_profiling.txt


title: 02202018-G05-NA19204


title: 02202018-F04-NA19203


title: ShML3-2_Mono

description:
monosome
Polysome_profiling.txt


title: ShML3-3_Input

description:
Input
Polysome_profiling.txt


title: 02202018-F03-NA19203


title: 02202018-F01-NA19203


title: 02202018-F05-NA19159


title: ShGFP_Mono

description:
monosome
Polysome_profiling.txt


title: 02202018-E12-NA19203


title: ShGFP_Input

description:
Input
Polysome_profiling.txt


title: ShML3-2_Poly

description:
polysome
Polysome_profiling.txt


title: 02202018-E11-NA19159


title: 02202018-E10-NA19203


title: HeLa_Poly

description:
polysome
Polysome_profiling.txt


title: 02202018-F02-NA19203


title: 02202018-E09-NA19159


title: HeLa_Mono

description:
monosome
Polysome_profiling.txt


title: HeLa_Input

description:
Input
Polysome_profiling.txt


title: 02202018-E08-NA19159


title: 02202018-E03-NA19159


title: 02202018-E05-NA19203


title: Input – H3K27me3

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

library_source: genomic

data_processing:
ChIP was essentially performed as described previously (Mohn et al., 2008). Briefly, after trypsinization and quenching 25 million Hap ES cells were washed once in PBS before fixing for 7 min by addition of formaldehyde to a final concentration of 1%. Crosslinking was then quenched by addition of 2.5 M glycine (0.125 M final concentration) and cells were then incubated on ice.  Crosslinked cells were spun at 600 3 g for 5 min, nuclei were prepared by consecutive washes with Rinse 1 buffer (final: 50 mM HEPES pH 8.0, 140 mM NaCl, 10% glycerol, 0.5% NP40, 0.25% Triton X100, 1 mM EDTA) followed by Rinse 2 buffer (final: 10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Pellets were resuspended in 2 ml total volume of Sonication buffer (0.1% SDS, 1mM EDTA, pH 8, 10mM Tris HCl, pH 8 with protease inhibitors complete mini (Roche)) and then  sonicated with a Covaris E220 sonicator (Covaris settings: 5% duty cycle, PIP 140, 200cyles/ burst, 15 minutes). ChIP was perfomed in ChIP buffer (final: 50 mM HEPES/KOH pH 7.5, 300 mM NaCl , 1 mM EDTA, 1 % Triton X100, 0.1 % DOC, 0.1% SDS) with the indicated antibody.
The reads are aligned with Bowtie2 (standard parameter).
MACS (1.4) is used for peak calling of ATAC, H3K4me3, H3K27ac. Broad peaks of H3K27me3 are called with SICER (W1000, G3000).
Genome_build: mm10
Supplementary_files_format_and_content: Standard BED files of MACS and SICER

molecule: genomic DNA

organism: Mus musculus

source_name: HapES cells (AN3-12)

growth_protocol: Haploid ES cells were grown in standard ES cell medium with serum and LIF. ES cell medium contains of 450 ml DMEM (Sigma D1152); 75 ml FCS  (Invitrogen); 5,5 ml P/S  (Sigma P0781); 5,5 ml NEAA  (Sigma M7145); 5,5 ml LGlu (Sigma G7513); 5,5 ml NaPyr (Sigma S8636); 0,55 ml bME   Merck 805740 (dilute 10 l bME in 2.85 ml PBS for a 1000x stock); and ESGRO Millipore ESG1107 (according to instructions by the manufacturer).

extract_protocol: Illumina NEBNext kit

tag: antibody


title: Input – H3K27Ac


title: ShGFP_Poly

description:
polysome
Polysome_profiling.txt


title: 02202018-E02-NA19159


title: Bcl11bKO_1%_input-rep1

city: Pasadena

first: Maile

last: Romero-Wolf

state: CA

address: 1200 E California Blvd

department: BBE

institute: California Institute of Technology

data_processing:
ChIP-seq data were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED-files  All genomic coordinates are relative to mm9 mouse assembly.

source_name: Lin- BM derived Bcl11bKO cells

growth_protocol: [Lin- BM isolation / culture protocol] ChIP-seq; Bone marrow (BM) was removed from the femurs and tibiae of 2-3 month-old mice.  Suspensions of BM cells were prepared and stained for lineage markers using biotin-conjugated lineage antibodies (CD11b, CD11c, Gr1, TER-119, NK1.1, CD19, CD3ε, B220), then incubated with streptavidin-coated magnetic beads (Miltenyi Biotec), and passed through a magnetic column (Miltenyi Biotec).  Then, Lin-, Sca1+, Kit+ (LSK) cells were sorted on a FACSAria (BD Bioscience).  LSK cells were cultured on OP9-DL1 monolayers using OP9 medium (α-MEM, 20% FCS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).  On day 7, cultured cells were disaggregated, filtered through 40-μm nylon mesh, and cultured on OP9-DL1 monolayers with medium containing 5 ng/ml of IL-7, 5 ng/ml of Flt3L and 120nM of 4-OHT (Sigma-Aldrich).  Two days later 4-OHT was removed, and cells were cultured for an additional 5 days on OP9-DL1 with 1 ng/ml of IL-7, 1 ng/ml of Flt3L, and subjected to further analysis.

extract_protocol:
ChIP-seq; Ten million of BM-derived DN3 cells with 1% formaldehyde for 10 min.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Five ug per 10^7 cells of anti-H3K27Ac Abs (ab4729, Abcam) were hybridized to Dynabeads anti-Rabbit (Invitrogen) and added to the diluted chromatin complex.  They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 ug/ml proteinase K).  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.
ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

tag: strain

value: Cultured on OP9DL1

tag: chip antibody


title: WT_DN3_1%_input-rep2

source_name: Lin- BM derived WT DN3 cells


title: WT_DN3_1%_input-rep1


title: 02202018-E01-NA19203


title: 02202018-E06-NA19159


title: 02202018-D11-NA18913


title: ShML3-2_Input

description:
Input
Polysome_profiling.txt


title: Bcl11bKO_aH3K27Ac-ChIP-rep1

value: anti-H3K27Ac Ab (Abcam, catalog# ab4729, lot# GR3216173-1)


title: WT_DN3_aH3K27Ac-ChIP-rep2


title: 02202018-D10-NA19159


title: WT_DN3_aH3K27Ac-ChIP-rep1


title: 02202018-E04-NA19159


title: HippCulture_UVp_rep3

city: Sapporo

first: Shinichi

last: Nakagawa

state: Hokkaido

address: Kita 12-jo Nishi 6-chome, Kita-ku

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Hokkaido University

description: UPA-Seq replicate 3

data_processing:
RNA-Seq reads are aligned to mm10 or hg38 using tophat 2.1.1.
Read counts are calculated using featureCounts allowing overlapping reads.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts mapped to each gene.

source_name: Primary hippocampal culture

extract_protocol:
RNAs were purified using TriZol reagents using manufacturer's protocol. Lysates were treated with 55ºC for 10 minutes before addition of chroloform.
rRNAs were removed using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat), and library was constructed using TruSeq Stranded mRNA Library Preparation Kit Set.

value: Primary culture of hippocampal neurons derived from E16.5 embryos


title: 02202018-D09-NA19159


title: Input – ATACseq and H3K4me3


title: 02202018-D06-NA18913


title: 02202018-D07-NA19159


title: Bcl11bKO_1%_input-rep2


title: HippCulture_UVp_rep1

description: UPA-Seq replicate 1


title: HippCulture_UVp_rep2

description: UPA-Seq replicate 2


title: 02202018-D12-NA19159


title: Bcl11bKO_aH3K27Ac-ChIP-rep2


title: 02202018-D04-NA19159


title: 02202018-D05-NA19159


title: HippCulture_UVm_rep2

description: control RNA-Seq replicate 2


title: HippCulture_UVm_rep1

description: control RNA-Seq replicate 1


title: 02202018-D03-NA19159


title: Neuro2a_UVp_rep3

description: UPA-Seq replicate 3

value: Mouse neuroblastoma cell


title: 02202018-E07-NA19159


title: Neuro2a_UVp_rep2

description: UPA-Seq replicate 2


title: 02202018-D02-NA18913


title: 02202018-C11-NA19203


title: 02202018-D01-NA19159


title: 02202018-C12-NA19159


title: 02202018-D08-NA18913


title: Neuro2a_UVp_rep1

description: UPA-Seq replicate 1


title: Neuro2a_UVm_rep2

description: control RNA-Seq replicate 2


title: Neuro2a_UVm_rep3

description: control RNA-Seq replicate 3


title: 02202018-C07-NA19203


title: 02202018-C08-NA19204


title: Neuro2a_UVm_rep1

description: control RNA-Seq replicate 1


title: 02202018-C06-NA19204


title: 02202018-C05-NA19203


title: 02202018-C04-NA19159


title: 02202018-C02-NA19159


title: 02202018-C01-NA19204


title: 02202018-C03-NA18913


title: 02202018-B11-NA18913


title: 02202018-B12-NA19159


title: Vav_Bcl11b_HOM_RNA-rep3

data_processing:
RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014) for removal of adapter ?and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).  Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings ?--output-genome-bam --sampling-for-bam? was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf.  The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with ?keepAll setting).  For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the ?noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

source_name: DN thymocytes

extract_protocol:
Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).
Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

tag: genotype/variation

value: Bcl11b flx/flx Vav1-iCre

value: YFP+CD25+ cells


title: HippCulture_UVm_rep3

description: control RNA-Seq replicate 3


title: Vav_Bcl11b_HOM_RNA-rep2


title: 02202018-B10-NA19204


title: 02202018-B08-NA19204


title: Vav_Bcl11b_HET_RNA-rep4

value: Bcl11b flx/+ Vav1-iCre


title: Vav_Bcl11b_HET_RNA-rep3


title: Vav_Bcl11b_HOM_RNA-rep1


title: 02202018-B05-NA19159


title: 02202018-C10-NA19159


title: Vav_Bcl11b_HET_RNA-rep2


title: Vav_Bcl11b_HET_RNA-rep1


title: 02202018-B09-NA19159


title: 02202018-B04-NA19204


title: 02202018-C09-NA19204


title: 02202018-B07-NA19159


title: 02202018-B03-NA18913


title: 02202018-B01-NA19159


title: Vav_Bcl11b_WT_RNA-rep1

value: Bcl11b +/+ Vav1-iCre


title: 02202018-B06-NA19159


title: Lck_Bcl11b_HOM_RNA-rep5

value: Bcl11b flx/flx Lck-Cre


title: 02202018-A12-NA18913


title: Lck_Bcl11b_HOM_RNA-rep4


title: Lck_Bcl11b_HOM_RNA-rep3


title: 02202018-A10-NA19204


title: Lck_Bcl11b_HET_DN3_RNA-rep6

value: Bcl11b flx/+ Lck-Cre

value: YFP+CD25+ DN3 cells


title: Lck_Bcl11b_HOM_RNA-rep1


title: 02202018-A09-NA18913


title: 02202018-A08-NA19204


title: Lck_Bcl11b_HET_DN3_RNA-rep5


title: Vav_Bcl11b_WT_RNA-rep2


title: Lck_Bcl11b_HET_DN3_RNA-rep3


title: Lck_Bcl11b_HET_DN3_RNA-rep4


title: 02202018-A06-NA19159


title: 02202018-A07-NA18913


title: Lck_Bcl11b_HET_DN3_RNA-rep2


title: 02202018-A02-NA19159


title: Lck_Bcl11b_HET_DN3_RNA-rep1


title: 02202018-B02-NA19159


title: Lck_Bcl11b_HET_DN2_RNA-rep5

value: YFP-CD25+ DN2 cells


title: Lck_Bcl11b_HET_DN2_RNA-rep4


title: 02192018-H11-NA19210


title: 02202018-A01-NA19204


title: 02192018-H12-NA19193


title: Lck_Bcl11b_HET_DN2_RNA-rep1


title: 02202018-A03-NA19159


title: Lck_Bcl11b_HET_DN2_RNA-rep3


title: Lck_Bcl11b_HET_DN2_RNA-rep2


title: Lck_Bcl11b_WT_DN3_RNA-rep5

value: Bcl11b +/+ Lck-Cre


title: 02192018-H10-NA19193


title: 02192018-H09-NA19210


title: Lck_Bcl11b_HOM_RNA-rep2


title: 02192018-H08-NA18517


title: Lck_Bcl11b_WT_DN3_RNA-rep3


title: Lck_Bcl11b_WT_DN3_RNA-rep4


title: 02192018-H07-NA19193


title: 02202018-A05-NA19159


title: 02202018-A04-NA19159


title: 02202018-A11-NA18913


title: 02192018-H06-NA19193


title: Lck_Bcl11b_WT_DN3_RNA-rep2


title: Lck_Bcl11b_WT_DN3_RNA-rep1


title: 02192018-H05-NA18913


title: 02192018-H04-NA18517


title: Lck_Bcl11b_WT_DN2_RNA-rep4


title: 02192018-H03-NA19193


title: Lck_Bcl11b_WT_DN2_RNA-rep2


title: Lck_Bcl11b_WT_DN2_RNA-rep1


title: 02192018-H02-NA18517


title: 02192018-H01-NA19210


title: Bone marrow U

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

data_processing:
Data were analyzed using Cell Ranger V2.0.0 (10X Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger generated one mtx file and two tsv files for gene ID and cell barcode ID.

source_name: Bone marrow

growth_protocol: Using standard operating procedures, mononuclear cells from 20 healthy donors' bone marrow aspirates were isolated using Ficoll density gradient separation and cryopreserved in 90% FBS/ 10% DMSO for storage in 72 liquid nitrogen.

extract_protocol:
scRNAseq was performed using 10X Genomics Single Cell 3’ Solution, version 2 according to manufacturer’s instructions (protocol rev A).
Droplet-based scRNAseq

treatment_protocol: No treatment

value: bone marrow cells

tag: age

value: 46 years old


title: Bone marrow Sk1

description: Biological replicate of S1

value: 55 years old


title: Bone marrow W

value: 28 years old


title: Bone marrow R

value: 31 years old


title: Bone marrow Sk2

description: Technical replicate of Sk1


title: Bone marrow Q

value: 66 years old


title: Bone marrow T

value: 24 years old


title: Bone marrow P

value: 58 years old


title: 02192018-G12-NA18517


title: sgBcl11b_Zbtb16_RNA-rep2

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

data_processing:
ChIP-seq data were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.
RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).  Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf.  The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with –keepAll setting).  For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED-files  All genomic coordinates are relative to mm9 mouse assembly.

extract_protocol:
ChIP-seq: Ten million of BM-derived DN3 cells or Schd.adh.2c2 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Six μg per 107 cells of anti-Bcl11b Abs (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)), anti-Chd4 (A301-081A), anti-Mta2 (sc-9447), anti-Hdac2 (ab12169), anti-Rest (12C11-1B11), anti-Ring1b (A302-869A), anti-LSD1 (ab17721) or anti-Runx1 (ab23980) were hybridized to Dynabeads anti-Rabbit, Dynabeads anti-Mouse or Dynabeads Protein A/G (Invitrogen) and added to the diluted chromatin complex.  They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg/ml proteinase K).  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.
RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

treatment_protocol:
Lin- BM isolation and culture protocol:
ChIP-seq; Bone marrow (BM) was removed from the femurs and tibiae of 2-3 month-old mice.  Suspensions of BM cells were prepared and stained for lineage markers using biotin-conjugated lineage antibodies (CD11b, CD11c, Gr1, TER-119, NK1.1, CD19, CD3ε, B220), then incubated with streptavidin-coated magnetic beads (Miltenyi Biotec), and passed through a magnetic column (Miltenyi Biotec).  Then, Lin-, Sca1+, Kit+ (LSK) cells were sorted on a FACSAria (BD Bioscience).  LSK cells were cultured on OP9-DL1 monolayers using OP9 medium (α-MEM, 20% FBS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).  On day 7, cultured cells were disaggregated, filtered through 40-μm nylon mesh, and cultured on OP9-DL1 monolayers with medium containing 5 ng/ml of IL-7, 5 ng/ml of Flt3L and 120nM of 4-OHT (Sigma-Aldrich).  Two days later 4-OHT was removed, and cells were cultured for an additional 5 days on OP9-DL1 with 1 ng/ml of IL-7, 1 ng/ml of Flt3L, and subjected to further analysis.
RNA-seq; Cultured Lin- BM cells for 7 days were disaggregated, filtered through 40-μm nylon mesh, transferred onto RetroNectin-coated virus bound plates, and cultured with OP9 medium supplemented with 5 ng/ml of IL-7, 5 ng/ml of Flt3L and 10 ng/ml of SCF.  Infected cells were cultured for an additional 7 days on OP9-DL1 and subjected to further analysis.  For sorting, cells were stained with CD45, CD25, and a biotin-conjugated lineage cocktail (CD8α, CD11b, CD11c, Gr1, TER-119, NK1.1, CD19, TCRβ, TCRγδ), and were sorted for CD25+ infected cells (Lin-CD45+CD25+CFP+).

value: Lin- BM derived DN3 cells

tag: cultured on


title: Bone marrow O

tag: cell type

value: 50 years old


title: sgBcl11b_Zbtb16_RNA-rep1


title: Bone marrow N

value: 67 years old


title: 02192018-G11-NA19193

tag: experiment


title: Bone marrow M

value: 60 years old


title: 02192018-G10-NA18913

tag: well


title: Bone marrow K

value: 84 years old


title: sgBcl11b_Id2_RNA-rep2


title: Bone marrow J

value: 43 years old


title: Bone marrow S2

description: Technical replicate of S1

value: 56 years old


title: sgBcl11b_Id2_RNA-rep1


title: Bone marrow L

value: 57 years old


title: Bone marrow S1


title: Lck_Bcl11b_WT_DN2_RNA-rep3

value: Bcl11b +/+ Lck-Cre

value: YFP-CD25+ DN2 cells


title: 02192018-G09-NA18913

tag: individual


title: Bone marrow G

value: bone marrow cells


title: Bone marrow H


title: 02192018-G08-NA19210

tag: batch


title: sgZbtb16_RNA-rep2


title: 02192018-G07-NA18913


title: sgZbtb16_RNA-rep1


title: Bone marrow C1


title: Bone marrow C2

description: Technical replicate of C1


title: Bone marrow B

value: 47 years old


title: Bone marrow Ck

description: Biological replicate of C1

value: 59 years old


title: 02192018-G06-NA19210


title: sgId2_RNA-rep1


title: Bone marrow A


title: MP_Penti_2

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
The miRNA normalized counts was generated as in Farazi et al., Cancer research 2011 (GEO accession number GSE28884)
Genome_build: hg19
Supplementary_files_format_and_content: format: xlsx content: Normalized counts

source_name: HeyA8 cells treated with Plenti

growth_protocol: HeyA8 cells are cultured in RPMI1640 medium supplemented with 10% FBS and 1% L-Glutamine. HCT116 cell lines were cultured in McCoy's 5A medium, supplemented with 10% FBS and 1% L-Glutamine.

extract_protocol:
AGO1-4 were pulled down from whole cell lysate (Hauptmann et al., 2015 PNAS).  The RNA was isolated using Trizol.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: cells were treated where indicated with plenti or hFasL

tag: cell line

tag: passages

tag: pull down

value: Pull down with Pan-AGO peptide (Hauptmann et al., 2015 PNAS)


title: 02192018-G05-NA19193


title: 02192018-G04-NA19210


title: MP_Penti_1


title: sgBcl11b_RNA-rep4


title: sgBcl11b_RNA-rep3


title: 02192018-G03-NA19193


title: MP_hFasL_2

source_name: HeyA8 cells treated with hFasL


title: sgControl_RNA-rep4


title: MP_hFasL_1


title: 02192018-G02-NA18517


title: Bone marrow F

value: 41 years old


title: Bone marrow E

value: 30 years old


title: sgId2_RNA-rep2


title: sgControl_RNA-rep3


title: sgRunx1_RNA-rep2


title: miRNA_HTC116_plenti2

source_name: HCT116 cells treated with plenti


title: 02192018-G01-NA18517


title: 02192018-F12-NA19193


title: miRNA_HTC116_plenti1


title: miRNA_HTC116_hFasL2

source_name: HCT116 cells treated with hFasL


title: sgRunx1_RNA-rep1


title: sgLSD1_RNA-rep2


title: 02192018-F11-NA19193


title: miRNA_HTC116_hFasL1


title: 02192018-F10-NA19193


title: 02192018-F09-NA18913


title: sgRing1a_b_RNA-rep2


title: miRNA_Drosha_plenti2

source_name: Drosha KO cells treated with plenti


title: miRNA_Drosha_plenti1


title: 02192018-F08-NA19193


title: 02192018-F07-NA18517


title: sgRing1a_b_RNA-rep1


title: sgRest_RNA-rep2


title: 02192018-F06-NA19193


title: T 0 min vs. T 15 min I

type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For calculation of mRNA half-lives, first the ratio of median values (GenePix Pro 6.0) reflecting the relative mRNA level changes were normalized for each array hybridization separately using a normalization factor. This factor was calculated for each hybridization based on the log base 2 of the non-normalized ratio of median values of the Spike-In (+)E1A_r60_1 and (+)E1A_r60_a20 RNAs as internal controls, each having 32 spots randomly scattered over the array. Both RNAs are present in A mix and B mix at an expected ratio amount (A/B) of 1:1 (Agilent Technologies). Accordingly, the factor was calculated that the log base 2 of the factor-normalized ratio of median values of the 1:1 control RNAs is 0 on average. Subsequently, the ratio of median value for each gene was normalized with the calculated factor. A normalized ratio value was included in the calculation of the average of the triplicates for each time point if the following quality filter was fulfilled by the spot data (GenePix Pro 6.0): i) Flags ≥0 and ii) signal/noise ≥3 for Cy5 (F635Median / B635Median) or Cy3 (F532Median / B532Median). The resulting data matrix with the average values of the four time points was used to calculate the mRNA half-lives and R2 in Excel (Microsoft) by linear fit.

organism: Gluconobacter oxydans 621H

source_name: G.oxydans T0

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm (2003)  Appl. Environm. Microbiol. 69:2521-2532, yet for pairwise comparisons the A mix and the B mix of the Agilent Spike-In Kit (Agilent Technologies) was used to spike t0 and tx RNA samples.

growth_protocol: In this study the wild type Gluconobacter oxydans 621H strain DSM 2343 from the German Collection of Microorganisms and Cell Cultures (DSMZ) was used. The cells were cultivated in mannitol medium containing 220 mM (4% w/v) mannitol, 5 g/L yeast extract, 1 g/L KH2PO4, 1 g/L (NH4)2SO4, 2.5 g/L MgSO4 x 7 H2O, and 50 µg/mL cefoxitin as antibiotic. Cells were grown in 500 mL shaking flasks with three baffles containing 50 mL of the mannitol medium (30°C, 140 rpm). Cell growth in liquid culture was followed by measuring the optical density at 600 nm (OD600) using a spectrophotometer. If rifampicin was applied, it was added to a cell culture at OD600 of 0.6 to 0.8 from a stock (50 mg/mL in methanol) to obtain the final concentration of 150 µg/mL.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004), Mol Microbiol 54: 420-438.)

tag: agent

value: control

tag: time

source_name: G.oxydans T15

value: rifampicin


title: T 0 min vs. T 10 min III

source_name: G.oxydans T10


title: T 0 min vs. T 15 min III


title: miRNA_Drosha_hFasL1

source_name: Drosha KO cells treated with hFasL


title: 02192018-F05-NA19193

source_name: LCL-derived iPSC


title: sgRest_RNA-rep1

value: Lin- BM derived DN3 cells


title: sgMta1_2_RNA-rep2


title: sgLSD1_RNA-rep1


title: 02192018-F04-NA18517


title: T 0 min vs. T 10 min I


title: T 0 min vs. T 5 min II csw

source_name: G.oxydans T5


title: sgMta1_2_RNA-rep1


title: ChIP-seq from lung (ENCLB527SEL)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR254NDP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR254NDP
assay title: ChIP-seq
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB527SEL

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female embryo (96 days) lung tissue

extract_protocol: extraction method: see document

value: Control

value: lung

value: tissue

tag: description

value: Primary lung tissue from a healthy day 96 female fetus from Ian Glass of University of Washington, Congenital Defects Lab.

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: embryonic

value: 96 day

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS611ZZU at ENCODE; https://www.encodeproject.org/ENCBS611ZZU/

value: Derived from ENCODE donor ENCDO370HUJ; https://www.encodeproject.org/ENCDO370HUJ/


title: T 0 min vs. T 5 min III


title: T 0 min vs. T 15 min II csw


title: T 0 min vs. T 10 min II csw


title: T 0 min vs. T 2 min II csw

source_name: G.oxydans T2


title: miRNA_Drosha_hFasL2


title: 02192018-F03-NA19210


title: sgChd4_RNA-rep2

tag: strain

tag: cultured on


title: T 0 min vs. T 5 min I


title: T 0 min vs. T 2 min III


title: T 0 min vs. T 2 min I


title: sgChd4_RNA-rep1

tag: cell type


title: 02192018-F01-NA18517

tag: experiment

tag: well


title: 02192018-F02-NA19210

tag: individual

tag: batch


title: 02192018-E12-NA19210


title: sgBcl11b_RNA-rep1


title: sgBcl11b_RNA-rep2


title: 02192018-E10-NA19193


title: 02192018-E11-NA19193


title: sgControl_RNA-rep1


title: 02192018-E08-NA18517


title: Scid.adh.2c2_shBcl11b_1%_input

tag: cell line

value: Scid.adh.2c2 cells

tag: transduced with


title: 02192018-E09-NA18517


title: neo_Tcells_1

city: Paris

first: Sebastien

last: LEMOINE

address: 149 rue de Sèvres, Bat. Hamburger, 5e étage, p507

country: France

institute: Necker Hospial

hyb_protocol: The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.5 µg Cy3-labeled cDNA were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K, AMADID 028004) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile for 30 sec

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES, 10.7.3.1) was used to read out and process the microarray image files

data_processing: Raw data were background corrected using the normexp method and normalized using the quantile method

source_name: neonatal naive T cells (CD3+ CD4+ CD56- CD25- CD45RO-)

label_protocol: 250 nanograms of purified PCR product was labeled with Cy3-dCTP (Amersham) in a Klenow Fragment (10 U) reaction for 1:50 h at 37°C before inactivating through addition of 5µl 0.5M EDTA pH 8.0. 0.5 µg Cy3-labeled and purified (Cy- Scribe GFX Purification Kit, GE Healthcare)

extract_protocol: For the generation of amplified cDNA (SuperAmp Service, Miltenyi Biotec), the mRNA was extracted from the lysed cell samples using magnetic beads and transcribed into cDNA using tagged random and oligo(dT) primer

treatment_protocol: Dendritic cells were left unstimulated or were stimulated with either poly I:C + R848, Bacillus Calmette–Guérin (BCG) or Respiratory Syncytial Virus (RSV) for 6h in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

tag: tissue

value: Cord Blood

tag: age

value: Neonatal

tag: stimulation

value: Unstimulated


title: neo_cDC2b_RSV_3

source_name: neonatal cord blood cDC2b (CD20- CD11c+ CD14- BDCA1+ CD11b+)

value: RSV


title: neo_cDC2b_BCG_3

value: neonatal cord blood cDC2b (CD20- CD11c+ CD14- BDCA1+ CD11b+)

value: BCG


title: 02192018-E07-NA18517


title: sgControl_RNA-rep2

value: Lin- BM derived DN3 cells


title: neo_mono_none_3

source_name: Neonatal monocytes (CD11c+ CD14+)

value: Neonatal monocytes (CD11c+ CD14+)


title: neo_cDC2b_TLR_3

value: TLR


title: neo_cDC2b_none_3


title: neo_cDC2_BCG_3

source_name: neonatal cord blood cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-)


title: Scid.adh.2c2_shControl_1%_input

value: shControl-GFP


title: 02192018-E06-NA18517


title: neo_cDC2_RSV_3

value: neonatal cord blood cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-)


title: Scid.adh.2c2_shControl_aRest

tag: chip antibody

value: anti-Rest Ab (12C11-1B11, Caltech protein center)


title: 02192018-E05-NA18517


title: Scid.adh.2c2_shBcl11b_aRest


title: 02192018-E04-NA19193


title: Scid.adh.2c2_shControl_aMta2

value: anti-Mta2 Ab (sc-9447, Santa Cruz)


title: Scid.adh.2c2_shBcl11b_aMta2


title: genomic DNA from PBMC 58 [DrKuo-I1212]

type: genomic

city: Taipei

first: Kang-Yi

last: Su

address: No.1, Jen-Ai Road

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: male offspring from the Yucheng' neighborhood referents with similar backgrounds.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Illumina GenomeStudioTM software (version XXV2011.1, Methylation Module 1.9) methylation module
The non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood mononuclear cells using Qiagen DNeasy Kit according to standard instructions

tag: sample group

tag: gender

value: Male

value: whole blood

value: peripheral blood mononuclear cells (PBMC)


title: 02192018-E03-NA18517


title: neo_cDC2_TLR_3


title: neo_mono_none_2


title: neo_cDC2_none_3


title: genomic DNA from PBMC 56 [DrKuo-5011]

source_name: male offspring from the Yucheng' neighborhood referents with similar backgrounds


title: Scid.adh.2c2_shBcl11b_aHdac2

value: Scid.adh.2c2 cells

value: anti-Hdac2 Ab (ab12169, Abcam)


title: neo_cDC2b_RSV_2

value: Cord Blood

value: Neonatal


title: Scid.adh.2c2_shControl_aHdac2


title: Scid.adh.2c2_shBcl11b_aChd4

value: anti-Chd4 Ab (A301-081A, Bethyl)


title: 02192018-E02-NA18517


title: genomic DNA from PBMC 54 [DrKuo-L1311]

value: the Yucheng' neighborhood referents with similar backgrounds


title: genomic DNA from PBMC 59 [DrKuo-2822]


title: neo_cDC2b_BCG_2

value: neonatal cord blood cDC2b (CD20- CD11c+ CD14- BDCA1+ CD11b+)

value: BCG


title: 02192018-E01-NA19210


title: Scid.adh.2c2_shControl_aChd4


title: genomic DNA from PBMC 53 [DrKuo-7921]


title: genomic DNA from PBMC 57 [DrKuo-2732]


title: neo_cDC2b_none_2

value: Unstimulated


title: 02192018-D11-NA19210


title: neo_cDC2b_TLR_2

value: TLR


title: 02192018-D12-NA18913


title: genomic DNA from PBMC 52 [DrKuo-R0211]


title: genomic DNA from PBMC 55 [DrKuo-4521]


title: genomic DNA from PBMC 51 [DrKuo-P0311]


title: genomic DNA from PBMC 60 [DrKuo-0521]


title: 02192018-D10-NA19193


title: Bcl11bKO_1%_input-rep2

value: Lin- BM derived Bcl11bKO cells


title: Bcl11bKO_1%_input-rep1

value: Lin- BM derived Bcl11bKOcells


title: 02192018-D09-NA18517


title: 02192018-D08-NA18913


title: WT_DN3_1%_input-rep2

value: Lin- BM derived WT DN3 cells


title: 02192018-D07-NA18517


title: genomic DNA from PBMC 47 [DrKuo-9010]

description: male offspring from the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort

source_name: male offspring from the Yucheng cohort


title: 02192018-D06-NA18517


title: genomic DNA from PBMC 49 [DrKuo-9222]


title: genomic DNA from PBMC 48 [DrKuo-4410]

value: the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort


title: neo_cDC2_RSV_2

value: neonatal cord blood cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-)

value: RSV


title: neo_cDC2_none_2


title: genomic DNA from PBMC 50 [DrKuo-N0411]

value: Male

value: whole blood

value: peripheral blood mononuclear cells (PBMC)


title: neo_cDC2b_RSV_1

value: Cord Blood


title: neo_cDC2b_BCG_1

value: Neonatal


title: neo_cDC2_TLR_2


title: genomic DNA from PBMC 46 [DrKuo-1310]


title: WT_DN3_1%_input-rep1


title: Bcl11bKO_aBcl11b-ChIP-rep1

value: a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)


title: Bcl11bKO_aBcl11b-ChIP-rep2


title: 02192018-D05-NA19210


title: genomic DNA from PBMC 45 [DrKuo-0820]


title: WT_DN3_aBcl11b-ChIP-rep2


title: genomic DNA from PBMC 44 [DrKuo-0210]


title: neo_mono_none_1

value: Neonatal monocytes (CD11c+ CD14+)


title: 02192018-D03-NA19210


title: Bcl11bKO_aRunx1-ChIP-rep2

value: anti-Runx1 Ab (ab23980, Abcam)


title: WT_DN3_aBcl11b-ChIP-rep1


title: 02192018-D02-NA19193


title: 02192018-D01-NA19193


title: Bcl11bKO_aRunx1-ChIP-rep1


title: WT_DN3_aRunx1-ChIP-rep2


title: genomic DNA from PBMC 43 [DrKuo-0810]


title: 02192018-C12-NA19193


title: neo_cDC2b_TLR_1

value: neonatal cord blood cDC2b (CD20- CD11c+ CD14- BDCA1+ CD11b+)


title: WT_DN3_aRunx1-ChIP-rep1


title: neo_cDC2_TLR_1


title: neo_cDC2_RSV_1


title: genomic DNA from PBMC 39 [DrKuo-9020]


title: genomic DNA from PBMC 40 [DrKuo-1120]


title: genomic DNA from PBMC 42 [DrKuo-0310]


title: 02192018-C10-NA18913


title: Bcl11bKO_aLSD1-ChIP-rep2

value: anti-LSD1 Ab (ab17721, Abcam)


title: 02192018-C11-NA18913


title: neo_cDC2_BCG_1

value: BCG


title: genomic DNA from PBMC 38 [DrKuo-7130]


title: genomic DNA from PBMC 37 [DrKuo-7120]


title: genomic DNA from PBMC 41 [DrKuo-H0110]


title: neo_cDC2_none_1

value: Unstimulated


title: Bcl11bKO_aLSD1-ChIP-rep1

value: Lin- BM derived Bcl11bKOcells


title: adult_cDC2_BCG_3

source_name: Peripheral blood adult cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-)

value: Peripheral blood

value: Adult


title: 02192018-C07-NA18517


title: 02192018-C08-NA19193


title: 02192018-C09-NA19210


title: WT_DN3_aLSD1-ChIP-rep2

value: Lin- BM derived WT DN3 cells


title: adult_cDC2_TLR_3

value: Peripheral blood adult cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-)

value: TLR


title: adult_cDC2_RSV_3

value: RSV


title: WT_DN3_aLSD1-ChIP-rep1


title: neo_cDC2_BCG_2

value: neonatal cord blood cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-)


title: genomic DNA from PBMC 36 [DrKuo-L1020]

value: the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort

value: Male

value: whole blood

value: peripheral blood mononuclear cells (PBMC)


title: genomic DNA from PBMC 32 [DrKuo-7-2]

value: the Yucheng' neighborhood referents with similar backgrounds


title: Bcl11bKO_aRing1b-ChIP-rep2

value: Lin- BM derived Bcl11bKO cells

value: anti-Ring1b Ab (A302-869A, Bethyl)


title: 02192018-C06-NA19193


title: adult_cDC2_none_3


title: 02192018-D04-NA18913


title: genomic DNA from PBMC 34 [DrKuo-4810]


title: adult_cDC2_BCG_2

value: BCG


title: 02192018-C05-NA19193


title: genomic DNA from PBMC 35 [DrKuo-H0130]


title: genomic DNA from PBMC 33 [DrKuo-6921]


title: adult_cDC2_RSV_2


title: Bcl11bKO_aRing1b-ChIP-rep1


title: neo_cDC2b_none_1

value: neonatal cord blood cDC2b (CD20- CD11c+ CD14- BDCA1+ CD11b+)

value: Cord Blood

value: Neonatal

value: Unstimulated


title: adult_cDC2_TLR_2

value: Peripheral blood

value: Adult


title: WT_DN3_aRing1b-ChIP-rep1

value: Lin- BM derived WT DN3 cells


title: WT_DN3_aRing1b-ChIP-rep2


title: Bcl11bKO_aRest-ChIP-rep2

value: anti-Rest Ab (12C11-1B11, Caltech protein center)


title: genomic DNA from PBMC 29 [DrKuo-N1011]


title: 02192018-C04-NA19193


title: 02192018-C03-NA18913


title: genomic DNA from PBMC 30 [DrKuo-N0711]


title: 02192018-C02-NA19210


title: Bcl11bKO_aRest-ChIP-rep1

value: Lin- BM derived Bcl11bKOcells


title: 02192018-C01-NA18913


title: 02192018-B12-NA18913


title: WT_DN3_aRest-ChIP-rep2


title: WT_DN3_aRest-ChIP-rep1


title: 02192018-B11-NA19193


title: adult_cDC2_RSV_1

value: Peripheral blood adult cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-)

value: RSV


title: adult_cDC2_none_2


title: genomic DNA from PBMC 31 [DrKuo-2312]

value: Male

value: whole blood


title: adult_cDC2_BCG_1


title: Bcl11bKO_aHdac2-ChIP-rep2

value: anti-Hdac2 Ab (ab12169, Abcam)


title: genomic DNA from PBMC 28 [DrKuo-L1812]

value: the Yucheng' neighborhood referents with similar backgrounds

value: peripheral blood mononuclear cells (PBMC)


title: 02192018-B10-NA18913


title: adult_cDC2_TLR_1

value: TLR


title: Bcl11bKO_aHdac2-ChIP-rep1


title: genomic DNA from PBMC 25 [DrKuo-9312]


title: 02192018-B09-NA18517


title: genomic DNA from PBMC 26 [DrKuo-0211]


title: adult_cDC2_none_1


title: genomic DNA from PBMC 27 [DrKuo-5222]


title: WT_DN3_aHdac2-ChIP-rep2


title: 02192018-B08-NA19193


title: Mouse gastrocnemius muscle, Ursolic acid added high-fat diet, rep3

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

country: South Korea

institute: Kyungpook National University

description:
MUR3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: biotin

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, USA) to yield biotinylated cRNA

growth_protocol: Thirty male C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) at 4 weeks of age. All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the AIN-76 semi-purified diet for a one-week acclimation period after arrival

extract_protocol: Total RNA was extracted from the adipose tissue and liver using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were fed a normal diet (ND, n=10), high-fat diet consisting of 20% fat and 1% cholesterol (HFD, n=10) or HFD with 0.05% (w/w) ursolic acid (Sigma Chemical, MO) (UR, n=10) for 16 weeks

value: male

tag: treatment

value: Ursolic acid added high-fat diet

value: gastrocnemius muscle


title: WT_DN3_aHdac2-ChIP-rep1


title: 02192018-B06-NA18517


title: 02192018-B07-NA19210


title: Bcl11bKO_aMta2-ChIP-rep2

value: Lin- BM derived Bcl11bKO cells

value: anti-Mta2 Ab (sc-9447, Santa Cruz)


title: genomic DNA from PBMC 24 [DrKuo-4812]


title: Bcl11bKO_aMta2-ChIP-rep1


title: genomic DNA from PBMC 22 [DrKuo-1121]


title: 02192018-B05-NA18517


title: Mouse gastrocnemius muscle, Ursolic acid added high-fat diet, rep1

description:
MUR1
replicate 1


title: Mouse gastrocnemius muscle, High-fat diet, rep2

description:
MHFD2
replicate 2

value: High-fat diet


title: 02192018-B04-NA19193


title: genomic DNA from PBMC 23 [DrKuo-1212]


title: WT_DN3_aMta2-ChIP-rep2

value: Lin- BM derived WT DN3 cells


title: WT_DN3_aMta2-ChIP-rep1


title: genomic DNA from PBMC 19 [DrKuo-6931]


title: Mouse gastrocnemius muscle, High-fat diet, rep3

description:
MHFD3
replicate 3


title: Mouse gastrocnemius muscle, High-fat diet, rep1

description:
MHFD1
replicate 1


title: Mouse gastrocnemius muscle, Normal diet, rep3

description:
MND3
replicate 3

source_name: Mouse gastrocnemius muscle, Normal diet

value: Normal diet


title: 02192018-B03-NA18517


title: Mouse gastrocnemius muscle, Ursolic acid added high-fat diet, rep2

description:
MUR2
replicate 2


title: Bcl11bKO_aChd4-ChIP-rep2

value: anti-Chd4 Ab (A301-081A, Bethyl)


title: 02192018-B02-NA19210


title: Bcl11bKO_aChd4-ChIP-rep1

value: Lin- BM derived Bcl11bKOcells


title: genomic DNA from PBMC 18 [DrKuo-7121]


title: 02192018-B01-NA18517


title: genomic DNA from PBMC 20 [DrKuo-1312]


title: WT_DN3_aChd4-ChIP-rep2


title: genomic DNA from PBMC 21 [DrKuo-9012]


title: WT_DN3_aChd4-ChIP-rep1


title: 02192018-A11-NA18913


title: Mouse gastrocnemius muscle, Normal diet, rep2

description:
MND2
replicate 2


title: Mouse gastrocnemius muscle, Normal diet, rep1

description:
MND1
replicate 1


title: 02192018-A10-NA18517


title: Mouse Epididymal adipose tissue, Ursolic acid added high-fat diet, rep3

description:
EUR3
replicate 3

value: Epididymal adipose tissue


title: genomic DNA from PBMC 17 [DrKuo-S0811]

value: Male


title: genomic DNA from PBMC 16 [DrKuo-2112]

value: whole blood


title: genomic DNA from PBMC 15 [DrKuo-S0410]

value: the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort


title: 02192018-A08-NA18913


title: 02192018-A07-NA18913


title: Mouse Epididymal adipose tissue, Ursolic acid added high-fat diet, rep2

description:
EUR2
replicate 2


title: 02192018-A06-NA19193


title: genomic DNA from PBMC 14 [DrKuo-J0210]


title: genomic DNA from PBMC 12 [DrKuo-I1520]


title: genomic DNA from PBMC 13 [DrKuo-L0710]


title: 02192018-A05-NA19193


title: genomic DNA from PBMC 11 [DrKuo-6120]


title: genomic DNA from PBMC 10 [DrKuo-L1810]


title: Mouse Epididymal adipose tissue, Ursolic acid added high-fat diet, rep1

description:
EUR1
replicate 1


title: 02192018-A09-NA19193


title: 02192018-A04-NA18913


title: Day2 rep3 [miRNA]

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

description: processed data file: Counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering is carried out to obtain clean reads to remove low quality reads present in the raw reads. The procedure includes following steps: 1) Remove reads in which the unknown bases (N) is presented; 2) Remove low quality reads, if the reads have low quality base (base with quality value ≤5), the reads were removed. The reads were mapped to known miRNA deposited in miRBase (release 22) using BLASTN. The calculated reads count per miRNA were used for comparing the difference of miRNA expression among samples.
Using R version 3.4.2 software (limma package) to find differential genes.
Genome_build: miRBase (Release 22)
Supplementary_files_format_and_content: Counts.txt: Tab-delimited text file includes read counts.

organism: Sus scrofa

source_name: Whole blood

growth_protocol: The piglets of Duroc × Landrace × Yorkshire crossbred were used. Piglets were raised in climate-controlled, fully enclosed isolation facilities.

extract_protocol:
Total RNA were extracted by PAXgene blood miRNA kit using the standard protocols. All samples were quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The pigs were tested fecal negative for Salmonella three times before intranasal challenge with 10^9 colony forming units (cfu) of Salmonella enterica serovar Typhimurium LT2 at four weeks of age.

tag: breed

value: Duroc x Landrace x Yorkshire crossbreed

value: Peripheral blood

value: 4 weeks

tag: time

value: Day 2


title: Mouse Epididymal adipose tissue, Normal diet, rep3

description:
END3
replicate 3

value: male

tag: strain


title: Day2 rep2 [miRNA]

description: processed data file: Counts.txt

value: Salmonella enterica serovar Typhimurium LT2


title: 02192018-A03-NA19210


title: 02192018-A02-NA18913


title: Mouse Epididymal adipose tissue, High-fat diet, rep2

description:
EHFD2
replicate 2


title: Mouse Liver, Ursolic acid added high-fat diet, rep2

description:
LUR2
replicate 2

value: Ursolic acid added high-fat diet

value: Liver


title: genomic DNA from PBMC 8 [DrKuo-2820]

tag: cell type

value: peripheral blood mononuclear cells (PBMC)


title: genomic DNA from PBMC 7 [DrKuo-2110]


title: Day2 rep1 [miRNA]

description: processed data file: Counts.txt


title: Mouse Epididymal adipose tissue, High-fat diet, rep1

description:
EHFD1
replicate 1

value: High-fat diet


title: Mouse Epididymal adipose tissue, Normal diet, rep1

description:
END1
replicate 1

value: Normal diet


title: 02192018-A01-NA18517

tag: experiment


title: Mouse Liver, Ursolic acid added high-fat diet, rep3

description:
LUR3
replicate 3


title: Mouse Epididymal adipose tissue, Normal diet, rep2

description:
END2
replicate 2


title: Day0 rep3 [miRNA]

description: processed data file: Counts.txt

value: Untreated

value: Day 0


title: genomic DNA from PBMC 9 [DrKuo-4520]


title: Mouse Liver, Ursolic acid added high-fat diet, rep1

description:
LUR1
replicate 1


title: Mouse Liver, High-fat diet, rep3

description:
LHFD3
replicate 3

source_name: Mouse Liver, High-fat diet


title: genomic DNA from PBMC 6 [DrKuo-4720]


title: HEK293_UVp_rep3

description: UPA-Seq replicate 3

value: Human embryonic kidney cells


title: genomic DNA from PBMC 4 [DrKuo-4710]

value: Male


title: Day0 rep1 [miRNA]

description: processed data file: Counts.txt


title: HEK293_UVp_rep2

description: UPA-Seq replicate 2


title: genomic DNA from PBMC 3 [DrKuo-2410]

value: whole blood


title: Mouse Liver, High-fat diet, rep2

description:
LHFD2
replicate 2


title: genomic DNA from PBMC 5 [DrKuo-4820]

value: the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort


title: HEK293_UVp_rep1

description: UPA-Seq replicate 1


title: 02192018-A12-NA19210

tag: well


title: HEK293_UVm_rep2

description: control RNA-Seq replicate 2


title: HEK293_UVm_rep3

description: control RNA-Seq replicate 3


title: C3KO_11

city: Chongqing

first: Haoran

last: Zha

address: Shaping Street #31

institute: Institute of Cancer, Xinqiao Hospital,Third Military Medical University

description: processed data file: TAM.gene.fpkm.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: TAM.gene.fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: CT26-Sg-C3 implanted tumor

extract_protocol:
TAMs were isolated from tumors by flow cytometry, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared using an MGIEasy™ mRNA kit.

tag: strain/background

value: BALB/C

tag: genotype/variation

value: wild type

value: Tumor-associated macrophages


title: HEK293_UVm_rep1

description: control RNA-Seq replicate 1

tag: cell line


title: SGC3_13

description: processed data file: TAM.gene.fpkm.txt


title: C3KO_12

description: processed data file: TAM.gene.fpkm.txt


title: CON_C

description: processed data file: TAM.gene.fpkm.txt

source_name: CT26-Sg-Con implanted tumor


title: TAM_B

description: processed data file: TAM.gene.fpkm.txt


title: TAM_A

description: processed data file: TAM.gene.fpkm.txt


title: Mouse Epididymal adipose tissue, High-fat diet, rep3

description:
EHFD3
replicate 3

value: Epididymal adipose tissue


title: Mouse Liver, High-fat diet, rep1

description:
LHFD1
replicate 1

value: male


title: Mouse Liver, Normal diet, rep3

description:
LND3
replicate 3

source_name: Mouse Liver, Normal diet


title: Mouse Liver, Normal diet, rep1

description:
LND1
replicate 1


title: Mouse Liver, Normal diet, rep2

description:
LND2
replicate 2


title: 4T1 KD2/3 + Vav3 rep 2

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: miRNA expression from 4T1 cells

hyb_protocol: GeneChip miRNA 1.0 array (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.3.1).

source_name: 4T1 cells transduced with lentiviral shRNAs to Vav2 and Vav3 transcripts, rescued with Vav3

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used according to the manufacturer's instructions (Affymetrix).

growth_protocol: 4T1 cells were cultured in RPMI medium supplemented with 10% fetal calf serum (FCS), at 37ºC with 5% CO2

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

treatment_protocol: The shRNA-mediated knockdown was carried out with prepackaged Mission TRC lentiviral particles (Sigma-Aldrich) according to the manufacturer's protocol

value: Breast

value: Vav3-rescued knock down


title: 4T1 KD2/3 + Vav3 rep 3

description: miRNA expression from 4T1 cells


title: 4T1 KD2/3 + Vav2 rep 3

description: miRNA expression from 4T1 cells

source_name: 4T1 cells transduced with lentiviral shRNAs to Vav2 and Vav3 transcripts, rescued with Vav2

value: Vav2-rescued knock down


title: genomic DNA from PBMC 1 [DrKuo-L0410]

value: peripheral blood mononuclear cells (PBMC)


title: genomic DNA from PBMC 2 [DrKuo-5220]


title: 4T1 KD2/3 + Vav3 rep 1

description: miRNA expression from 4T1 cells


title: 4T1 KD2/3 + Vav2 rep 1

description: miRNA expression from 4T1 cells


title: 4T1 KD2/3 + Vav2 rep 2

description: miRNA expression from 4T1 cells


title: DrhoExp_2: S. aureus rho mutant_exponential phase_rep2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

hyb_protocol: 75 ng of Cy5-labeled cDNA and 75 ng of Cy3-labeled cDNAwere hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 11.5.1.1, Agilent Technologies).
The normalization/ dye bias correction method as defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol GE2_105_Dec08) is: Linear and Lowess.

organism: Staphylococcus aureus

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol: For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D (final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye, GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: S. aureus HG001 wild-type and its isogenic Δrho mutant were grown under vigorous agitation at 37 °C in RPMI medium (with L-glutamine, without phenol red and HEPES).

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

treatment_protocol: At OD600 of 0.2 (early exponential phase), the wild-type culture was split in pre-warmed flasks. BCM was added in concentrations of 40 or 80 µg/ml. Samples were taken at OD600 of 0.2 and 70 min later.

source_name: S. aureus rho mutant_exponential phase

tag: genotype

value: rho mutant

tag: growth phase

value: exponential


title: 4T1 KD2/3 expB rep 1

description: miRNA expression from 4T1 cells

source_name: 4T1 cells transduced with lentiviral shRNAs to Vav2 and Vav3 transcripts, clone B

tag: tissue

value: Knock down B


title: 4T1 KD2/3 expB rep 2

description: miRNA expression from 4T1 cells


title: wtBCM40_1: S. aureus wild type_exponential_BCM40_rep1

source_name: S. aureus wild type_exponential_BCM40


title: wtBCM80_2: S. aureus wild type_exponential_BCM80_rep2

source_name: S. aureus wild type_exponential_BCM80


title: DrhoOD0.2_2: S. aureus rho mutant_early exponential phase_rep2

value: early exponential


title: 4T1 pLKO rep 3

description: miRNA expression from 4T1 cells

source_name: 4T1 cells harboring the empty pLKO lentiviral vector

value: Control


title: DrhoExp_1: S. aureus rho mutant_exponential phase_rep1


title: wtExp_2: S. aureus wild type_exponential phase_rep2

source_name: S. aureus wild type_exponential phase


title: 4T1 KD2/3 expB rep 3

description: miRNA expression from 4T1 cells


title: 4T1 KD2/3 expA rep 1

description: miRNA expression from 4T1 cells

source_name: 4T1 cells transduced with lentiviral shRNAs to Vav2 and Vav3 transcripts, clone A

value: Knock down A


title: wtBCM40_2: S. aureus wild type_exponential_BCM40_rep2


title: wtOD0.2_1: S. aureus wild type_early exponential phase_rep1


title: HIV3_CSF

status: Public on Sep 20 2018

city: New Haven

first: Shelli

last: Farhadian

state: CT

address: 135 College St

institute: Yale University School of Medicine

data_processing:
The reads from the sequencer were processed with the DropSeq analysis pipeline DropSeqtools version 1.13 (http://mccarrolllab.com/dropseq/).
The reads are concatenated such that there is only one file for Read1 and one for Read2.  The Fastq files are then converted to SAM format using FastqToSam.
The unaligned SAM file is then tagged with the cell barcode.  The cell-barcode tagged reads are then tagged with molecular barcode.
The reads are further trimmed of the PolyA signal, and converted back to fastq.  These files are then aligned with the reference genome using STAR.  The alignemnt files are then tagged with the geneId, and finally converted into a digital expression matrix.
Genome_build: hg19
Supplementary_files_format_and_content: The files are digital expression matrices generated by the DropSeq pipeline.  Each column is a cell, and each row is the gene.  The value in in each cell denotes number of times the transcript/Cell barcode combination was seen in the data.

source_name: CSF

extract_protocol:
SeqWell
Nextera

tag: hiv ab status


title: Uninfected2_CSF

value: uninfected


title: Uninfected1_CSF


title: HIV2_Bld

source_name: PBMCs


title: 4T1 pLKO rep 2

description: miRNA expression from 4T1 cells


title: 4T1 KD2/3 expA rep 2

description: miRNA expression from 4T1 cells


title: 4T1 KD2/3 expA rep 3

description: miRNA expression from 4T1 cells


title: 4T1 pLKO rep 1

description: miRNA expression from 4T1 cells


title: DrhoOD0.2_1: S. aureus rho mutant_early exponential phase_rep1


title: wtBCM80_1: S. aureus wild type_exponential_BCM80_rep1


title: wtOD0.2_2: S. aureus wild type_early exponential phase_rep2


title: wtExp_1: S. aureus wild type_exponential phase_rep1


title: HIV1_Bld


title: HIV1_CSF


title: t821.KIT-2

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Quality of reads was verified using FASTQC analysis
RNA-Seq reads were aligned to the hg38 human genome build using STAR.
Density files for the positive and negative strands were generated for RNA-seq data using bedtools and uploaded to the UCSC genome browser
Fragments per Kilobase of transcript per Million mapped reads (FPKM) values for each gene were extracted using Cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph

source_name: AML patient #2 with t(8;21) translocation

extract_protocol:
RNA was extracted using the Machery-Nagel Nucleospin kit. 1μg RNA was used to make cDNA with 0.5 μg OligoDT primer, Murine Moloney Reverse Transcriptase and RNase Inhibitor (Promega, USA) according to manufacturer’s protocol.  RT-PCR was performed using Sybr Green mix (Applied Biosystems, UK), at 2x dilution.  Primers were used at 100nM concentration. A 7900HT system (Applied Biosystems, UK) was used to perform qPCR.  Analyses were performed in technical duplicates using a standard curve derived from the untreated cell line.
RNA-seq libraries were prepared with a Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina, USA) according to manufacturer’s instructions with the following alterations: 15 cycles of PCR was undertaken to amplify the library and adaptors for multiplexing were used at a 1:4 dilution. Library quality was checked by running the samples on a Bioanalyser and libraries were quantified using a Kapa library quantification kit (Kapa Biosystems, USA) and run in a pool of eight indexed libraries in two lane of a HiSeq 2500 (Illumina, USA) using rapid run chemistry with 100bp paired end reads.

value: t(8;21) translocation

tag: disease state

value: AML


title: t821.ITDx2-5

source_name: AML patient #5 with t(8;21) translocation


title: t821-1_rel

source_name: AML patient #1 with t(8;21) translocation relapse

value: t(8;21) translocation relapse


title: HIV2_CSF


title: t821-1

source_name: AML patient #1 with t(8;21) translocation


title: FLT3-ITD captureHiC

data_processing:
Quality of reads was verified using FASTQC analysis
The capture Hi-C paired-end sequencing reads were alighned using HiCUP tools (PMID: 26835000). The raw sequencing reads are separated and mapped against the positions of the human genome (hg38). The reads were then filtered for experimental artefacts and duplicate reads
Functions provided with HOMER (PMID: 20513432) were used for HiC data processing and to obtain interactions
Genome_build: hg38
Supplementary_files_format_and_content: tab text

source_name: CHiC from AML paitent with FLT3-ITD and NPM1 mutation

extract_protocol:
AML cells from patient peripheral blood were first purified by density gradient centrifugation (Lymphoprep™) and then using CD34 antibody coupled beads. 5× 107 t(8;21) blasts (patient t(8;21)-1R) and FLT3-ITD/NPM1 blasts (patient ITD/NPM1-2) were fixed in 37 ml of RPMI-1640 supplemented with 15% FBS and 2% formaldehyde for 10 minutes at room temperature. 6 ml of 1M glycine (0.125 M final concentration) was added to quench the reaction and cells were incubated at room temperature for 5 min, followed by 15 minutes on ice before pelleting the cells at 4 °C and washing them in ice cold PBS. Each sample was flash frozen in liquid nitrogen, and stored at −80 °C. Cells were lysed in a tight dounce homogeniser (ten cycles) with 3ml of cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, one tablet protease inhibitor cocktail (Roche complete, EDTA-free, 11873580001)). Cells were left on ice for five minutes then homogenised another ten times. The lysed cells, in 3 ml lysis buffer, were added to 47ml of lysis buffer and incubated on ice for 30 minutes with occasional mixing. Chromatin was pelleted and resuspended in 1ml of 1.25x NEBuffer 2 and split into four. Each sample was then pelleted at 1000 rpm and resuspended in 358 µl of 1.25x NEBuffer 2. 11 µl 10% SDS was added and each tube was incubated at 37°C for 60 minutes, rotating at 950 rpm. Samples were mixed by pipetting up and down every 15 minutes. SDS was quenched with 75µl 10% Triton X-100 and incubated at 37˚C for 60 minutes. The chromatin was digested overnight with 1500 units of HindIII (NEB R0104T), rotating (950 rpm) at 37 °C. The HindIII cleavage of its restriction site (5’ AAGCTT 3’) generates a 5’ overhang (5’-AGCT-3’), which was repaired to include a biotinylated nucleotide, allowing the enrichment of Hi-C ligation products. To do this, 6µl 10x NEB2, 2µl H2O, 1.5µl 10mM dCTP, 1.5µl 10mM dGTP, 1.5µl 10mM dTTP, 37.5µl 0.4mM biotin-14-dATP (Life Technologies 19524-016), and 10μl 5U/μl Klenow (DNA polymerase I large fragment, NEB M0210L) were added to each tube. Samples were mixed carefully and incubated for 60 minutes at 37˚C, with mixing by pipetting every ten minutes. The digested chromatin mixture was added to a falcon tube with 8 ml of ligation buffer (750µl 10x ligation buffer (NEB B0202S), 75 μl 10mg/ml BSA (NEB B9001S) and 50 μl  1U/μl T4 DNA ligase (Invitrogen 15224-025). These dilute conditions favour ligation of fragments crosslinked within the same chromatin complex (intra-molecular ligation). The tubes were mixed by inversion and incubated overnight at 16 °C. The following day, samples were incubated for a further 30 minutes at room temperature.
Crosslinks were reversed and proteins degraded by incubating the tubes over night at 65 ˚C, with 60µl 10mg/ml proteinase K (Roche 03115879001). After the overnight incubation, another 60 µl of 10 mg/ml proteinase K per tube was added, followed by a 2 hour incubation at 65˚C. The reaction mixtures were cooled to room temperature and 12.5 µl of 10 mg/ml RNase A (Roche 10109142001) was added. Samples were incubated at 37˚C for 60 minutes. The DNA in these tubes was purified with two phenol extractions. After ethanol precipitation, the DNA pellets were resuspended in 25µl 1x TE and the four samples were pooled. The Quant-iT assay was used to determine the DNA concentration of the resultant HiC library using a Qubit® 3.0 Fluorometer (Thermo Scientific). To check the library was sufficiently ligated, a 1/10 dilution was resolved on a 0.8% agarose gel. The majority of the library should run at around 10 kb. To confirm that blunt-end ligation was successful, the fact that fill-in and ligation of a HindIII site (AAGCTT) creates a NheI restriction site (GCTAGC) was exploited. A particular ligation product formed by the MYC promoter and a known 1.8 MB long range interaction was amplified with 3C PCR (see table 12 for primer sequences). The same was done for a ligation product formed by the MYC promoter and an adjacent restriction fragment. 200ng of the purified PCR products were split into four and digested with HindIII, NheI or both enzymes, with undigested DNA is used as a control. The resultant DNA samples were run on a 1.5% gel.  To avoid pulling down any non-ligated fragments, biotin was removed from free ends using the exonuclease activity of T4 DNA polymerase. 8 reactions of  5μg of Hi-C library, 0.5μl 10 mg/ml BSA, 5μl 10x NEBuffer 2, 2μl 2.5mM dATP, and 5μl T4 DNA polymerase (NEB M0203L) in a total volume of 50μl were made and incubated at 20˚C for 4 hours. The reaction was stopped by adding 2ml of 0.5M EDTA pH 8.0. Two reactions were pooled to generate four tubes of approximately 10ug DNA. The DNA was purified via phenol:chloroform extraction and ethanol precipitation. Each sample was reconstituted in 130 μl H2O. An E220 focused-ultrasonicator (Covaris) was used to fragment the DNA with the intensity set to 4, the duty cycle set to 10% and with 200 cycles per burst for 55 seconds. After sonication,  the entire volume of each sample was transferred into a fresh Eppendorf tube and 18μl 10x ligation buffer (NEB B0202S),18μl 2.5mM dNTP mix, 6.5μl T4 DNA polymerase (NEB M0203L),6.5μl T4 DNA Polynucleotide kinase (NEB M0201L) and 1.3μl Klenow (NEB M0210L) were added. The reaction was left for 30 minutes at room temperature. Each sample was then split into two and purified with a MinElute column (Qiagen 28004), according to the manufacturer’s instructions. Each column was eluted twice with 15 μl TLE (10mM Tris pH8.0, 0.1mM EDTA). To the sheared and end repaired DNA , 5 μl of NEBuffer 2 10x, 11.5 μl dATP 1mM and 3.5 μl Klenow exo- (NEB M0212L) were added. The reaction was incubated for 30 minutes at 37 ˚C. To inactivate the enzyme, each reaction was incubated at 65˚C for 20 minutes, and put on ice immediately afterwards. Fragments between 200 and 650 base pairs were size selected by double-sided SPRI bead (ampure) size selection (0.6x followed by 0.9x), following the manufacturers protocol.  All Hi-C library samples were then pooled and quantified with the Quant-iT™ High-Sensitivity DNA Assay Kit (Invitrogen) and assayed on the Qubit™ Fluorometer (Invitrogen). The biotin marked fragments were immobilized via MyOne Strapavidin C1 DynaBeads (Invitrogen) following manufacturers protocol. The fragments were ligated to illumina paired-end adaptors. The immobilized Hi-C fragments were amplified via PCR, using PE PCR primers 1 and 2 with 7 cycles. The Hi-C library was then purified twice with solid phase reversible immobilization (SPRI) beads (Beckman Coulter Ampure XP beads A63881) with a 1:1.8 DNA to SPRI bead ratio.

value: FLT3-ITD and NPM1 mutation


title: RUNX1-T_JAK-2

source_name: AML patient #2 with RUNX1 and JAK2 mutation

value: RUNX1 and JAK2 mutation


title: SRSF2-1

source_name: AML patient #1 with SRSF2 mutation

value: SRSF2 mutation


title: t(8;21) captureHiC

source_name: CHiC from AML paitent with t(8;21) translocation


title: SRSF2-2

source_name: AML patient #2 with SRSF2 mutation


title: RUNX1-DT-1

source_name: AML patient #1 with RUNX1 mutation

value: RUNX1 mutation


title: RUNX1-D-5

source_name: AML patient #5 with RUNX1 mutation


title: RUNX1-T_CEBPA-6

source_name: AML patient #6 with RUNX1 and CEBPA mutation

value: RUNX1 and CEBPA mutation


title: RUNX1-D_JAK-1

source_name: AML patient #1 with RUNX1 and JAK2 mutation


title: PBSC-1

source_name: CD34+ human healthy donor


title: RUNX1-DT-3

source_name: AML patient #3 with RUNX1 mutation


title: RUNX1x2-DT-4

source_name: AML patient #4 with RUNX1 double mutation

value: RUNX1 double mutation


title: RUNX1-T-7

source_name: NHL patient with RUNX1 mutation


title: RUNX1-DT_CEBPA-2

source_name: AML patient #2 with RUNX1 and CEBPA mutation


title: NPM1-1

source_name: AML patient #1 with NPM1 mutation

value: NPM1 mutation


title: ITDNPM1-5

source_name: AML patient #5 with FLT3-ITD and NPM1 mutation


title: ITDNPM1-6

source_name: AML patient #6 with FLT3-ITD and NPM1 mutation


title: NPM1-2

source_name: AML patient #2 with NPM1 mutation


title: NPM1RAS-3 (2)

source_name: AML patient with NPM1 and RAS mutation

value: NPM1 and RAS mutation


title: ITDNPM1-4

source_name: AML patient #4 with FLT3-ITD and NPM1 mutation


title: ITDNPM1-2

source_name: AML patient #2 with FLT3-ITD and NPM1 mutation


title: ITD-3

source_name: AML patient #3 with FLT3-ITD mutation

value: FLT3-ITD mutation


title: ITD2x_NPM1-2

source_name: AML patient #2 with FLT3-ITD double mutation

value: FLT3-ITD double mutation


title: ITD2x_NPM1-1

source_name: AML patient #1 with FLT3-ITD double mutation


title: ITD-1

source_name: AML patient #1 with FLT3-ITD mutation


title: inv3RAS-3

source_name: AML patient #2 with inv(3) and RAS mutation

value: inv(3) and RAS mutation


title: inv3RAS-1

source_name: AML patient #1 with inv(3) and RAS mutation


title: inv16-2

source_name: AML patient #2 with inv(16)


title: CEBPAx2-3

source_name: AML patient #3 with CEBPA double mutation

value: CEBPA double mutation


title: CEBPAx2-2

source_name: AML patient #2 with CEBPA double mutation


title: CEBPAx2-1

source_name: AML patient #1 with CEBPA double mutation


title: CEBPA-5

source_name: AML patient #5 with CEBPA mutation

value: CEBPA mutation


title: ITDNPM1-3

source_name: AML patient #3 with FLT3-ITD and NPM1 mutation


title: CD34Plus_CB

source_name: CD34+ human coord blood

value: CD34+ coord blood


title: ITDNPM1-1

source_name: AML patient #1 with FLT3-ITD and NPM1 mutation


title: RUNX1-DT_CEBPA-2 DHS

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
The aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools and then converted to big wig file using "wigToBigWig" function
Genome_build: hg38
Supplementary_files_format_and_content: wiggle

source_name: AML patient #2 DHS with RUNX1 and CEBPA mutation

extract_protocol:
DNase I digestions of permeabilized cells were performed briefly as follows: live cells were added directly to a solution of DNase I (DPFF, Worthington) in dilute Nonidet P40, digested for 3 min at 22oC, and the reactions then terminated by addition of SDS to 0.5%. DNase I was typically used in the range of 2-6 μg/ml using a final 1.5 x 107 cells/ml.
DNase I (DPFF) was obtained from Worthington Biochemical Corporation and typically used in the range of 2-6 μg/ml using a final 1.5 x 107 cells/ml. The DNA digestion extent was comparable in all the generated samples as measured by RT-PCR. DNase-Seq libraries were then prepared.  Levels of DNase I digestion were assessed using quantitative real-time PCR, measuring the ratio of the presence of known DNase I hypersensitive regions compared to a more resistant inactive region. Sequences of the PCR primers used for this purpose were, for the active region, TBP promoter 5´- CTGGCGGAAGTGACATTATCAA and 5´- GCCAGCGGAAGCGAAGTTA; and for the inactive region, a region of chromosome 18: 5´- ACTCCCCTTTCATGCTTCTG and 5´- AGGTCCCAGGACATATCCATT. DNase-Seq samples were generated from a size selection of DNase I-digested DNA fragments comprised within a range of 100 to 250 bp (not including linkers) and subjected to library preparation as per manufacturer´s instruction (Illumina).

value: DHS with RUNX1 and CEBPA mutation


title: RUNX1-T_JAK-2 DHS

source_name: AML patient #2 DHS with RUNX1 and JAK mutation

value: DHS with RUNX1 and JAK mutation

value: AML


title: RUNX1x2-DT-4 DHS

source_name: AML patient #4 DHS with RUNX1 double mutation

value: DHS with RUNX1 double mutation


title: t821-3 DHS

source_name: AML patient #3 DHS with t(8;21) translocation

value: DHS with t(8;21) translocation


title: RUNX1-T_CEBPA-6 DHS

source_name: AML patient #6 DHS with RUNX1 and CEBPA mutation


title: t821-1_rel DHS

source_name: AML patient #1 DHS with t(8;21) translocation relapse

value: DHS with t(8;21) translocation relapse


title: t821-1 DHS

source_name: AML patient #1 DHS with t(8;21) translocation


title: RUNX1-DT-1 DHS

source_name: AML patient #1 DHS with RUNX1 mutation

value: DHS with RUNX1 mutation


title: RUNX1-D_JAK-1 DHS

source_name: AML patient #1 DHS with RUNX1 and JAK mutation


title: RUNX1-DT-3 DHS

source_name: AML patient #3 DHS with RUNX1 mutation


title: t821KIT-2 DHS

source_name: AML patient #2 DHS with t(8;21) translocation and KIT mutation


title: RUNX1-T-7 DHS

source_name: NHL patient DHS with RUNX1 mutation


title: RUNX1-D-5 DHS

source_name: AML patient #5 DHS with RUNX1 mutation


title: ITD-2

source_name: AML patient #2 with FLT3-ITD mutation


title: NPM1RAS-3

source_name: AML patient with DHS NPM1 and RAS mutation

value: DHS NPM1 and RAS mutation


title: inv16-3

source_name: AML patient #3 with inv(16)


title: NPM1-1 DHS

source_name: AML patient #1 DHS with NPM1 mutation

value: DHS with NPM1 mutation


title: inv16-1

source_name: AML patient #1 with inv(16)


title: ITDNPM1-5 DHS

source_name: AML patient #5 DHS with FLT3-ITD and NPM1 mutation

value: DHS with FLT3-ITD and NPM1 mutation


title: NPM1-2 DHS

source_name: AML patient #2 DHS with NPM1 mutation


title: ITDNPM1-3 DHS

source_name: AML patient #3 DHS with FLT3-ITD and NPM1 mutation


title: ITDNPM1-2 DHS

source_name: AML patient #2 DHS with FLT3-ITD and NPM1 mutation


title: ITDNPM1-4 DHS

source_name: AML patient #4 DHS with FLT3-ITD and NPM1 mutation


title: Day0 rep2 [miRNA]

description: processed data file: Counts.txt

source_name: Whole blood

value: Duroc x Landrace x Yorkshire crossbreed

value: Peripheral blood

tag: age

value: 4 weeks

value: Untreated

value: Day 0


title: ITD-2 DHS

source_name: AML patient #2 DHS with FLT3-ITD mutation

value: DHS with FLT3-ITD mutation


title: ITD-1 DHS

source_name: AML patient #1 DHS with FLT3-ITD mutation


title: ITD2x_NPM1-2 DHS

source_name: AML patient #2 DHS with FLT3-ITD double mutation

value: DHS with FLT3-ITD double mutation


title: ITD2x_NPM1-1 DHS

source_name: AML patient #1 DHS with FLT3-ITD double mutation


title: inv3RAS-1 DHS

source_name: AML patient #1 DHS with inv(3) and RAS mutation

value: DHS with inv(3) and RAS mutation


title: ITDNPM1-1 DHS

source_name: AML patient #1 DHS with FLT3-ITD and NPM1 mutation


title: CEBPAx2-2 DHS

source_name: AML patient #2 DHS with CEBPA double mutation

value: DHS with CEBPA double mutation


title: CEBPAx2-3 DHS

source_name: AML patient #3 DHS with CEBPA double mutation

value: AML


title: inv16-2 DHS

source_name: AML patient #2 DHS with inv(16)

value: DHS with inv(16)


title: inv3CBL-2 DHS

source_name: AML patient #2 DHS with inv(3) and CBL mutation

value: DHS with inv(3) and CBL mutation


title: inv16-1 DHS

source_name: AML patient #1 DHS with inv(16)


title: CEBPAx2-1 DHS

source_name: AML patient #1 DHS with CEBPA double mutation


title: 3744-MS-85: SD Rat Heart, 24 h, High (100 mg/kg thioacetamide)

city: Frederick

first: Patric

last: Schyman

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description: Treatment

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.2) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Rattus norvegicus transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Genome_build: Rattus norvegicus transcriptome (Rnor_6.0)
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Frozen whole kidney and heart samples were powdered in liquid nitrogen, since these organs are histologically heterogeneous. Total RNA was isolated from liver, powdered kidney, and powdered heart, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: Sprague-Dawley

value: Heart

tag: duration

tag: dose

value: High (100 mg/kg thioacetamide)


title: 3744-MS-84: SD Rat Heart, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-66: SD Rat Heart, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-82: SD Rat Heart, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment

value: Low (25 mg/kg thioacetamide)


title: 3744-MS-63: SD Rat Heart, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-83: SD Rat Heart, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-80: SD Rat Heart, 24 h, Vehicle (3 ml/kg saline)

description: Control

value: Vehicle (3 ml/kg saline)


title: 3744-MS-65: SD Rat Heart, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-62: SD Rat Heart, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-86: SD Rat Heart, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-79: SD Rat Heart, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-81: SD Rat Heart, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-61: SD Rat Heart, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-87: SD Rat Heart, 8 h, High (100 mg/kg thioacetamide)

description: Treatment

value: 8 h


title: inv16-3 DHS

source_name: AML patient #3 DHS with inv(16)


title: 3744-MS-77: SD Rat Heart, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-74: SD Rat Heart, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-68: SD Rat Heart, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-64: SD Rat Heart, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-72: SD Rat Heart, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-78: SD Rat Heart, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-89: SD Rat Heart, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-90: SD Rat Heart, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-76: SD Rat Heart, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-69: SD Rat Heart, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-71: SD Rat Heart, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-88: SD Rat Heart, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-67: SD Rat Heart, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-73: SD Rat Heart, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-54: SD Rat Kidney, 24 h, High (100 mg/kg thioacetamide)

description: Treatment

source_name: Kidney

value: Kidney


title: 3744-MS-106: SD Rat Kidney, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-37: SD Rat Kidney, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-36: SD Rat Kidney, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-56: SD Rat Kidney, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-33: SD Rat Kidney, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-70: SD Rat Heart, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-32: SD Rat Kidney, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-51: SD Rat Kidney, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-105: SD Rat Kidney, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-35: SD Rat Kidney, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-52: SD Rat Kidney, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-109: SD Rat Heart, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-50: SD Rat Kidney, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-34: SD Rat Kidney, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-103: SD Rat Kidney, 24 h, Vehicle (3 ml/kg saline)

description: Control