title: FTO-GFP RNA-seq rep 3

status: Public on Jul 01 2020

data_processing:
Fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14)
Trimmed reads were aligned to the ENSEMBL human genome version GRCh38 using STAR (2.5.2)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
Cutom bash and R scripts were used for generating figures and performing statisitcal analyses
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: ascites

growth_protocol: GFP or FTO overexpressed ovcarian cancer cells were culutured with high glucose DMEM medium contain 10% FBS and 1% penicillin/streptomycin, and MENNA.

extract_protocol:
RNA was harvested using Trizol reagent. gDNA was removed using QIAGEN Rneasy mini kit. And then mRNA was isolated with Ambion Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.

value: ovarian cancer cell

tag: tumor stage

value: high grade serous

tag: passage

value: 4 to 6


title: DM503_MNase_rep1_120_min

status: Public on Jul 04 2020

type: SRA

city: Durham

first: David

middle: M

last: MacAlpine

state: North Carolina

address: Duke University

department: Department of Pharmacology and Cancer Biology

country: USA

institute: Duke University Medical Center

description: MNase chromatin at T=120 following Cd addition

library_source: genomic

data_processing:
Reads were aligned using Bowtie 0.12.7 with parameters "-n 2 -l 20 -m 1 -k 1 -X 1000" to release 64 (sacCer3) of the S.cerevisiae genomic sequence obtained from downloads.yeastgenome.org.
Data processing code from github.com/HarteminkLab/cadmium-paper was run against aligned reads. The following steps from this code were performed:
Chromatin replicates were merged and randomly sampled to equivalent proportions for each time point.
For each base pair at each ORF of the genome, chromatin characterization of transcription factors and nucleosomes were computed relative to TSSs obtained from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973313/bin/supp_42_6_3736__index.html
Transcription factor occupancy was characterized using MNase reads shorter than 100 base pairs and within 200 base pairs upstream of TSSs, defined as the "small fragment promoter occupancy" for each ORF.
Nucleosomes were characterized through cross correlating a bivariate Gaussian distribution against MNase reads at high scoring nucleosomes obtained from GEO/GSE36063. An information entropy score was computed using this per base pair cross correlation for first three nucleosomes downstream of each ORF’s TSS, defined as a gene's "gene body nucleosome disorganization".
RNA reads were counted at non-intronic regions inside ORF boundaries. TPM was computed by scaling read counts by ORF length and normalizing to an equivalent sum for each time point.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown in rich medium at 30C to an OD600 0.8.

extract_protocol:
Chromatin were prepared as in Belsky et. al. Genes and Development, 2015
See Belsky et al.

treatment_protocol: Samples were removed for both MNase treatment and RNA-seq as a 0 time point before addition of Cadmium Chloride to a final concentration of 1mM for 120 min.

tag: strain

tag: treatment

value: 1 mM Cd

tag: time

value: 120 min


title: FTO-GFP RNA-seq rep 1

city: CHICAGO

first: Manoj

last: Kandpal

state: Illinois

address: 1256 W NORTHSHORE AVE, 3R

institute: Northwestern University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: FTO-GFP RNA-seq rep 2


title: GFP RNA-seq rep 3


title: RNA_rep1_15_min

description: RNA at T=15 following Cd addition

value: 15 min


title: FTO-GFP m6A-seq m6A pull-down rep 2

description: diff_peak.bed, diff_peak.xls

data_processing:
Fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14)
Trimmed reads were aligned to the ENSEMBL human genome version GRCh38 using STAR (2.5.2)
Exomepeak (in R) is used for estimating RNA methylation sites and differntial peaks between two conditions.
IGVtool and MEME-chip is used for geneating tracks and predicting enriched motifs
Genome_build: GRCh38
Supplementary_files_format_and_content: xls, bed

extract_protocol:
Magna MeRIP m6A kit (Millipore, Billerica, MA) was used to examine m6A modifications . Methylated RNAs were immunoprecipitated with beads, eluted by competition with free m6A, and recovered with the RNeasy kit
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.
MERIP


title: GFP RNA-seq rep 2


title: FTO-GFP m6A-seq m6A pull-down rep 1

description: diff_peak.bed, diff_peak.xls


title: GFP RNA-seq rep 1


title: GFP m6A-seq m6A pull-down rep 2

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq m6A pull-down rep 1

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq m6A pull-down rep 3

description: diff_peak.bed, diff_peak.xls


title: MG189B_NOIGD_HHT

status: Public on Aug 03 2020

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger mkfastq function from 10X Genomics 2.2.0.
Reads were aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the Cell Ranger count function.
The resulting output was loaded into Seurat v.2.3.4 for analysis.
Cells with less than 50 genes detected, or mitochondrial content above 0.2 of all transcripts were discarded.
Genome_build: GCRhg38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv, features.tsv & genes.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
B cells were isolated from PBMCs by Human Pan B cell immunomagnetic negative selection kit (StemCell) per manufacturer’s instructions.
Libraries were prepared using the Chromium Single-cell5′ Reagent Kit (10x Genomics) for version 3 chemistry per the manufacturer’s protocol.

value: B-lymphocytes

tag: mgfa class

value: IIb

tag: isolate


title: FTO-GFO m6A-seq input rep 1

description: diff_peak.bed, diff_peak.xls


title: FTO-GFO m6A-seq input rep 3

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq input rep 3

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq input rep 2

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq input rep 1

description: diff_peak.bed, diff_peak.xls


title: WT1GFP-3

status: Public on Jun 27 2020

city: Rochester

first: Eric

last: Small

state: NY

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

data_processing:
Basecalls by bcl2fastq version 1.8.4
Quality filtering and adapter removal were performed using Trimmomatic version 0.32 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15".
Processed/cleaned reads were then mapped to the GRCm38 reference genome using the SHRiMP version 2.2.3 and the following parameters: " --qv-offset 33 --all-contigs".
Uniquely aligned and multi-mapped reads were counted within the gencode GRCm38 gene annotations, in a strand specific manner, using the cuffdiff tool from the cufflinks-2.0.2 package and the following parameters: “--FDR 0.05 -u -b GENOME”
Differential expression analyses and data normalization were performed using DESeq2-1.14.1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimitted gene counts

organism: Mus musculus

source_name: Epicardium-derived cells

growth_protocol: Hearts were removed from mouse embryos at  embryonic age 12.5. Ex vivo hearts were cultured for 48 hours in a mixture of M199/DMEM High Glucose media containing 1% FBS and 1% Pen-Strep. Hearts were maintained at conditions of 5% CO2 and 37℃.

extract_protocol:
Ex vivo wild-type and MRTFdKO hearts were removed from culture media and whole heart tissue was digested with collagenase type IV at 37℃ for 20 minutes. A single cell suspension was subjected to fluorescence-activated cell sorting to collect GFP-positive epicardium-derived cells directly into TRIzol to isolate RNA.
The Clontech Ultralow RNA Kit in conjunction with NexteraXT DNA Library Prep Kit was used for next generation sequencing library construction per manufacturer’s protocols.
low input RNA-Seq

treatment_protocol: Ex vivo MRTF-A wild-type ; MRTF-B wild-type hearts were treated with adenovirus to express b-galactosidase in the first 24 hours of culture. Ex vivo MRTF-A -/- ; MRTF-B flox/flox hearts were treated with adenovirus to express Cre and delete MRTF-B alleles in the first 24 hours of culture. Additionally, wild-type and MRTFdKO hearts were treated with adenovirus to express GFP. Adenoviruses are validated to infect the first cell layer of the heart, also known as the epicardium. Both wild-type and MRTFdKO hearts were treated with TGFb1 [10ng/mL] and PDGF-BB [20ng/mL] for an additional 24 hours to induce epithelial-to-mesenchymal transition.

tag: background strain

tag: genotype

value: MRTF-A wild-type ; MRTF-B wild-type

tag: developmental stage

value: embryonic day 12.5

tag: tissue

value: heart

value: epicardium-derived cells

value: adenovirus expressing b-galactosidase and GFP (24 hours) ; recombinant TGFb1 [10ng/mL] and PDGF-BB [20ng/mL] (24 hours)


title: MRTFdKO-4

value: MRTF-A -/- ; MRTF-B flox/flox

value: adenovirus expressing Cre and GFP (24 hours) ; recombinant TGFb1 [10ng/mL] and PDGF-BB [20ng/mL] (24 hours)


title: DM502_MNase_rep1_60_min

description: MNase chromatin at T=60 following Cd addition

value: 60 min


title: MRTFdKO-2


title: WT1GFP-2


title: WT1GFP-1


title: MRTFdKO-1


title: 0777A_ETO_Input_DNA

status: Public on Jun 25 2020

city: New York

first: Junfei Zhao

last: Zhao

address: 1130 St. Nicholas Ave

institute: Columbia University

description: 0777A ETO Input

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem.
peaks were called using macs2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2.

source_name: 0777A glioma cells

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam, TOP2B Abcam) was incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

treatment_protocol: 50x10e6 cells were treated with etoposide or DMSO, crosslinked using formaldehyde 1%.

tag: agent

value: ETO

tag: cell line

value: glioma cells

tag: chip antibody


title: 0777A_DMSO_Input_DNA

description: 0777A DMSO Input

value: DMSO


title: FTO-GFP m6A-seq m6A pull-down rep 3

description: diff_peak.bed, diff_peak.xls

value: ovarian cancer cell

value: high grade serous

value: 4 to 6


title: SNB19_Input_DNA

description: SNB19 Input

source_name: SNB19 glioma cells


title: NU01722_Input_DNA

description: NU01722 Input

source_name: Glioma cells


title: DMSO_BT142_Input_DNA

source_name: BT142 glioma cells

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.


title: NU01482_Input_DNA

description: NU01482 Input


title: ETO_TS543_Input_DNA


title: FTO-GFO m6A-seq input rep 2

description: diff_peak.bed, diff_peak.xls


title: DMSO_TS543_Input_DNA

source_name: TS543 glioma cells


title: pPCH2-FLAG tag-Pch2 wild_type_ChIP rep1

status: Public on Jun 14 2020

city: Dortmund

first: Richard

last: Cardoso da Silva

state: North Rhine Westfallen

department: Mechanistic Cell Biology

country: Germany

institute: Max Planck Institute of Mol Physiol

data_processing:
Basecalls performed using (CLC Genomics Workbench 10)
ChIP-seq and Input reads were aligned and mapped to the S. cerevisiae genome background (SacCer3) assembly with CLC Genomics Workbench 10, allowing for maximal 2 mismatches in 100bp.
Peak calling was performed using the CLC shape-based peak caller (CLC Genomics Workbench 10). ChIP peakswere obtained through normalization with inputs. A p-value of 1e-15 was used for calling the peaks.
Genome_build: SacCer3
Supplementary_files_format_and_content: wig files of averaged data

source_name: 3X-FLAG Pch2 wild type

growth_protocol: Cells were patched from glycerol stocks onto YPG plates and grown overnight. Patched cells were transferred to YPD and further grown overnight. Cells were cultured in liquid YPD at 23°C overnight and diluted at OD600 0.3 into pre-sporulation media (BYTA; phthalate-buffered yeast extract, tryptone and acetate). Cells were grown in BYTA for 16-18 hours at 30°C, washed twice in water and resuspended in sporulation media (0.3% KAc) at OD600 1.9 to induce meiosis. Sporulation cultures were grown at 30°C

extract_protocol:
Cells were resuspended and broken with glass beads using a bead beater. Chromatin was sheared using a Diagenode Bioruptor UCD 200 (25 cycles of 30 seconds on/off, high power at 4°C). Cells were centrifuged at 13000 rpm for 10 min at 4°C
Preparation of paired-end sequencing libraries was performed using the Illumina TruSeq ChIP library preparation kit Set-A (15034288),  according to the manufacturer’s guidelines. Ligation products were size-selected (250-300 bp) and purified from a 2% low-melting agarose gel using the MinElute Gel Extraction Kit (Qiagen). Ampure XP beads (Agilent) were used for cleanup steps and size selection. The final purified product was quantitated using Picogreen in a QuantiFluor dsDNA System (Promega). Paired-end sequencing (2 X 150bp) was performed on the Illumina HiSeq 3000 platform
TrueSeq ChIP

tag: genotype/variation

value: 3X-FLAG Pch2 wild type

value: cells undergoing meiosis in sporulation medium

tag: passages

value: 4h in SPO (ndt80delta)

value: α-Flag-M2 affinity gel (Sigma-Aldrich, A2220)


title: pPCH2-FLAG tag-Pch2 wild_type_ChIP rep3


title: pPCH2-FLAG tag-Pch2 wild_type_ChIP rep2


title: pPCH2-FLAG tag-Pch2 E399Q_ChIP rep1


title: pPCH2-FLAG tag-Pch2 E399Q _input rep3

value: input


title: pPCH2-FLAG tag-Pch2 E399Q_ChIP rep3


title: pPCH2-FLAG tag-Pch2 wild_type _input rep3


title: pPCH2-FLAG tag-Pch2 E399Q _input rep2


title: pPCH2-FLAG tag-Pch2 wild_type _input rep1

data_processing: Preliminary quality control of raw reads was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Illumina raw reads were filtered for removal of low quality and duplicated reads, adapters and low-quality bases using the SAM tools (version 1.2). Paired-sequencing reads from three biological independent replicas (ChIPed DNA and their respective inputs from 3XFLAG-Pch2 and 3XFLAG-tagged-Pch2-E399Q expressing cells) were mapped to the yeast genome S288C (SacCer3) using Bowtie2 (version 2.3.4.3) with default parameters. Non-unique reads were removed using SAMtools (Version 1.2). The dataset was pooled and the Model-based Alignment of ChIP-Seq (MACS2) program was used to call peaks of Pch2 occupancy using the input as a control (P-value = e10-15).


title: DM500_MNase_rep1_15_min

description: MNase chromatin at T=15 following Cd addition

value: 1 mM Cd

value: 15 min


title: pPCH2-FLAG tag-Pch2 E399Q_ChIP rep2


title: Kidney_LdlrKO_Male_ST5

status: Public on Jun 01 2020

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

data_processing:
Raw RNA-seq reads were aligned to the GRCm38 build of the mouse genome by STAR v2.7.6a, with the following command line parameters: --outSAMunmapped Within KeepPairs--outFilterMismatchNmax33--seedSearchStartLmax33--alignSJoverhangMin 8. Additionally, STAR was provided with the gene models (Ensembl v91) in GTF format during alignments.
Data were normalized and quantified at both gene and exon-intron level, using a downsampling strategy implemented in the PORT pipeline (github.com/itmat/Normalization -v0.8.45e-beta).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files contain PORT-normalized/quantified gene-level read counts from uniquely-aligned reads that map to single genes.

source_name: kidney medulla

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap

extract_protocol:
Heart atria and kidney medulla were collected from animals perfused with ice-cold PBS dissolved in UltraPure DEPC-treated water to minimize degradation of RNA. The tissues were immediately stored separately in RNAlater solution at 4ºC. After 24h, the tissue samples were transferred to -80ºC for storage until analyses. RNA was extracted using TRIzol Reagent and RNeasy Kit following the manufacturer’s protocol.
RNA integrity was checked on an Agilent Technologies 2100 Bioanalyzer. RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA Library Prep Kit.

treatment_protocol: Mice of both genders were fed a high salt diet (HSD, 8% NaCl, TD.92012, Harlan Teklad, Madison, WI) and saline containing 0.9% NaCl (Hospira, Lake Forest, IL) from 8-10 weeks of age for two weeks. Mice were weighed before and after the HSD feeding.

value: kidney medulla

value: Ldlr KO

tag: gender

value: male

tag: library barcode

value: CGGCTATG-ACGTCCTG


title: Kidney_DKO_Male_ST15

value: Ipr/Ldlr DKO

value: TCCGGAGA-GTCAGTAC


title: Kidney_DKO_Male_ST14

value: AGCGATAG-ACGTCCTG


title: Kidney_DKO_Male_ST13

value: TCCGCGAA-ACGTCCTG


title: Kidney_DKO_Male_ST12

value: TAATGCGC-ACGTCCTG


title: Kidney_LdlrKO_Male_ST4

value: CTGAAGCT-ACGTCCTG


title: Kidney_LdlrKO_Male_ST8

value: CGCTCATT-GTCAGTAC


title: Kidney_LdlrKO_Male_ST2

value: CGCTCATT-ACGTCCTG


title: Kidney_LdlrKO_Male_ST3

value: ATTCAGAA-ACGTCCTG


title: Kidney_LdlrKO_Male_ST1

value: ATTACTCG-ACGTCCTG


title: ACP40-QD-D3

status: Public on Apr 07 2020

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent FeatureCounts for gene level abundance estimation
Limma-voom was employed for DEA
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix, raw count, tab delimited

source_name: ACP40 QD D3

extract_protocol:
RNA was extracted per manufacturer's instructions (RNAeasy kit, Qiagen, Germantown, MD or ZR-Duet kit, Zymo Research, Irvine, CA).
Libraries were prepared with TruSeq Stranded total RNA Library Preparation Gold Kit (Illumina, San Diego, CA).

treatment_protocol: CD19+ PBMCs were purified by positive immunomagnetic selection (Miltenyi Biotec, Bergisch Gladbach, Germany).

tag: sample type

value: LN


title: Kidney_DKO_Male_ST10

value: GAGATTCC-ACGTCCTG


title: Kidney_LdlrKO_Male_ST6

value: TCTCGCGC-ACGTCCTG


title: pPCH2-FLAG tag-Pch2 E399Q _input rep1

value: cells undergoing meiosis in sporulation medium

value: 4h in SPO (ndt80delta)

tag: strain

value: input


title: pPCH2-FLAG tag-Pch2 wild_type _input rep2

value: 3X-FLAG Pch2 wild type


title: Kidney_LdlrKO_Male_ST7

value: kidney medulla

value: Ldlr KO

value: male

value: ATTACTCG-GTCAGTAC


title: Kidney_DKO_Male_ST9

value: Ipr/Ldlr DKO

value: TCCGGAGA-ACGTCCTG


title: Kidney_DKO_Male_ST16

value: GAGATTCC-GTCAGTAC


title: ACP38-BID-D4-PB

source_name: ACP38 BID D4

value: CD19+ PBMC


title: ACP39-QD-Pre

source_name: ACP39 QD Pre


title: ACP38-BID-C1-PB

source_name: ACP38 BID C1


title: ACP40-QD-Pre

source_name: ACP40 QD Pre


title: ACP39-QD-D3

source_name: ACP39 QD D3


title: ACP38-BID-C6-PB

source_name: ACP38 BID C6


title: ACP38-BID-Pre-PB

source_name: ACP38 BID Pre


title: Kidney_DKO_Male_ST11

value: GAATTCGT-ACGTCCTG


title: ACP37-BID-C6-PB

source_name: ACP37 BID C6


title: ACP37-BID-C1-PB

source_name: ACP37 BID C1


title: ACP36-BID-C6-PB

source_name: ACP36 BID C6


title: ACP37-BID-Pre-PB

source_name: ACP37 BID Pre


title: ACP37-BID-Pre


title: ACP36-BID-C1-PB

source_name: ACP36 BID C1


title: ACP30-QD-C6-PB

source_name: ACP30 QD C6


title: ACP36-BID-Pre-PB

source_name: ACP36 BID Pre


title: ACP36-BID-D5

source_name: ACP36 BID D5


title: ACP30-QD-C1-PB

source_name: ACP30 QD C1


title: ACP37-BID-D4

source_name: ACP37 BID D4


title: ACP30-QD-Pre-PB

source_name: ACP30 QD Pre


title: ACP37-BID-D4-PB


title: ACP34-QD-D4

source_name: ACP34 QD D4


title: ACP36-BID-Pre


title: ACP38-BID-Pre


title: ACP29-QD-C1-PB

source_name: ACP29 QD C1


title: ACP29-QD-D3

source_name: ACP29 QD D3


title: ACP29-QD-Pre-PB

source_name: ACP29 QD Pre


title: ACP29-QD-C6-PB

source_name: ACP29 QD C6


title: ACP30-QD-Pre


title: ACP28-QD-D4

source_name: ACP28 QD D4


title: ACP28-QD-Pre

source_name: ACP28 QD Pre


title: ACP30-QD-D3

source_name: ACP30 QD D3


title: ACP29-QD-Pre


title: ACP24-QD-D4-PB

source_name: ACP24 QD D4


title: ACP24-QD-C1-PB

source_name: ACP24 QD C1


title: ACP24-QD-Pre-PB

source_name: ACP24 QD Pre


title: ACP24-QD-D4


title: ACP34-QD-Pre

source_name: ACP34 QD Pre


title: ACP24-QD-Pre


title: ACP23-BID-C6-PB

source_name: ACP23 BID C6


title: ACP23-BID-Pre

source_name: ACP23 BID Pre


title: ACP22-BID-D5

source_name: ACP22 BID D5


title: ACP22-BID-Pre

source_name: ACP22 BID Pre


title: ACP23-BID-C1-PB

source_name: ACP23 BID C1


title: ACP23-BID-D5

source_name: ACP23 BID D5


title: ACP20-QD-C6-PB

source_name: ACP20 QD C6


title: ACP20-QD-C1-PB

source_name: ACP20 QD C1


title: ACP20-QD-D3

source_name: ACP20 QD D3


title: ACP19-BID-Pre

source_name: ACP19 BID Pre


title: ACP17-QD-C6-PB

source_name: ACP17 QD C6


title: ACP24-QD-C6-PB

source_name: ACP24 QD C6


title: ACP17-QD-C1-PB

source_name: ACP17 QD C1


title: ACP23-BID-Pre-PB


title: ACP20-QD-Pre

source_name: ACP20 QD Pre


title: ACP17-QD-Pre-PB

source_name: ACP17 QD Pre


title: ACP19-BID-C6-PB

source_name: ACP19 BID C6


title: ACP19-BID-Pre-PB


title: ACP19-BID-D4-PB

source_name: ACP19 BID D4


title: ACP19-BID-C1-PB

source_name: ACP19 BID C1


title: ACP19-BID-D4


title: ACP17-QD-Pre


title: ACP17-QD-D3

source_name: ACP17 QD D3


title: ACP20-QD-Pre-PB


title: ACP15-QD-C6-PB

source_name: ACP15 QD C6


title: ACP15-QD-C1-PB

source_name: ACP15 QD C1


title: ACP15-QD-D4-PB

source_name: ACP15 QD D4


title: ACP15-QD-Pre-PB

source_name: ACP15 QD Pre


title: ACP15-QD-Pre


title: ACP14-BID-D4

source_name: ACP14 BID D4


title: ACP14-BID-Pre

source_name: ACP14 BID Pre


title: ACP13-QD-C6-PB

source_name: ACP13 QD C6


title: ACP13-QD-C1-PB

source_name: ACP13 QD C1


title: ACP13-QD-D4-PB

source_name: ACP13 QD D4


title: ACP12-BID-C6-PB

source_name: ACP12 BID C6


title: ACP13-QD-Pre-PB

source_name: ACP13 QD Pre


title: ACP12-BID-C1-PB

source_name: ACP12 BID C1


title: ACP12-BID-Pre-PB

source_name: ACP12 BID Pre


title: ACP12-BID-Pre


title: ACP11-QD-C6-PB

source_name: ACP11 QD C6


title: ACP10-BID-C1-PB

source_name: ACP10 BID C1


title: ACP11-QD-Pre-PB

source_name: ACP11 QD Pre


title: ACP11-QD-C1-PB

source_name: ACP11 QD C1


title: ACP11-QD-D4-PB

source_name: ACP11 QD D4


title: ACP10-BID-C6-PB

source_name: ACP10 BID C6


title: ACP10-BID-D4

source_name: ACP10 BID D4


title: ACP12-BID-D5

source_name: ACP12 BID D5


title: ACP09-QD-D4

source_name: ACP09 QD D4


title: ACP08-QD-C1-PB

source_name: ACP08 QD C1


title: ACP08-QD-C6-PB

source_name: ACP08 QD C6


title: ACP08-QD-Pre-PB

source_name: ACP08 QD Pre


title: ACP10-BID-Pre

source_name: ACP10 BID Pre


title: ACP08-QD-D4

source_name: ACP08 QD D4


title: ACP08-QD-Pre


title: ACP09-QD-Pre

source_name: ACP09 QD Pre


title: ACP15-QD-D4

source_name: ACP15 QD D4


title: ACP07-BID-Pre-PB

source_name: ACP07 BID Pre


title: ACP07-BID-C1-PB

source_name: ACP07 BID C1


title: ACP07-BID-Pre


title: ACP07-BID-C6-PB

source_name: ACP07 BID C6


title: ACP06-BID-C6-PB

source_name: ACP06 BID C6


title: ACP07-BID-D5

source_name: ACP07 BID D5


title: ACP06-BID-D5

source_name: ACP06 BID D5


title: ACP06-BID-Pre-PB

source_name: ACP06 BID Pre


title: ACP10-BID-Pre-PB


title: ACP06-BID-C1-PB

source_name: ACP06 BID C1


title: ACP05-QD-D3

source_name: ACP05 QD D3


title: ACP05-QD-Pre

source_name: ACP05 QD Pre


title: ACP06-BID-Pre


title: ACP04-BID-D4

source_name: ACP04 BID D4


title: ACP04-BID-Pre-PB

source_name: ACP04 BID Pre


title: ACP04-BID-Pre


title: ACP04-BID-D4-PB


title: ACP02-QD-Pre-PB

source_name: ACP02 QD Pre


title: ACP02-QD-C1-PB

source_name: ACP02 QD C1


title: ACP04-BID-C6-PB

source_name: ACP04 BID C6


title: ACP02-QD-Pre


title: ACP01-BID-D4

source_name: ACP01 BID D4


title: ACP02-QD-D3

source_name: ACP02 QD D3


title: ACP01-BID-Pre

source_name: ACP01 BID Pre


title: ACP04-BID-C1-PB

source_name: ACP04 BID C1


title: ACP02-QD-C6-PB

source_name: ACP02 QD C6


title: iBAT

status: Public on Feb 04 2020

city: Bronx

first: Kosaku

last: Shinoda

state: New York

address: 1301 Morris Park Avenue

department: Endocrinology

institute: Albert Einstein College of Medicine

data_processing:
10X genomics cellranger count
Genome_build: modified refdata-cellranger-mm10-3.0.0 (pre-mrna included)
Supplementary_files_format_and_content: tab seprated values file and mtx file with expression values  for each gene for each nucleus

source_name: interscapular BAT adipocyte nuclei

extract_protocol:
Adipose tissue was digested, the mature fraction isolated, followed by nuclei isolation
10X genomics Chromium V3 protocol

tag: age

value: 8 weeks

value: brown adipocytes


title: Normal-8080086

status: Public on Feb 10 2020

type: RNA

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: 8080086-M, Normal Pregnancy

hyb_protocol: Hybridization was processed according to the protocol for the Affymetrix GeneChip® Hybridization Control Kit.

scan_protocol: Scanning is carried out on an Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions.

data_processing: All 24 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output in base 2 logarithmic scale.

label: Biotin

source_name: PAXgene whole blood

label_protocol: Biotinylated-cRNA was prepared according to Affymetrix manufacturers protocol.

growth_protocol: Not applicable.

extract_protocol: Total RNA was isolated from whole blood using the PAXgene Blood RNA Kit (Qiagen®) according to manufacturers protocol. The Ambion Globin Clear kit (Ambion®) was used to remove alpha and beta globin mRNA from the sample to increase the sensitivity of gene expression assays through improving the detection rate of expressed genes. The RNA was quantified using the Nanodrop 8000 and checked for high integrity before preparation of cDNA. The integrity of RNA samples was assessed using the Agilent 2100 Bioanalyzer.  Sample purity was confirmed using the NanoDrop spectrophotometer and RNA Integrity Number (RIN ≥ 8).

treatment_protocol: Not applicable.

tag: recruitment id

tag: Sex

value: Female

tag: ethnicity

value: Black or African American

tag: age years

tag: pregnancy condition

value: Normal Pregnancy

tag: delivery gestation age week

tag: blood draw at gestation week

tag: study site

value: St Louis

tag: vitamin 25(oh) d measured in blood of mother at 10-18 weeks of gestation (ng/ml)


title: Normal-8023002

description: 8023002-M, Normal Pregnancy


title: Normal-5067199

description: 5067199-M, Normal Pregnancy

value: White


title: Preterm-7048174

description: 7048174-M, Spontaneous Preterm Births

value: Spontaneous Preterm Births


title: Normal-5079624

description: 5079624-M, Normal Pregnancy


title: Normal-5022821

description: 5022821-M, Normal Pregnancy

value: Asian


title: Preterm-2020274

description: 2020274-M, Spontaneous Preterm Births

value: Boston


title: Normal-4019058

description: 4019058-M, Normal Pregnancy


title: Normal-3092708

description: 3092708-M, Normal Pregnancy


title: Normal-2089477

description: 2089477-M, Normal Pregnancy


title: Normal-7007377

description: 7007377-M, Normal Pregnancy


title: Normal-1005587

description: 1005587-M, Normal Pregnancy


title: Preterm-4089320

description: 4089320-M, Spontaneous Preterm Births


title: Normal-9089352

description: 9089352-M, Normal Pregnancy

value: San Diego


title: Normal-6096334

description: 6096334-M, Normal Pregnancy


title: Preterm-9005717

description: 9005717-M, Spontaneous Preterm Births


title: Preterm-5061869

description: 5061869-M, Spontaneous Preterm Births


title: Normal-4084775

description: 4084775-M, Normal Pregnancy


title: Preterm-2097081

description: 2097081-M, Spontaneous Preterm Births


title: Preterm-2090501

description: 2090501-M, Spontaneous Preterm Births


title: Normal-2049192

description: 2049192-M, Normal Pregnancy


title: ACP38-BID-D4

source_name: ACP38 BID D4

value: LN


title: Normal-1093607

description: 1093607-M, Normal Pregnancy


title: Mo.6C-II-.Bl_2

status: Public on Jan 23 2020

first: Brian

last: Brown

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Critical threshold (Ct) values were obtained from qPCR profiling with an upper limit of 40. Across sample normalization was performed for each qPCR plate separately as follows: i) the arithmetic mean of all assays for each sample was calculated. ii) the median of sample means was divided by the arithmetic mean for each sample to create a scaling factor. iii) Ct values for each sample were multiplied by their scaling factor. Following normalization, individual assay outliers were identified either by visual inspection or based on a Z-score greater than 4, relative to all other samples. Next, normalization was redone with outlier assays set as missing. Missing values were then imputed using the mice package in R with default settings and 10 iterations.
Batch correction was performed only for a subset of miRNAs (223 total) that were assessed to have a significant association with batch, because batch correcting all miRNAs would have removed signal from cell type specific miRNAs that were only seen in a limited number of batches. Batch associated miRNAs were selected in 2 rounds. The first was a broad round of selection that included all cell types that had at least one replicate in 2 different batches. Variation due to cell type was removed using the removeBatchEffect function from the limma package, then an F-test in limma was performed with respect to batch for each miRNA on the resulting values. miRNAs were selected for batch correction if they had a Bonferroni adjusted p value <0.01 and a mean Ct value <35 across all samples involved. After miRNA selection, batch correction was performed using ComBat only for the selected miRNAs.
Following normalization and batch correction, Ct values were converted to arbitrary units (AU) for easier interpretation. We determined a limit of reliable detection at a Ct value of 28, which was assessed through the standard curves of 10 miRNAs and inter-replicate variability at different Ct thresholds. Our AU scale was designed so that a Ct value of 28 corresponded to a value of 1 AU. Ct values were converted to AU with the formula: 2^(28 - exp[i,j]), where exp is the Ct value matrix for all samples and miRNAs, i is a given miRNA, and j is a given cell type. A pseudocount of 0.1 was added to all assays following conversion.

label: SYBR

source_name: primary

growth_protocol: Primary cells harvested from 6-8 week old mice

extract_protocol: miRNeasy Micro Kit (Qiagen)

tag: organ

value: Blood

tag: cell type

value: Ly6Clow monocytes

tag: cell markers

tag: isolation date

tag: lab

tag: cell count (thousands)

tag: rna concentration (ng/ul)

tag: processing batch

value: male


title: Preterm-7049736

description: 7049736-M, Spontaneous Preterm Births

tag: recruitment id


title: Normal-3077230

description: 3077230-M, Normal Pregnancy

tag: Sex


title: normal tissue_normal_1

status: Public on Apr 02 2019

city: HeFei

first: Yong

last: Jiang

address: 218 Jixi Road

country: China

institute: First Affiliated Hospital of Anhui Medical University

description: no

hyb_protocol: Cy3-labeled cDNA were hybridized to Agilent Human mRNA microarray (4*44K) Design ID：014850.

scan_protocol: Fluorescence was detected using the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Images were analyzed using Feature Extraction software (version 10.7.1.1, Agilent Technologies).

source_name: normal tissue,replicate 1

label_protocol: RNA was amplified and labeling of CTP with cyanine-3 (cy3) was done with Agilent one-color labeling kits (Agilent Technologies).

extract_protocol: Tissues were suspended in TRIzol and total RNA was extracted with an RNeasy MiniKit (Qiagen, Hilden, Germany).

treatment_protocol: Tissue samples were originated from HCC patients, and we freezed them in refrigerator (-80°C).

tag: gender

value: Male

tag: tissue

value: martched normal liver tissue


title: tumor tissue_HCC_2

description: no

source_name: tumor tissue,replicate 2

value: Hepatocellular carcinoma tissue


title: MB157_untreated_CTCF_ChIPseq_rep2

status: Public on Feb 27 2019

first: YEQIAO

last: ZHOU

address: 421 Curie Boulevard

data_processing:
Reads from all ChIP-seq experiments were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.25.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 329).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

source_name: MB157 cell line

growth_protocol: MB157 (female) cells were grown in DMEM (Corning, cat# 10-013-CV) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03) and 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI). When passaged cells were detached with 0.25% trypsin, EDTA-free (Gibco, cat# 15090-046) to avoid activation of Notch signaling.

extract_protocol:
ChIP-seq was performed as previously described (Ryan et al., 2017). Briefly, chromatin samples prepared from appropriate number of fixed cells (10^7 for histone modifications and 4 x 10^7 for transcription factors) were sonicated and cleared with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated with antibodies recognizing Notch1 (Wang et al., 2014), RBPJ (D10A4) (CST, cat# 5313), H3K27ac (Active Motif, cat# 39133), H3K27me3 (EMD Millipore cat# 07-449), H3K4me1 (Abcam, cat# ab8895), Smc1a (Bethyl, cat# A300-055A) and CTCF (EMD Millipore cat# 07-729). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. After reversal of cross-linking, RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment were performed and DNA was purified with QIAquick PCR Purification Kit (Qiagen, cat# 28106).
Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Single end sequencing (75 bp) or Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.

treatment_protocol: Untreated.

tag: cell line

value: Triple-negative breast cancer cell line

tag: chip antibody

value: CTCF

tag: drug treatment

value: untreated


title: normal tissue_normal_2

description: no

source_name: normal tissue,replicate 2

value: Female


title: MB157_WO_RBPJ_ChIPseq_rep1

treatment_protocol: Cells were treated with the GSI compound E (1 μM, Calbiochem cat# 565790) for 72 hours, washed, and then cultured for 5 hours in media containing 1μM GSI (mock washout) or DMSO (washout) as previously described (Weng et al., 2006).

value: RBPJ

value: GSI-washout


title: MB157_untreated_SMC1a_ChIPseq_rep1


title: MB157_WO_RBPJ_ChIPseq_rep2


title: MB157_WO_H3K27me3_ChIPseq_rep2


title: MB157_GSI_RBPJ_ChIPseq_rep1

value: GSI-mock-washout


title: MB157_GSI_NICD1_ChIPseq_rep2


title: MB157_untreated_SMC1a_ChIPseq_rep2


title: MB157_ChIPseq_input

value: input


title: MB157_WO_H3K4me1_ChIPseq_rep1


title: MB157_GSI_H3K4me1_ChIPseq_rep2


title: MB157_WO_H3K4me1_ChIPseq_rep2


title: MB157_GSI_H3K4me1_ChIPseq_rep1


title: MB157_GSI_NICD1_ChIPseq_rep1


title: MB157_WO_H3K27ac_ChIPseq_rep2


title: MB157_WO_NICD1_ChIPseq_rep1


title: MB157_WO_H3K27me3_ChIPseq_rep1


title: tumor tissue_HCC_1

description: no

source_name: tumor tissue,replicate 1


title: MB157_untreated_CTCF_ChIPseq_rep1


title: MB157_WO_NICD1_ChIPseq_rep2

extract_protocol:
ChIP-seq was performed as previously described (Ryan et al., 2017). Briefly, chromatin samples prepared from appropriate number of fixed cells (107 for histone modifications and 4 x 107 for transcription factors) were sonicated and cleared with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated with antibodies recognizing Notch1 (Wang et al., 2014), RBPJ (D10A4) (CST, cat# 5313), H3K27ac (Active Motif, cat# 39133), H3K27me3 (EMD Millipore cat# 07-449), H3K4me1 (Abcam, cat# ab8895), Smc1a (Bethyl, cat# A300-055A) and CTCF (EMD Millipore cat# 07-729). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. After reversal of cross-linking, RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment were performed and DNA was purified with QIAquick PCR Purification Kit (Qiagen, cat# 28106).
Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Single end sequencing (75 bp) or Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.


title: MB157_WO_H3K27ac_ChIPseq_rep1


title: MB157_GSI_H3K27ac_ChIPseq_rep2


title: MB157_GSI_RBPJ_ChIPseq_rep2


title: SWD007: Cachectic from C26m2 metastasis model

status: Public on Jul 01 2018

data_processing:
We use RTA (Illumina) for base calling. Sanger/Illumina 1.9
We map the reads to a reference genome (Mouse: NCBIm37) using Tophat (version 2.1.0) with very-fast (-D 5 -R 1 -N 0 -L 22 -i S,0,2.50) option
Reads across junctions were checked and indicated in the supplied GFF (--no-novel-juncs).
Bam files obtained from TopHat were used to generate the differential gene using the module Cuffdiff (cufflinks-2.2.1) with default settings
The cutoff for the differential gene list was set as q-val less than 0.05
Genome_build: NCBIm37
Supplementary_files_format_and_content: Excel files containing differential list of genes, obtained using cuffdiff

source_name: skeletal muscle

growth_protocol: Mice were housed in the animal facility at Columbia University Medical Center (CUMC) under conventional conditions with constant temperature and humidity and fed a standard diet. Treatment of mice was in accordance with the institutional guidelines of CUMC’s Institute of Comparative Medicine.

extract_protocol:
Total RNA was extracted using Trizol® reagent following manufacturer’s instructions (Thermo Fisher). RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest following the manufacturer’s instructions (QIAGEN). RNA was quantified spectrophotometrically (Nanodrop, Thermo Scientific) and assessed for quality by capillary gel electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies, Inc.).
poly-A pull-down to enrich mRNAs from total RNA samples and Illumina TruSeq RNA prep kit to prepare library.

treatment_protocol: For RNA sequencing, Luciferase labeled C26m2 and 4T1 tumors were resected 2-3 weeks post tumor cell injection. After confirmation of metastasis by bioluminescence imaging and with appearance of cachectic symptoms, mice were euthanized 5 weeks post tumor cell injection. Tibialis anterior muscles from tumor-bearing and age-matched healthy control mice were isolated, snap frozen for subsequent RNA isolation.

tag: strain

value: tibialis anterior muscle

tag: age

value: 12-14 weeks


title: SWD008: Cachectic from C26m2 metastasis model


title: MB157_GSI_H3K27ac_ChIPseq_rep1


title: MB157_GSI_H3K27me3_ChIPseq_rep2


title: MB157_GSI_H3K27me3_ChIPseq_rep1


title: SWD006: CD2F1 healthy control


title: SWD005: CD2F1 healthy control


title: SWD004: Cachectic from 4T1 metastasis model

value: Balb/c


title: SWD002: Balb/c healthy control


title: SWD001: Balb/c healthy control


title: sgTAF12_4.1_MOLM13

status: Public on Jan 08 2018

city: Cold Spring Harbor

first: Yali

last: XU

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: processed data file: sgTAF12 VS sgROSA_MOLM13.txt

data_processing:
Single-end 50bp sequencing reads were mapped into mm9 genome using TopHat with default settings
Structural RNAs were masked
Differentially expressed genes were identified using Cuffdiff, normalized to total mapped reads
Genome_build: mm9/hg19
Supplementary_files_format_and_content: txt files generated from Cuffdiff

source_name: human MOLM-13 AML cell line

growth_protocol: RN2 cells derived from MLL-AF9/NrasG12D AML mouse model were cultured in RPMI with 10%FBS and P/S under 7.5% CO2. Bone marrow-derived myeloid progenitor cells were cultured in 10%FBS with 10 ng/ul SCF, 2 ng/ul IL-3, 2 ng/ul IL-6 and 50 uM beta-ME under 7.5% CO2. Human AML cell line was cultured in RPMI with 10%FBS and P/S under 7.5% CO2.

extract_protocol:
RNA was extracted using TRIzol following manufacture’s protocol. 2ug total RNA was used for constructing RNA-seq library
RNA-seq libraries were constructed using the Illumina TruSeq sample prep kit v2 following manufacture’s protocol. Briefly, RNA was polyA selected and enzymatically fragmented. cDNA was synthesized using Super Script II master mix, followed by end repair, A-tailing and PCR amplification.

treatment_protocol: For RNA-seq in cells transduced with dox-regulated shRNA, cells were treated with dox for 24 hrs prior to RNA extraction.

tag: cell types

value: cells transduced with sgRNA in LRG vecor

tag: mouse strain

tag: treatment time

value: day 4 post-infection


title: sgROSA_MOLM13_repeat1

description: processed data file: sgMYB VS sgROSA_MOLM13.txt

value: day 3 post-infection


title: MOLM13_sgSIK3e1

status: Public on Mar 12 2018

first: Yusuke

last: Tarumoto

data_processing:
Sequencing reads were mapped into reference human genome hg19 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: txt, normalized RPKM

source_name: actue myeloid luekemia

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout, or treated with DMSO or 100 nM HG-9-91-01 for 2 hrs

value: MOLM-13 cell

tag: treatment

value: day 5 after sgSIK3e1 guideRNA infection


title: MOLM13_sgMEF2Ce3.3

value: day 5 after sgMEF2Ce3.3 guideRNA infection


title: sgTAF12_4.4_MOLM13


title: sgROSA_MOLM13_repeat2


title: EGKX_S6

status: Public on Dec 11 2017

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
Adaptor sequences and low quality bases with PHERD scores (Q) ≤ 30 were removed. And we employed Trimmomatic for removal of adapter sequences.
The read mapping into assembled transcriptome was performed using tophat2
Finally, HTSeq-count was employed for quantification.
Genome_build: We used watermelon reference genome (97103) version 1 in Curcurbit Genomics Database.
Supplementary_files_format_and_content: TSV file for each sample

organism: Gallus gallus

source_name: Embryonic cell

extract_protocol:
Total RNA was prepared from the samples and Total RNA was extracted using TRIzol reagent (MRC).
Libraries were prepared based on Illimina instruction

tag: developmental stage

value: EGKX


title: EGKX_S7


title: MOLM13_sgMEF2Ce2.1

value: day 5 after sgMEF2Ce2.1 guideRNA infection


title: sgMYB_5.2_MOLM13


title: MOLM13_sgSIK3e4

value: day 5 after sgSIK3e4 guideRNA infection


title: EGKX_S5


title: TruSeq70_IP_rep3

status: Public on Oct 30 2017

city: Baltimore

first: yang

last: song

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence. In order to maintain the best quality, all the reads were further trimmed to 60bp and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM)  and count per Million mapped reads(CPM) were calculated for each sample.
We evaluated the robustness of different kits for detecting enrichment (IP/input RNA > 1) or depletion (IP/input RNA < 1) of transcripts in the translatome (IP samples) compared to the transcriptome (input samples). Features with raw read counts ≥ 20 in input samples and with enrichment or depletion factor ≥ 2 were included as enriched (IP/Input ≥ 2) or depleted transcripts (Input/IP ≥ 2).
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

growth_protocol: Mice were kept until P30

extract_protocol:
Cell-type specific RNA from livers of P30 mice was obtained using the RiboTag protocol. Briefly, liver tissue expressing HA-tagged ribosomes in specific cells was homogenized followed by immunoprecipitation of the tagged ribosomes using an HA antibody. The RNA was extracted from the immunoprecipitated ribosomes to obtain cell-type specific enriched transcripts (IP samples). An aliquot of the homogenized tissue before immunoprecipitation was used for total RNA extraction (input samples).
Libraries were prepared from 0.25ng/4ng/70ng using NuGEN Ovation RNA-Seq system V2, TaKaRa SMARTer Stranded Total RNA-Seq Kit , TaKaRa SMART-Seq v4 Ultra Low Input RNA kit , Illumina TruSeq RNA Library Prep Kit v2 and NEBNext® Ultra™ Directional RNA Library Prep Kit,  per manufacturer’s instructions, with minor modification for NuGEN prepared samples. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Untreated

value: neonatal pups P1

value: liver

tag: antibody

value: HA


title: TruSeq70_input_rep2


title: TruSeq70_IP_rep1


title: TruSeq70_input_rep3


title: sgMYB_4.9_MOLM13


title: MOLM13_sgNeg3

value: day 5 after sgNeg3 guideRNA infection


title: TruSeq4_IP_rep1


title: TruSeq70_input_rep1


title: TruSeq4_IP_rep3


title: TruSeq4_IP_rep2


title: MOLM13_sgNeg2

value: day 5 after sgNeg2 guideRNA infection


title: TruSeq4_input_rep1


title: TruSeq4_input_rep3


title: SMARTer_IP_rep2


title: SMARTer_IP_rep3


title: SWD003: Cachectic from 4T1 metastasis model

value: tibialis anterior muscle


title: TruSeq70_IP_rep2


title: SMARTer_IP_rep1


title: SMARTer_input_rep2


title: SMARTer_input_rep1


title: NuGEN_IP_rep2


title: SMARTer_input_rep3


title: NuGEN_input_rep3


title: NEB_IP_rep3


title: NuGEN_input_rep2


title: NuGEN_IP_rep3


title: NuGEN_input_rep1


title: NuGEN_IP_rep1


title: NEB_input_rep3


title: SMARTseq4_input_rep3


title: SMARTseq0.25_input_rep3


title: SMARTseq4_input_rep1


title: SMARTseq0.25_IP_rep3


title: SMARTseq4_IP_rep1


title: SMARTseq0.25_IP_rep2


title: SMARTseq4_input_rep2


title: SMARTseq4_IP_rep3


title: SMARTseq4_IP_rep2


title: SMARTseq0.25_input_rep1


title: TruSeq4_input_rep2


title: NEB_input_rep1


title: NEB_IP_rep1


title: NEB_input_rep2


title: SMARTseq0.25_IP_rep1


title: SMARTseq0.25_input_rep2


title: NEB_IP_rep2


title: lymphocytes_0Gy_rep220

status: Public on Jan 30 2017

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: RNA was hybridised to HT HG-U133+ PM GeneChip® arrays (Affymetrix, Santa Clara CA, USA) according to the manufacturer’s protocol.

scan_protocol: Scanning of the array was conducted by the MicroArray Department of the University of Amsterdam, and images were processed to obtain an intensity value for each oligonucleotide probe.

data_processing: Data were normalized and summarized to the probe set level using the robust multi-array average (RMA) method with default settings (function rma, package affy; version 1.44.0).

label: biotin

label_protocol: Biotin-labeled cRNA probes were generated according to the manufacturer’s protocol.

growth_protocol: Peripheral lymphocytes were isolated using Ficoll (Ficoll-Paque PLUS, GE Healthcare) gradient separation, and stored in liquid nitrogen.

extract_protocol: Isolation of RNA was executed 24h post radiation using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol. RIN value and RNA quality of both treated as untreated RNA was assessed with a BD Bioanalyzer.

treatment_protocol: Lymphocytes were cultured stimulated by phytohemagglutinin (concentration of 1μg/ml). After two weeks, half of the cells were irradiated at room temperature with 2Gy gamma rays from a 137Cs source, dose rate of approximately 0.5Gy/min and the other half of the cells was left untreated.

value: lymphocytes

tag: irradiation

tag: batch

tag: study

value: retrospective (new)


title: lymphocytes_0Gy_rep217

value: retrospective (old)


title: lymphocytes_2Gy_rep214


title: lymphocytes_2Gy_rep219


title: lymphocytes_2Gy_rep215


title: lymphocytes_2Gy_rep218


title: lymphocytes_2Gy_rep212


title: lymphocytes_0Gy_rep210


title: lymphocytes_0Gy_rep208


title: lymphocytes_2Gy_rep217


title: lymphocytes_2Gy_rep220


title: lymphocytes_0Gy_rep218


title: lymphocytes_2Gy_rep208


title: lymphocytes_0Gy_rep216


title: lymphocytes_0Gy_rep212


title: lymphocytes_2Gy_rep209


title: lymphocytes_0Gy_rep214


title: lymphocytes_2Gy_rep216


title: lymphocytes_0Gy_rep215


title: lymphocytes_2Gy_rep213


title: lymphocytes_0Gy_rep207


title: lymphocytes_0Gy_rep209


title: lymphocytes_2Gy_rep210


title: lymphocytes_0Gy_rep206

value: prospective


title: lymphocytes_2Gy_rep211


title: lymphocytes_2Gy_rep207


title: lymphocytes_0Gy_rep211


title: lymphocytes_0Gy_rep219


title: lymphocytes_0Gy_rep213


title: lymphocytes_2Gy_rep206


title: lymphocytes_2Gy_rep203


title: lymphocytes_2Gy_rep204


title: lymphocytes_0Gy_rep204


title: lymphocytes_0Gy_rep201


title: lymphocytes_2Gy_rep200


title: lymphocytes_0Gy_rep197


title: lymphocytes_2Gy_rep199


title: lymphocytes_0Gy_rep199


title: lymphocytes_0Gy_rep203


title: lymphocytes_2Gy_rep196


title: lymphocytes_2Gy_rep202


title: lymphocytes_2Gy_rep205


title: lymphocytes_0Gy_rep202


title: lymphocytes_0Gy_rep195


title: lymphocytes_2Gy_rep197


title: lymphocytes_0Gy_rep200


title: lymphocytes_2Gy_rep192


title: lymphocytes_2Gy_rep195


title: lymphocytes_0Gy_rep194


title: lymphocytes_2Gy_rep201


title: lymphocytes_0Gy_rep196


title: lymphocytes_2Gy_rep198


title: lymphocytes_0Gy_rep205


title: lymphocytes_2Gy_rep191


title: lymphocytes_2Gy_rep193


title: lymphocytes_0Gy_rep193


title: lymphocytes_0Gy_rep198


title: lymphocytes_0Gy_rep192


title: lymphocytes_2Gy_rep188


title: lymphocytes_2Gy_rep194


title: lymphocytes_0Gy_rep190


title: lymphocytes_0Gy_rep184


title: lymphocytes_0Gy_rep182


title: lymphocytes_2Gy_rep189


title: lymphocytes_2Gy_rep184


title: lymphocytes_0Gy_rep181


title: lymphocytes_2Gy_rep190


title: lymphocytes_2Gy_rep181


title: lymphocytes_0Gy_rep177


title: lymphocytes_2Gy_rep183


title: lymphocytes_0Gy_rep189


title: lymphocytes_2Gy_rep182


title: lymphocytes_2Gy_rep180


title: lymphocytes_2Gy_rep177


title: lymphocytes_0Gy_rep183


title: lymphocytes_0Gy_rep191


title: lymphocytes_0Gy_rep179


title: lymphocytes_0Gy_rep188


title: lymphocytes_2Gy_rep178


title: lymphocytes_2Gy_rep179


title: lymphocytes_0Gy_rep180


title: lymphocytes_0Gy_rep187


title: lymphocytes_0Gy_rep185


title: lymphocytes_2Gy_rep187


title: lymphocytes_0Gy_rep178


title: lymphocytes_2Gy_rep185


title: lymphocytes_2Gy_rep176


title: lymphocytes_0Gy_rep173


title: lymphocytes_0Gy_rep176


title: lymphocytes_0Gy_rep174


title: lymphocytes_2Gy_rep173


title: lymphocytes_0Gy_rep175


title: lymphocytes_0Gy_rep172


title: lymphocytes_2Gy_rep172


title: lymphocytes_2Gy_rep167


title: lymphocytes_2Gy_rep169


title: lymphocytes_2Gy_rep175


title: lymphocytes_2Gy_rep171


title: lymphocytes_0Gy_rep169


title: lymphocytes_0Gy_rep166


title: lymphocytes_2Gy_rep163


title: lymphocytes_0Gy_rep170


title: lymphocytes_0Gy_rep163


title: lymphocytes_0Gy_rep171


title: lymphocytes_2Gy_rep162


title: lymphocytes_0Gy_rep165


title: lymphocytes_2Gy_rep170


title: lymphocytes_2Gy_rep166


title: lymphocytes_0Gy_rep164


title: lymphocytes_0Gy_rep168


title: lymphocytes_0Gy_rep167


title: lymphocytes_2Gy_rep168


title: lymphocytes_2Gy_rep164


title: lymphocytes_2Gy_rep165


title: lymphocytes_0Gy_rep162


title: lymphocytes_0Gy_rep160


title: lymphocytes_0Gy_rep157


title: lymphocytes_2Gy_rep160


title: lymphocytes_2Gy_rep161


title: lymphocytes_2Gy_rep155


title: lymphocytes_0Gy_rep161


title: lymphocytes_2Gy_rep159


title: lymphocytes_0Gy_rep159


title: lymphocytes_0Gy_rep153


title: lymphocytes_2Gy_rep152


title: lymphocytes_2Gy_rep157


title: lymphocytes_0Gy_rep149


title: lymphocytes_2Gy_rep148


title: lymphocytes_2Gy_rep154


title: lymphocytes_2Gy_rep158


title: lymphocytes_0Gy_rep152


title: lymphocytes_2Gy_rep151


title: lymphocytes_0Gy_rep154


title: lymphocytes_2Gy_rep153


title: lymphocytes_2Gy_rep174


title: lymphocytes_0Gy_rep150


title: lymphocytes_0Gy_rep155


title: lymphocytes_0Gy_rep156


title: lymphocytes_0Gy_rep148


title: lymphocytes_2Gy_rep150


title: lymphocytes_2Gy_rep156


title: lymphocytes_0Gy_rep151


title: lymphocytes_2Gy_rep149


title: lymphocytes_2Gy_rep147


title: lymphocytes_0Gy_rep158


title: lymphocytes_2Gy_rep146


title: lymphocytes_0Gy_rep147


title: lymphocytes_0Gy_rep145


title: lymphocytes_0Gy_rep144


title: lymphocytes_0Gy_rep143


title: lymphocytes_2Gy_rep145


title: lymphocytes_2Gy_rep140


title: lymphocytes_2Gy_rep142


title: lymphocytes_2Gy_rep139


title: lymphocytes_0Gy_rep146


title: lymphocytes_2Gy_rep143


title: lymphocytes_0Gy_rep140


title: lymphocytes_0Gy_rep142


title: lymphocytes_0Gy_rep139


title: lymphocytes_2Gy_rep141


title: lymphocytes_2Gy_rep137


title: lymphocytes_2Gy_rep136


title: lymphocytes_0Gy_rep138


title: lymphocytes_0Gy_rep136


title: lymphocytes_2Gy_rep138


title: lymphocytes_0Gy_rep133


title: lymphocytes_0Gy_rep134


title: lymphocytes_2Gy_rep135


title: lymphocytes_0Gy_rep141


title: lymphocytes_2Gy_rep132


title: lymphocytes_2Gy_rep134


title: lymphocytes_2Gy_rep144


title: lymphocytes_2Gy_rep133


title: lymphocytes_0Gy_rep135


title: lymphocytes_0Gy_rep132


title: lymphocytes_2Gy_rep131


title: lymphocytes_0Gy_rep130


title: lymphocytes_0Gy_rep129


title: lymphocytes_0Gy_rep131


title: lymphocytes_2Gy_rep130


title: lymphocytes_2Gy_rep127


title: lymphocytes_2Gy_rep125


title: lymphocytes_2Gy_rep129


title: lymphocytes_2Gy_rep128


title: lymphocytes_2Gy_rep126


title: lymphocytes_0Gy_rep124


title: lymphocytes_0Gy_rep125


title: lymphocytes_0Gy_rep127


title: lymphocytes_0Gy_rep128


title: lymphocytes_0Gy_rep126


title: lymphocytes_2Gy_rep120


title: lymphocytes_2Gy_rep117


title: lymphocytes_2Gy_rep124


title: lymphocytes_0Gy_rep137


title: lymphocytes_2Gy_rep123


title: lymphocytes_2Gy_rep122


title: lymphocytes_0Gy_rep121


title: lymphocytes_0Gy_rep119


title: lymphocytes_0Gy_rep122


title: lymphocytes_2Gy_rep121


title: lymphocytes_2Gy_rep116


title: lymphocytes_2Gy_rep118


title: lymphocytes_0Gy_rep123


title: lymphocytes_2Gy_rep119


title: lymphocytes_0Gy_rep118


title: lymphocytes_0Gy_rep120


title: lymphocytes_0Gy_rep117


title: lymphocytes_2Gy_rep114


title: lymphocytes_2Gy_rep115


title: lymphocytes_0Gy_rep112


title: lymphocytes_2Gy_rep110


title: lymphocytes_0Gy_rep111


title: lymphocytes_0Gy_rep113


title: lymphocytes_2Gy_rep109


title: lymphocytes_2Gy_rep111


title: lymphocytes_2Gy_rep113


title: lymphocytes_0Gy_rep114


title: lymphocytes_2Gy_rep107


title: lymphocytes_0Gy_rep110


title: lymphocytes_0Gy_rep109


title: lymphocytes_0Gy_rep115


title: lymphocytes_2Gy_rep112


title: lymphocytes_0Gy_rep108


title: lymphocytes_2Gy_rep105


title: lymphocytes_2Gy_rep106


title: lymphocytes_0Gy_rep107


title: lymphocytes_2Gy_rep104


title: lymphocytes_0Gy_rep102


title: lymphocytes_0Gy_rep103


title: lymphocytes_0Gy_rep105


title: lymphocytes_0Gy_rep101


title: lymphocytes_2Gy_rep103


title: lymphocytes_0Gy_rep100


title: lymphocytes_2Gy_rep102


title: lymphocytes_2Gy_rep108


title: lymphocytes_0Gy_rep106


title: lymphocytes_2Gy_rep101


title: lymphocytes_0Gy_rep104


title: lymphocytes_0Gy_rep99


title: lymphocytes_0Gy_rep98


title: lymphocytes_2Gy_rep98


title: lymphocytes_0Gy_rep92


title: lymphocytes_2Gy_rep97


title: lymphocytes_0Gy_rep94


title: lymphocytes_2Gy_rep96


title: lymphocytes_2Gy_rep94


title: lymphocytes_2Gy_rep100


title: lymphocytes_0Gy_rep97


title: lymphocytes_0Gy_rep95


title: lymphocytes_0Gy_rep96


title: lymphocytes_0Gy_rep93


title: lymphocytes_2Gy_rep93


title: lymphocytes_2Gy_rep89


title: lymphocytes_2Gy_rep99


title: lymphocytes_2Gy_rep90


title: lymphocytes_2Gy_rep88


title: lymphocytes_0Gy_rep90


title: lymphocytes_0Gy_rep88


title: lymphocytes_2Gy_rep95


title: lymphocytes_0Gy_rep89


title: lymphocytes_2Gy_rep91


title: lymphocytes_2Gy_rep87


title: lymphocytes_0Gy_rep87


title: lymphocytes_0Gy_rep85


title: lymphocytes_2Gy_rep86


title: lymphocytes_2Gy_rep85


title: lymphocytes_0Gy_rep86


title: lymphocytes_0Gy_rep84


title: lymphocytes_2Gy_rep84


title: lymphocytes_0Gy_rep91


title: lymphocytes_0Gy_rep82


title: lymphocytes_2Gy_rep81


title: lymphocytes_2Gy_rep74


title: lymphocytes_2Gy_rep83


title: lymphocytes_0Gy_rep78


title: lymphocytes_0Gy_rep79


title: lymphocytes_2Gy_rep75


title: lymphocytes_2Gy_rep80


title: lymphocytes_0Gy_rep83


title: lymphocytes_2Gy_rep82


title: lymphocytes_0Gy_rep75


title: lymphocytes_0Gy_rep76


title: lymphocytes_2Gy_rep78


title: lymphocytes_0Gy_rep77


title: lymphocytes_2Gy_rep76


title: lymphocytes_0Gy_rep81


title: lymphocytes_2Gy_rep77


title: lymphocytes_2Gy_rep79


title: lymphocytes_0Gy_rep72


title: lymphocytes_0Gy_rep80


title: lymphocytes_0Gy_rep74


title: lymphocytes_0Gy_rep116


title: lymphocytes_2Gy_rep72


title: lymphocytes_0Gy_rep71


title: lymphocytes_0Gy_rep73


title: lymphocytes_2Gy_rep70


title: lymphocytes_2Gy_rep71


title: lymphocytes_0Gy_rep68


title: lymphocytes_0Gy_rep67


title: lymphocytes_2Gy_rep64


title: lymphocytes_2Gy_rep73


title: lymphocytes_2Gy_rep63


title: lymphocytes_0Gy_rep70


title: lymphocytes_2Gy_rep62


title: lymphocytes_0Gy_rep60


title: lymphocytes_2Gy_rep59


title: lymphocytes_2Gy_rep60


title: lymphocytes_2Gy_rep65


title: lymphocytes_0Gy_rep65


title: lymphocytes_0Gy_rep64


title: lymphocytes_2Gy_rep68


title: lymphocytes_2Gy_rep92


title: lymphocytes_0Gy_rep63


title: lymphocytes_2Gy_rep67


title: lymphocytes_2Gy_rep66


title: lymphocytes_2Gy_rep69


title: lymphocytes_0Gy_rep66


title: lymphocytes_0Gy_rep69


title: lymphocytes_0Gy_rep61


title: lymphocytes_2Gy_rep61


title: lymphocytes_0Gy_rep62


title: lymphocytes_0Gy_rep59


title: lymphocytes_0Gy_rep58


title: lymphocytes_2Gy_rep58


title: lymphocytes_2Gy_rep55


title: lymphocytes_0Gy_rep56


title: lymphocytes_2Gy_rep56


title: lymphocytes_2Gy_rep54


title: lymphocytes_0Gy_rep54


title: lymphocytes_2Gy_rep53


title: lymphocytes_0Gy_rep52


title: lymphocytes_2Gy_rep52


title: lymphocytes_0Gy_rep55


title: lymphocytes_2Gy_rep48


title: lymphocytes_0Gy_rep57


title: lymphocytes_2Gy_rep49


title: lymphocytes_2Gy_rep51


title: lymphocytes_0Gy_rep48


title: lymphocytes_0Gy_rep47


title: lymphocytes_2Gy_rep50


title: lymphocytes_0Gy_rep49


title: lymphocytes_2Gy_rep47


title: lymphocytes_0Gy_rep53


title: lymphocytes_0Gy_rep51


title: lymphocytes_0Gy_rep50


title: lymphocytes_2Gy_rep46


title: lymphocytes_2Gy_rep44


title: lymphocytes_2Gy_rep45


title: lymphocytes_0Gy_rep44


title: lymphocytes_2Gy_rep39


title: lymphocytes_0Gy_rep41


title: lymphocytes_2Gy_rep42


title: lymphocytes_0Gy_rep45


title: lymphocytes_0Gy_rep43


title: lymphocytes_0Gy_rep38


title: lymphocytes_2Gy_rep38


title: lymphocytes_0Gy_rep35


title: lymphocytes_2Gy_rep35


title: lymphocytes_0Gy_rep36


title: lymphocytes_0Gy_rep37


title: lymphocytes_0Gy_rep34


title: lymphocytes_0Gy_rep33


title: lymphocytes_2Gy_rep32


title: lymphocytes_0Gy_rep42


title: lymphocytes_2Gy_rep43


title: lymphocytes_2Gy_rep37


title: lymphocytes_0Gy_rep31


title: lymphocytes_2Gy_rep33


title: lymphocytes_0Gy_rep32


title: lymphocytes_2Gy_rep31


title: lymphocytes_2Gy_rep34


title: lymphocytes_2Gy_rep36


title: lymphocytes_2Gy_rep30


title: lymphocytes_2Gy_rep28


title: lymphocytes_0Gy_rep28


title: lymphocytes_2Gy_rep27


title: lymphocytes_0Gy_rep26


title: lymphocytes_0Gy_rep29


title: lymphocytes_0Gy_rep25


title: lymphocytes_2Gy_rep23


title: lymphocytes_0Gy_rep21


title: lymphocytes_2Gy_rep18


title: lymphocytes_0Gy_rep20


title: lymphocytes_2Gy_rep22


title: lymphocytes_2Gy_rep26


title: lymphocytes_0Gy_rep24


title: lymphocytes_2Gy_rep25


title: lymphocytes_0Gy_rep22


title: lymphocytes_2Gy_rep16


title: lymphocytes_2Gy_rep20


title: lymphocytes_0Gy_rep27


title: lymphocytes_0Gy_rep23


title: lymphocytes_2Gy_rep17


title: lymphocytes_0Gy_rep18


title: lymphocytes_0Gy_rep17


title: lymphocytes_0Gy_rep19


title: lymphocytes_2Gy_rep29


title: lymphocytes_2Gy_rep21


title: lymphocytes_2Gy_rep19


title: lymphocytes_2Gy_rep24


title: lymphocytes_0Gy_rep16


title: lymphocytes_2Gy_rep57


title: lymphocytes_2Gy_rep15


title: lymphocytes_2Gy_rep14


title: lymphocytes_0Gy_rep15


title: lymphocytes_0Gy_rep14


title: lymphocytes_0Gy_rep13


title: lymphocytes_2Gy_rep11


title: lymphocytes_2Gy_rep13


title: lymphocytes_0Gy_rep11


title: lymphocytes_0Gy_rep10


title: lymphocytes_0Gy_rep9


title: lymphocytes_2Gy_rep9


title: lymphocytes_0Gy_rep6


title: lymphocytes_0Gy_rep46


title: lymphocytes_0Gy_rep12


title: lymphocytes_2Gy_rep10


title: lymphocytes_0Gy_rep7


title: lymphocytes_2Gy_rep7


title: lymphocytes_0Gy_rep3


title: lymphocytes_0Gy_rep8


title: lymphocytes_2Gy_rep12


title: lymphocytes_2Gy_rep8


title: lymphocytes_2Gy_rep6


title: lymphocytes_2Gy_rep5


title: lymphocytes_2Gy_rep3


title: lymphocytes_0Gy_rep5


title: lymphocytes_0Gy_rep4


title: lymphocytes_2Gy_rep2


title: lymphocytes_2Gy_rep4


title: lymphocytes_0Gy_rep2


title: lymphocytes_0Gy_rep1


title: lymphocytes_2Gy_rep1


title: lymphocytes_0Gy_rep30