title: RNA-seq for isolated mouse brain microglia, LPS group, replicate 3

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

data_processing:
RNA-seq mapping to mouse genome (mm10) was performed using STAR aligner (Dobin et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: txt files for read counts at gene level (Ensembl) generated by STAR aligner

source_name: isolated brain microglia

extract_protocol:
For Ptbp2-KO brain cortex RNA-seq, E18.5 mouse cortex RNA (three biological replicates) from Ptbp2-KO mice (Licatalosi et al., 2012) was prepared using Trizol (Ambion); ribosomal RNA was removed from 1 μg RNA using Ribo-Zero rRNA removal Kit (Illumina). For microglia isolation, mice were perfused with 30ml of heparinized PBS. Brains were excised, minced and two brains were placed into C tube and processed as per instructions for the Neural Tissue Dissociation Kit P (Miltenyi Biotec) using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, protocol 37_ABDK). Once digested, the debris and myelin was removed using the Debris Removal Solution (Miltenyi Biotec) followed by CD11b positive selection using Microglia CD11b beads (Miltenyi). Cells were counted, washed in PBS and pelleted prior to isolation of RNA. Total RNA from isolated microglia was prepared using Trizol (Ambion) and High Pure RNA Isolation Kit (Roche).  The Total RNA was then further purified for polyadenylated RNA by using 150ng Total RNA in Dynabeads mRNA Purification Kit (Ambion).
RNA-seq libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina) following manufacturer’s instructions.

treatment_protocol: To activate microglia, adult wildtype B6 mice received daily intraperitoneally injection of 1mg/Kg lipopolysaccharide (L4524, Sigma) or phosphate-buffered saline for 4 consecutive days before sacrifice.

tag: sample type

value: replicate 3

tag: genotype/variation

value: WT

tag: agent

value: LPS

value: brain

value: microglia


title: RNA-seq for isolated mouse brain microglia, LPS group, replicate 2

status: Public on Sep 13 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: replicate 2

tag: strain

tag: tissue

tag: cell type


title: RNA-seq for isolated mouse brain microglia, LPS group, replicate 1

value: replicate 1


title: V03_mRNA

status: Public on Sep 14 2017

city: Beijing

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

country: China

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

data_processing:
[miRNA] The small RNA tags were mapped to reference sequence (Amel_4.5) by Bowtie. The characteristics of hairpin structure of miRNA precursor can be used to predict new miRNA. The available software miREvo60 and mirdeep261 were integrated to predict new miRNA. Predicting the target gene of miRNA was performed by miRanda.
[mRNA and lncRNA] Index of reference genome (Amel_4.5) was built using Bowtie V2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (FPKM, expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Readcount_TPM_miRNA.txt, mRNA_FPKM_mRNA.txt

organism: Apis mellifera

source_name: ovaries

extract_protocol:
Trizol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA, according to the manufacturer’s instructions. miRNA sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA and lncRNA sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols
For miRNA library preparation, a total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated. A total of twelve small libraries were constructed using ovaries of virgin queens, normal queens, caged queens and released queens.
A total amout of 3 μg total RNA per sample was used as input material for the mRNA and lncRNA library. Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The libraries were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. A total of twelve libraries were constructed using ovaries of virgin queens, normal queens, caged queens and released queens.

value: ovaries

tag: age

value: virgin queen

tag: treatment


title: RNA-seq for isolated mouse brain microglia, PBS group, replicate 3

value: PBS


title: p65 IP in Tconv, unstim, rep2

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

description:
p65_Tcon_US_2
processed data file:
p65_Tcon_US.pooled_peaks.noBlacklist.idr_conservative.narrowPeak

library_source: genomic

data_processing:
Raw FASTQs were adapter and quality trimmed with Trim Galore! v0.4.1
Trimmed reads were aligned to mm10 with BWA mem v0.7.15-r1140
Conservative peaks were called per group using MACS v2.1.1.20160309 within the Irreproducible Discovery Rate framework outlined by ENCODE (https://sites.google.com/site/anshulkundaje/projects/idr)
Blacklisted sites were excluced (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated representing coverage of estimated fragment length extended alinged reads, normalized by library size over autosomal chromosomes and scaled to the equivalent of 1X coverage

molecule: genomic DNA

source_name: Tconv unstimulated

growth_protocol: Isolated Tconv and Treg cells were cultured on a plate coated with anti-CD3 antibody in the presence of soluble anti-CD28 antibodies for 3 hours. 2 ng/ml IL-2 was added to Tconv culture and 10 ng/ml IL-2 was added to Treg culture.

extract_protocol:
After nuclear isolation, nuclear lysates were sonicated by using bioruptor followed by immunoprecipitating with anti-p65 antibody+ Dynabeads protein A
Library was constructed on immunoprecipitated DNA according to manufacturer's recommendations (KAPA Hyper Prep Kit). Samples were enriched with PCR with 12 cycles.Afterward, double size selection was performed with AMPure XP beads

tag: mouse strain

tag: tissues

value: Spleens+Lymph nodes

value: Conventional T cells

tag: cell subtype

value: Tconv unstimulated

tag: chip antibody

value: anti-mouse p65 (Santa Cruz, sc-372, #K-0615)


title: p65 IP in Tconv, anti-CD3/CD28 stim, rep2

description:
p65_Tcon_S_2
processed data file:
p65_Tcon_S.pooled_peaks.noBlacklist.idr_conservative.narrowPeak

source_name: Tconv + anti-CD3/CD28 stim

value: Tconv + anti-CD3/CD28 stim


title: RNA-seq for isolated mouse brain microglia, PBS group, replicate 1


title: RNA-seq for isolated mouse brain microglia, PBS group, replicate 2


title: Input chromatin, rep2

source_name: Treg + Tconv  stim + unstim input chromatin

value: Treg+Tconv


title: bpl21

city: Stanford

first: Michael

middle: Warren

last: Guernsey

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

data_processing:
Adapter sequences and low quality bases were trimmed using trim_galore v 0.3.3
The resulting sequences were aligned to the wallaby genome (m.eug_v1.0) using STAR (version 2.5.1b).
Raw counts were assigned to significantly transcribed regions using UniPeak v1.0.
Regions were then associated with the nearest gene using HOMER (version 4.7)
Multiple regions mapping to the same gene were summed to give a final read count for each gene.
Genome_build: m.eug_v1.0
Supplementary_files_format_and_content: Tab-delimited file containing summed read counts for each transcript

organism: Notamacropus eugenii

source_name: bilaminar omphalopleure

extract_protocol:
For fresh tissue, total RNA was isolated from placenta using a phenol–chloroform purification with Trizol (Invitrogen) and mRNA was subsequently isolated using Dynabeads Oligo (dT)25.
the samples were given a short heat-shearing treatment immediately followed by cDNA synthesis. The resulting cDNA was repaired using 3’A-tailing and ligated to linkers containing unique illumina barcodes for sequencing. An agarose gel was used for size selection and the samples were then PCR amplified for 15(fresh)-17(fixed) cycles and purified using AMPure XP beads. Quality of the libraries was assessed using both Qubit and Bioanlyzer technology and then sequenced

value: day 21 of gestation

value: placenta (bilaminar omphalopleure)

tag: tissue state

value: fresh, snap frozen


title: PAPERCLIP for CL57/B6J liver

description: Index 5: AGTC

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011).  Only reads that are at least 25-nt in length are retained for mapping to reference genome (mm10).
Mapping was performed using Novoalign (http://www.novocraft.com) without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Unique reads from both replicates were merged.  CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster. The clusters were filtered by PH before downstream analysis.  For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site.  The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends.  Please refer to the citation for further information.
Note: The submitted raw files are de-multiplexed and quality-filtered without further processing.
Genome_build: mm10
Supplementary_files_format_and_content: txt files for unique read counts at gene level (RefSeq)

source_name: mouse liver

extract_protocol:
Sample preparation, immunoprecipitation, SDS-PAGE and RNA extraction were performed using the PAPERCLIP protocol (Hwang et al. 2016).  Mouse monoclonal anti-GFP antibodies clone 19F7 and 19C8 (Heiman et al. 2014) were used for immunoprecipitation.
The sequencing library was constructed using the PAPERCLIP method (Hwang et al. 2016).  The library contains a 11-nt degenerate linker sequence at the 5′ end (3-nt degenerate sequence, 4-nt sample multiplexing index and 7-nt random barcode).
Other (cTag-PAPERCLIP)

value: liver


title: p65 IP in Tconv, anti-CD3/CD28 stim, rep1

description:
p65_Tcon_S_1
processed data file:
p65_Tcon_S.pooled_peaks.noBlacklist.idr_conservative.narrowPeak


title: C2_Ctr

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

description:
circRNAs of human 6 samples _rRNA_HSV1_CIRCexplorer.fa
Candidate_lncRNAs of human 6 samples_rRNA_HSV1.fa
isoforms.fpkm_expression
circRNA.fpkm_expression
Genes.fpkm_expression
lncRNA_Prediction.fpkm_expression

data_processing:
Raw reads of FASTQ files were obtained and assessed for quality using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). The reads containing adapter, ploy-N and low quality reads were removed using Cutadapt (https://pypi.python.org/pypi/cutadapt/1.4.2) [2] to obtain clean reads with high quality.
For circRNA analysis, clean paired-end RNA-seq reads with 150 bp in length of were aligned to the human reference genome hg38 (GRCh38.p7) using Tophat (v2.1.0) (Tophat2, -N 2 -r 50 --library-type fr-firststrand --mate-std-dev20 -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 ) for linear transcripts. For the mapped reads, they were assembled into know and novel linear transcripts using Cufflinks (v2.1.1) (Cufflinks2, -I 40000 --max-bundle-frags 1000000 -p 26 -u -L CUFF). All transcripts were pooled and merged to generate final transcriptome using Cuffmerge (v 2.1.1) (Cuffmerge2, -p 26). In contrast, the unmapped reads were aligned to the AGM reference genome for fusion transcripts using Tophat-Fusion (v2.1.0) (Tophat-Fusion2, -N 2 --library-type fr-firststrand -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 --fusion-search --no-coverage-search --bowtie1). Fusion transcripts from TopHat-Fusion and the transcripts from the assembled linear RNAs were analyzed with circExplorer to identify candidate circRNAs.
For mRNA analysis, the human reference genome hg38 (GRCh38.p7) was served as mRNA annotation reference.
For lncRNA analysis, transcripts that met the following criteria were further analyzed: (1) RNA length ≥200 bp; (2) transcript reads ≥3; (3) exon number ≥1. Subsequently, transcripts were subjected to protein coding potential evaluation by CNCI (v2) [7] and CPC (0.9-r2) [8] with default parameters. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts predicted without coding potential were considered as lncRNAs.
Genome_build: human reference genome hg38 (GRCh38.p7)
Supplementary_files_format_and_content: fasta files and fpkm expression value of circRNAs, lncRNAs and genes

organism: Homo sapiens

source_name: human fibroblast KMB17 cells

growth_protocol: Human fibroblast KMB17 strain (Institute of Medical Biology, CAMS), a normal diploid cell line that was originated from fetal lung tissue, was cultured in Minimum Essential Medium (MEM) supplemented with 10% bovine serum (Minhai Biotech, Beijing, China) at 37°C in 5% CO2.

extract_protocol:
At 48 h postinfection, total RNA from HSV-1 infected and uninfected KMB17 cells was isolated with Trizol regeant (Invitrogen) followed by digestion with DNase I (Epicentre) for 15 min at 37°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KMB17 cells were mock- infected or infected with HSV-1 at a multiplicity of infection (m.o.i) of 1.

tag: cell line

value: Human fetal lung tissue-derived fibroblast cells

tag: passages

tag: infection


title: cTag-PAPERCLIP for Camk2a-Cre; Ctag-PABP mouse cortex, replicate 2

description: Index 3: CGAT

source_name: mouse cortex

value: brain cortex


title: cTag-PAPERCLIP for Gad2-Cre; Ctag-PABP mouse cortex, replicate 2

description: Index 4: TAGC

value: replicate 2


title: Input chromatin, rep1

value: Treg + Tconv  stim + unstim input chromatin


title: cTag-PAPERCLIP for Camk2a-Cre; Ctag-PABP mouse cortex, replicate 1

description: Index 5: AGTC

value: replicate 1


title: cTag-PAPERCLIP for Gfap-Cre; Ctag-PABP mouse cortex, replicate 2

description: Index 4: TAGC


title: cTag-PAPERCLIP for Gfap-Cre; Ctag-PABP mouse cortex, replicate 1

description: Index 3: CGAT


title: Tia1 iCLIP LPS-activated B cells Replicate 1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

description:
RNA-Tia1 complex
5'barcode ACTNNNN_0

data_processing:
library strategy: CLIP-Seq
See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Raw sequence reads were trimmed to remove both barcodes and adapters. 5' barcodes are 5' GAANNNN_0 and 5'ACTNNNN_0. Linker L34 oligo sequence: P-AUAGAUCGGAAGAGCGGUUCAG-Puromycin; P5/P3 solexa primers for library amplification are AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
Remaining sequences were mapped to the mouse mm9 genome (Ensembl59 genome annotation) using Bowtie (Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).).
Deduplication and identification of unique cDNA counts was performed based on the 4 random bases present in the 5' barcode.
Position -1 of uniquely annotated reads to the genome was annotated as the TTP crosslink site.
Peak enrichment analysis of Tia1 binding sites was performed in iCount for both independent replicates and  the sum of both files. Unique Tia1 crosslink sites were identified as previously described (See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Briefly, 15 nucleotide windows flanking the crosslink site were generated, 100 permutations were allowed and multiple test correction of p-values (Benjamini-Hochberg) was performed to calculate FDR.
Lift over to mm10 genome (Ensembl75 annotation).
Genome_build: mm9 (Ensembl59 genome annotation)
Supplementary_files_format_and_content: Bed files contain the annotation of unique individual Tia1-nucleotide crosslinks (prior and after peak call, FDR<0.05) for each and the sum of experiments performed.

source_name: Tia1 iCLIP LPS-activated B cells

growth_protocol: Splenic B cells are purified using the B cell isolation kit from Miltenyi Biotec.

extract_protocol:
Cytoplasmic extracts were isolated from 2-3 x 10E7 cells after irradiation with 300mJ/cm2 UV-C light in a Stratalinker. RNA-protein complexes were purified using a 2 µg of goat anti-Tial1 (C-18) antibody (sc-1749) after partial RNA digestion with RNAse I (0.3 U/ml)
See König et al, 2010 Nature Structural and Molecular Biology, 17, 909-915. Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP). Samples were multiplexed based on a 7 bases barcode (annotated under sample description)

treatment_protocol: B cell lines were grown on 10 cm dishes using Dutch-modified RPMI containing 2 mM L-glutamine, 5% (v/v) FCS, 50 µM 2-mercapto-ethanol, 100 U penicillin G/ml, 100 mg/ml streptomycin and non-essential amino acids. Cells were treated with LPS (10 µg/ml) for 48 hours.

value: Splenic B cells (cytoplasm)

value: primary cells

tag: stimulation

value: 48h LPS

tag: ip antibody

value: Goat anti-Tial1 (C-18) antibody (sc-1749)


title: Tia1 iCLIP LPS-activated B cells Replicate 2

description:
RNA-Tia1 complex
5'barcode GAANNNN_0


title: GFP_3

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Library strategy: DamID-seq
Reads were mapped to Danio Rerio genome GRCz10 using bwa mem (v0.7.12) using default parameters
Mapped Reads were sorted and converted into BAM format using samtools(v1.2) using default parameters
Bigwig files were generated by first geneterating wiggle files from .bam files using igvtools (v2.3.60) and then converting bigwig format using wigToBigWig(v4)
Genome_build: GRCz10
Supplementary_files_format_and_content: bigWig

organism: Danio rerio

source_name: TB stage embryos

growth_protocol: Embryos obtained from natural mating were maintained at 28.5C until TB stage

extract_protocol:
gDNA was collected from TB stage zebrafish embryos following instructions for the Qiagen DNeasy kit.
Adenine-methylated gDNA was digested with DpnI, followed by ligation of DamID adaptors. Unmethylated DNA was destroyed by DpnII digestion, and methylated regions were PCR amplified in 2 parallel reactions per sample. Adaptors were removed by additional DpnII digest followed by addition of sequencing idexes.

treatment_protocol: WT embryos were injected at one-cell stage with synthetic mRNA encoding Gon4l-Dam or GFP-Dam

tag: geotype/variation

value: control GFP-Dam


title: Udu_3


title: mRNA_Tbx21_WT_NK_IL15_48h_rpt2

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description:
sample21_RNA13
exp ID: 150224_212_213_s19
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

data_processing:
RNA-seq, alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to mouse genome mm9 using TopHat 2.0.8.
RNA-seq, RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bw: bigWig files include ChIP-seq peaks.
Supplementary_files_format_and_content: JEM_RPKM_table.xlsx: Excel file includes RPKM values.

source_name: mouse primary splenic NK cells

growth_protocol: RNAseq IL-15 (version 2): 0.5-2 x 10^5 CD3- CD19- NKp46+ NK cells were purified from spleens of mice by cell sorting (>98% purity; FACSAria III; Becton Dickinson) and cultured for 48 hours in the presence of recombinant mouse IL-15 (20 ng/ml; eBioscience). These were then collected and resuspended in Trizol reagent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 0.2-0.5 million cells/ml in flat bottomed, 96 well tissue culture-treated plates (CoStar).

extract_protocol:
RNA-seq: Total RNA was extracted from 50-500K cells by phenol-chloroform method with GlycoBlue as co-precipitant (7 μg per sample; Life Technologies).
RNA-seq: Single-end libraries were prepared from 0.1-0.5 μg of total RNA using the TruSeq RNA Sample Preparation Kit V2 (Illumina).
RNA-seq: Indexed libraries were multiplexed and sequenced for 50 single read cycles on Illumina HiSeq 2000 or 2500 instruments according to the manufacturer's instructions.

tag: strain/background

tag: genotype/variation

value: WT

value: primary splenic NK cells

tag: culture condition

value: 48 hour in vitro culture with IL-15.


title: mRNA_Tbx21_KO_NK_IL15_48h_rpt2

description:
sample22_RNA14
exp ID: 150224_212_213_s22
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

tag: cell type


title: GFP_1


title: Udu_2


title: mRNA_Tbx21_WT_NK_IL15_48h_rpt1

description:
sample19_RNA11
exp ID: 150224_212_213_s13
mRNA
Processed data file: Villarino JEM RPKM table.xlsx


title: GFP_2


title: MZudu TB B2

data_processing:
Reads were mapped to Danio Rerio genome GRCz10 using STAR (v2.4.2a) with default parameters to create sorted BAM files.
Bigwig files were generated by first geneterating wiggle files from .bam files using igvtools (v2.3.60) and then converting bigwig format using wigToBigWig(v4)
Genome_build: GRCz10
Supplementary_files_format_and_content: BigWig formatted files for each sample

extract_protocol:
Embryos were lysed and mRNA isolated using a Dynabeads mRNA Direct kit (Ambion).
Libraries were prepared according to instructions for the ScriptSeq RNA-seq Library Prep kit (Illumina).

value: Mzudu


title: mRNA_WT_NK_IL15_16h_rpt1

description:
sample14_RNA6
exp ID: 121026_SN7001365_0031_s11
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

growth_protocol: RNAseq IL-15 (version 1): 0.5-2 x 10^5 CD3- CD19- NKp46+ NK cells were purified from spleens of mice by cell sorting (>98% purity; FACSAria III; Becton Dickinson) and cultured overnight (12-18 hours) in the presence of recombinant mouse IL-15 (20 ng/ml; eBioscience). These were then collected and resuspended in Trizol reagent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 0.2-0.5 million cells/ml in flat bottomed, 96 well tissue culture-treated plates (CoStar).

value: 16 hour in vitro culture with IL-15.


title: MZudu TB B1


title: mRNA_WT_NK_ExVivo_rpt1

description:
sample13_RNA5
exp ID: 121026_SN7001365_0031_s7
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

growth_protocol: RNAseq ex vivo: 0.5-2 x 10^5 CD3- CD19- NKp46+ NK cells were purified from spleens of mice by cell sorting (>98% purity; FACSAria III; Becton Dickinson) and stored in Trizol reagent (Invitrogen) for subsequent RNA isolation.

value: ex vivo


title: MZudu TB A2


title: MZudu TB A1


title: WT TB B2


title: WT TB B1


title: WT TB A1


title: panSTAT5_WT_NK_IL15_2h_rpt1

description:
sample2_ChIP2
exp ID: 131126_0082_s7

data_processing:
ChIP-seq, alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were aligned to mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Only uniquely mapped, non-redundant reads were used for peak calling.
ChIP-seq, peaks: Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0 E-05.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bw: bigWig files include ChIP-seq peaks.
Supplementary_files_format_and_content: JEM_RPKM_table.xlsx: Excel file includes RPKM values.

growth_protocol: ChIPseq IL-15 cultures: 1 x 10^7 NK cells were purified from spleens of WT mice by magnetic bead separation (90% purity; negative selection kit by Miltenyi Biotec, Bergisch Gladbach, Germany),  treated with recombinant mouse IL-15 (2 hrs; 20 ng/ml) and fixed with 1% formaldehyde.  Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 2 million cells/ml in 6 well tissue culture-treated plates (CoStar).

extract_protocol:
ChIP-seq: Cells were chemically cross-linked by 1% formaldehyde. Lysates were made by sonication (10,000,000 cells/sample) and protein-DNA complexes isolated using the indicated antibodies.
ChIP-seq: Single-end libraries were prepared for STAT5-bound fragments, along with un-precipitated input controls, using the NEBNext ChIP-Seq Library Prep kit for Illumina (New England Biolabs). Briefly, DNA fragments were end-repaired to generate phosphorylated blunt ends. These were then treated with Taq polymerase and dATP to generate 3-prime 'A' base overhangs for ligation to adapters containing complementary 'T' base overhangs. After ligation, DNA was PCR amplified for 15 cycles with indexed primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-seq: Indexed libraries were multiplexed and sequenced for 50 single read cycles on Illumina HiSeq 2000 or 2500 instruments according to the manufacturer's instructions.

value: 2 hour in vitro culture with IL-15.

value: pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969, Lot #GR93813-4)


title: panSTAT5_WT_NK_ExVivo_2h_rpt1

description:
sample1_ChIP1
exp ID: 131126_0082_s6

growth_protocol: ChIPseq ex vivo: 1 x 10^7 NK cells were purified from spleens of WT mice by magnetic bead separation (90% purity; negative selection kit by Miltenyi Biotec, Bergisch Gladbach, Germany) and fixed with 1% formaldehyde directly ex vivo.


title: Input_WT_NK_IL15_2h_rpt1

description:
sample4_ChIP4
exp ID: 131126_0082_s29


title: cTag-PAPERCLIP for Gad2-Cre; Ctag-PABP mouse cortex, replicate 1

description: Index 3: CGAT

tag: sample type

tag: tissue

value: brain cortex


title: RNA-seq for Ptbp2-KO mouse, E18.5 brain cortex, replicate 3

source_name: brain cortex

value: replicate 3

tag: age


title: Input_WT_NK_ExVivo_2h_rpt1

description:
sample3_ChIP3
exp ID: 131126_0082_s28


title: WT TB A2


title: RNA-seq for Ptbp2-KO mouse, E18.5 brain cortex, replicate 2

value: replicate 2


title: RNA-seq for Ptbp2-KO mouse, E18.5 brain cortex, replicate 1

value: replicate 1


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, LPS treatment, replicate 3

description: Index 4: TAGC

source_name: mouse brain

value: brain


title: mRNA_Tbx21_KO_NK_IL15_48h_rpt1

description:
sample20_RNA12
exp ID: 150224_212_213_s16
mRNA
Processed data file: Villarino JEM RPKM table.xlsx


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, LPS treatment, replicate 2

description: Index 6: GACT


title: Udu_1


title: LPS+KU55933+Etoposide treated B cells_Replicate 4

description:
LEKU4_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LEKU_vs_LPS.csv
res_dds_LEKU_vs_LE.csv

data_processing:
Sample demultiplexing (6 samples per lane).
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (cutadapt version 1.2.1). Example: command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC lane2_L1_CGATGT_L002_R1.fastq.gz
Remaining sequences were mapped to Mus_musculus.GRCm38.70.gtf annotation with TopHat (v2.0.12) using tophat -p 6 -g 2 parameters.
Read counting was performed using HT-Seq (Mus_musculus.GRCm38.78.gtf annotation)
Differential gene expression analysis was performed using DESeq2_1.6.3 package. [DESeq2 ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable_MF,directory = directory,design= ~Condition). dds<-DESeq(ddsHTSeq). res_dds_LEvsLPS<-results(dds,contrast = c("Condition","LE","LPS")). res_dds_LEKUvsLE<-results(dds,contrast = c("Condition","LEKU","LE")). res_dds_LEKUvsLPS<-results(dds,contrast = c("Condition","LEKU","LPS")). NA omit. Cut off: padj<0.01
Genome_build: mm10
Supplementary_files_format_and_content: csv files. DESeq2 results and DESeq2 normalized gene counts

molecule: polyA RNA

source_name: LPS+KU55933+Etoposide treated B cells

growth_protocol: Splenic B cells from C57BL6_Babr mice were isolated using a B cell isolation kit from Miltenyi Biotech. Mice were maintained under Babraham Institute AWEEC and UK home Office regulation.

extract_protocol:
RNA extraction using TriZol (life Technologies)
Illumina TruSeq mRNA sample prep kit (Barcodes used for sample multiplexing: index 2, CGATGT; index 4, TGACCA; index 5, ACAGTG; index 7, CAGATC; index 12, CTTGTA; index 19, GTGAAA)

treatment_protocol: After isolation, splenic B cells were cultured in RPMI 1640 Medium (Dutch Modification) plus 5% FCS, antibiotics, 2 mM L-glutamine and Beta-mercaptoethanol (5 microMolar) at a density of 5x10^5 cells/ml. They were activated with LPS (10 micrograms/ml) for 47 hours prior adding the ATM kinase inhibitor KU55933 (10 microMolar) for 1 hour. Then, DNA damage was induced with etoposide (20 microMolar) for 4 hours. Cells were collected for RNA extraction.

tag: strain

value: Splenic B cells

value: primary B cells

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

tag: illumina index

value: GTGAAA


title: LPS+KU55933+Etoposide treated B cells_Replicate 3

description:
LEKU3_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LEKU_vs_LPS.csv
res_dds_LEKU_vs_LE.csv

value: ACAGTG


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, LPS treatment, replicate 1

description: Index 4: TAGC


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, PBS treatment, replicate 1

description: Index 3: CGAT


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, replicate 2

description: Index 4: TAGC


title: LPS+KU55933+Etoposide treated B cells_Replicate 2

description:
LEKU2_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LEKU_vs_LPS.csv
res_dds_LEKU_vs_LE.csv


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, PBS treatment, replicate 3

description: Index 3: CGAT


title: LPS+KU55933+Etoposide treated B cells_Replicate 1

description:
LEKU1_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LEKU_vs_LPS.csv
res_dds_LEKU_vs_LE.csv


title: WT Treg stim_RNA-seq

first: Hyunju

last: Oh

address: 701 West 168th Street

department: Microbiology and Immunology

institute: Columbia University Medical Center

description:
No-deletion control for the tat-cre treated group
HS032

data_processing:
Illumina RTA was used for base calling
Bcl2fastq was used for converting BCL to fastq format, coupled with adaptor trimming. The, the reads were mapped to mm9 using Tophat with 4 mismatches and 10 maximum multiple hits.
We estimated the relative abundance (FPKM) of genes and splice isoforms using cufflinks with default setting.
Genome_build: mm9
Supplementary_files_format_and_content: CSV files including general abundance information of genes: gene name, gene id, gene length, FPKM

source_name: Spleen, LN

extract_protocol:
RNA was extracted by using Qiagen Rneasy mini kit or Rneasy micro kit depending on the cell number
Library was prepared by using Illumina TruSeq RNA prep kit

treatment_protocol: For stimulated samples, cells were incubated with 2 μg/ml CD3 and CD28 antibodies in the presence of IL-2 for three hours

value: spleen and lymph node

value: Regulatory T cells

tag: genotype

value: WT


title: p65 IP in Tconv, unstim, rep1

description:
p65_Tcon_US_1
processed data file:
p65_Tcon_US.pooled_peaks.noBlacklist.idr_conservative.narrowPeak

tag: mouse strain

tag: tissues

value: Spleens+Lymph nodes

value: Conventional T cells

tag: cell subtype

value: Tconv unstimulated

tag: chip antibody

value: anti-mouse p65 (Santa Cruz, sc-372, #K-0615)


title: FoxP3 del Treg stim_RNA-seq

description:
Induced deletion by tat-cre followed by CD3/CD28 stimiulation
HS033

value: FoxP3 del


title: LPS+Etoposide treated B cells_Replicate 4

description:
LE4_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LE.csv

source_name: LPS+Etoposide treated B cells

tag: stimulation

value: LPS (48 hours) + Etoposide (4 hours)

value: CTTGTA


title: NFkB del Treg stim_RNA-seq

description:
Induced deletion by tat-cre followed by CD3/CD28 stimiulation
HSO34

value: NF-kB del


title: WT Tconv stim_RNA-seq

description:
No-deletion control for the tat-cre treated group
HS031


title: LPS+Etoposide treated B cells_Replicate 3

description:
LE3_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LE.csv

value: TGACCA


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, replicate 1

description: Index 3: CGAT

value: replicate 1

value: brain


title: cTag-PAPERCLIP for Cx3cr1-Cre; Ctag-PABP mouse brain, PBS treatment, replicate 2

description: Index 5: AGTC

value: replicate 2


title: LPS+Etoposide treated B cells_Replicate 2

description:
LE2_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LE.csv

value: Splenic B cells

value: primary B cells


title: LPS+Etoposide treated B cells_Replicate 1

description:
LE1_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LE.csv


title: DKO Treg stim rep2_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS030

value: spleen and lymph node

value: p65 c-Rel DKO


title: cRelKO Treg stim_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS028

value: Regulatory T cells

value: c-RelKO


title: cRelKO Treg rep2_RNA-seq


title: p65KO Treg rep3_RNA-seq


title: LPS-activated B cells_Replicate 4

description:
L4_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LPS.csv

source_name: LPS-activated B cells

value: LPS (48 hours)

value: CAGATC


title: LPS-activated B cells_Replicate 3

description:
L3_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LPS.csv

value: CGATGT


title: LPS-activated B cells_Replicate 2

description:
L2_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LPS.csv


title: LPS-activated B cells_Replicate 1

description:
L1_RNA-Seq
processed data file:
Normalized_counts_mRNAseq
res_dds_LE_vs_LPS.csv
res_dds_LEKU_vs_LPS.csv


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 16_Replicate 4

data_processing:
Sample demultiplexing (39-40 samples per lane) based on Illumina first read (10 bp; not provided).
Location and length analysis of the longest consecutive A tract in raw reads (20 nucleotide long A tract expected). Removal of the A-tract from reads was performed according to the following rules (tail length, A tract length, allowed mismatches in tract): (20, 17, 2), (19, 16, 2), (18, 15, 2), (17, 14, 2), (16, 13, 1), (15, 12, 1), (14, 11, 1), (13, 10, 1), (12, 10, 1), (11, 9, 1), (10, 8, 1), (9, 8, 1), (8, 7, 0), (7, 6, 0), (6, 5, 0), (5, 3, 0), (4, 3, 0).
Reads containing internal A-tracts are cut according to rule (minimal A tract length, allowed mismatches in tract): (17, 2). Remove any remaining A from the end of read.
Reads were mapped to GRCm38/mm10 genome (Ensembl 66.8 annotation)with TopHat (v2.0.12) using tophat -p 6 -g 2 parameters.
Read counting was performed using HT-Seq (Mus_musculus.GRCm38.78.gtf annotation)
Differential gene expression analysis was performed using DESeq2_1.6.3 package. (GLM; read.counts ~ condition + polysome.fraction + condition:polysome.fraction)
Genome_build: mm10
Supplementary_files_format_and_content: Read counts

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 16

extract_protocol:
mRNA was precipitated using 8M guanidine hydrochloride and absolute ethanol
Custom protocol (described in the associated publication).

treatment_protocol: After isolation, splenic B cells were cultured in RPMI 1640 Medium (Dutch Modification) plus 5% FCS, antibiotics, 2 mM L-glutamine and Beta-mercaptoethanol (5 microMolar) at a density of 5x10^5 cells/ml. They were activated with LPS (10 micrograms/ml) for 47 hours prior adding the ATM kinase inhibitor KU55933 (10 microMolar) for 1 hour. Then, DNA damage was induced with etoposide (20 microMolar) for 4 hours. Cells were then treated with cycloheximide (100 microgrames per ml) for 3 minutes prior isolation of cytoplasmic extracts and polysome fractionation using sucrose gradients (10-30%). 1 ml fractions containing monosomes (fractions 4 to 7), light polysomes (fractions 8 to 10) or heavy polysomes (fractions 11 to 16) were collected .

value: primary, splenic B cells

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

tag: cell fraction

value: Polysomes

tag: fraction id

value: Polysome fraction 16


title: WT Tconv stim rep2_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS022

value: Conventional T cells

value: WT


title: WT Treg rep4_RNA-seq


title: WT Tconv rep2_RNA-seq


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 15_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 15

value: Polysome fraction 15


title: c-RelKO Treg rep1_RNA-seq


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 14_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 14

value: Polysome fraction 14


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 13_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 13

value: Polysome fraction 13


title: DKO Treg stim rep1_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS015


title: DKO Treg rep2_RNA-seq


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 9_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 9

value: Polysome fraction 9


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 11_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 11

value: Polysome fraction 11


title: WT Treg rep3_RNA-seq

value: spleen and lymph node


title: WT Tconv stim rep1_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS011


title: DKO Treg rep1_RNA-seq

value: Regulatory T cells

value: p65 c-Rel DKO


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 12_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 12

value: Polysome fraction 12


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 10_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 10

value: Polysome fraction 10


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 8_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 8

value: Polysome fraction 8


title: WT Treg stim rep2_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS024


title: p65KO Treg stim_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS026


title: WT Treg rep2_RNA-seq


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 7_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 7

value: primary, splenic B cells

value: Polysome fraction 7


title: p65KO Treg rep2_RNA-seq


title: p65KO Treg rep1_RNA-seq


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 5_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 5

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

value: Polysomes

value: Polysome fraction 5


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 4_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 4

value: Polysome fraction 4


title: WT Treg rep1_RNA-seq

value: WT


title: LPS-Etoposide 2 48-4 h pf 16_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 16

value: LPS (48 hours) + Etoposide (4 hours)

value: Polysome fraction 16


title: LPS-Etoposide 2 48-4 h pf 15_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 15

value: Polysome fraction 15


title: LPS-Etoposide 2 48-4 h pf 14_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 14

value: Polysome fraction 14


title: WT Treg stim rep1_RNA-seq

description:
3 hour CD3/CD28 stimulation
HS013

source_name: Spleen, LN

value: spleen and lymph node


title: LPS-Etoposide 2 48-4 h pf 13_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 13

value: Polysome fraction 13


title: WT Tconv rep1_RNA-seq

value: Conventional T cells


title: LPS-Etoposide 2 48-4 h pf 11_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 11

value: Polysome fraction 11


title: LPS-Etoposide 2 48-4 h pf 12_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 12

value: Polysome fraction 12


title: AML 38

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

description: small RNA from AML patient

data_processing: Alignment: sequence reads were obtained and mapped to the miRNA database (miRBase 15, http://www.mirbase.org), functional RNA database (fRNAdb, http://www.ncrna.org/frnadb), piRNA database (piRNAbank, http://pirnabank.ibab.ac.in), human genome reference sequence (build 36, March 2006) and the genomic tRNA database (GtRNADB, http://gtrnadb.ucsc.edu) using Novoalign V 2.05 software (http://www.novocraft.com). Only uniquely aligned reads were reported.

source_name: Peripheral Blood

growth_protocol: Total RNA was extracted from cryopreserved patient samples, either BM or PB, using TRIzol (Invitrogen Life Technologies)

extract_protocol: Size fractionated library of small RNAs were prepared for each sample from 1 ug of total RNA with the DGE-Small RNA Sample Preparation Kit, v 1.5 Protocol (Illumina) according to manufacturer's instructions. Libraries were processed using DGE-Small RNA Cluster Generation Kit and sequenced with a 36 Cycle Sequencing Kit v 3

value: Peripheral Blood

tag: age at diagnosis

tag: morphology (fab)

tag: cytogenetic group

value: Normal Karyotype (NK)

tag: disease state

value: AML patient


title: AML 37

description: small RNA from AML patient


title: LPS-Etoposide 2 48-4 h pf 9_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 9

tag: cell type

value: primary, splenic B cells

value: Polysome fraction 9


title: AML 32

description: small RNA from AML patient

tag: tissue


title: AML 40

description: small RNA from AML patient

source_name: Bone Marrow

value: Bone Marrow


title: AML 39

description: small RNA from AML patient


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 6_Replicate 4

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 6

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

value: Polysomes

value: Polysome fraction 6


title: AML 33

description: small RNA from AML patient


title: AML 30

description: small RNA from AML patient


title: LPS-Etoposide 2 48-4 h pf 7_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 7

value: LPS (48 hours) + Etoposide (4 hours)

value: Polysome fraction 7


title: LPS-Etoposide 2 48-4 h pf 8_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 8

value: Polysome fraction 8


title: AML 27

description: small RNA from AML patient


title: LPS-Etoposide 2 48-4 h pf 5_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 5

value: Polysome fraction 5


title: Normal Control 41 (rep II)

description: small RNA from healthy donor

value: normal

value: Normal BM

value: healthy donor


title: LPS-Etoposide 2 48-4 h pf 4_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 4

value: Polysome fraction 4


title: APML 26 (rep II)

description: small RNA from AML patient

source_name: Peripheral Blood (IBM enriched)

value: Peripheral Blood (IBM enriched)


title: LPS 2 48h pf 15_Replicate 4

source_name: LPS 2 48h pf 15

value: LPS (48 hours)

value: Polysome fraction 15


title: LPS 2 48h pf 14_Replicate 4

source_name: LPS 2 48h pf 14

value: primary, splenic B cells

value: Polysome fraction 14


title: AML 25

description: small RNA from AML patient

value: Peripheral Blood

value: AML patient


title: AML 24

description: small RNA from AML patient


title: LPS 2 48h pf 16_Replicate 4

source_name: LPS 2 48h pf 16

value: Polysomes

value: Polysome fraction 16


title: LPS 2 48h pf 13_Replicate 4

source_name: LPS 2 48h pf 13

value: Polysome fraction 13


title: AML 36

description: small RNA from AML patient


title: AML 22

description: small RNA from AML patient

value: Bone Marrow


title: LPS 2 48h pf 12_Replicate 4

source_name: LPS 2 48h pf 12

value: Polysome fraction 12


title: LPS 2 48h pf 10_Replicate 4

source_name: LPS 2 48h pf 10

value: Polysome fraction 10


title: AML 31 (rep II)

description: small RNA from AML patient


title: AML 23

description: small RNA from AML patient


title: LPS 2 48h pf 11_Replicate 4

source_name: LPS 2 48h pf 11

value: Polysome fraction 11


title: AML 21

description: small RNA from AML patient


title: AML 18

description: small RNA from AML patient

value: Complex


title: Normal Control 28 (rep I)

description: small RNA from healthy donor

value: normal

value: Normal BM

value: healthy donor


title: AML 29

description: small RNA from AML patient


title: AML 16

description: small RNA from AML patient


title: LPS 2 48h pf 9_Replicate 4

source_name: LPS 2 48h pf 9

value: LPS (48 hours)

value: Polysome fraction 9


title: AML 19

description: small RNA from AML patient

source_name: Peripheral Blood

value: Other


title: LPS-Etoposide 2 48-4 h pf 6_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 6

value: primary, splenic B cells

value: LPS (48 hours) + Etoposide (4 hours)

value: Polysome fraction 6


title: AML 17 (rep I)

description: small RNA from AML patient

value: Peripheral Blood

value: AML patient


title: LPS 2 48h pf 7_Replicate 4

source_name: LPS 2 48h pf 7

value: Polysomes

value: Polysome fraction 7


title: LPS 2 48h pf 6_Replicate 4

source_name: LPS 2 48h pf 6


title: AML 15

description: small RNA from AML patient


title: LPS 2 48h pf 5_Replicate 4

source_name: LPS 2 48h pf 5

value: Polysome fraction 5


title: AML 14

description: small RNA from AML patient

value: Normal Karyotype (NK)


title: LPS 2 48h pf 4_Replicate 4

source_name: LPS 2 48h pf 4

value: Polysome fraction 4


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 16_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 16

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

value: Polysome fraction 16


title: AML 13

description: small RNA from AML patient

value: Complex


title: APML 12

description: small RNA from AML patient

source_name: Bone Marrow

value: Bone Marrow


title: LPS-Etoposide 2 48-4 h pf 10_Replicate 4

source_name: LPS-Etoposide 2 48-4 h pf 10

value: Polysome fraction 10


title: LPS 2 48h pf 8_Replicate 4

source_name: LPS 2 48h pf 8

value: LPS (48 hours)

value: Polysome fraction 8


title: AML 11

description: small RNA from AML patient


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 14_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 14

value: primary, splenic B cells

value: Polysome fraction 14


title: APML 9 (rep I)

description: small RNA from AML patient

source_name: Peripheral Blood (IBM enriched)

value: Peripheral Blood (IBM enriched)


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 15_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 15

value: Polysome fraction 15


title: AML 10

description: small RNA from AML patient

value: Peripheral Blood

value: AML patient


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 11_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 11

value: Polysomes

value: Polysome fraction 11


title: APML 8

description: small RNA from AML patient


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 12_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 12

value: Polysome fraction 12


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 13_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 13

value: Polysome fraction 13


title: AML 7

description: small RNA from AML patient

value: Other


title: APML 5

description: small RNA from AML patient


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 9_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 9

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

value: Polysome fraction 9


title: AML 6

description: small RNA from AML patient

value: Bone Marrow


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 8_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 8


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 5_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 5

value: Polysome fraction 5


title: LPS-Etoposide 1 48-4 h pf 16_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 16

value: LPS (48 hours) + Etoposide (4 hours)

value: Polysome fraction 16


title: APML 4

description: small RNA from AML patient

source_name: Peripheral Blood


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 6_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 6

value: primary, splenic B cells

value: Polysome fraction 6


title: AML 2

description: small RNA from AML patient


title: AML 1

description: small RNA from AML patient


title: AML 3

description: small RNA from AML patient


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 4_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 4

value: Polysome fraction 4


title: LPS-Etoposide 1 48-4 h pf 11_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 11


title: LPS-Etoposide 1 48-4 h pf 15_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 15

value: Polysome fraction 15


title: LPS-Etoposide 1 48-4 h pf 10_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 10

value: Polysome fraction 10


title: LPS-Etoposide 1 48-4 h pf 13_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 13


title: LPS-Etoposide 1 48-4 h pf 14_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 14

value: Polysome fraction 14


title: LPS-Etoposide 1 48-4 h pf 9_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 9

value: Polysomes


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 7_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 7

value: Polysome fraction 7


title: LPS 1 48h pf 16_Replicate 3

source_name: LPS 1 48h pf 16

value: LPS (48 hours)


title: LPS 1 48h pf 15_Replicate 3

source_name: LPS 1 48h pf 15


title: LPS 1 48h pf 13_Replicate 3

source_name: LPS 1 48h pf 13

value: Polysome fraction 13


title: LPS 1 48h pf 14_Replicate 3

source_name: LPS 1 48h pf 14


title: LPS-Etoposide 1 48-4 h pf 8_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 8

value: Polysome fraction 8


title: LPS-Etoposide-KU55933 1 48-4-1 h pf 10_Replicate 3

source_name: LPS-Etoposide-KU55933 1 48-4-1 h pf 10

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)


title: LPS 1 48h pf 11_Replicate 3

source_name: LPS 1 48h pf 11

value: Polysome fraction 11


title: LPS-Etoposide 1 48-4 h pf 4_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 4


title: LPS-Etoposide 1 48-4 h pf 5_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 5


title: LPS 1 48h pf 10_Replicate 3

source_name: LPS 1 48h pf 10


title: LPS-Etoposide 1 48-4 h pf 7_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 7


title: LPS 1 48h pf 12_Replicate 3

source_name: LPS 1 48h pf 12

value: Polysome fraction 12


title: LPS 1 48h pf 5_Replicate 3

source_name: LPS 1 48h pf 5

value: Polysome fraction 5


title: LPS-Etoposide 1 48-4 h pf 12_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 12

value: LPS (48 hours) + Etoposide (4 hours)


title: LPS 1 48h pf 7_Replicate 3

source_name: LPS 1 48h pf 7


title: LPS 1 48h pf 6_Replicate 3

source_name: LPS 1 48h pf 6


title: LPS 1 48h pf 4_Replicate 3

source_name: LPS 1 48h pf 4


title: LPS 1 48h pf 9_Replicate 3

source_name: LPS 1 48h pf 9

value: Polysome fraction 9


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 15_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 15

value: primary, splenic B cells


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 14_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 14


title: LPS-Etoposide 1 48-4 h pf 6_Replicate 3

source_name: LPS-Etoposide 1 48-4 h pf 6

value: Polysome fraction 6


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 13_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 13


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 11_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 11


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 10_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 10


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 12_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 12


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 9_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 9


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 8_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 8


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 6_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 6


title: LPS 1 48h pf 8_Replicate 3

source_name: LPS 1 48h pf 8


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 5_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 5


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 7_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 7


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 4_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 4

value: Polysome fraction 4


title: LPS-Etoposide 2 48-4 h pf 15_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 15

value: Polysome fraction 15


title: LPS-Etoposide-KU55933 2 48-4-1 h pf 16_Replicate 2

source_name: LPS-Etoposide-KU55933 2 48-4-1 h pf 16

value: Polysome fraction 16


title: LPS-Etoposide 2 48-4 h pf 14_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 14

value: Polysome fraction 14


title: LPS-Etoposide 2 48-4 h pf 16_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 16

value: Polysomes


title: mRNA_WT_NK_IL15_16h_rpt3

description:
sample18_RNA10
exp ID: 130124_0182_s17
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

source_name: mouse primary splenic NK cells

tag: strain/background

tag: genotype/variation

value: WT

value: primary splenic NK cells

tag: culture condition

value: 16 hour in vitro culture with IL-15.


title: LPS-Etoposide 2 48-4 h pf 12_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 12

tag: strain


title: LPS-Etoposide 2 48-4 h pf 13_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 13

value: Polysome fraction 13


title: mRNA_WT_NK_IL15_16h_rpt2

description:
sample16_RNA8
exp ID: 121126_SN923_0170_s5
mRNA
Processed data file: Villarino JEM RPKM table.xlsx


title: LPS-Etoposide 2 48-4 h pf 11_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 11


title: LPS-Etoposide 2 48-4 h pf 9_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 9


title: mRNA_WT_NK_ExVivo_rpt2

description:
sample15_RNA7
exp ID: 121126_SN923_0170_s1
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

value: ex vivo


title: mRNA_WT_NK_ExVivo_rpt3

description:
sample17_RNA9
exp ID: 130124_0182_s13
mRNA
Processed data file: Villarino JEM RPKM table.xlsx


title: LPS-Etoposide 2 48-4 h pf 10_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 10

value: Polysome fraction 10


title: LPS-Etoposide 2 48-4 h pf 8_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 8

value: Polysome fraction 8


title: mRNA_STAT5_AAB_NK_ExVivo_rpt2

description:
sample12_RNA4
exp ID: 130815_SN923_0208_s27
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

value: mixed 129/C57BL/6

value: STAT5A-/- STAT5B+/-


title: mRNA_STAT5_AAB_NK_ExVivo_rpt1

description:
sample10_RNA2
exp ID: 130506_SN923_0197_s15
mRNA
Processed data file: Villarino JEM RPKM table.xlsx


title: LPS-Etoposide 2 48-4 h pf 7_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 7

value: LPS (48 hours) + Etoposide (4 hours)

value: Polysome fraction 7


title: mRNA_STAT5_WT_NK_ExVivo_rpt2

description:
sample11_RNA3
exp ID: 130815_SN923_0208_s23
mRNA
Processed data file: Villarino JEM RPKM table.xlsx


title: LPS-Etoposide 2 48-4 h pf 6_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 6

value: primary, splenic B cells

value: Polysome fraction 6


title: LPS-Etoposide 2 48-4 h pf 5_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 5

value: Polysome fraction 5


title: Input_WT_NK_IL15_2h_rpt2

description:
sample8_ChIP8
exp ID: 151211_0411_s19

value: 2 hour in vitro culture with IL-15.


title: Input_WT_NK_ExVivo_rpt2

description:
sample7_ChIP7
exp ID: 151211_0411_s10


title: LPS-Etoposide 2 48-4 h pf 4_Replicate 2

source_name: LPS-Etoposide 2 48-4 h pf 4

value: Polysome fraction 4


title: LPS 2 48h pf 17_Replicate 2

source_name: LPS 2 48h pf 17

value: LPS (48 hours)

value: Polysomes

value: Polysome fraction 17


title: LPS 2 48h pf 16_Replicate 2

source_name: LPS 2 48h pf 16

value: Polysome fraction 16


title: panSTAT5_WT_NK_ExVivo_rpt2

description:
sample5_ChIP5
exp ID: 151211_0411_s11

value: WT

value: primary splenic NK cells

value: pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969, Lot #GR93813-4)


title: panSTAT5_WT_NK_IL15_2h_rpt2

description:
sample6_ChIP6
exp ID: 151211_0411_s13


title: LPS 2 48h pf 15_Replicate 2

source_name: LPS 2 48h pf 15

value: Polysome fraction 15


title: LPS 2 48h pf 14_Replicate 2

source_name: LPS 2 48h pf 14

value: Polysome fraction 14


title: LPS 2 48h pf 13_Replicate 2

source_name: LPS 2 48h pf 13

value: Polysome fraction 13


title: LPS 2 48h pf 12_Replicate 2

source_name: LPS 2 48h pf 12

value: Polysome fraction 12


title: 24H-Bex_RNA-seq_replicate_1

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
Sequencing reads were aligned to the mouse genome build mm9 using TopHat and guided by transcripts from the Ensembl 67 database. Transcript assembly was performed using Cufflinks to obtain expression values.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq FPKM_tracking files were output from cufflinks and represent expression values for all mapped genes.

source_name: C2C12 myoblasts

growth_protocol: Cells of the murine myoblasts cell line C2C12 (ATCC) were maintained in growth medium (GM), Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% Fetal Bovine Serum, at 37ºC with 5% CO2. To induce differentiation, the medium of 80% confluent cell cultures was changed to differentiation medium (DM), D-MEM supplemented with 2% horse serum and 50 nM of bexarotene was added for treatment conditions.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen_74104) according to manufacturer’s instructions and  sent for sequencing to the McGill University Genome Quebec Innovation Centre using Illumina HiSeq 2000 platform.
RNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.

tag: cell line


title: 24H-Ctl_RNA-seq_replicate 2


title: LPS 2 48h pf 8_Replicate 2

source_name: LPS 2 48h pf 8

value: Polysome fraction 8


title: 12H-Bex_RNA-seq_replicate_1


title: 24H-Bex_RNA-seq_replicate_2


title: 24H-Ctl_RNA-seq_replicate 1


title: LPS 2 48h pf 9_Replicate 2

source_name: LPS 2 48h pf 9

value: primary, splenic B cells

value: Polysome fraction 9


title: 12H-Bex_RNA-seq_replicate_2


title: Serum_LG1_rep1

city: Nijmegen

first: Menno

last: ter Huurne

address: Geert Grooteplein 26

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

data_processing:
Bowtie was used to map reads to mouse gene annotation (Ensemble release 67) and gene expression levels were determined by MMSeq.
Genome_build: mm9

source_name: Serum ESCs

growth_protocol: Mouse ESCs were fully adapted (over 20 days) to either serum or 2i conditions.

extract_protocol: Libraries were prepared according to Illumina's instructions.

value: Embryonic Stem cell

tag: treatment protocol

value: Serum

tag: developmental stage

value: Late G1-phase


title: 12H-Ctl_RNA-seq_replicate 2


title: 2i_LG1_rep1

source_name: 2i ESCs


title: LPS 2 48h pf 6_Replicate 2

source_name: LPS 2 48h pf 6

value: LPS (48 hours)

value: Polysome fraction 6


title: 12H-Ctl_RNA-seq_replicate 1


title: Proliferating_RNA-seq_replicate 2


title: LPS 2 48h pf 7_Replicate 2

source_name: LPS 2 48h pf 7

value: Polysomes

value: Polysome fraction 7


title: mRNA_STAT5_WT_NK_ExVivo_rpt1

description:
sample9_RNA1
exp ID: 130506_SN923_0197_s22
mRNA
Processed data file: Villarino JEM RPKM table.xlsx

source_name: mouse primary splenic NK cells

value: mixed 129/C57BL/6

value: WT

value: ex vivo


title: LPS 2 48h pf 10_Replicate 2

source_name: LPS 2 48h pf 10

value: Polysome fraction 10


title: WV_KO_5496

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

data_processing:
De-multiplexing was performed with bcl2fastq v2.17.1.14
Reads were aligned to the mm9 reference genome with TopHat v2.0.14 with the parameters -M --GTF mm9.gtf –mate-inner-dist fragment_size
PCR duplicates and low quality reads were filtered out using Picard 2.2.4 and samtools 0.1.19
Reads were assigned to genes using featureCounts 1.4.6 and a custom meta-annotation derived from mm9 that merges together overlapping transcripts
Differential expression analysis was performed with edgeR using a standard approach to pair-wise comparisons with no confounding factors as described in the edgeR manual
Genome_build: mm9
Supplementary_files_format_and_content: BAT_counts.tsv and WV_counts.tsv contain raw counts for each gene in all BAT or WV samples respectively. UCSC gene ids, official gene symbols, and gene lengths are provided for each gene.

source_name: White vastus lateralis

extract_protocol:
RNAs were extracted using Rneasy kit from Qiagen following manufacturer's protocol.
mRNA was purified from 200 ng of total RNA using the NEBNext rRNA Depletion Kit (catalog E6310X, NEB) per manufacturer instructions. cDNA was generated using random hexamer primers (catalog SO142, Thermo Fisher Scientific) and Maxima H Minus Reverse Transcriptase (catalog EP0753, Thermo Fisher Scientifc) for first strand synthesis, followed by NEBNext Second Strand Synthesis Module (catalog E6111L, NEB). Sequencing libraries were then generated from cDNA using the Nextera XT DNA Library Preparation Kit (catalog FC-131-1096, Illumina).

tag: genotype

value: BATI4 KO

value: White vastus lateralis


title: LPS 2 48h pf 5_Replicate 2

source_name: LPS 2 48h pf 5

tag: stimulation

value: Polysome fraction 5


title: LPS 2 48h pf 4_Replicate 2

source_name: LPS 2 48h pf 4

tag: cell fraction

value: Polysome fraction 4


title: WV_KO_5495


title: LPS-Etoposide-KU55933 48-4-1 h pf 16_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 16

value: primary, splenic B cells

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

tag: fraction id

value: Polysome fraction 16


title: WV_KO_5493


title: WV_KO_5494


title: LPS 2 48h pf 11_Replicate 2

source_name: LPS 2 48h pf 11

value: Polysome fraction 11


title: LPS-Etoposide-KU55933 48-4-1 h pf 15_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 15

value: Polysome fraction 15


title: WV_KO_5492


title: WV_FX_5514

value: Floxed


title: LPS-Etoposide-KU55933 48-4-1 h pf 13_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 13

value: Polysome fraction 13


title: H3K27me3_Proliferating_ChIP-seq

description: chip antibody: H3K27me3 (Abcam_ab6002)

data_processing:
Sequencing reads were mapped to the mouse genome build mm9 using Bowtie, allowing for 3 mismatches and reporting the single best alignment per 50bp read. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end, and converted to bedgraph format using the bedtools2 package.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated with the bedtools2 package for ChIP-seq datasets and represent coverage depth of sequencing over the genome.

extract_protocol:
Cells were crosslinked in formaldehyde and sonicated with a Bioruptor (Diagenode). DNA was precipitated with the appropriate antibody and sent for sequencing to the McGill University Genome Quebec Innovation Centre using Illumina HiSeq 2000 platform.
Genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.


title: WV_FX_5503


title: H3K27ac_24H-Ctl_ChIP-seq

description: chip antibody: H3K27ac (Abcam_ab4729)


title: LPS-Etoposide-KU55933 48-4-1 h pf 12_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 12

value: Polysomes

value: Polysome fraction 12


title: WV_FX_5497


title: WV_FX_5415


title: LPS-Etoposide-KU55933 48-4-1 h pf 10_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 10


title: LPS-Etoposide-KU55933 48-4-1 h pf 11_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 11


title: H3K18ac_24H-Ctl_ChIP-seq

description: chip antibody: H3K18ac (Abcam_ab1191)

source_name: C2C12 myoblasts


title: H3K18ac_24H-Bex_ChIP-seq

description: chip antibody: H3K18ac (Abcam_ab1191)


title: LPS-Etoposide-KU55933 48-4-1 h pf 9_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 9

value: Polysome fraction 9


title: H3K27ac_24H-Bex_ChIP-seq

description: chip antibody: H3K27ac (Abcam_ab4729)


title: BAT_KO_5494

source_name: Brown adipose tissue

value: Brown adipose tissue


title: H3K27ac_Proliferating_ChIP-seq

description: chip antibody: H3K27ac (Abcam_ab4729)


title: WV_FX_5413


title: Proliferating_RNA-seq_replicate 1


title: BAT_KO_5492


title: LPS-Etoposide-KU55933 48-4-1 h pf 7_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 7

value: Polysome fraction 7


title: LPS-Etoposide-KU55933 48-4-1 h pf 6_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 6

value: Polysome fraction 6


title: H3K9ac_24H-Bex_ChIP-seq

description: chip antibody: H3K9ac (Abcam_ab4441)


title: BAT_KO_3

value: BATI4 KO


title: H3K9ac_24H-Ctl_ChIP-seq

description: chip antibody: H3K9ac (Abcam_ab4441)


title: LPS-Etoposide-KU55933 48-4-1 h pf 14_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 14

value: Polysome fraction 14


title: LPS-Etoposide-KU55933 48-4-1 h pf 5_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 5

value: Polysome fraction 5


title: BAT_KO_5414


title: BAT_KO_2


title: H3K9ac_Proliferating_ChIP-seq

description: chip antibody: H3K9ac (Abcam_ab4441)


title: BAT_KO_1


title: H4K8ac_24H-Bex_ChIP-seq

description: chip antibody: H3K8ac (Abcam_ab15823)


title: H4K8ac_24H-Ctl_ChIP-seq

description: chip antibody: H3K8ac (Abcam_ab15823)


title: BAT_FX_5503


title: H4K8ac_Proliferating_ChIP-seq

description: chip antibody: H3K8ac (Abcam_ab15823)


title: LPS-Etoposide 48-4 h pf 16_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 16

value: LPS (48 hours) + Etoposide (4 hours)


title: BAT_FX_5497


title: Input_histone marks_ChIP-seq


title: LPS-Etoposide-KU55933 48-4-1 h pf 8_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 8

value: primary, splenic B cells

value: Polysome fraction 8


title: BAT_FX_2


title: BAT_FX_3


title: LPS-Etoposide 48-4 h pf 14_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 14


title: BAT_FX_1


title: H3K18ac_Proliferating_ChIP-seq

description: chip antibody: H3K18ac (Abcam_ab1191)


title: LPS-Etoposide 48-4 h pf 12_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 12


title: 2i_LG1_rep2

source_name: 2i ESCs

value: Embryonic Stem cell

value: Late G1-phase


title: LPS-Etoposide 48-4 h pf 9_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 9


title: Serum_LG1_rep2

source_name: Serum ESCs

value: Serum


title: LPS-Etoposide 48-4 h pf 11_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 11

value: Polysome fraction 11


title: gDNA_iPS

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bwa.
Genome_build: mm9
Supplementary_files_format_and_content: # reads per chromosome per sample. No other processed data available. The data of the TNGA sample is public already and has been referred to in the manuscript.

growth_protocol: Mouse ESCs were fully adapted to serum conditions.

value: iPS  cells


title: gDNA_EB5


title: LPS-Etoposide 48-4 h pf 7_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 7

value: Polysomes


title: gDNA_E14


title: LPS-Etoposide-KU55933 48-4-1 h pf 4_Replicate 1

source_name: LPS-Etoposide-KU55933 48-4-1 h pf 4

value: LPS (47 hours) + KU59933 (1 hour) + Etoposide (4 hours)

value: Polysome fraction 4


title: LPS-Etoposide 48-4 h pf 10_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 10

value: Polysome fraction 10


title: ChIP_2i-E2f1-Rep2

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (http://code.google.com/p/phantompeakqual-tools/). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the three studied histone marks at p-value of 1e-8 and peak-coverage was determined by bedtools multicov.
Genome_build: mm9

tag: chip antibody


title: LPS-Etoposide 48-4 h pf 6_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 6


title: LPS-Etoposide 48-4 h pf 5_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 5


title: LPS-Etoposide 48-4 h pf 15_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 15

value: Polysome fraction 15


title: LPS-Etoposide 48-4 h pf 13_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 13

value: Polysome fraction 13


title: ChIP_2i-E2f1-Rep1


title: LPS 48h pf 16_Replicate 1

source_name: LPS 48h pf 16

value: LPS (48 hours)

value: Polysome fraction 16


title: ChIP_Serum-E2f1-Rep1


title: LPS-Etoposide 48-4 h pf 4_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 4


title: ChIP_Serum-E2f1-Rep2


title: LPS 48h pf 14_Replicate 1

source_name: LPS 48h pf 14

value: Polysome fraction 14


title: LPS 48h pf 15_Replicate 1

source_name: LPS 48h pf 15


title: LPS 48h pf 13_Replicate 1

source_name: LPS 48h pf 13


title: LPS 48h pf 12_Replicate 1

source_name: LPS 48h pf 12

value: Polysome fraction 12


title: LPS 48h pf 11_Replicate 1

source_name: LPS 48h pf 11

value: primary, splenic B cells


title: HL-48 and HL-58 Xylose Rep4

city: Richland

first: Ryan

middle: Scott

last: McClure

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T24

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD  sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters
Counts were then determined for each gene in either Halomonas sp. HL-48 and Marinobacter sp. HL-58 using SOLiD LifeScope software version 2.5 using the default parameters
Normalized expression values and differentially expressed genes were then determined using DESeq2
Genome_build: Nucleotide sequence is available through the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under accessions GCA_000686925.1 (Halomonas sp. HL-48) and GCA_000686085.1 (Marinobacter sp. HL-58), and annotated genome data is available through IMG (http://img.jgi.doe.gov).
Supplementary_files_format_and_content: HL48_Norm_Exp_Values.csv (Normalized expression values for HL-48), HL58_Norm_Exp_Values.csv (Normalized expression values for HL-58)

organism:
Halomonas sp. HL48
Halomonas sp. HL58

source_name: Halomonas sp. HL-48 and Halomonas sp. HL-58

growth_protocol: These strains were grown under both axenic and co-culture conditions in a defined media named Hot Lake Heterotrophic (HLH) medium: 400 mM MgSO4·7H2O, 80 mM Na2SO4, 20 mM KCl, 0.189 mM Na2CO3, 0.175 mM K2HPO4, 5 mM NH4Cl, 10 mM TES, 22.3 µM NH4Fe(III) citrate, 10 mM NaHCO3. HLH was amended with 1× Wolfe's vitamins 21 and with either glucose or xylose (to 5 mM) as the sole carbon source

extract_protocol:
RNA was extracted using Trizol following by DNAseI treatment using Qiagen RNAseay mini column
Template cDNA was prepared using the Applied Biosystems SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) according to manufacturer's protocol. Sequencing was carried using the SOLiDTM 5500XL protocol (Life Technologies).

treatment_protocol: Strains were grown either axenically or in co-culture with glucose, in co-culture with xylose or axenically with xylose (Halomonas sp. HL-48 only).

tag: carbon source

value: Growth on xylose

tag: growth condition

value: Co-culture


title: LPS-Etoposide 48-4 h pf 8_Replicate 1

source_name: LPS-Etoposide 48-4 h pf 8

value: LPS (48 hours) + Etoposide (4 hours)

value: Polysome fraction 8


title: HL-58 Glucose Rep4

description:
HL58_Norm_Exp_Values.csv
T9

organism: Halomonas sp. HL58

source_name: Halomonas sp. HL-58

value: Growth on glucose

value: Axenic


title: HL-58 Glucose Rep2

description:
HL58_Norm_Exp_Values.csv
T7


title: HL-58 Glucose Rep5

description:
HL58_Norm_Exp_Values.csv
T10


title: HL-58 Glucose Rep1

description:
HL58_Norm_Exp_Values.csv
T6


title: HL-48 and HL-58 Xylose Rep2

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T22


title: HL-48 and HL-58 Xylose Rep3

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T23


title: HL-58 Glucose Rep3

description:
HL58_Norm_Exp_Values.csv
T8


title: HL-48 Xylose Rep4

description:
HL48_Norm_Exp_Values.csv
T19

organism: Halomonas sp. HL48

source_name: Halomonas sp. HL-48


title: LPS 48h pf 8_Replicate 1

source_name: LPS 48h pf 8

value: Polysomes


title: LPS 48h pf 9_Replicate 1

source_name: LPS 48h pf 9

value: Polysome fraction 9


title: LPS 48h pf 7_Replicate 1

source_name: LPS 48h pf 7

value: Polysome fraction 7


title: HL-48 and HL-58 Xylose Rep1

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T21


title: LPS 48h pf 6_Replicate 1

source_name: LPS 48h pf 6

value: Polysome fraction 6


title: HL-48 Xylose Rep1

description:
HL48_Norm_Exp_Values.csv
T16


title: HL-48 and HL-58 Glucose Rep5

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T15


title: HL-48 and HL-58 Glucose Rep3

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T13


title: LPS 48h pf 5_Replicate 1

source_name: LPS 48h pf 5

value: Polysome fraction 5


title: HL-48 Glucose Rep4

description:
HL48_Norm_Exp_Values.csv
T5


title: HL-48 and HL-58 Glucose Rep4

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T14


title: HL-48 Glucose Rep3

description:
HL48_Norm_Exp_Values.csv
T4


title: LPS 48h pf 4_Replicate 1

source_name: LPS 48h pf 4

value: Polysome fraction 4


title: HL-48 and HL-58 Glucose Rep2

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T12


title: HL-48 and HL-58 Glucose Rep1

description:
HL48_Norm_Exp_Values.csv and HL48_Norm_Exp_Values.csv
T11


title: LPS 48h pf 10_Replicate 1

source_name: LPS 48h pf 10

value: LPS (48 hours)

value: Polysome fraction 10


title: HL-48 Glucose Rep1

description:
HL48_Norm_Exp_Values.csv
T1


title: RLY9025_replicate 1

status: Public on Sep 12 2017

city: Baltimore

first: Wahid

middle: A

last: Mulla

address: 855 North Wolfe Street

institute: Johns Hopkins University

data_processing:
Reads were aligned to the sacCer3 reference genome using  using bowtie software
Read counts were normalized to chromosome copy number.
The resulting binary alignment/map (BAM) files were sorted and indexed using SAM tools (Li, Handsaker et al. 2009).
Differential gene expression was evaluated using the edgeR library (Robinson, McCarthy et al. 2010),
p-values were adjusted by the Benjamini-Hochberg procedure.
Genome_build: sacCer3
Supplementary_files_format_and_content: edge.R; txt format

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Cells were grown in SC medium for 18 hours at 25°C; cultures were then diluted to a starting OD600 of 0.2 and grown for five to six hours to an OD600 of 0.6.

extract_protocol:
RNA samples were prepared from ten OD600 units of the final yeast culture using a standard acid–phenol/chloroform extraction method (Collart and Oliviero 2001), and contaminating gDNA was removed by treating with DNase I (Sigma-Aldrich, Saint Louis, MO).
PolyA-selected, 50 bp single-end RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample prep kit (Illumina, Inc., San Diego, CA), quantified using a Bioanalyzer (Agilent, Santa Clara, CA), and sequenced on an Illumina HiSeq 2000 platform.
PolyA-selected, 50 bp single-end RNA-seq

tag: replicate

value: First

tag: karyotype

value: Aneuploid


title: RLY9025_replicate 3

value: Third


title: HL-48 Glucose Rep2

description:
HL48_Norm_Exp_Values.csv
T2


title: RLY9017_replicate 3

value: Euploid


title: RLY9017_replicate 1


title: IRI28d-R3

city: Los Angeles

first: Jing

last: Liu

state: California

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

description: 28 days post IRI

data_processing:
RNA-seq samples were aligned to mm10 genome assembly with STAR aligner (version 2.5.0b). The mapping index was generated using GENCODE release M4 (GRCm38.p3) gene annotations. In addition to read mapping, STAR was also used to remove duplicates, generate read-count tables and wiggle files. Differentially-expressed genes were called for each time point with DESeq2.
Genome_build: mm10

source_name: adult kidneys, IRI

extract_protocol:
Qiagen Rneasy mini kit
Illumina TruSeq RNA Sample Prep kit v2 protocol was followed with the exception that the final PCR amplification was performed for 12 and not 15 cycles. Libraries were visualized on the Agilent Bioanalzyer and quantified using the Kapa Biosystems Library Quantification Kit according to manufacturer’s instructions.  Libraries were applied to an Illumina flow cell at a concentration of 16 pM on a version 3 flow cell and run on the Illumina HiSeq 2000 as a paired end read for 100 cycles each side.  On average, 3 samples were loaded to each lane of a flow cell.

tag: tissue

value: kidney

tag: surgery

value: IRI

tag: time points

value: 28 days


title: RLY9017_replicate 2

value: Second


title: IRI12m-R2

description: 12 months post IRI

value: 12 months


title: RLY9025_replicate 2


title: IRI28d-R2

description: 28 days post IRI


title: HL-48 Xylose Rep2

description:
HL48_Norm_Exp_Values.csv
T17

value: Growth on xylose

value: Axenic


title: IRI28d-R1

description: 28 days post IRI


title: IRI12m-R1

description: 12 months post IRI


title: IRI14d-R3

description: 14 days post IRI

value: 14 days


title: IRI14d-R2

description: 14 days post IRI


title: IRI14d-R1

description: 14 days post IRI


title: IRI7d-R3

description: 7 days post IRI

value: 7 days


title: IRI7d-R2

description: 7 days post IRI


title: IRI7d-R1

description: 7 days post IRI


title: IRI72h-R2

description: 72 hours post IRI

value: 72 hours


title: IRI72h-R1

description: 72 hours post IRI


title: IRI48h-R3

description: 48 hours post IRI

value: 48 hours


title: IRI72h-R3

description: 72 hours post IRI


title: IRI12m-R3

description: 12 months post IRI


title: IRI48h-R2

description: 48 hours post IRI


title: IRI24h-R3

description: 24 hours post IRI

value: 24 hours


title: IRI24h-R2

description: 24 hours post IRI


title: IRI24h-R1

description: 24 hours post IRI


title: IRI2h-R2

description: 2 hours post IRI

value: 2 hours


title: SHAM12m-R3

description: 12 months post sham surgery

value: sham


title: IRI2h-R3

description: 2 hours post IRI


title: IRI4h-R1

description: 4 hours post IRI

value: 4 hours


title: IRI2h-R1

description: 2 hours post IRI


title: IRI4h-R2

description: 4 hours post IRI


title: SHAM24h-R1

description: 24 hours post sham surgery

source_name: adult kidneys, sham


title: SHAM24h-R3

description: 24 hours post sham surgery


title: SHAM4h-R2

description: 4 hours post sham surgery


title: SHAM12m-R2

description: 12 months post sham surgery


title: SHAM24h-R2

description: 24 hours post sham surgery


title: SHAM4h-R3

description: 4 hours post sham surgery


title: SHAM4h-R1

description: 4 hours post sham surgery


title: IRI6mN-R4

description: 6 months post IRI

value: 6 months


title: IRI6mN-R2

description: 6 months post IRI


title: IRI6mN-R1

description: 6 months post IRI


title: IRI6mN-R3

description: 6 months post IRI


title: NORM15m-R3

description: 15-month old age matched control without surgery

source_name: adult kidneys, uninjured

value: no


title: IRI48h-R1

description: 48 hours post IRI

value: kidney


title: NORM15m-R1


title: NORM9m-R3

description: 9-month old age matched control without surgery


title: NORM9m-R2


title: NORM9m-R1


title: NORM3m-R2

description: 3-month old age matched control without surgery

value: 0 month


title: IRI4h-R3

description: 4 hours post IRI

value: IRI


title: SHAM12m-R1

description: 12 months post sham surgery


title: c7CT_PGCLC_1

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: 3'-RNAseq amplified from 1ng RNA

data_processing:
Adaptor removal, mapping and abundance measurement were performed as described in GSE63266. All SOLiD reads were processed by cutadapt v1.11 with the "-c -e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAA" option. Illuina reads were processed by cutadapt v1.11 with the "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT" option.
Reads with 30 bases and longer were mapped onto mouse mm10 genome and reference genes using  tophat v1.4.1/bowtie 1.0.1 with the "--no-coverage-search" option. Abundance measurement was performed using cufflinks-2.2.0 using the “--compatible-hits-norm”, “--no-length-correction” and “--library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs.
Abundance of ERCC spike-in transcripts were counted separately from bam files produced by tophat.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

source_name: PGC like cells

growth_protocol:
The ESC culture and PGCLC induction were performed as described previously with a few modifications.  ESCs were maintained under a 2i+LIF condition on a dish coated with poly-L-ornithine (0.01%; Sigma) and Laminin (300 ng/ml; BD Biosciences) or on mouse embryonic fibroblasts (MEF).  EpiLCs were induced by plating 1.0 × 105 ESCs on wells of a 12-well plate coated with human plasma fibronectin (16.7 ug/ml; Millipore) in N2B27 medium containing activin A (20 ng/ml; Peprotech), bFGF (12 ng/ml; Life Technology) and KSR (1%; Thermo Fisher).  42-46 hrs after the EpiLC induction, PGCLCs were induced under a floating condition by plating 2.0 × 103 EpiLCs in wells of a low-cell-binding 96-well Lipidure-coat plate (Thermo Fisher) in 200 ml of GK15 medium with BMP4 (500 ng/ml; R&D Systems), LIF (1000 u/ml; Merck Millipore), SCF (100 ng/ml; R&D Systems), and EGF (50 ng/ml; R&D Systems).  The GK15 medium was composed of GMEM (Thermo Fisher) with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin and 2 mM L-glutamine. The PGC/PGCLC culture was performed as described previously.  Briefly, d4 PGCLC aggregates were collected, washed with PBS, and dissociated with TrypLE Express (Thermo Fisher).  They were then washed with DMEM+0.1%BSA (Gibco) and filtered by a cell strainer (BD Bioscience) to remove large clumps of cells.  Next, the samples were centrifuged, resuspended in 0.1% BSA-PBS and sorted by FACS (Aria lll; BD Bioscience).  The BV (+) cells were plated onto mitomycin C (MMC)-treated m220 feeder cells in the PGC/PGCLC-expansion medium.  The PGC/PGCLC-expansion medium was composed of GMEM with 10% KSR, 2.5% FBS, 0.1 mM NEAA, 1 mM sodium pyruvate, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 10 mM Forskolin and 10 mM Rolipram.  The entire medium was changed every 2 days from c3.  The cytokines/chemicals for the induction of the female fate were provided from c3 to the end of the culture.  The concentrations of RA and BMP used were 100 nM and 300 ng/mL, respectively, unless otherwise specified.
To obtain PGCs and male and female germ cells, ICR female mice were mated with Dppa3-EGFP male mice or Ddx4-RFP male mice.

extract_protocol:
Total RNAs from collected cells were extracted with an RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
cDNA synthesis and amplification from isolated RNAs/single cells were perfomed essentially as reported in [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. Library constructions for NextSeq500 (illumina) System were performed according to the procedure described in [Nakamura et.al., Nuceic Acids Res. (2015)] with a few modifications.

treatment_protocol: E9.5 to E13.5 germ cells were sorted as GFP(+) cells by FACS, E14.5 and E15.5 germ cells as RFP(+) cells, d4PGCLCs as BV(+) cells, and cultured PGCLCs as SC(+) cells.

value: germ cells derived from ESCs

value: culture day9


title: HL-48 Xylose Rep3

description:
HL48_Norm_Exp_Values.csv
T18

value: Growth on xylose


title: c0CT_PGCLC_1

description: 3'-RNAseq amplified from 1ng RNA

value: culture day2


title: c0RB_PGCLC_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK3_c9_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK3_c7_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA

value: culture day7


title: c7_PGCLC_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK3_c3_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA

value: culture day3


title: d4c0_PGCLC_1

description: 3'-RNAseq amplified from 1ng RNA

value: culture day0


title: SK1_c7_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA


title: SK1_c9_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA


title: WT_c7_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA

value: Prdm1-mVenusTg/0; Dppa3-ECFPTg/0


title: NORM3m-R3


title: NORM15m-R2

value: 12 months


title: WT_c9_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA


title: SK1_c3_PGCLC_CT_2

description: 3'-RNAseq amplified from 1ng RNA


title: WT_c5_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day5


title: WT_c3_PGCLC_CT_2

description: 3'-RNAseq amplified from 1ng RNA


title: SK2_c9_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK2_c3_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK1_c9_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK1_c7_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK1_c5_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: NORM3m-R1


title: SK1_c3_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA


title: c7RB_PGCLC_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK1_c5_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA


title: SK3_c5_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: WT_c9_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK2_c5_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: SK2_c7_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: WT_c5_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: c9_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA


title: WT_c7_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: c9_PGCLC_RA_2

description: 3'-RNAseq amplified from 1ng RNA


title: c7_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA


title: c5_PGCLC_RA_2

description: 3'-RNAseq amplified from 1ng RNA


title: c7_PGCLC_RA_2

description: 3'-RNAseq amplified from 1ng RNA


title: c5_PGCLC_CT_2

description: 3'-RNAseq amplified from 1ng RNA


title: c5_PGCLC_RB_2

description: 3'-RNAseq amplified from 1ng RNA


title: c3_PGCLC_CT_2

description: 3'-RNAseq amplified from 1ng RNA


title: d4_PGCLC_2

description: 3'-RNAseq amplified from 1ng RNA


title: c9_PGCLC_CT_2

description: 3'-RNAseq amplified from 1ng RNA


title: WT_c3_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA


title: c9_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: c9_PGCLC_RA_1

description: 3'-RNAseq amplified from 1ng RNA


title: c7_PGCLC_RA_1

description: 3'-RNAseq amplified from 1ng RNA


title: c7_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: c9_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA


title: c7_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA


title: c5_PGCLC_RA_1

description: 3'-RNAseq amplified from 1ng RNA


title: c5_PGCLC_RB_1

description: 3'-RNAseq amplified from 1ng RNA


title: c5_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA


title: d4_PGCLC_1

description: 3'-RNAseq amplified from 1ng RNA


title: c7_PGCLC_CT_2

description: 3'-RNAseq amplified from 1ng RNA


title: E15.5_GC_female_2

description: 3'-RNAseq amplified from 1ng RNA

source_name: fetal oocytes

value: germ cells


title: c3_PGCLC_CT_1

description: 3'-RNAseq amplified from 1ng RNA


title: E15.5_GC_male_2

description: 3'-RNAseq amplified from 1ng RNA

source_name: prospermatogonia


title: E14.5_GC_female_2

description: 3'-RNAseq amplified from 1ng RNA


title: E15.5_GC_male_1

description: 3'-RNAseq amplified from 1ng RNA


title: E15.5_GC_female_1

description: 3'-RNAseq amplified from 1ng RNA


title: E14.5_GC_male_2

description: 3'-RNAseq amplified from 1ng RNA


title: E14.5_GC_male_1

description: 3'-RNAseq amplified from 1ng RNA


title: E13.5_PGC_female_2

description: 3'-RNAseq amplified from 1ng RNA

source_name: primordial germ cells


title: E14.5_GC_female_1

description: 3'-RNAseq amplified from 1ng RNA


title: E13.5_PGC_female_1

description: 3'-RNAseq amplified from 1ng RNA


title: E13.5_PGC_male_1

description: 3'-RNAseq amplified from 1ng RNA


title: E12.5_PGC_female_2

description: 3'-RNAseq amplified from 1ng RNA


title: E12.5_PGC_female_1

description: 3'-RNAseq amplified from 1ng RNA


title: E11.5_PGC_1

description: 3'-RNAseq amplified from 1ng RNA


title: E11.5_PGC_2

description: 3'-RNAseq amplified from 1ng RNA


title: E10.5_PGC_2

description: 3'-RNAseq amplified from 1ng RNA


title: E9.5_PGC_1

description: 3'-RNAseq amplified from 1ng RNA


title: E10.5_PGC_1

description: 3'-RNAseq amplified from 1ng RNA


title: E12.5_PGC_male_2

description: 3'-RNAseq amplified from 1ng RNA


title: E9.5_PGC_2

description: 3'-RNAseq amplified from 1ng RNA


title: bulk cell sequencing 3wks-2_1

city: Shanghai

first: shi

last: zhanping

address: 1239 siping road

department: School of Medicine

institute: Tongji University

description:
bulk cell cDNA
3 weeks bulk

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using HISAT2 with parameters -p 8 -dta
Genes expression level is quantified by a software package called Stringtie.
Reads aligned to genes were calculated using featurecounts.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: FPKM(Fragments Per Kilobase Million) for each Sample

source_name: adult neural stem cells

extract_protocol:
SVZ tissue was digested by papain, flow cytometry sorting single cell. Then lysis the single cell and reverse Transcription. cDNA was amplyfied
Libraries were prepared according to DNA Library Prep Kit for Illumina kit from NEB (Cat# E7370S/L)
smart seq2

tag: genetic background

tag: organ

value: mouse brain

value: SVZ


title: bulk cell sequencing 3wks-1_1

description:
bulk cell cDNA
3 weeks bulk


title: single cell sequencing P_24_2

description:
Single cell cDNA
Prom1+, 24 months


title: bulk cell sequencing 18mths-3_1

description:
bulk cell cDNA
18 months bulk


title: bulk cell sequencing 18mths-1_1

description:
bulk cell cDNA
18 months bulk


title: single cell sequencing P_24_1

description:
Single cell cDNA
Prom1+, 24 months


title: bulk cell sequencing 18mths-2_1

description:
bulk cell cDNA
18 months bulk


title: E13.5_PGC_male_2

description: 3'-RNAseq amplified from 1ng RNA

tag: strain


title: single cell sequencing P_1_2

description:
Single cell cDNA
Prom1+, 1 month


title: single cell sequencing P_1_3

description:
Single cell cDNA
Prom1+, 1 month


title: single cell sequencing P_1_1

description:
Single cell cDNA
Prom1+, 1 month


title: single cell sequencing P_24_3

description:
Single cell cDNA
Prom1+, 24 months


title: E12.5_PGC_male_1

description: 3'-RNAseq amplified from 1ng RNA


title: single cell sequencing G_24_3

description:
Single cell cDNA
Gfap+, 24 months


title: single cell sequencing G_24_5

description:
Single cell cDNA
Gfap+, 24 months


title: single cell sequencing G_1_2

description:
Single cell cDNA
Gfap+, 1 month


title: single cell sequencing G_24_4

description:
Single cell cDNA
Gfap+, 24 months


title: single cell sequencing D_24_3

description:
Single cell cDNA
Dlx2+/Dcx+, 24 months


title: single cell sequencing G_1_1

description:
Single cell cDNA
Gfap+, 1 month


title: single cell sequencing D_24_4

description:
Single cell cDNA
Dlx2+/Dcx+, 24 months


title: single cell sequencing G_24_1

description:
Single cell cDNA
Gfap+, 24 months


title: single cell sequencing G_24_2

description:
Single cell cDNA
Gfap+, 24 months


title: single cell sequencing D_1_5

description:
Single cell cDNA
Dlx2+/Dcx+, 1 month


title: single cell sequencing D_1_4

description:
Single cell cDNA
Dlx2+/Dcx+, 1 month


title: single cell sequencing D_1_1

description:
Single cell cDNA
Dlx2+/Dcx+, 1 month


title: single cell sequencing D_24_1

description:
Single cell cDNA
Dlx2+/Dcx+, 24 months


title: single cell sequencing D_24_2

description:
Single cell cDNA
Dlx2+/Dcx+, 24 months


title: bulk cell sequencing 3wks-3_1

description:
bulk cell cDNA
3 weeks bulk


title: single cell sequencing D_1_3

description:
Single cell cDNA
Dlx2+/Dcx+, 1 month


title: single cell sequencing D_1_2

description:
Single cell cDNA
Dlx2+/Dcx+, 1 month


title: 18B_72_plus_14_off

city: Heidelberg

first: Tatsiana

last: Ryl

address: Im Neuenheimer Feld 280

department: Theoretical Systems Biology

country: Germany

institute: German Cancer Research Center

data_processing:
RTA 1.17.21.3
Raw reads were aligned to hg19 genome by STAR (v2.4.0h1)
counts of genes were generated by Htseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with counts for each samples

source_name: cell line

growth_protocol: MYCN-high (without doxycycline) and MCN-low cells (with doxycycline) were grown in RPMI1640 media supplemented with 100 U/ml Penicillin and 10% FCS in 10cm2 dishes.

extract_protocol:
RNA was extracted from 106 cells using RNeasy mini kit (Qiagen) with a separate step for DNAse I digestion (Qiagen). ERCC Spike-in control mix-1 (Life technologies) was added to each sample prior to processing (1 μl of a 1:10 dilution of mix-1). RNA from each sample was processed using the RiboGold kit (Epicentre) to remove rRNA
The rRNA-depleted was used to prepare libraries for sequencing using ScriptSeq Complete Gold Kit low input  (Epicenter).

treatment_protocol: Cells were treated with 0.1µg/ml Doxorubicin for 72 hours. After treatment the medium with DOX was washed out and replaced with a normal growth medium.

tag: time

tag: mycn level

value: mycnLow

tag: treatment


title: 17B_72_plus_14_on

value: mycnHigh


title: 14B_72_plus_8_off


title: 19C_72_plus_14_on


title: 15C_72_plus_8_on


title: 16C_72_plus_8_off