title: Cell__number_92


title: 2013_024_011 [ccRCC]

status: Public on Oct 31 2016

type: SRA

city: Bonnn

first: Jörg

last: Ellinger

state: NRW

address: Sigmund-Freud-Straße 25

department: Urologie

country: Germany

institute: Universitätsklinikum Bonn

description: Gene expression in ccRCC tissue

library_source: transcriptomic

data_processing:
After adapter trimming, reads were collapsed and mapped to the genome using Bowtie (Langmead et al., 2009)
Mapped reads were subsequently annotated to different contaminants (tRNA, rRNA, sn(o)RNA, piRNA, ...) and mature miRNAs using genome annotation data from Ensembl, UCSC and miRBase v20.
Prior to normalization, data were filtered using a cutoff of 4 reads. miRNA expression data were normalized based on the total read count per sample. Read count for each miRNA was divided by the total read count in that sample and multiplied by the median total read count across all samples. After normalization, data were log2-transformed.
The expression level of each miRNA unit is measured by the number of sequenced fragments that map to the transcript and represent count data. This measure is different from gene probe-based methods, such as microarrays or RT-qPCR.
Genome_build: Ensembl, UCSC and miRBase v20
Supplementary_files_format_and_content: abundance measurements; annex_*_phase1_*.txt contains processed data for GSM1891367-74; annex_*_phase2_*.txt contains processed data for GSM1891375-402; A brief description of each file is included in the 'readme.txt'

molecule: total RNA

organism: Homo sapiens

source_name: ccRCC

extract_protocol:
Fresh-frozen tissue samples (approximately 50 mg) were cut on liquid nitrogen and homogenized with Yttrium stabilized Zirkonoxid-Beads (Silibeads, Sigmund-Lindner, Warmensteinach, Germany) using a Precellys24 tissue homogenizer. Total RNA was isolated using the mirVana miRNA Isolation Kit (Ambion, Foster City, CA, USA) according to the manufacturers recommendation. To remove residual DNA fragments, we treated the isolate twice with DNase (DNA-free Kit, Ambion).
Libraries for small RNA sequencing were prepared using the TruSeq small RNA library kit (Illumina) according to the manufacturer’s instructions. 500 ng of total RNA was used as input for RNA adapter ligation, followed by reverse transcription and PCR amplification with bar-coded primers. Small RNA libraries were sequenced on a NextSeq500 (Illumina).

tag: gender

value: male

tag: age (yrs)

tag: tissue type

value: ccRCC

tag: pt-stage

tag: lymph node metastasis

tag: distand metastasis

tag: grading

tag: ajcc stage

tag: tumor size (cm)


title: Cell__number_94

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

institute: German Cancer Research Center (DKFZ)

data_processing:
Basecalls performed using RTA 1.18.64
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL Release 80) using STAR_2.4.2a.
Expression level of each gene was quantified in unites by transcript per million (TPM) and fragments per kilobase of transcript per million fragments mapped (FPKM) using RSEM 1.2.21 with default parameters.To compare expression levels of different genes across samples, we performed an additional TMM (trimmed mean of M-values) normalization on TPM using Trinity9 (http://trinityRNA-seq.github.io/) based on edgeR (abbreviated TMM-TPM). The purpose of this normalization is to account for differences in total cellular RNA production across all cells.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.PCA analysis was performed on cells passed quality control using all genes expressed in more than two cells and with a variance in log2 (TMM-TPM+1) across all single cells greater than 0.5. Subsequently, genes with the highest correlation coefficient with one of the first three or four principal components were identified using dimdesc function in FactoMineR. Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices (TPM value) of each gene in each cells in CSV format

molecule: polyA RNA

organism: Mus musculus

growth_protocol: C57BL/6 male mice used for this experiments were 12 weeks of age. Mice were purchased from Charles River or bred in house at the DKFZ Center for Preclinical Research facility. Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Mice were perfused with 20ml HBSS (Gibco), the pancreas was extracted and adipose tissue removed. Four solutions were prepared, including D solution: 1mg/ml Collagenase Type CLS IV supplemented with 0.25% BSA (Sigma-Aldrich), R solution: 1% BSA dissolved in PBS, C solution: 4% BSA in PBS and I solution: 0.1% BSA in PBS. The tissue was chopped into small pieces and incubated in 10ml of D solution at 37°C for 30 minutes. The digestion product was filtered through a 70μm cell strainer (Islets of Langerhans were thereby removed). 10ml of R solution was pipetted on the cell strainer. A quarter of the filtered cell suspension was gently transferred on top of 6ml C solution to achieve layer separation of the liquids. Acini were spun down at 50g for 2 minutes and washed with C solution and I solution successively. Purified acini were treated with 2ml Accutase (Sigma-Aldrich) for 5min to acquire acinar cell suspension containing single cells and clusters of acinar cells
Single cell RNA seq library preparation protocol was based on the SMART seq2 protocol by Picelli et al., 2014 with following modifications: Acinar cells were isolated as described in the section “Acinar Cell Isolation and Culture” and resuspended in DPBS without Ca2+ and Mg2+ (Beckman Coulter). Cells were collected in a volume of 0.5µl and transferred to a reaction tube containing 4µl of 6M Guanidine-HCl (Sigma-Aldrich) and 0.1% (vol/vol) Triton X-100 (Sigma-Aldrich). The tube was immediately transferred into liquid nitrogen and kept there for the duration of cell collection. Next, 2.2x RNA SPRI beads (Beckman Coulter) was added directly to the lysis buffer and incubated for 5 min at room temperature. The beads were washed twice with 70% Ethanol. Air-dried beads were resuspended in a solution containing 2µl H20, 1 µl oligo-dT primer and 1µl dNTP mix (primer and nucleotides used as in 4). 24 cells contained ERCC Spike-In RNAs (1:10 000 – Mix2, Ambion) Mix in addition to primer and nucleotides. Beads were incubated for 3 min at 72°C and reverse transcription and PCR (19 cycles) were performed as described in Picelli et al., 2014. PCR product was cleaned up using 0.8x DNA SPRI beads (Beckman Coulter) and air dried beads were resuspended in 15µl H2O. Quality of cDNA library was assessed for each cell on a high sensitivity DNA Bioanalyzer chip. Subsequent steps (tagmentation, amplification, multiplexing) were done as previously described in Llorens-Bobadilla et al., 2015

treatment_protocol: All mice used in this study were untreated

tag: strain

tag: cell type

value: acinar

tag: age

tag: tissue

value: pancreas

value: Male


title: Sample_TPM8c

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

country: USA

institute: University of Pennsylvania

description: counts.txt.gz

data_processing:
For bulk samples and those generated with C1 SMARTer, BaseSpace Fastq generation algorithm was used for base calling (Illumina). For aRNA and Nugen Ovation samples,  Casava 1.8.2 was used.
For diluted HBR and UHR samples: Low confidence nucleotides (with Phred score less than 20) were treated as unknown and replaced with Ns. Unknown nucleotides (Ns) at the ends of reads were trimmed. Poly-A and method-specific adapter sequences were trimmed from the 3’ end of reads using in-house software. Reads were aligned to the human reference genome, build hg19, and to ERCC spike-in transcript sequences using STAR (Spliced Transcripts Alignment to a Reference) aligner version 2.4.0. We provided STAR with GENCODE18 annotations to generate a splice-junction loci database for use in alignment. We retained reads that aligned to at least 40% (paired-end) or 60% (single-end) of trimmed length or 30bp, whichever was greater. In addition, we discarded reads with greater than 30% mismatched positions in trimmed length.
For diluted HBR and UHR samples: Uniquely aligned reads were assigned to GENCODE18 gene annotations and to ERCC transcripts using HTSeq and htseq-counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non-empty method.
For bulk HBR and UHR samples: raw sequencing data from all three ribosome-depleted bulk HBR or UHR replicates were pooled resulting in a single sample for each HBR and UHR. Sequencing characteristics of bulk RNA sequencing are relatively well known and we used a model theoretic method to estimate reference gene expression, as implemented in RSEM (RNA-seq by Expectation-Maximization, version 1.2.18, using Bowtie version 1.1.1) strand-specific quantification. Poly-A tails were not added to transcripts. RSEM gene abundances were normalized to transcripts per million (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: [txt.gz] htseq abundance measurements: tab-delimited text files with raw counts
Supplementary_files_format_and_content: [RSEM.gz] RSEM abundance measurements: tab delimited text files including gene abundance estimates as generated by RSEM

source_name: Human Brain Reference

extract_protocol: Illumina TruSeq stranded mRNA, modified to begin with amplified aRNA

tag: amount of starting rna

value: 10 pg

tag: ercc spike-in dilution used

tag: single-cell amplification protocol used

value: aRNA


title: Cell__number_95


title: Cell__number_97


title: Cell__number_93


title: Sample_ERCC_10

description: counts.txt.gz


title: Sample_TPM7c

description: counts.txt.gz


title: 2013_024_006 [non pathological renal tissue]

description: Gene expression in non pathological renal tissue

source_name: non pathological renal tissue

value: non pathological renal tissue

value: CTRL


title: Sample_HBR_10pC

description: counts.txt.gz


title: Cell__number_98


title: Sample_ERCC_6

description: counts.txt.gz


title: Cell__number_99


title: 2013_024_004 [non pathological renal tissue]


title: 2013_024_003 [ccRCC]

description: Gene expression in ccRCC tissue


title: Sample_HBR_10pD

description: counts.txt.gz


title: Sample_HBR_10pA

description: counts.txt.gz


title: 2014_001_011 [ccRCC]

description: Gene expression in ccRCC tissue

value: female


title: 2013_024_002 [non pathological renal tissue]


title: 2013_024_001 [ccRCC]

description: Gene expression in ccRCC tissue


title: 2014_001_008 [non pathological renal tissue]


title: 2014_001_007 [ccRCC]

description: Gene expression in ccRCC tissue


title: dMCs_D2_1

city: Beijing

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

country: China

institute: Peking University School and Hospital of Stomatology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm10
Supplementary_files_format_and_content: TXT files including tau values for each RNA-seq samples, and TPM values are generated for all the samples.

source_name: mouse dental mesenchymal cells

extract_protocol:
Total RNA was extracted using the RNeasy® Mini Kit
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: ICR mouse embyonic dental mesenchymal cells

tag: passage

value: ICR


title: dMCs_D2_2


title: 2013_024_005 [ccRCC]

description: Gene expression in ccRCC tissue

tag: gender


title: dMCs_D1_2


title: 2014_001_004 [non pathological renal tissue]

tag: age (yrs)


title: 2014_001_005 [ccRCC]

description: Gene expression in ccRCC tissue

tag: tissue type


title: dMCs_D1.5_3


title: 2014_001_002 [non pathological renal tissue]

tag: pt-stage


title: 2014_001_003 [ccRCC]

description: Gene expression in ccRCC tissue

tag: lymph node metastasis


title: dMCs_D2_3


title: 2014_001_006 [non pathological renal tissue]

tag: distand metastasis


title: Sample_HBR_10pB

description: counts.txt.gz


title: dMCs_tissue

value: tissue


title: dMCs_D1.5_2


title: dMCs_D1_1


title: dMCs_D0.5_2


title: 2014_001_001 [ccRCC]

description: Gene expression in ccRCC tissue

tag: grading


title: dMCs_D0.5_1


title: UvrY - ChIP-exo

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

institute: University of Florida

library_source: genomic

data_processing:
Library strategy: ChIP-exo
Peconic LLC performed data processing
ChIP-exo reads were aligned using BWA with  default parameters
Peaks were called with GeneTrack 1.0.3 (s=5, e=10)
Peaks on opposing strands were paired with Genetrack (u=0, d=80, b=2, m=mode)
Singleton peaks (standard deviation =0) and peaks without matched peaks on the opposing strand where discarded
Genome_build: NC_000913.3
Genome_build: NC_016856.1
Supplementary_files_format_and_content: Bedgraphs files representing the extracted peak data
Supplementary_files_format_and_content: chromosome chromosomeStartPosition chromosomeStopPosition readCoverage(positive values on + strand, negative on - strand)

molecule: genomic DNA

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

source_name: UvrY (Response regulator of the BarA/UvrY two-component system)

growth_protocol:
E. coli cells were grown in Kornberg medium (1.1% [wt/vol] K2HPO4, 0.85% [wt/vol] KH2PO4, 0.6% [wt/vol] yeast extract containing 0.5% [wt/vol] glucose) to mid-exponential phase (OD600 = ~0.6) at 37C and shaking 250rpm
S. Typhimurium cells were grown in LB (supplemented with 10mM glucose) to mid-exponential phase (OD600 = ~0.6) at 37C and shaking 250rpm

extract_protocol:
E. coli and S. Typhimurium cells (at mid-exponential growth phase) were fixed with formaldehyde (1% final concentration) for  20 min at 30°C with shaking. The crosslinking reaction was then quenched by the addition of glycine (0.33M final concentrationg) for 5 minutes at room temperature with gentle mixing.  Cells where then lysed on ice with lysozyme and sonication.
Samples were used for on-bead enzymatic reactions of the ChIP-exo procedure and Illumina Tru-seq sequencing libraries were construction as described in Rhee and Pugh, 2012

tag: chip antibody

value: Monoclonal anti-FLAG antibody, Murine  IgG

tag: chip antibody manufacturer/lot#

value: Sigma-Aldrich, M8823-1ML, Lot #  SLBD7244V


title: RNA-seq of CD8 T cells from spleen-exhausted_PD-L1-day235

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

data_processing:
Sequenced libraries were aligned to the mm10 reference genome using STAR
Gene expression from RefSeq genes was quantified using Cufflinks and reported as FPKM values
Genome_build: mm10

source_name: Spleen

extract_protocol:
Total RNA from sorted cells was extracted using the Applied Biosystems Arcturus PicoPure RNA isolation kit
Double stranded cDNA was generated using the Clontech SMRT-seq v4 method and was fragmented using the Covaris S220 in microTubes. Indexed Illumina-compatible sequencing libraries were generated from fragmented cDNA using the NEBNext Ultra IImethodology
Libraries were quantified using Kapa Library QC kit for Illumina, pooled, and sequenced on an Illumina NextSeq 500 for 75 cycles (single end)

value: Spleen

value: 6-8 weeks


title: RNA-seq of CD8 T cells from spleen-exhausted_PD-L1-day160


title: dMCs_D0_2

tag: strain


title: RNA-seq of CD8 T cells from spleen-exhausted_untreated-day160


title: dMCs_D0_1

tag: cell type


title: RNA-seq of CD8 T cells from spleen-exhausted_untreated-day235

tag: age


title: dMCs_D1.5_1


title: dMCs_D1_3


title: RNA-seq of CD8 T cells from spleen-exhausted_PD-L1, 4

tag: tissue


title: dMCs_D0_3


title: RNA-seq of CD8 T cells from spleen-exhausted_untreated, 2


title: RNA-seq of CD8 T cells from spleen-exhausted_PD-L1, 3


title: RNA-seq of CD8 T cells from spleen-exhausted_untreated, 3


title: RNA-seq of CD8 T cells from spleen-exhausted_PD-L1, 2


title: RNA-seq of CD8 T cells from spleen-Naïve, 1


title: RNA-seq of CD8 T cells from spleen-exhausted_untreated, 1


title: BMDM_LPS_240 chromatin input

city: New York

first: Steven

middle: Zvi

last: Josefowicz

state: NY

address: 1300 York Ave, Box 69

department: Laboratory of Epigenetics and Immunity

institute: Weill Cornell Medicine

description: crosslinked chromatin (10' 1% PFA)

data_processing:
ChIP-seq data was aigned using bowtie (version 1.0.1) to the mouse mm9 genome reporting only unique reads in the best stratum, with up to 2 mismatches (bowtie -p 8 -S -q -v 2 -m 1 -k 1 --best –strata).
Samtools (version 0.1.19) was used to split mapped and unmapped reads and remove duplicate reads. Mapped files were sorted, duplicate removed, and indexed.
BAM files were converted to BED files using bedtools (vers12ion 2.19.1).
Estimated fragment length was determined by strand cross-correlation analysis using MaSC (version 1.2.1).
TDF files were generated using igvtools (version 2.3.32) with fragments extended to match MaSC predicted fragment length.
Genome_build: mm9
Supplementary_files_format_and_content: TDF files contained tag density data for all ChIPseq samples
RNA-seq reads were aligned to the mouse mm9 reference genome with a mouse transcriptome guide (NCBI37) using Tophat v2.0.11 Reads that mapped to the genome with two or fewer mismatches, and up to a maximum of 20 hits per read were kept.
Transcript abundances were quantified using Cufflinks v2.2.1
LPS-induced transcripts were defined as those with FPKM >= 1 and 5 fold or greater increase in transcript abundance at 60 min after stimulation with LPS. Unexpressed transcripts were defined as those with FPKM = 0
Genome_build: mm9
Supplementary_files_format_and_content: TDF files contained tag density data for all RNAseq reads; isoforms.tracking_fpkm file contains cuffdiff output for all RNAseq datasets with normalized FPKM values.

source_name: Bone marrow derived macrophage- stimulated 240'

growth_protocol: Bone marrow derived macrophages (BMDM) were generated from the in vitro culture of bone marrow precursor cells isolated from the femurs of C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME). Briefly, cells were resuspended at a concentration of 5x105 cells/mL in DMEM (Corning, Union City, CA) supplemented with 10% FBS, 2mM L-glutamine, 100 U/mL penicillin/streptomycin, 0.1 mM Non-essential amino acids, 55 uM b-mercaptoethanol, 5 ng/mL each of IL-3 and CSF-1 (Peprotech, Rocky Hill, NJ). Cells were plated (day 0) in non-treated 6-well, 10 cm, or 15 cm CytoOne tissue culture plates (USA Scientific, Ocala, FL). On day five of culture, media was supplemented with BMDM culture media by 1.5x original plating volume and using 1.5x cytokine concentrations. One day 10 media was replaced (non-adherent cells gently rinsed away) with BMDM culture media free of cytokines. Cells were then harvested 2-4 days following initiation of cytokine-free resting phase of culture. BMDM were assessed for differentiated status and purity (consistently >98% CD11b+F4/80+) upon harvest. BMDM were stimulated with 100 ng/mL S. typhosa LPS (Sigma-Aldrich, St. Louis, MO, Cat. #2387). When possible cells were fixed in situ on plates with 1% formaldehyde solution or Foxp3 Fix/Perm staining buffer (Affymetrix/eBioscience, San Diego, CA, Cat. # 00-5523).

extract_protocol:
Crosslinking ChIP was performed as described in (Lee et al. 2006)1 with slight modifications. Chromatin shearing was performed with a Covaris S2 focused-ultrasonicator using settings (time 20 min, duty cycle 5%, intensity 4, cycles per burst 200, temperature 4C, power mode frequency sweeping, degassing mode continuous). Immunoprecipitation was performed using 15 ug of antibody bound to 100 uL of Dynabead Protein A magnetic beads. DNA purification after immunoprecipitation and decrosslinking was perfomed using the QIAGEN Qiaquick PCR purification kit. RNA was isolated from 1x106 or more BMDM cells using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD) and then samples were prepared as instructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA). H3S28p antibody: MABE13 (Millipore); H3K27ac antibody: Active Motif (39133).
Eluted DNA was used to construct sequencing libraries using the Illumina TruSeq ChIP Sample Prep Kit. 50 cycle, single-end read sequencing was performed with the Illumina HiSeq 2000.
Illumina adapters # 5,8,12,16 were used to 4-plex all samples into groups of 4/sequencing lane.

treatment_protocol: BMDM cells were treated with 100 ng/mL S. typhosa LPS for the indicated time

value: Bone marrow derived macrophage

tag: s. typhosa lps time

tag: small molecule inhibitor treatement

value: input


title: BMDM_LPS_30 chromatin input

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- stimulated 30'


title: BMDM_LPS_60 chromatin input

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- stimulated 60'


title: BMDM_LPS_RMM64_30 chromatin input

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- stimulated 30'/DMSO treated

value: RMM64 5 uM


title: BMDM_LPS_0 chromatin input

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- unstimulated


title: BMDM_LPS_120 chromatin input

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- stimulated 120'


title: BMDM_LPS_SB747651A_0 chromatin input

description: crosslinked chromatin (10' 1% PFA)


title: Exhausted_cells_ATAC-Seq 2

data_processing:
Library strategy: ATAC-Seq
Paired-end reads were mapped to the mm10 reference genome using Bowtie2
Only concordantly mapped pairs were kept for further analysis
Peak calling was performed using MACS v1.4 to identify areas of sequence tag enrichment
BedTools was used to find common intersection between identified peaks (1bp minimum overlap) and to create a merged peak list
ATAC-seq tag enrichment, DNA motif analysis across the merged peak list,and GO term assessment were computed using HOMER (homer.salk.edu)
Genome_build: mm10
Supplementary_files_format_and_content: bed files generated by peak calling

source_name: P14 CD8 Tcells day35 post infection LCMV-Clone13

extract_protocol:
Nuclei were isolated from 50,000-150,000 sorted cells per replicate
Transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 45 minutes at 37oC.Transposed DNA fragments were purified using a Qiagen MinElute Kit, barcoded with dualindexes (Illumina Nextera) and PCR amplified using NEBNext High Fidelity 2x PCR master mix(New England Labs).

tag: infection

tag: time

value: day35 post infection

value: CD8 T cells


title: Exhausted+a-PD-L1_cells_ATAC-Seq 2

source_name: P14 CD8 Tcells day35 post infection LCMV-Clone13+anti-PD-L1

tag: treatment


title: Exhausted+a-PD-L1_cells_ATAC-Seq 1


title: BMDM_LPS_FMK_30 chromatin input

description: crosslinked chromatin (10' 1% PFA)

value: FMK 5 uM


title: BMDM_LPS_FMK_0 chromatin input

description: crosslinked chromatin (10' 1% PFA)


title: Procr-EC

city: Shanghai

first: Qing Cissy

last: Yu

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institute of Biological Sciences

data_processing:
Quality control using Illumina 1.5+
Basecalling usingHCS1.5.15.1+RTA1.13.48+OLB-1.9.4
Map to mouse genome mm10
Alignment: Soap (2.21), no more than 2 mismatches were allowed in the alignment
Differential gene expression analysis using FDR≤0.001 AND |log2Ratio|≥1
Genome_build: mm10
Quantification of gene expression using RPKM algorithm and screening of differentially expressed genes using Poisson distribution model.

source_name: Freshly sorted Procr-expressing mouse mammary vascular endothelial cells

growth_protocol: cells were freshly sorted from mouse mammary gland

extract_protocol:
total RNA from freshly isolated Lin-, CD105+, CD31+, Sca1+, Procr+ and Procr- cells were extracted with Trizol.
 RNA-seq libraries were prepared according to the manufacturer’s instructions (Illumina) and then applied to sequencing on Illumina HiSeq 2000 in BGI-tech, Beijing.
Single reads for each sample were obtained and uniquely mapped to the mm10 mouse genome with around 80% of mapping rate for both samples.

value: Mouse mammary gland endothelium

tag: developmental stage

value: adult virgin 8wk


title: Exhausted_cells_ATAC-Seq 1


title: Memory_cells_ATAC-Seq 2

source_name: P14 CD8 Tcells day33 post infection LCMV-Armstrong

value: LCMV-Armstrong

value: day33 post infection


title: RNA-seq of CD8 T cells from spleen-exhausted_PD-L1, 1


title: RNA-seq of CD8 T cells from spleen-Naïve, 2


title: Memory_cells_ATAC-Seq 1


title: EC

source_name: Freshly sorted non-Procr-expressing mouse mammary vascular endothelial cells

treatment_protocol: cells were freshly sorted from mouse mammary gland


title: BMDM_LPS_240 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_DMSO_30 chromatin input

description: crosslinked chromatin (10' 1% PFA)

value: DMSO (control)


title: BMDM_LPS_RMM64_0 chromatin input

description: crosslinked chromatin (10' 1% PFA)


title: Effector_cells_ATAC-Seq 1

source_name: P14 CD8 Tcells day8 post infection LCMV-Armstrong

value: day8 post infection


title: Naive_cells_ATAC-Seq 2

source_name: Sorted naive T cells

value: naïve


title: BMDM_LPS_120 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_DMSO_0 chromatin input

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- unstimulated/DMSO treated


title: BMDM_LPS_60 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_180 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- stimulated 180'


title: BMDM_LPS_0 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_FMK_0 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_SB747651A_30 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_DMSO_30 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_30 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_SB747651A_30 chromatin input

description: crosslinked chromatin (10' 1% PFA)


title: Naive_cells_ATAC-Seq 1


title: BMDM_LPS_120 chromatin H3K27ac

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_RMM64_0 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_240 chromatin H3K27ac

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_DMSO_0 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_FMK_30 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_0 chromatin H3K27ac

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_SB747651A_0 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_30 chromatin H3K27ac

description: crosslinked chromatin (10' 1% PFA)


title: cbp20 root 4 hour ethylene Small RNAseq, rep2

city: Austin

first: FAN

last: ZHANG

address: 2506 speedway, NMS5.324

institute: The University of Texas at Austin

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie with default parameters
Remove structural RNAs such as tRNA, rRNA, snRNA, and snoRNA. The perfect matched reads between 18-28 nucleotides (nts) in length were selected
Putative precursor sequence was folded using RNAfold from Vienna RNA software package
Using the miRNA annotation information of Arabidopsis thaliana in miRBase 21 (http://www.mirbase.org), all members of miRNA candidate families of the known miRNAs were selected
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include RP18M values for each sample.

organism: Arabidopsis thaliana

source_name: cbp20 root 4 hour ethylene Small RNAseq

growth_protocol: Arabidopsis seeds were dark-grown and treated with air (hydrocarbon-free air (Zero grade air, AirGas)) at 24 ºC for 3 days

extract_protocol:
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the Small RNA Library Kit (NEB #E7330S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

tag: ecotype background

value: Col

tag: genotype/variation

value: cbp20 mutant

tag: treated with

value: ethylene for 4hrs

value: root

tag: molecule subtype

value: small RNA


title: cbp20 root 4 hour ethylene Small RNAseq, rep1


title: BMDM_LPS_C646_60 RNA

description:
RNA
isoforms.fpkm_tracking

value: Bone marrow derived macrophage


title: BMDM_LPS_C646_120 chromatin

description:
RNA
isoforms.fpkm_tracking


title: BMDM_LPS_C646_0 RNA

description:
RNA
isoforms.fpkm_tracking


title: BMDM_LPS_SB747651A_120 RNA

description:
RNA
isoforms.fpkm_tracking


title: Col root 4 hour ethylene Small RNAseq, rep2

source_name: Col root 4 hour ethylene Small RNAseq

value: wild type


title: Col root 4 hour ethylene Small RNAseq, rep1


title: cbp20 root 4 hour air Small RNAseq, rep2

source_name: cbp20 root 4 hour air Small RNAseq

value: air for 4hrs


title: BMDM_LPS_SB747651A_60 RNA

description:
RNA
isoforms.fpkm_tracking


title: BMDM_LPS_SB747651A_0 RNA

description:
RNA
isoforms.fpkm_tracking


title: Col root 4 hour air Small RNAseq, rep2

source_name: Col root 4 hour air Small RNAseq


title: BMDM_LPS_RMM64_120 RNA

description:
RNA
isoforms.fpkm_tracking

value: RMM64 5 uM


title: Col root 4 hour air Small RNAseq, rep1


title: BMDM_LPS_RMM64_30 chromatin H3S28ph

description: crosslinked chromatin (10' 1% PFA)


title: BMDM_LPS_RMM64_60 RNA

description:
RNA
isoforms.fpkm_tracking


title: cbp20 shoot 4 hour ethylene Small RNAseq, rep2

value: shoot


title: cbp20 root 4 hour air Small RNAseq, rep1


title: BMDM_LPS_60 chromatin H3K27ac

description: crosslinked chromatin (10' 1% PFA)

source_name: Bone marrow derived macrophage- stimulated 60'


title: BMDM_LPS_RMM64_0 RNA

description:
RNA
isoforms.fpkm_tracking

source_name: Bone marrow derived macrophage- stimulated 30'/DMSO treated


title: cbp20 shoot 4 hour ethylene Small RNAseq, rep1


title: BMDM_LPS_DMSO_120 RNA

description:
RNA
isoforms.fpkm_tracking


title: cbp20 shoot 4 hour air Small RNAseq, rep2

source_name: cbp20 shoot 4 hour air Small RNAseq


title: BMDM_LPS_DMSO_60 RNA

description:
RNA
isoforms.fpkm_tracking


title: Col shoot 4 hour ethylene Small RNAseq, rep2

source_name: Col shoot 4 hour ethylene Small RNAseq


title: Col shoot 4 hour ethylene Small RNAseq, rep1


title: cbp20 shoot 4 hour air Small RNAseq, rep1


title: Col shoot 4 hour air Small RNAseq, rep2

source_name: Col shoot 4 hour air Small RNAseq


title: Col shoot 4 hour air Small RNAseq, rep1


title: cbp20 root 4 hour ethylene RNAseq, rep2

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using TopHat version 2.0.9 with default parameters
Differential expressed genes were calculated by Cuffdiff version 2.2.1
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, generated by Cuffdiff version 2.2.1

source_name: cbp20 root 4 hour ethylene RNAseq

extract_protocol:
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L)


title: cbp20 root 4 hour ethylene RNAseq, rep1


title: cbp20 root 4 hour air RNAseq, rep1

source_name: cbp20 root 4 hour air RNAseq


title: cbp20 root 4 hour air RNAseq, rep2


title: shCtrl_1_RA_D4

city: Rochester

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
Basecalls performed using CASAVA version
Sequenced reads were trimmed for barcode sequence
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all the samples

source_name: 46c mES cells (N2B27,+RA, day4)

growth_protocol: ESCs  were cultured in N2B27 medium supplemented with 2 mM Glutamax (100 × Life Technology), 0.1 mM 2-mercaptoethanol and with 5nM retinod acid(RA, millipore) for four days.

extract_protocol:
Differentiated ES cells were harvested at day 4. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: embryonic stem cells

value: add 5nM RA in N2B27 medium, day4

tag: cell line


title: shSox21os_1_RA_D4

tag: barcode

value: GTACCTT


title: shPou3f3os_2_RA_D4


title: shPou3f3os_1_RA_D4

value: GATGTCT


title: Col root 4 hour ethylene RNAseq, rep1

source_name: Col root 4 hour ethylene RNAseq


title: shFendrr_1_D5

source_name: CJ9 mES cells (-LIF, day5)

growth_protocol: ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for five days.

extract_protocol:
Differentiated ES cells were harvested at day 5. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: LIF withdrawal, day5

value: CAGATGT


title: shFendrr_2_D5

value: TCACGTT


title: shNr2f1as_1_RA_D4


title: shCtrl_2_Fendrr_D5

value: AGCTCAT


title: Effector_cells_ATAC-Seq 2

source_name: P14 CD8 Tcells day8 post infection LCMV-Armstrong

value: LCMV-Armstrong

value: day8 post infection

value: CD8 T cells


title: shCtrl_1_Fendrr_D5


title: Col root 4 hour air RNAseq, rep1

source_name: Col root 4 hour air RNAseq

value: Col

value: root


title: shNr2f1as_2_RA_D4

value: CTGAAGT


title: BMDM_LPS_DMSO_0 RNA

description:
RNA
isoforms.fpkm_tracking

source_name: Bone marrow derived macrophage- unstimulated/DMSO treated

value: Bone marrow derived macrophage

value: DMSO (control)


title: shCtrl_2_RA_D4


title: cbp20 shoot 4 hour ethylene RNAseq, rep1

source_name: cbp20 shoot 4 hour ethylene RNAseq

value: cbp20 mutant

value: ethylene for 4hrs

value: shoot


title: cbp20 shoot 4 hour ethylene RNAseq, rep2


title: shLhx1os_D6

source_name: CJ9 mES cells (-LIF, day6)

growth_protocol: ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for six days.

extract_protocol:
Differentiated ES cells were harvested at day 6. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: embryonic stem cells

value: LIF withdrawal, day6


title: shEVX1_2_D4

source_name: CJ9 mES cells (-LIF, day4)

growth_protocol: ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for four days.

value: LIF withdrawal, day4


title: shEVX1_1_D4


title: cbp20 shoot 4 hour air RNAseq, rep2

source_name: cbp20 shoot 4 hour air RNAseq

value: air for 4hrs


title: Col root 4 hour ethylene RNAseq, rep2

value: wild type


title: shEvx1as_1_D4

source_name: CJ7 mES cells (-LIF, day4)


title: shEvx1as_2_D4


title: Col root 4 hour air RNAseq, rep2


title: Col shoot 4 hour ethylene RNAseq, rep2

source_name: Col shoot 4 hour ethylene RNAseq


title: Col shoot 4 hour air RNAseq, rep2

source_name: Col shoot 4 hour air RNAseq


title: WT 3 M1lo

status: Public on Oct 30 2016

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Indexed sample libraries were sequenced using the 75 cycle high output kit v2 chemistry for the Illumina NextSeq 500 sequencing instrument
Reads were aligned to the mouse genome by Rsubread version 1.18.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Thymus T Cells

extract_protocol:
Sorted cells were preserved in RNAlater (ThermoFisher Scientific) and frozen at -80°C, then RNA was isolated with RNeasyPlus Mini kit (Qiagen)
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions

tag: mhc class i phenotype

value: Low

tag: genotype

value: Wildtype

tag: mouse

value: Wildtype 3

value: CD69+ MHC I low


title: shCtrl_Evx1as_D4

tag: cell type

tag: strain

value: AGCTCAT


title: WT 2 M1lo

value: Wildtype 2


title: WT 3 M1hi

value: High

value: CD69+ MHC I high


title: WT 2 M1hi


title: WT 1 M1lo

value: Wildtype 1


title: shCtrl_Lhx1os_D6


title: WT 1 M1hi


title: 17806_B-isox_RNA-Seq_Orb2_WT_supernatant_rep6

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

description: B-isoxasole sample

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1.
RNA-seq:
Samples were processed with the RNA-seq Tuxedo pipeline (tophat and cufflinks).
Genome_build: dm3
Supplementary_files_format_and_content: The b-isox RNA-seq data is stored as cufflinks output files on the gene level.

organism: Drosophila melanogaster

source_name: RNAseq b-isox precipitation fly heads

growth_protocol: Semi-defined medium, 25ºC

extract_protocol: B-isoxasole precipitation (Han et al., Cell 2012)

tag: tissue

value: head

value: head extract

value: Orb2 WT-GFP (Kruttner et al., 2012)

tag: experimental procedure

value: RNA-Seq (b-isox)


title: Sharpin 3 M1lo

value: Sharpin

value: Sharpin 3


title: 15766_B-isox_RNA-Seq_Orb2_WT_pellet_rep5

description: B-isoxasole sample


title: 17805_B-isox_RNA-Seq_Orb2_WT_pellet_rep6

description: B-isoxasole sample


title: 15765_B-isox_RNA-Seq_Orb2_WT_supernatant_rep5

description: B-isoxasole sample


title: Sharpin 3 M1hi


title: 21434_B-isox_RNA-Seq_Orb2_WT_supernatant_rep3

description: B-isoxasole sample


title: 21436_B-isox_RNA-Seq_Orb2_WT_supernatant_rep4

description: B-isoxasole sample


title: 21435_B-isox_RNA-Seq_Orb2_WT_pellet_rep3

description: B-isoxasole sample


title: 21437_B-isox_RNA-Seq_Orb2_WT_pellet_rep4

description: B-isoxasole sample


title: Sharpin 2 M1lo

value: Sharpin 2


title: 21433_B-isox_RNA-Seq_Orb2_WT_pellet_rep2

description: B-isoxasole sample


title: shCtrl_EVX1_D4

value: embryonic stem cells

value: LIF withdrawal, day4


title: cbp20 shoot 4 hour air RNAseq, rep1

value: Col

value: cbp20 mutant

value: air for 4hrs

value: shoot


title: Col shoot 4 hour ethylene RNAseq, rep1

value: wild type

value: ethylene for 4hrs


title: Sharpin 1 M1lo

value: Low

value: Sharpin 1

value: CD69+ MHC I low


title: Sharpin 2 M1hi

value: High

value: CD69+ MHC I high


title: Col shoot 4 hour air RNAseq, rep1


title: 21432_B-isox_RNA-Seq_Orb2_WT_supernatant_rep2

description: B-isoxasole sample

value: head

value: head extract

value: Orb2 WT-GFP (Kruttner et al., 2012)

value: RNA-Seq (b-isox)


title: 21431_B-isox_RNA-Seq_Orb2_WT_pellet_rep1

description: B-isoxasole sample


title: Hoil 3 M1lo

value: Hoil

value: Hoil 3


title: 21430_B-isox_RNA-Seq_Orb2_WT_supernatant_rep1

description: B-isoxasole sample


title: Hoil 3 M1hi


title: Hoil 2 M1lo

value: Hoil 2


title: CLIP_Orb2B_WT_ctrl_replicate_4b

description: sequenced strained (https://stockcenter.ucsd.edu)

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1.
RNA-seq:
Reads were mapped to the dm3 genome and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
PAR/iCLIP:
Reads were first processed by a series of filters before the alignment step: (i) remove bases with Phred quality score < 13 from the 3' end, (ii) collapse identical sequences (putative PCR duplicates), (iii) trim off 10bp linker sequences from the 5' end (contains a random 4bp random sequences to sort out PCR duplicates), (iv) remove adapter sequence (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) from the 3' end using cutadapt (Marcel Martin, EMBnet.journal 2011) (v) remove low complexity and N containing reads and (vi) remove reads matching to ribosomal sequences. After these filters, reads that were longer than 15bp were mapped to the dm3 genome using novoalign (-d INDEX -f READS.FA -F FA -t 90 -l 25 -s 1 -o SoftClip -r None). Mapped reads from different replicate sequencing runs (e.g. rep1a, rep1b) were merged. Using an in-house developed pipeline, CLIP binding clusters where called from overlapping reads and scored by the fraction of T>C conversions and their contribution to a single locus. In addition, putative binding sites were predicted using PARalyzer (Corcoran et al., Genome Biol. 2011). Read density profiles were computed from mapped reads and normalized to 1 million mapped reads per library.
Genome_build: dm3
Supplementary_files_format_and_content: Processed RNA-seq data is stored as text files with FlyBase gene identifiers, gene names, and CG numbers and the associated RPKM expression value for each library. For the CLIP libraries, read density profiles normalized to 1 million mapped reads are provided.

source_name: CLIP S2 cells

growth_protocol: 27°C, 5% CO2, Schneider's Drosophila medium + 10% FCS +PenStrep

extract_protocol: iCLIP (König et al., Nat. Struct. Mol. Biol. 2010)

treatment_protocol: 250μM CuSO4, 300 μg/ml hygromycin B, PAR CLIP 4-SU treatment (Hafner et al., Cell 2010)

value: S2 cells


title: CLIP_Orb2B_WT_ctrl_replicate_6


title: CLIP_Orb2B_WT_ctrl_replicate_5


title: Hoil 2 M1hi


title: CLIP_Orb2B_WT_ctrl_replicate_4a


title: CLIP_Orb2B_WT_ctrl_replicate_3


title: CLIP_Orb2B_WT_ctrl_replicate_1


title: Hoil 1 M1hi

value: Hoil 1


title: CLIP_OrbF_WT_ctrl_replicate_2


title: CLIP_Orb2B_Znf


title: CLIP_OrbF_WT_ctrl_replicate_1


title: CLIP_Orb2B_WT_ctrl_replicate_2b


title: CLIP_Orb2B_WT_ctrl_replicate_2a


title: CLIP_OrbF_WT_ctrl_replicate_3


title: Trsp knockout Rep2 (rna-seq)

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

description:
polyA enriched
10689X10

data_processing:
Adapter sequences were trimmed from all sequences using the Hannon laboratory FastX toolkit. Sequences from ribosome profiling and polyA enriched libraries that aligned uniquely to selenoprotein mRNAs, allowing for two mismatches, were identified using bowtie (v. 0.12.8).
RefSeq entries used for selenoprotein gene alignments included, NM_027652.2 Seli, NM_027905 Selo, NM_007860.3 Dio1, NM_013759.2 Msrb1, NM_024439.3, Sels, NM_015762.2 Txnrd1, NM_008160.6 Gpx1, NM_008162.2 Gpx4, NM_009155.3 Sepp1, NM_053102.2 Sep15, NM_013711.3 Txnrd2, NM_019979.2 Selk, NM_001040396.2 Selt, NM_009156.2 Sepw1, NM_009266.3 Sephs2, NM_030677.2 Gpx2, NM_001178058.1 Txnrd3, NM_029100.2 Sepn1, NM_053267.2 Selm, NM_008161.3 Gpx3, NM_001033166.2 Selh, NM_172119.2 Dio3, NM_010050.2 Dio2, NM_175033.3 Selv.
Total mapped reads used to derive RPKM calculations were determined by aligning sequences against RefSeq entries obtained from the UCSC genome browser (mm9) in which all mRNAs derived from the same gene were reduced to a single entry corresponding to the longest isoform.
For RPFs, the 5’ end of RPFs were offset 15 nts to approximate the position of the A-site (See Figure S1). Reads with the A-site mapping to the first and last 15nts of the annotated coding sequence were excluded to avoid bias at the initiation and termination codon.

source_name: Liver

extract_protocol:
Whole livers were isolated from three young adult (5-8 weeks) male mice for each genetic background, Secisbp2 KO, Trsp KO, and matched male littermates carrying wild type alleles. Livers were rapidly frozen in liquid nitrogen and pulverized. For ribosome profiling,~100 mg of tissue were digested with RNase I and monosomes were isolated by centrifugation through 50% sucrose and purification using qiazol and the miRNAeasy kit (Qiagen). For RNA-Seq, pulverized liver was extracted with Qiazol and polyA RNA encriched using the polyA purist Mag kit (Ambion). Ribosome footprints and randomly fragmented mRNA were size selected (20 - 40 nts) on a 15% TBE Urea gel prior to library construction.
Small RNA sequencing libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit (Illumina), according to the manufacturer’s instructions. Libraries were subjected to 50-cycle single-end sequencing on the Illumina HiSeq 2000 Instrument.

value: liver

tag: age

value: 5-8 weeks

value: Alb-Cre; Trspfl/fl


title: CLIP_Orb2B_RRM12


title: Sharpin 1 M1hi

value: Sharpin


title: CLIP_Orb2B_WT_replicate_6


title: Trsp knockout Rep1 (rna-seq)

description:
polyA enriched
10689X9


title: Trsp wild type Rep3 (rna-seq)

description:
polyA enriched
10689X6

value: wild type


title: CLIP_Orb2B_WT_replicate_5


title: CLIP_Orb2B_WT_replicate_7b

treatment_protocol: 250μM CuSO4, 300 μg/ml hygromycin B, PAR CLIP 6-SG treatment (Hafner et al., Cell 2010)


title: CLIP_Orb2B_WT_replicate_7a


title: CLIP_Orb2B_WT_replicate_4a


title: Trsp wild type Rep1 (rna-seq)

description:
polyA enriched
10689X4


title: CLIP_Orb2B_WT_replicate_4b


title: Trsp wild type Rep2 (rna-seq)

description:
polyA enriched
10689X5


title: Hoil 1 M1lo

value: Low

value: CD69+ MHC I low


title: CLIP_Orb2B_WT_replicate_2b


title: Secisbp2 knockout Rep1 (rna-seq)

description:
polyA enriched
10929X3

value: Alb-Cre; Secisbp2fl/fl


title: Cal51

city: Cincinnati

first: Kakajan

last: Komurov

state: Ohio

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
calling was carried out using CASAVA v 1.8
aligned to reference genome(hg19) using MapSplice. Resulting BAM file is sorted by chromosome and translated to transcriptome coordinates using ubu package
reads with zero mapping quality were removed from the transcriptome BAM file. Transcript quantification from the filtered file were done using RSEM
Normalized gene and isoform counts were obtained by dividing raw counts by the 75th percentile and then multiplying by 1000.
Genome_build: hg19
Supplementary_files_format_and_content: excel file contain gene expression data for each sample

source_name: Mammary gland:Breast: pleural effusion

extract_protocol:
Total RNA was extracted from the cells using Tri reagent(Sigma). RNase-free DNase was used to remove all genomic DNA contamination. The RNA was precipitated with Isopropanol, washed with ice cold 75% ethanol and air dried prior to resuspension in 20μl of DEPC-treated water.
Library was prepared using PrepX mRNA Library kit (WaferGen) and Apolllo 324 NGS automatic library prep system.

tag: disease

value: BreastCarcinoma

tag: morphology

value: epithelial

tag: growth protocol

value: RPMI 1640 medium with 10% fetal bovine serum.


title: T47D

source_name: Mammary gland:Breast: derived from metastatic site. pleural effusion

value: Ductal Carcinoma


title: MB453

source_name: Mammary gland:Breast: derived from metastatic site. perecardial effusion

value: Metastatic Carcinoma

value: IMEM medium with 20% fetal bovine serum.


title: CLIP_Orb2B_WT_replicate_2a


title: Secisbp2 wild type Rep2 (rna-seq)

description:
polyA enriched
10610X8


title: Secisbp2 wild type Rep1 (rna-seq)

description:
polyA enriched
10610X6


title: MB415

value: Adenocarcinoma

value: Leibovitz's L-15 medium with 2mM L-glutamine supplemented with 10 mcg/ml insulin and 10 mcg/ml glutathione, 15% fetal bovine serum


title: Trsp knockout Rep2 (ribo-seq)

description:
Rnase 1 resistant
10689X8


title: SKBR3

value: RPMI 1640 medium with 20% fetal bovine serum.


title: CLIP_OrbF_WT_replicate_2

value: S2 cells


title: UACC812

source_name: Mammary gland:Breast

value: Leibovitz's L-15 medium with 2 mM L-glutamine supplemented with 20 ng/ml human EGF and 20% fetal bovine serum.


title: CLIP_OrbF_WT_replicate_4


title: CLIP_OrbF_WT_replicate_1


title: RNAseq_S2_Orb2B_overexpressing_rep2

source_name: mRNAseq S2 cells

extract_protocol: TRIzol (Invitrogen) extraction, DNA-free (Ambion) rDNase I treatment, 2 rounds Dynabeads mRNA purification (Invitrogen), RNA fragmentation, RNeasy column (Qiagen) purification, reverse transcription (Superscript III, Invitrogen) and 2nd strand synthesis, Minielute column (Qiagen) purification, primer ligation, pre-PCR and NGS at CSF NGS Unit (http://csf.ac.at/)

treatment_protocol: 250μM CuSO4, 300 μg/ml hygromycin B


title: RNAseq_S2_Orb2B_overexpressing_rep1


title: Trsp wild type Rep3 (ribo-seq)

description:
Rnase 1 resistant
10689X3

value: liver

value: 5-8 weeks


title: Secisbp2 knockout Rep1 (ribo-seq)

description:
Rnase 1 resistant
10929X1


title: Trsp wild type Rep2 (ribo-seq)

description:
Rnase 1 resistant
10689X2

value: wild type


title: Trsp knockout Rep1 (ribo-seq)

description:
Rnase 1 resistant
10689X7

value: Alb-Cre; Trspfl/fl


title: RNAseq_S2_background_rep2

treatment_protocol: 250μM CuSO4


title: CLIP_OrbF_WT_replicate_3


title: Secisbp2 knockout Rep2 (ribo-seq)

description:
Rnase 1 resistant
10929X2


title: Secisbp2 wild type Rep2 (ribo-seq)

description:
Rnase 1 resistant
10610X4


title: RNAseq_S2_background_rep1


title: Secisbp2 wild type Rep1 (ribo-seq)

description:
Rnase 1 resistant
10610X2


title: CLIP_Orb2B_WT_replicate_3


title: CLIP_Orb2B_WT_replicate_1


title: Trsp wild type Rep1 (ribo-seq)

description:
Rnase 1 resistant
10689X1


title: Secisbp2 knockout Rep2 (rna-seq)

description:
polyA enriched
10929X4


title: rad21_input_3h_rep_1 [re-used]

status: Public on Oct 29 2016

city: La Jolla

first: Ian

last: Quigley

state: CA

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

description: input

data_processing:
RNAseq reads aligned to transcriptome with RNA-STAR (PMID: 23104886)
RNAseq aligned reads counted with eXpress (PMID: 23160280)
RNAseq counts normalized and differential expression tested with DESeq (PMID: 23975260)
RNAseq and ChIPseq reads aligned to genome with bowtie2 (PMID: 22388286)
Peaks called with HOMER (PMID: 20513432) using input as background (input reads from NCBI GEO: GSE78176, It was pooled reads from GSM2068810 through GSM2068815 (i.e., 6 accessions total)).
BigWigs made with HOMER (PMID: 20513432)
Genome_build: Genome: v7.1, http://www.xenbase.org/
Genome_build: Transcriptome: Mayball interim models, http://daudin.icmb.utexas.edu/
Supplementary_files_format_and_content: RNAseq files are output from eXpress
Supplementary_files_format_and_content: ChIPseq files are bed files from HOMER

organism: Xenopus laevis

source_name: epithelial progenitors (animal cap)

growth_protocol: Animal caps (ectoderm) dissected from embryos at stage 10 and cultured in 0.5x MMR. 20 animal caps per condition were used for RNAseq.

extract_protocol:
mRNAs were obtained with proteinase K digestion, phenol chloroform extraction and precipitated with ethanol, treated with DNAse, extracted with phenol chloforom, and precipitated with lithium and again with ethanol. See our manuscript (PMID: 24934224) for a more detailed protocol.  RNAseq libraries were constructed with Illumina Truseq v2 non-stranded mRNA kits.
Chromatin was obtained as in Ma et al. 2014 (PMID: 24934224)
Illumina Truseq v2, poly-a+

treatment_protocol: Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.

tag: harvest time/stage

value: 3h @ 22 deg after mid-11 (stage 18)

tag: injection


title: myb-GFP_input_9h_rep_1 [re-used]

description: input

value: 9h @ 22 deg after mid-11 (stage 18)

value: myb-GFP


title: foxj1-FLAG_input_9h_rep_1 [re-used]

description: input


title: myb-GFP_mcidas_input_9h_rep_1 [re-used]

description: input

value: myb-GFP, mcidas-HGR


title: histone_input_9h_rep_1 [re-used]

description: input


title: histone_input_9h_rep_2 [re-used]

description: input


title: foxn4+mcidas_ChIPseq_rep_1

description: chromatin/gDNA

source_name: animal cap (dissected ectoderm)

value: animal cap (dissected ectoderm)

value: 9h @ 22 deg after mid-11 (st 18)

value: Foxn4-GFP-HGR + Multicilin mRNA


title: foxn4_ChIPseq_rep_1

description: chromatin/gDNA


title: MCIDAS_9h_RNAseq_rep_1 [re-used]

description:
Poly-A mrNA
RNAseq (non-stranded)

source_name: animal cap (ectoderm)

value: animal cap (ectoderm)

value: 9h @ 22 deg  after mid-11 (st 18)

tag: injected mrna

value: MCIDAS-HGR


title: MCIDAS_9h_RNAseq_rep_3 [re-used]

description:
Poly-A mrNA
RNAseq (non-stranded)


title: foxn4_MO_RNAseq_rep_1

description: poly-a+ mRNA

value: Multicilin mRNA + foxn4 morpholino


title: MCIDAS_9h_RNAseq_rep_2 [re-used]

description:
Poly-A mrNA
RNAseq (non-stranded)


title: foxn4_crispr_RNAseq_9h_rep_2

description: poly-a+ mRNA

value: Multicilin mRNA + (cas9 protein + foxn4 gRNA)


title: foxn4_crispr_RNAseq_9h_rep_1

description: poly-a+ mRNA


title: foxj1_crispr_RNAseq_9h_rep_2

description: poly-a+ mRNA

value: Multicilin mRNA + (cas9 protein + foxj1 gRNA)


title: foxj1_crispr_RNAseq_9h_rep_1

description: poly-a+ mRNA


title: IL_6_4

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

description: Sample 61

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to miRBase Version19 using miRDeep2.
The expression of miRNAs in each library was normalized to counts per million reads (CPM) by the following method: CPM = (miRNA reads number / total reads number per library) × 1000000
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Tab-delimited text files include reads number for each Sample

organism: Bos taurus

source_name: Ileum

extract_protocol:
Rumen, mid-jejunum and ileum were collected from cavles, flash frozen on dry ice, and RNA was harvested using mirVana™ miRNA Isolation Kit (Ambion, Carlsbad, CA). Illumina TruSeq Small RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ileum


title: IL_6_3

description: Sample 60


title: IL_6_1

description: Sample 58


title: IL_6_6

description: Sample 63


title: IL_6_2

description: Sample 59


title: IL_6_5

description: Sample 62


title: IL_3_3

description: Sample 54


title: IL_3_5

description: Sample 56


title: IL_3_6

description: Sample 57


title: IL_3_2

description: Sample 53


title: IL_3_1

description: Sample 52


title: IL_1_6

description: Sample 51


title: foxn4_MO_RNAseq_rep_2

description: poly-a+ mRNA


title: IL_1_5

description: Sample 50


title: IL_1_2

description: Sample 47


title: IL_1_4

description: Sample 49


title: IL_1_3

description: Sample 48


title: IL_1_1

description: Sample 46


title: IL_0_3

description: Sample 45

value: 30 min after birth


title: IL_3_4

description: Sample 55


title: MJ_6_2

description: Sample 38

source_name: Mid-jejunum

value: Mid-jejunum


title: IL_0_1

description: Sample 43


title: MJ_3_6

description: Sample 36


title: MJ_6_5

description: Sample 41


title: MJ_6_1

description: Sample 37


title: MJ_6_3

description: Sample 39


title: MJ_3_5

description: Sample 35


title: MJ_3_4

description: Sample 34


title: MJ_6_6

description: Sample 42


title: MJ_1_6

description: Sample 30


title: MJ_1_2

description: Sample 26


title: MJ_3_1

description: Sample 31


title: MJ_1_5

description: Sample 29


title: MJ_1_3

description: Sample 27


title: MJ_1_4

description: Sample 28


title: MJ_3_2

description: Sample 32


title: MJ_3_3

description: Sample 33


title: MJ_1_1

description: Sample 25


title: Macrophage_2DG/1018_rep2

city: Vancouver

first: Erin

last: Gill

state: British Columbia

address: 2259 Lower Mall

institute: University of British Columbia

data_processing:
basecalls and demultiplexing were done using CASAVA
alignment to the human genome was done using Bowtie2 and Tophat2
read count table generation performed using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files containing read counts for each gene

source_name: macrophage

growth_protocol: Venous blood was collected from healthy volunteers into vacutainer tubes containing the anti-coagulant sodium heparin.

extract_protocol:
The Qiagen RNeasy Isolation Kit was used to extract RNA from cell lysates. The RNA concentration, integrity and purity were assessed using the RNA Nano Kit with the Agilent 2100 Bioanalyzer.
Truseq RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Macrophages were pretreated or not with 20mM 2DG for 5 minutes then stimulated or not with 20μg/ml IDR-1018 for four hours.

tag: agent

value: 2-deoxy-d-glucose + IDR-1018

tag: donor

value: macrophage


title: IL_0_2

description: Sample 44


title: MJ_0_3

description: Sample 24


title: Macrophage_2DG/1018_rep3


title: Macrophage_2DG/1018_rep1


title: MJ_6_4

description: Sample 40


title: Macrophage_1018_rep2


title: Macrophage_1018_rep1


title: Macrophage_2DG_rep3


title: Macrophage_2DG_rep2


title: Macrophage_2DG_rep1


title: Macrophage_untreated_rep3

value: untreated


title: RU_6_6

description: Sample 21

source_name: Rumen

value: Rumen


title: RU_6_5

description: Sample 20


title: RU_6_4

description: Sample 19


title: Macrophage_untreated_rep2


title: Macrophage_untreated_rep1


title: RU_6_3

description: Sample 18


title: RNAseq_ES_Cont_1

city: Edinburgh

first: Julie

last: Rodor

address: Western General Hospital

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: processed data file: RNAseq_RBM10_KO_ES_transcript_tpm

data_processing:
iCLIP: sequencing data from the iCLIP experiments were processed as followed using mostly the tools on Galaxy server https://usegalaxy.org/. Taking advantage of the iCLIP specific barcodes, identical reads, corresponding to PCR duplicates, were removed. Sequencing artefacts were discarded. Adapter sequences at the 3’ end were removed from the reads using CLIP tool. Barcode splitter tool attributed reads to each replicates. Reads were mapped to the Mouse July 2007 (NCBI37/mm9) genome data using Bowtie51, allowing only one mismatch in the seed. Only reads with only one genomic hit were kept. As reads come from cDNAs that have been truncated prematurely at the cross-linked nucleotide, we can deduce the cross-linked nucleotide positions that corresponds to the upstream nucleotide on the genome and obtain a number of reads at each position.
RNAseq: Reads mapping and transcript quantification were done using Sailfish (Rapid Alignment-free Quantification of Isoform Abundance) (Patro, Mount, & Kingsford, 2014) using the mm10 annotation of the mouse genome. The TPM (transcripts per million) value for each transcript was obtained.
Genome_build: mm9 (iCLIP) and mm10 (RNAseq)
Supplementary_files_format_and_content: iCLIP processed file: interval.txt file containing the cross-linked nucleotide positions (O based - half open coordinates) with the number of reads observed at each position

growth_protocol: Cells were cultured in gelatin-coated plates in GMEM medium supplemented with 15% FCS, 2mM glutamine, 1mM sodium pyruvate, 100uM non-essential amino acids, 100 µM b-mercaptoethanol, antibiotics and LIF.

extract_protocol:
RNA extractions were performed using RNeasy Mini Kit (Qiagen) with DNAse treatment on column.
The libraries have been obtained using the Truseq Transcriptome kit (polyA transcript enrichment) at the Beijing Genomics Institute (BGI).

tag: cell line

tag: cell line source

value: parental cell line (obtained from BayGenomics)

tag: genotype/variation

value: wild type (control)


title: RNAseq_ES_RBM_KO_1

value: hemizygote RBM10Y/− gene trap ES cells (obtained from Baygenomics)

value: RBM10 KO


title: RNAseq_ES_Cont_2


title: Macrophage_1018_rep3


title: RU_6_2

description: Sample 17


title: MJ_0_2

description: Sample 23


title: RNAseq_ES_RBM_KO_3


title: RNAseq_ES_Cont_3


title: RU_6_1

description: Sample 16


title: RNAseq_md_Cont_3

description: processed data file: RNAseq_RBM10_KO_md_transcript_tpm

growth_protocol: Cells were cultured in medium (DMEM, 10% FCS, 1% penicillin/streptomycin) containing 100 U ml-1 murine -interferon (Peprotech) at 33 °C in an atmosphere containing 5% CO2.

value: Mouse mandibular MEPA (Mouse Embryonic Pharyngeal Arch)

value: 11.5 d.p.c. embryos from CD1 females crossed with a male 'Immortomouse' (Benko et al, 2009).


title: RU_3_6

description: Sample 15


title: RU_3_5

description: Sample 14


title: RNAseq_ES_RBM_KO_2


title: RNAseq_md_Cont_1


title: RU_3_4

description: Sample 13


title: Sample_2B-M1T1_DSTP

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

data_processing:
Primary sequencing data that produced by Illumina Hiseq 2000, called as raw reads were subjected to quality control to determine if resequencing step is needed. After QC, raw reads were filtered into clean reads which were then aligned to reference sequence Streptococcus pyogenes MGAS5005 NC_007297.1 with SOAPaligner/SOAP2 v2.20 [Li. R, Yu,C., LiY et al  Bioinformatics :Doi:10.1093/bioinformatics/btp336.  259(15)1966-1967]. the alignment data were utilized to calculate distribution of reads on reference genes and perform coverage analysis. Upon QC pass, down stream analysis including gene expression, novel transcript prediction and annotation were done. Gene ontology enrichment analysis were used for pathway enrichment analysis. In order to assess the effectiveness of selected mapping tool, the comparative analysis between SOAPAligner/SOAP2 and other popular-alignment tool BOWTIE [Langmead B. et al (2009)genome biology 10:25-34/ http://Bowtie-bio.sourceforge.net/index.shtml].  Because the SOAPaligner/SOAP2 performed better, quantification analysis of gene expression was done with SOAPaligner/SOAP2. For significance of didgital gene expression profile, algorithms as published [ Audic et al (1997) Gemome Res. 7:986-985] was employed. We used FDR< 0.001 [benjamini and Yekutieli(2001)Ann Statistics29:1165-1188] and the absolute value Log2 ratio > 1 as the threshold to judge the significance of gene expression difference. KEGG was used to perform Pathway enrichment analysis. For gene refinement, transcripts reads were assemble by using CUFFLINK software [Roberts et al Bioinformatics: doi:10.1093/bioinformatics. btr355].
Genome_build: NC_007297.1
Supplementary_files_format_and_content: *xls…..DEGS and RPKM, Pvalue and FDR etc

organism: Streptococcus pyogenes

source_name: Late-log phase culture

growth_protocol: All cultures were grown in Todd Hewitt broth supplemented with 0.5% yeast extract. Cultures were grown at 37oC till O.D. reached at 0.8. (wt) mutant (0.65) i.e. till late log phase. The cultures were then centrifuged at 4oC  and washed once with sterile autoclaved PBS. The cells were then resuspended in PBS in the 1/50th of the starting culture volume.

extract_protocol:
Total RNA was extracted using  Norgen RNA isolation kit (canada) as described by the manufacturer's instructions.
The high quality total RNA samples were obtained by DNase treatment. The samples were then sent to BGI Americas. rRNA was removed from the total RNA samples.cDNA was then made using mRNA as template. Short fragments were made by heat treatment and were purified and resolved  with EB buffer for endrepairation and single nucleotide A ( adenine) addition. Short fragments were then connected to adapters. Subsequently, following agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification. All qc steps i.e. for quantification and quality of sample library, ABI bioanalyzer and ABI StepOnePlus realtime PCR system were used. Library were sequenced using IlluminaHiseq 2000.
mRNA-seq transcriptome library was sequenced using Illumina HiSeq2000 sequencer.

treatment_protocol: Using pFW6 vector, the S. pyogenes mutant lacking SP-STP was derived from type M1 strain M1T15448 as described [Agarwal et al (2011) JBC 286:41368-41380]. The washed concentrated bacterial pellet was suspended in  Tris/HCl  buffer pH 7.4 containing phage-lysin and RNase free DNAse to lyse the bacterial cells and digest DNA.

tag: genotype

value: mutant

tag: phosphatase

value: Lacking -SP-PTP


title: RU_3_3

description: Sample 12


title: RNAseq_md_RBM_KO4


title: Sample_2A-M1T1_DSTP

tag: strain


title: MJ_0_1

description: Sample 22

tag: tissue


title: RU_3_2

description: Sample 11


title: sample_1B-M1T1_WT

value: wild-type

value: Intact SP-PTP


title: RU_3_1

description: Sample 10


title: RU_1_6

description: Sample 9


title: RNAseq_md_RBM_KO3


title: RNAseq_md_RBM_KO2


title: sample_1A-M1T1_WT


title: RNAseq_md_RBM_KO1


title: RU_1_5

description: Sample 8


title: RU_1_3

description: Sample 6


title: RU_1_4

description: Sample 7


title: iCLIP_Cont_2

data_processing:
library strategy: iCLIP-seq
iCLIP: sequencing data from the iCLIP experiments were processed as followed using mostly the tools on Galaxy server https://usegalaxy.org/. Taking advantage of the iCLIP specific barcodes, identical reads, corresponding to PCR duplicates, were removed. Sequencing artefacts were discarded. Adapter sequences at the 3’ end were removed from the reads using CLIP tool. Barcode splitter tool attributed reads to each replicates. Reads were mapped to the Mouse July 2007 (NCBI37/mm9) genome data using Bowtie51, allowing only one mismatch in the seed. Only reads with only one genomic hit were kept. As reads come from cDNAs that have been truncated prematurely at the cross-linked nucleotide, we can deduce the cross-linked nucleotide positions that corresponds to the upstream nucleotide on the genome and obtain a number of reads at each position.
RNAseq: Reads mapping and transcript quantification were done using Sailfish (Rapid Alignment-free Quantification of Isoform Abundance) (Patro, Mount, & Kingsford, 2014) using the mm10 annotation of the mouse genome. The TPM (transcripts per million) value for each transcript was obtained.
Genome_build: mm9 (iCLIP) and mm10 (RNAseq)
Supplementary_files_format_and_content: iCLIP processed file: interval.txt file containing the cross-linked nucleotide positions (O based - half open coordinates) with the number of reads observed at each position

extract_protocol: iCLIP experiments were performed following a published protocol (Konig et al, 2011), with minor modifications (Rodor et al, 2016). The immunoprecipitation (IP) step was carried out using an anti-RBM10 antibody (ab72423, Abcam) that recognizes the two isoforms of the murine RBM10 proteins. Four independent experiments of the RBM10 protocol were performed. The four RBM10 iCLIP libraries with different barcodes were pooled together and sequenced on a single lane by single end sequencing 50nt on an Illumina HiSeq 2000 system (BGI). Equivalent volume of the control libraries was sequenced on a different lane.

treatment_protocol: Cells were irradiated once with 400 mJ/cm2 at 254 nm.

tag: clip antibody

value: Rabbit IgG, Millipore 12-370, Lot DAM1795390


title: RU_1_1

description: Sample 4

tag: age


title: RU_1_2

description: Sample 5


title: RU_0_3

description: Sample 3

value: 30 min after birth


title: iCLIP_Cont_4

value: Rabbit IgG, Millipore 12-370, Lot DAM1795392


title: iCLIP_RBM10_4

value: anti-RBM10 (ab72423, Abcam)


title: iCLIP_Cont_1

value: Rabbit IgG, Millipore 12-370, Lot DAM1795389


title: RU_0_1

description: Sample 1


title: RNAseq_md_Cont_2


title: iCLIP_RBM10_1


title: iCLIP_RBM10_2


title: RNAPII_replicate2

status: Public on Oct 28 2016

city: Nijmegen

first: Simon

last: van Heeringen

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

data_processing:
Basecalling and demultiplexing was performed using the default Illumina software.
Reads were mapped to the Xenopus laevis genome (J-Strain v9.1) using bwa mem (version 0.7.10-r789) with default settings. Duplicate reads were marked using bamUtil v1.0.2.
Where applicable (H3K4me3, p300) peaks were called using MACS (version 2.1.0.20140616) relative to the Input track using the options --broad -g 2.3e9 -q 0.001. --buffer-size 1000
Peaks were combined for replicates using bedtools intersect (version v.2.20.1).
Genome_build: J-Strain v9.1 (http://www.xenbase.org)
Supplementary_files_format_and_content: .bed files report peaks

source_name: whole embryo

extract_protocol:
Embryos (n= 35-90) were fixed in 1% formaldehyde for 30 minutes at the indicated developmental stage. Embryos were washed once in 125 mM glycine / 25% Marc's modified Ringer's medium (MMR) and twice in 25% MMR, homogenized on ice in sonication buffer (20 mM Tris•HCl, pH 8/10 mM KCl/1mM EDTA/10% glycerol/5 mM DTT/0.125% Nonidet P-40, and protease inhibitor cocktail (Roche)). Homogenized embryos were sonicated for 20 minutes using a Bioruptor sonicator (Diagenode). Sonicated extract was centrifuged at top speed in a cold table-top centrifuge and supernatants (ChIP extracts) were snap frozen in liquid nitrogen and stored at -20 degree C until used. Prior to assembling the ChIP reaction, the ChIP extract was diluted with IP buffer (50 mM Tris•HCl, pH 8/100 mM NaCl/2mM EDTA/1 mM DTT/1% Nonidet P-40, and protease inhibitor cocktail) and then incubated with 1-5 µg of antibody and 12.5 µl Prot A/G beads (Santa Cruz)  for an overnight  binding reaction on the rotating wheel in the cold room. The beads were sequentially washed, first with ChIP1 buffer (IP buffer plus 0.1% sodium deoxycholate),  then ChIP2 buffer (ChIP1 buffer with 500 mM NaCl final concentration), then ChIP3 buffer (ChIP1 buffer with 250 mM LiCl), then again with ChIP1 buffer, and lastly with TE buffer (10 mM Tris, pH 8/1 mM EDTA). The material was eluted in 1% SDS in 0.1M  sodium bicarbonate. Cross-linking was reversed by adding 16 µl  of 5M NaCl and incubating at 65°C for 4-5 hours. DNA was extracted using the Qiagen QIAquick PCR purification kit. ~ 10 ng input DNA was used  for sample preparation for high-throughput sequencing (according to manufacturer’s protocol).
Libraries were prepared using the Kapa Hyper Prep kit (Kapa Biosystems) according to manufacturer's protocol and sequenced on an Illumina HiSeq 2000 or an Illumina NextSeq.

tag: developmental stage

value: NF stage 10.5

tag: cell type

value: whole embryo

tag: chip antibody

value: RNA polymerase II (Diagenode, catalog# C15200004, lot# #001-11)


title: ST_96_3

city: Tucson

first: Megha

last: Padi

state: AZ

address: 1071 East Lowell St.

department: Molecular and Cellular Biology

institute: University of Arizona

data_processing:
Reads were mapped to a transcriptome index generated from the hg19 human reference genome and the Merkel cell polyomavirus sequence, using Tophat 2.0.4 and Bowtie1 with all default parameters except for the following: --no-novel-juncs --transcriptome-only -p 6.
Log-transformed FPKM (fragments per kilobase of transcript per million mapped reads) were quantified using Cufflinks 1.3.0 and correcting for biases and multi-mapped reads using the following parameters: -q -p 5 -u
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each transcript

source_name: IMR90_MCPyV ST_96

growth_protocol: IMR90 cells were cultured in Dulbecco’s modified eagle medium (DMEM) (Cellgro) supplemented with 1% Pen Strep (GIBCO), 1% Glutamax (GIBCO), 1% non-essential amino acids (GIBCO) and 15% fetal bovine serum (FBS) (Sigma)

extract_protocol:
Total RNA was purified using RNeasy Plus Mini Kit (Qiagen) and mRNA was isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs).
Sequencing libraries were prepared with NEBNext mRNA library Prep Master Mix Set for Illumina (New England BioLabs), passed Qubit, Bioanalyzer and qPCR QC analyses and sequenced on HiSeq 2000 system (Illumina).

treatment_protocol: Dox-inducible IMR90 lines expressing ST or GFP were seeded in 6 cm dishes 24 hours before initiation of timecourse with dox-containing DMEM. Cells were harvested every 8 hours for 96 hours. IMR90 cells were re-fed after 48 hours with dox-containing media.

value: lung embryonic fibroblast

tag: time (hrs)

tag: vector

value: MCPyV ST


title: iCLIP_Cont_3

value: Rabbit IgG, Millipore 12-370, Lot DAM1795391


title: ST_96_1


title: ST_80_3

source_name: IMR90_MCPyV ST_80


title: ST_88_1

source_name: IMR90_MCPyV ST_88


title: ST_96_2


title: ST_88_2


title: ST_88_3


title: iCLIP_RBM10_3

value: Mouse mandibular MEPA (Mouse Embryonic Pharyngeal Arch)


title: RU_0_2

description: Sample 2

value: Rumen


title: ST_80_2


title: ST_80_1


title: ST_72_1

source_name: IMR90_MCPyV ST_72


title: ST_64_1

source_name: IMR90_MCPyV ST_64


title: ST_72_3


title: ST_64_2


title: ST_64_3


title: ST_72_2


title: ST_56_2

source_name: IMR90_MCPyV ST_56


title: ST_56_1


title: ST_40_3

source_name: IMR90_MCPyV ST_40


title: ST_48_2

source_name: IMR90_MCPyV ST_48


title: ST_40_1


title: ST_48_3


title: ST_48_1


title: ST_40_2


title: ST_32_3

source_name: IMR90_MCPyV ST_32


title: ST_32_1


title: ST_24_3

source_name: IMR90_MCPyV ST_24


title: ST_24_2


title: ST_56_3


title: ST_24_1


title: ST_16_2

source_name: IMR90_MCPyV ST_16


title: ST_16_3


title: ST_16_1


title: GFP_88_3

value: GFP


title: ST_0_2

source_name: IMR90_MCPyV ST_0


title: ST_8_2

source_name: IMR90_MCPyV ST_8


title: ST_8_3


title: GFP_88_1


title: ST_0_3


title: ST_0_1


title: GFP_88_2


title: ST_32_2


title: GFP_96_2


title: GFP_96_1


title: GFP_64_1


title: GFP_80_2


title: GFP_72_3


title: GFP_64_2


title: GFP_72_1


title: GFP_72_2


title: GFP_80_3


title: GFP_64_3


title: GFP_80_1


title: GFP_56_3


title: ST_8_1


title: GFP_56_2


title: GFP_56_1


title: GFP_96_3


title: GFP_48_3


title: GFP_48_1


title: GFP_40_1


title: GFP_32_3


title: GFP_32_1


title: GFP_16_1


title: GFP_16_3


title: GFP_24_1


title: GFP_24_2


title: GFP_16_2


title: GFP_24_3


title: VCaP input 2

city: Bloomington

first: Vivekananda

last: Kedage

state: IN

address: 1001 E. third Street

institute: Indiana University

description: Vertebral-Cancer of the Prostate (VCaP)

data_processing:
Casava1.8.2 software was used for basecalling
Reads were aligned to Homo Sapien Genome (UCSC Hg19) uisng Bowtie2 (v0.12.8)
Peaks were called using Useq program (v8.4.0)
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab delimited text files with chromosome:start-end

source_name: VCaP Prostate cancer cell line

growth_protocol: VCaP cells were grown in DMEM media (Mediatech-cellgro) with 10%FBS and 1% penicillin/streptomycin

extract_protocol:
ChIP DNA was extracted as described in Hollenhorst et al., Genes and Dev. 2011
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol. ChIP DNA's were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

value: VCaP

value: prostate cancer

tag: antibody


title: VCaP input 1

description: Vertebral-Cancer of the Prostate (VCaP)


title: ERG ChIP-Seq

description: Vertebral-Cancer of the Prostate (VCaP)

value: Anti-ERG Clone 9FY Biocare # CM421 C


title: GFP_8_3


title: GFP_0_1


title: GFP_8_2


title: GFP_8_1


title: GFP_0_2


title: GFP_0_3


title: GFP_32_2


title: GFP_40_2


title: GFP_48_2


title: EX2

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
The small RNAs sequencing reads with good quality were subjected to 3’ adaptor sequence trimming by sRNAbench.
The miRNA expression (RPM) were caculated by: miRNA reads number/total mapped reads per library
Genome_build: Baylor Btau 4.6.1
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

source_name: exosomes

extract_protocol:
Sera were stored at -80°C, and the sera and exosomes RNAs were extracted using two commonly used commercial kits (Norgen and Invitrogen total RNA isolation kit), respectively. Illumina TruSeq samll RNA Sample Prep Kit (Cat#RS-200-0012) was used with 5 ul of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

tag: extracellular component

value: exosomes


title: SE4

source_name: Serum

value: Serum


title: EX3


title: SE2


title: EX4


title: SE3


title: GFP_40_3


title: SFB#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Data was separated by barcode and aligned using Tophat version 2.0.10 with default settings.
Transcripts were quantified using the Cufflinks suite version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: SI-LP

extract_protocol:
Cells were sorted into TCL buffer (Qiagen #1031576) + 2-Mercaptoethanol (Sigma-Aldrich# M6250) and then processed according to the Smart-Seq2 protocol by the Broad Technology Labs
The Smart-Seq2 protocol was performed by the Broad Technology Labs

treatment_protocol: Germ-free mice were left unmanipulated or colonized with different bacterial species for 2 weeks prior to sacrifice

value: CD4+ T cells

tag: bacterial species

value: SFB

value: 6 weeks

tag: Sex

value: Male

tag: phenotype markers

value: CD4+ TCRb+ CD45+ DAPI-


title: SFB#1


title: SE1


title: Nexabiotic#2

value: Nexabiotic


title: Germfree#3

value: Germ-free


title: Nexabiotic#1


title: Germfree#2


title: Badolescentis#4

value: B. adolescentis L2-32


title: Germfree#1


title: EX1


title: Badolescentis#1


title: Aire+/+ Lung Tgd17 #1

source_name: Lung

treatment_protocol: Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45+ TCRb- TCRgd+ CD27- Vg1,2,4,5-

value: Aire+/+

value: 10 weeks old

value: Female

value: gd T cells

tag: sorting markers


title: Badolescentis#2


title: Aire-/- Lung Tgd17 #2

tag: genotype

value: Aire-/-


title: KO Hepatoblastoma rep1

city: Pittsburgh

first: Edward

middle: V

last: Prochownik

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

data_processing:
Raw sequencing reads were quality checked for potential sequencing issues and contaminants using FastQC (Babraham Bioinformatics, Inc, Cambridge, UK.). Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and PRINSEQ (http://prinseq.sourceforge. net/manual.html). Reads with a remaining length of less than 20 bp after trimming were discarded. Paired end reads were mapped to the mouse genome (m10) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) in a strand specific manner. Read coverage on forward and reverse strands for genome browser visualization was computed using SAMtools, BEDtools, and UCSC Genome Browser utilities. Pairwise differential expression was quantified using Cuffdiff and DESeq [4, 5]. Cufflinks was used to determine FPKM levels for each gene from the TopHat alignment and was used as input for Cuffdiff. Significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05. DESeq was utilized
for raw read counts, which were calculated by HTSeq based on the TopHat alignment (http://www-huber.embl.de/users /anders/HTSeq/doc/count.html). Read counts were then normalized across all samples and significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Hepatoblastoma Tumor

extract_protocol:
Total RNAs were extracted using Qiagen RNeasy columns (Valencia, CA). Each RNA sample was assessed for quality and quantity using a Qubit 2.0 fluorometer and Agilent Bioanalyzer TapeStation 2200. The Sample preparation was replicated using Illumina TruSeq Stranded mRNA kit (San Diego, CA). mRNA was used to generate poly-A+ libraries using oligo-dT beads following 2 rounds of poly-A selection.
mRNA was fragmented to an average length of 260 nt by magnesium-catalyzed hydrolysis at 940C and then converted into cDNA by random priming. cDNA 3’ ends were adenylated, followed by adaptor ligation and a 9-cycle PCR to enrich DNA fragments. cDNA libraries were then validated using KAPA Biosystems (Wilmington, MA) primer premix kit with Illumina-compatible DNA primers on the Qubit 2.0 fluorometer and Tapestation 2200 systems described above. Libraries were diluted in 0.1% Tween 20 to concentrations of 2 nM for stabilization. The cDNA libraries were then pooled to final concentrations of 2.5 pM.

value: Liver

tag: tumor

value: hepatoblastoma

value: Myc-/-


title: KO Hepatoblastoma rep3

tag: strain


title: Aire-/- Lung Tgd17 #1


title: KO Hepatoblastoma rep5

tag: tissue


title: WT Hepatoblastoma rep5

value: WT


title: WT Hepatoblastoma rep2


title: WT Hepatoblastoma rep1


title: SFB#2

value: CD4+ T cells


title: KO heptatocyte rep3

source_name: hepatocyte

value: hepatocyte


title: KO heptatocyte rep4


title: WT Hepatoblastoma rep4


title: Badolescentis#3

value: 6 weeks


title: Aire+/+ Lung Tgd17 #2


title: KO heptatocyte rep2


title: KO heptatocyte rep1


title: WT hepatocyte rep3


title: WT Hepatoblastoma rep3


title: WT hepatocyte rep2


title: ES_shTet2-2 [small RNA-seq]

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

data_processing:
Adaptors were trimmed using trim_galore! v0.3.3 with the options ‘-q 0 --length 15’.
Trimmed reads were mapped to mm9 using bowtie2 v2.1.0 with default parameters, which reports multi-hit read alignments.
Reads in the size range of 19-32 nt that overlapped full-length (>5 kb) LINE1 elements were extracted and annotated with the respective LINE1.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the following fields: SAM file ‘flag’ denoting a top (0) or bottom (16) strand alignment, read sequence (‘read’), read coordinates (‘chr.read’, ‘start.read’, ‘end.read’), LINE1 coordinates (‘chr’, ‘start’, ‘end’), LINE1 ‘class’, LINE1 orientation (‘strand’).

source_name: ES_shTet2_small RNA-seq

growth_protocol: ESCs were cultured on gelatin-coated plates without feeders, in DMEM-based media (Gibco 10569010) supplemented with 15% fetal bovine serum, pen/strep, nonessential amino-acids, beta-mercaptoethanol and 1,000 U/ml LIF (Millipore).

extract_protocol:
RNA was extracted using either QIAzol (QIAGEN) or the Quick-RNA Midiprep kit (Zymo).
Libraries were prepared using the NEBNext small RNA library prep kit (NEB), followed by size selection (~120-150 bp, including adaptors) using gel extraction.

treatment_protocol: Lentiviral particles containing pLKO.1 shRNA vectors were produced by standard methods in 293T cells. Transduced ES cells were selected with 1 µg/ml puromycin 24 hours post-infection and collected after 3 days of selection.

tag: cell line

tag: strain background

value: embryonic stem (ES) cells

tag: shRNA


title: KO Hepatoblastoma rep4


title: ES_shTet1-2 [small RNA-seq]

source_name: ES_shTet1_small RNA-seq

tag: cell type


title: KO Hepatoblastoma rep2


title: ES_shTet1-1 [small RNA-seq]


title: ES_shScr-1 [small RNA-seq]

source_name: ES_shScr_small RNA-seq

value: shScr


title: ES_shTet2-5

description: processed data file: gene_expression_vsd.txt, repeat_expression_vsd.txt

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.3.3 with default parameters.
Trimmed reads were mapped to mm9 using tophat v2.0.9 with -g 1.
Raw read counts for each gene or repeat (from RepeatMasker annotation) were generated in Seqmonk with the RNA-seq quantitation pipeline. Reads from repeats belonging to the same class were pooled. Normalised gene and repeat expression values were calculated with the variance stabilizing transformation in DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file containing normalised gene or repeat expression values (log2) for each sample.

extract_protocol:
RNA was extracted using either QIAzol (QIAGEN) or the Quick-RNA Midiprep kit (Zymo).
Directional rRNA-depleted RNA-Seq libraries were generated from 400-600 ng of total RNA using the ScriptSeq Complete Gold kit (Epicentre).


title: ES_shTet2-2


title: ES_shTet2-4


title: ES_shTet1-5


title: ES_shTet2-1


title: ES_shTet1-3


title: ES_shTet1-4


title: ES_shTet1-2


title: ES_shTet2-3


title: ES_shTet1-1


title: ES_shScr-4


title: ES_shScr-5


title: ES_shScr-3


title: WT hepatocyte rep4


title: WT hepatocyte rep1


title: ES_shScr-2


title: ES_shTet2-1 [small RNA-seq]


title: PA1_Ctrl_Input_rep2

first: Areum

last: Han

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

description:
polyA+ RNA
RIP1_PA1_RPKM.xls

data_processing:
From the raw reads, we removed adaptor sequences using a Cutadapt tool, allowing some mismatches (The specific parameters we used were -n 2 -e 0.02 -O 15).
Then, the cleaned reads were aligned to the human genome/transcriptome (hg19 and corresponding UCSC gene model) using a TopHat2 software with the following parameters (--library-type=fr-unstranded --min-intron-length=10 --no-coverage-search --microexon-search --min-isoform-fraction=0).
To estimate expression levels for each gene, we counted aligned reads per gene and using a htseq-count tool. And calculated CPM (Counts Per Million) values were converted to RPKM (Reads Per Kilobase per Million mapped reads) values corresponding to gene lengths.
Genome_build: hg19
Supplementary_files_format_and_content: excel, RPKM values of genes after corresponding immunoprecipitation

source_name: PA1 cells

growth_protocol: PA1 cells (ATCC# CRL-1572) were maintained in DMEM/10% FBS.

extract_protocol:
Cells were harvested in cold PBS and immediately lysed in M2 lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing 100 U/ml RNasin (Promega) and 2X protease and phosphatase inhibitors (Pierce). FLAG-tagged LIN28 variants were purified using the anti-FLAG M2 affinity gel following the manufacturer’s specifications (Sigma). Parental PA1 cells (no FLAG) were used as controls for antibody specificity. RNA was isolated from the beads using Trizol (Invitrogen) and RNeasy columns (Qiagen). Purified RNA was subjected to polyA selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were prepared with the NEBNext Ultra RNA Library Prep Kit (NEB).

value: Embryonal carcinoma cells

tag: transgene

tag: rip antibody


title: PA1_S200D_Input_rep3

description:
polyA+ RNA
RIP1_PA1_RPKM.xls

value: FLAG-LIN28 (S200D)


title: PA1_Ctrl_Input_rep3

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_WT_Input_rep3

description:
polyA+ RNA
RIP1_PA1_RPKM.xls

value: FLAG-LIN28 (WT)


title: PA1_S200D_Input_rep1

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_S200D_IP_rep3

description:
polyA+ RNA
RIP1_PA1_RPKM.xls

data_processing:
From the raw reads, we removed adaptor sequences using a Cutadapt tool, allowing some mismatches (The specific parameters we used were -n 2 -e 0.1 -O 15 --quality-base=33).
Then, the cleaned reads were aligned to the human genome/transcriptome (hg19 and corresponding UCSC gene model) using a TopHat2 software with the following parameters (--library-type=fr-firststrand --min-intron-length=10 --no-coverage-search --microexon-search --min-isoform-fraction=0).
To estimate expression levels for each gene, we counted aligned reads per gene and using a htseq-count tool.
And calculated CPM (Counts Per Million) values were converted to RPKM (Reads Per Kilobase per Million mapped reads) values corresponding to gene lengths.
Genome_build: hg19
Supplementary_files_format_and_content: excel, RPKM values of genes after corresponding immunoprecipitation

value: FLAG M2 (Sigma #A2220)


title: PA1_WT_Input_rep1

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_S200D_Input_rep2

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_Ctrl_Input_rep1

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_WT_IP_rep3

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: ES_shScr-2 [small RNA-seq]


title: ES_shScr-1


title: RWPE1_INPUT

data_processing:
Casava1.8.2 software was used for basecalling
Reads were aligned to Homo sapiens Genome (UCSC Hg19) using Bowtie2 (v0.12.8)
Peaks were called using Useq program (v8.4.0)
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab delimited text files with chromosome:start-end

growth_protocol: VCaP cells were grown in DMEM media (Mediatech-cellgro) with 10%FBS and 1% penicillin/streptomycin. RWPE1 cells stably expressing either wild type (WT) or point mutant (P436A) of ERG were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract,  human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)

value: normal prostate


title: PA1_WT_IP_rep1

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_Ctrl_IP_rep2

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_WT_IP_rep2

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_Ctrl_IP_rep1

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: PA1_S200D_IP_rep1

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: EWS-ChIP_VCaP

value: VCaP

value: prostate cancer

value: Anti-EWS clone G5 sc-28327


title: ERG-ChIP_RWPE1-ERG(WT)_Rep1

value: Anti-ERG Clone 9FY Biocare # CM421 C


title: PA1_S200D_IP_rep2

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: ERG-ChIP_RWPE1-ERG(P436A)


title: EWS-ChIP_RWPE1-ERG(WT)


title: RWPE1 ERG-P436A replicate 2

data_processing:
Casava1.8.2 software was used for basecalling
Differential gene expression analysis was carried out with Tuxedo Suite RNA sequencing pipeline (Trapnell et al., Nature Protocol 2012). Sequence reads obtained from illumina sequencer was mapped to the human genome (hg19, UCSC) using Bowtie2. Differential gene expression was determined using Cuffdiff.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: Tab delimited text file of differential gene expression analysis. Output from CuffDiff

source_name: RWPE1 ERG-P436A

growth_protocol: RWPE1 cells were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract,  human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)

extract_protocol:
Total RNA from three biological replicates of RWPE1 cells expressing either vector, ERG-WT, ERG-P436A or ERG-WT with EWS knockdown shRNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol. Total RNA was DNase treated with RNase-Free DNase set (Qiagen) according to manufacturer’s protocol.
polyA containing RNA was purified using oligo(dT) beads (Invitrogen). cDNAs of polyA selected RNA was generated with SuperScript III reverse transcriptase enzyme using random hexamers (Invitrogen). Second strand synthesis from cDNAs was carried out with E. coli DNA ligase and E. coli DNA polymerase I (New England BioLabs). The double-stranded cDNAs were sheared to ~150 nucleotide fragments using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis.Sheared DNA was end-repaired and ligated to indexing primers provided in Truseq sample preparation kit (Illumina). DNA libraries were pooled and sequenced in Illumina NextSeq 500 according to manufacturers protocol.

value: human prostatic epithelial cell line

tag: genotype/variation

value: expressing ERG-P436A


title: EWS-ChIP_RWPE1-ERG(P436A)

tag: antibody


title: PA1_WT_Input_rep2

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: RWPE1 ERG-P436A replicate 3


title: ERG-ChIP_RWPE1-ERG(WT)_Rep2


title: RWPE1 ERG-P436A replicate 1


title: RWPE1 ERG-WT with EWS shRNA replicate 3

source_name: RWPE1 ERG-WT with EWS shRNA

value: expressing ERG-WT with EWS shRNA


title: RWPE1 ERG-WT with EWS shRNA replicate 2


title: RWPE1 ERG-WT replicate 2

source_name: RWPE1 ERG-WT

value: expressing ERG-WT


title: RWPE1 empty vector replicate 1

source_name: RWPE1 empty vector

value: expressing empty vector


title: RWPE1 empty vector replicate 2


title: RWPE1 ERG-WT replicate 3


title: PA1_Ctrl_IP_rep3

description:
polyA+ RNA
RIP1_PA1_RPKM.xls


title: RWPE1 empty vector replicate 3


title: RWPE1 ERG-WT replicate 1