title: DON2531A626


title: DON2531A620

status: Public on Jan 13 2017

type: SRA

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

library_source: transcriptomic

data_processing:
Adapter trimming: RNA-seq reads were trimmed for Nextera and Illumina  adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins
Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92
Read counts: Reads mapping uniquely to genes annotated in ENSEMBL release 75 were counted using featureCounts implemented in subread-v1.5.0
Genome_build: GRCh37
Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: additional_file_2.xlsx:  Contains multiple excel sheets with Sheet1= tpm table (subset for 13873 expressed genes);
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet2= cell metadata with information regarding chip, sequencing batch, imaging, and QC metrics;
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet3= wildtype differential expression;
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet4= knockout differential expression

molecule: total RNA

organism: Homo sapiens

source_name: HUES2 Embryonic stem cell line

growth_protocol:
Macrophages grown on fibronectin coated polaris chip in XVIVO 15 + MCSF + FCS + PS
LPS 100ng/ml in either XVIVO 15 + FCS + MCSF or from previously cultured Macrophages exposed to same batch of LPS

extract_protocol:
FluidigmC1 RNAseq protocol: cDNA was generated using SMARTer Ultra Low RNA Kit (Clontech)
Nextera XT DNA Library Preparation Kit (Illumina); Illumina RNAseq HiSeq4000 75bp PE

tag: cell line

tag: cell type

value: embryonic stem cell derived macrophage

tag: macrophage batch

value: KOD

tag: macrophage samhd1

value: dNTPase knockout

tag: macrophage culture time in hours

tag: macrophage culture media

value: standard media


title: DON2531A619

value: WTG

value: wildtype


title: DON2531A618

value: standard media with LPS


title: DON2531A655


title: DON2531A617


title: DON2531A643

value: KOC


title: DON2531A613

value: conditioned media with LPS


title: DON2531A611


title: DON2531A615

value: conditioned media


title: DON2531A604


title: DON2531A608


title: DON2531A609


title: DON2531A605


title: DON2531A616


title: DON2531A600


title: DON2531A595


title: DON2531A593

value: KOE

value: knockout


title: DON2531A597


title: DON2531A587


title: DON2531A596


title: DON2531A585


title: DON2531A584


title: DON2531A602


title: DON2531A579


title: DON2531A583


title: DON2531A580


title: DON2531A603


title: DON2531A591


title: DON2531A58


title: DON2531A59

value: WTB


title: DON2531A610


title: DON2531A578


title: DON2531A577


title: DON2531A575

value: WTA


title: DON2531A601


title: DON2531A573


title: DON2531A574


title: DON2531A572


title: DON2531A571


title: DON2531A592


title: DON2531A568


title: DON2531A567


title: DON2531A566


title: DON2531A565


title: DON2531A564


title: DON2531A562


title: DON2531A56


title: DON2531A551


title: DON2531A548


title: DON2531A556


title: DON2531A563


title: DON2531A550


title: DON2531A542


title: DON2531A546


title: DON2531A557


title: DON2531A537


title: DON2531A545


title: DON2531A536


title: DON2531A534


title: DON2531A538


title: DON2531A532


title: DON2531A533


title: DON2531A531


title: DON2531A53


title: DON2531A525


title: DON2531A529


title: DON2531A526


title: DON2531A522


title: DON2531A524


title: DON2531A520


title: DON2531A519


title: DON2531A515


title: DON2531A512


title: DON2531A544


title: DON2531A513


title: DON2531A510


title: DON2531A504


title: DON2531A502


title: DON2531A501


title: DON2531A50


title: DON2531A499


title: DON2531A5


title: DON2531A497


title: DON2531A500


title: DON2531A491


title: DON2531A492


title: DON2531A489


title: DON2531A490


title: DON2531A488


title: DON2531A487


title: DON2531A52


title: DON2531A521


title: DON2531A482


title: DON2531A483


title: DON2531A485


title: DON2531A472


title: DON2531A469


title: DON2531A51


title: DON2531A467


title: DON2531A468


title: DON2531A460


title: DON2531A463


title: DON2531A462


title: DON2531A464


title: DON2531A458


title: DON2531A46


title: DON2531A456


title: DON2531A455


title: DON2531A459


title: DON2531A453


title: DON2531A450


title: DON2531A452


title: DON2531A451


title: DON2531A446


title: DON2531A445


title: DON2531A443


title: DON2531A44


title: DON2531A437


title: DON2531A436


title: DON2531A432


title: DON2531A494


title: DON2531A434


title: DON2531A431


title: DON2531A461


title: DON2531A457


title: DON2531A426


title: DON2531A430


title: DON2531A423


title: DON2531A419


title: DON2531A420


title: DON2531A417


title: DON2531A416


title: DON2531A414


title: DON2531A415


title: DON2531A411


title: DON2531A413


title: DON2531A407


title: DON2531A406


title: DON2531A404


title: DON2531A403


title: DON2531A402


title: DON2531A399


title: DON2531A400


title: DON2531A398


title: DON2531A424


title: DON2531A395


title: DON2531A393


title: DON2531A396


title: DON2531A388


title: DON2531A387


title: DON2531A391


title: DON2531A383


title: DON2531A429


title: DON2531A381


title: DON2531A378


title: DON2531A379


title: DON2531A409


title: DON2531A410


title: DON2531A380


title: DON2531A405


title: DON2531A373


title: DON2531A372


title: DON2531A370


title: DON2531A366


title: DON2531A363


title: DON2531A362


title: DON2531A397


title: DON2531A360

value: KOF


title: DON2531A359


title: DON2531A36


title: DON2531A358


title: DON2531A357


title: DON2531A351


title: DON2531A355


title: DON2531A350


title: DON2531A347


title: DON2531A343


title: DON2531A376


title: DON2531A353


title: DON2531A342


title: DON2531A346


title: DON2531A368


title: DON2531A331


title: DON2531A365


title: DON2531A332


title: DON2531A335


title: DON2531A334


title: DON2531A340


title: DON2531A329


title: DON2531A324


title: DON2531A330


title: DON2531A323


title: DON2531A327


title: DON2531A328


title: DON2531A325


title: DON2531A322


title: DON2531A321


title: DON2531A320


title: DON2531A319


title: DON2531A315


title: DON2531A309


title: vitamin D receptor ChIP vitamin D treated

city: St Louis

first: Susana

last: Gonzalo

state: MO

address: 1100 S Grand Blvd

department: Biochemistry and Molecular Biology

country: USA

institute: Saint Louis University

library_source: genomic

data_processing:
Basecalling was performed by Torrent Suite version 4 software using default settings
Aligmentment to the human genome sequence was performed using the TMAP map4 algorithm without soft clipping (-g 3 option)
Aligned bam files for replicate sequencing of each sample were merged, and then separated into individual chromosomes using SAMtools
Genome coverage at each base pair for Input and each ChIP sample was calcluted using BEDtools genomecoveragebed (-d option)
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using custom R scripts as described in Swain et al. submitted. Coverage in each window was normalized to total genome coverage prior to normalization to Input.
Genome_build: hg19
Supplementary_files_format_and_content: sgr text graph files showing ChIP enrichment normalized to input

molecule: genomic DNA

growth_protocol: Normal human primary foreskin fibroblasts (BJ) immortalized with telomerase were grown in culture in complete DMEM-HG media, containing 10% FBS, antibiotic, and antimycotics.

extract_protocol:
BJ cells were grown to 80% confluence, cross-linked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubated for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. We washed cross-linked cells twice with cold phosphate-buffered saline, scraped them and lysed them at a density of 5X106 cells ml-1 for 10 min at 4°C in 1% SDS, 50 mM Tris-HCl (pH 8.0) and 10 mM EDTA containing protease inhibitors. We sonicated lysates to obtain chromatin fragments <1 kb and centrifuged them for 15 min in a microfuge at room temperature. We diluted lysate 1:10 with 1.1% Triton-X100, 2 mM EDTA, 150 mM NaCl and 20 mM Tris-HCl (pH 8.0) containing protease inhibitors, and precleared the lysates with blocked magnetic beads (Dynabeads with protein-G blocked in 1X PBS+0.5% BSA in dilution buffer). We incubated the fragments with 10 μg of VDR antibody or 10 μg of control IgG, together with 80 μl of Dynabeads mix at 4 °C overnight on a rotating platform. Next day, we washed the immunoprecipitates with 0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0) and 150 mM NaCl (one wash); 0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0) and 500 mM NaCl (one wash); 0.25 M LiCl, 1% Nonidet P-40, 1% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0 (one wash); and 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA (two washes). We then eluted the chromatin from the beads twice by incubation with 250 μl 1% SDS and 0.1 M NaHCO3 during 15 min at room temperature with rotation. After adding 20 μl of 5 M NaCl, we reversed the crosslinks for 4 h at 65 °C. Samples were supplemented with 20 μl of 1 M Tris-HCl (pH 6.5), 10 μl of 0.5 M EDTA, 20 μg of RNase A and 40 μg of proteinase K and incubated for 1 h at 45 °C. We recovered DNA by phenol-chloroform extraction and ethanol precipitation. For Input samples, we collected 20 μl of chromatin after sonication, and processed these with the rest of the samples at the point of reverse crosslinking.
Ion Torrent IonXpress barcoded sequencing libraries were constructed using the Ion Xpress Plus Fragment Library Kit (Life Technologies) according to the manufacturer's directions except that size selection was performed using Beckman Agencourt magnetic beads.

treatment_protocol: Vitamin D (1,25D 100 nM) resuspended in FBS was added to BJs growing in culture. FBS alone was added to the control sample. 24 h after initiating treatment, cells were crosslinked, sonicated, and chromatin isolated to perform ChIP analysis as described in Gonzalez-Suarez et al. EMBO J 2009. .

tag: treatment

value: vitamin D treated

value: primary foreskin fibroblasts


title: DON2531A341

value: embryonic stem cell derived macrophage


title: vitamin D receptor ChIP vehicle control

source_name: Normal human primary foreskin fibroblasts (BJ)

value: vehicle treated control


title: DON2531A308


title: input vitamin D treated


title: input vehicle treated control


title: DON2531A301


title: DON2531A302


title: DON2531A304


title: Normal Fibroblasts 1,25D treated

data_processing:
Basecalling and quality filtering was performed by Torrent Suite version 4 software using the default settings
Alignment to human genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The strand specific total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools, custom R code, and Microsoft Excel as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655.
Strand-specific bedgraph files of genome coverage for each sample were generated using BEDTools.
Genome_build: Homo sapiens release hg19
Supplementary_files_format_and_content: File with normalized basepair coverage for annotated genes with > 1000 base pair total coverage in all samples, and non-normalized strand-specific bedgraph files of genome coverage for each individual sample.

growth_protocol: Normal human primary fibroblasts (NF) were grown in culture in complete DMEM-HG media, containing 10% FBS, antibiotic, and antimycotics.

extract_protocol:
NF supplemented with 10-7 M 1,25D (1α,25-dihydroxyvitamin D3; Sigma-Aldrich) or FBS for 24 h using Aurum Total RNA Mini Kit (Bio-Rad) with DNaseI treatment following the manufacturer’s protocol.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total v2 kits (Life Technologies) according to the manufacturer's directions.

treatment_protocol: Vitamin D (1,25D 100 nM) resuspended in FBS was added to NF growing in culture. FBS alone was added to the control sample. 24 h after initiating treatment, cells were collected, and RNA extracted.

tag: 1,25d treatment

value: Vitamin D (1,25D in FBS) treatment for 24 h

value: normal human primary fibroblasts


title: DON2531A300


title: DON2531A296


title: Twist2-pos-2

city: Dallas

first: Stephen

last: Li

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

description: Skeletal muscle was harvested and digested, followed by sorting for tomato positive and negative cells.

data_processing:
Quality assessment of the RNA-Seq data was done using NGS-QC-Toolkit (Patel and Jain, 2012) with default setting
Quality filtered reads generated by the tool were then aligned to the mouse reference genome GRCm38 (mm10) using the Tophat2 (v 2.0.0 ) aligner (Kim et al., 2013) using default setting.
Differential gene expression analysis was done using the R package DESeq2 (v 1.6.3) (Anders and Huber, 2010).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Text file containing differential expression with FDR < 0.05. Expression values are normalized counts per million (column headers without "vs"). Columns with "vs" in the header are the fold-change.

organism: Mus musculus

source_name: freshly sorted cells from hind limb skeletal muscle

extract_protocol:
Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with Tamoxifen every other day for 3 total treatments 10 days prior to skeletal muscle harvesting to turn on tdTO labeling.

tag: tissue

value: Skeletal Muscle

tag: background strain

tag: developmental stage

value: adult

tag: genotype


title: Twist2-pos-1


title: DON2531A298

value: wildtype

value: standard media


title: DON2531A293


title: Twist2-neg-1


title: DON2531A288

value: WTG

value: conditioned media with LPS


title: DON2531A292

value: standard media with LPS


title: Pax7-neg


title: DON2531A285

value: conditioned media


title: Tw2-GM-1

description: Hind limb skeletal muscle was harvested and digested, followed by sorting for tomato positive cells and subsequent plating on matrigel.

source_name: Cultured freshly sorted cells from hind limb skeletal muscle

growth_protocol: Skeletal muscle derived twist2+ myoblasts were plated on matrigel in Ham's F10 media, 20% FBS, and 2% Primocin. Myoblasts were differentiated using DMEM high glucose, 2% Horse Serum, bFGF, and 2% Primocin


title: Tw2-GM-2


title: DON2531A284


title: DON2531A283

value: KOC

value: dNTPase knockout


title: Tw2-48hr-2


title: Tw2-48hr-1


title: DON2531A28

value: KOD


title: DON2531A282


title: Normal Fibroblasts vehicle treated

value: Vehicle (FBS) treatment for 24 h


title: Twist2-neg-2


title: Pax7-48-1


title: Pax7-48-2


title: Tw2-DM

description: Twist2-infected control Tw2 myoblasts 5 days post-differentiation

source_name: cultured twist2+ myoblast from skeletal muscle

growth_protocol: Skeletal muscle derived twist2+ myoblasts were cultured and passaged on matrigel in Ham's F10 media, 20% FBS, and 2% Primocin. Myoblasts were differentiated using DMEM high glucose, 2% Horse Serum, and 2% Primocin

extract_protocol:
Total RNA was extracted from Myoblasts using Trizol Chloroform purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Twist2+ myoblasts were infected with retrovirus for 24 hours followed by 24 hours in growth media. Cells were then either differentiated or harvested for GFP-GM and Tw2-GM RNAseq measurements.

tag: infected


title: DON2531A274


title: DON2531A271


title: DON2531A287


title: Pax7-pos


title: DON2531A267


title: DON2531A270


title: GFP-GM

description: GFP-infected control Tw2 myoblasts pre-differentiation

value: GFP


title: GFP-DM

description: GFP-infected control Tw2 myoblasts 5 days post-differentiation


title: DON2531A265

value: embryonic stem cell derived macrophage


title: DON2531A279


title: DON2531A260

value: KOF

value: knockout


title: DON2531A257


title: DON2531A258


title: DON2531A277


title: DON2531A256


title: Pax7-GM-2


title: Pax7-GM-1


title: DON2531A255


title: DON2531A278


title: DON2531A262


title: DON2531A254

value: WTB


title: DON2531A252


title: Tw2-GM

description: Twist2-infected control Tw2 myoblasts pre-differentiation

value: Skeletal Muscle


title: DON2531A253


title: DON2531A250


title: DON2531A249


title: DON2531A245


title: DON2531A244


title: DON2531A241


title: DON2531A232


title: DON2531A229


title: DON2531A230


title: DON2531A226


title: DON2531A222


title: DON2531A224


title: DON2531A221


title: DON2531A228


title: DON2531A219


title: DON2531A211

value: KOE


title: DON2531A208


title: DON2531A251

value: wildtype


title: DON2531A207

value: WTA


title: DON2531A206


title: DON2531A204


title: DON2531A210

value: standard media


title: DON2531A212


title: DON2531A197


title: DON2531A198


title: DON2531A194


title: DON2531A190


title: DON2531A19


title: DON2531A242


title: DON2531A189


title: DON2531A187


title: DON2531A186


title: DON2531A188


title: DON2531A225

value: conditioned media with LPS


title: DON2531A185


title: DON2531A184


title: DON2531A180

value: standard media with LPS


title: DON2531A182

value: conditioned media


title: DON2531A177


title: DON2531A173


title: DON2531A178


title: DON2531A172


title: DON2531A169


title: DON2531A193


title: DON2531A171


title: DON2531A18


title: DON2531A179


title: DON2531A14

value: KOC


title: DON2531A141


title: DON2531A144

value: dNTPase knockout


title: DON2531A143

value: KOD


title: DON2531A150


title: DON2531A146


title: DON2531A149


title: DON2531A138


title: DON2531A137


title: DON2531A132


title: DON2531A131


title: DON2531A126


title: DON2531A125


title: DON2531A160


title: DON2531A155


title: DON2531A159


title: DON2531A164


title: DON2531A163


title: DON2531A151


title: DON2531A161


title: DON2531A167


title: DON2531A154


title: DON2531A157


title: DON2531A168


title: control endometrial stromal cells of patient 9

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

data_processing:
RTA (Illumina, San Diego, CA, USA) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to FASTQ format, coupled with adaptor trimming
The reads were mapped to the human reference genome (NCBI/build37.2) using Tophat [32] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
The relative expression level of genes was estimate by FPKM (Fragments Per Kilobase of transcript per Million mapped reads) using cufflinks (version 2.0.2) with default settings.
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: Matrix (tab delimited txt file) with FPKMs

source_name: CESC 5

growth_protocol: Primary stromal cells were cultured on fibronectin-collagen (Gibco, Grand Island, NY) coated dishes in DMEM-F12 without phenol red (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine (Gibco) and 1% antibiotics –antimycotic (Gibco) up to passage 3. To exclude influences of the serum derived steroid hormones on DNA methylation and expression in the cultures, the cells were grown in culture medium containing 10% charcoal stripped fetal bovine serum (CS-FBS; Gibco).

extract_protocol:
RNA was isolated using TRIZOL reagent (Invitrogen, MA, USA)
Poly-A pull-down was used to enrich for mRNAs, and libraries were prepared using the Illumina TruSeq RNA kit. Libraries were pooled and sequenced on an Illumina HiSeq2000 machine with 100 bp paired-end reads.

tag: individual

value: patient 9

tag: disease state

value: control

tag: sites

value: Endometrial stroma

value: cell culture of endometrial stromal cells


title: DON2531A152

value: embryonic stem cell derived macrophage


title: DON2531A158

value: WTB


title: DON2531A156


title: DON2531A12


title: DON2531A119


title: DON2531A118


title: DON2531A117


title: DON2531A130


title: control endometrial stromal cells of patient 6

source_name: CESC 2

value: patient 6


title: control endometrial stromal cells of patient 5

source_name: CESC 1

value: patient 5


title: endometriotic stromal cells from ovarian ectopic sites of patient 4

source_name: OESC 4

value: patient 4

value: endometriosis

value: Ectopic endometriotic stroma :ovary

value: cell culture of endometriotic stromal cells


title: control endometrial stromal cells of patient 7

source_name: CESC 3

value: patient 7


title: S2_SV40

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

country: China

institute: Institute of Medical Biology

description:
circRNAs of cae 6 samples _rRNA_SV40_CIRCexplorer.fa
Candicate_lncRNAs of cae 6 samples_rRNA_SV40
mRNAs of cae 6 samples _rRNA_SV40
circRNA.fpkm_expression
Genes.fpkm_expression
lncRNA_Prediction.fpkm_expression

data_processing:
Raw reads of FASTQ files were obtained and assessed for quality using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). The reads containing adapter, ploy-N and low quality reads were removed using Cutadapt (https://pypi.python.org/pypi/cutadapt/1.4.2) [2] to obtain clean reads with high quality.
For circRNA analysis, clean paired-end RNA-seq reads with 150 bp in length of were aligned to the AGM reference genome using Tophat (v2.1.0) (Tophat2, -N 2 -r 50 --library-type fr-firststrand --mate-std-dev20 -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 ) for linear transcripts. For the mapped reads, they were assembled into know and novel linear transcripts using Cufflinks (v2.1.1) (Cufflinks2, -I 40000 --max-bundle-frags 1000000 -p 26 -u -L CUFF). All transcripts were pooled and merged to generate final transcriptome using Cuffmerge (v 2.1.1) (Cuffmerge2, -p 26). In contrast, the unmapped reads were aligned to the AGM reference genome for fusion transcripts using Tophat-Fusion (v2.1.0) (Tophat-Fusion2, -N 2 --library-type fr-firststrand -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 --fusion-search --no-coverage-search --bowtie1). Fusion transcripts from TopHat-Fusion and the transcripts from the assembled linear RNAs were analyzed with circExplorer to identify candidate circRNAs.
For mRNA analysis, the AGM reference transcripts were downloaded from the NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/409/795/GCF_000409795.2_Chlorocebus_sabeus_1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_rna.fna.gz) and served as mRNA annotation reference.
For lncRNA analysis, transcripts that met the following criteria were further analyzed: (1) RNA length ≥200 bp; (2) transcript reads ≥3; (3) exon number ≥1. Subsequently, transcripts were subjected to protein coding potential evaluation by CNCI (v2) [7] and CPC (0.9-r2) [8] with default parameters. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts predicted without coding potential were considered as lncRNAs.
Genome_build: African green monkey (AGM) (Chlorocebus aethiops) were download from NCBI GenBank (http://www.ncbi.nlm.nih.gov/assembly/) under assembly accession number CA_000409795.2 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/409/795/GCF_000409795.2_Chlorocebus_sabeus_1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz)
Supplementary_files_format_and_content: fasta files and fpkm expression value of novel circRNAs, lncRNAs and known mRNAs

organism: Chlorocebus aethiops

source_name: SV40-infected Vero cells

growth_protocol: African green monkey kindey-derived Vero cells, an established monkey kidney epithelial cell line, were obtained from the American Type Culture Collection (ATCC) and maintained in Dulbecco’s modified Eagle’s medium (DMEM; HyClone) supplemented with 10% fetal bovine serum (FBS; Gibico), 2 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 ug/ml) at 37 °c and 5% CO2 atmosphere.

extract_protocol:
After 72 h post-infection, the cells were harvested and total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) with DNase I digestion (Epicentre, Illumina, San Diego, CA, USA) for 15 minutes at 37℃. The integrity and quality of the total RNA was evaluated using an Agilent 2100 BioAnalyzer (Agilent Technologies) and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0. RNA quantity was measured using the NanoDrop 2000 (Thermo Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Vero cells were mock-infected or virus-infected with the SV40 strain 776 (GenBank: AF316139.1) at a multiplicity of infection of 5 PFU per cell (MOI = 5) in serum-free medium. After 1 h adsorption at 37 C, the medium was replaced with complete DMEM containing 10% FBS and incubated at 37 C.

value: African green monkey kindey-derived epithelial cells

tag: passages

tag: infection

value: SV40 strain 776 (GenBank:AF316139.1)


title: S3_SV40

tag: cell type


title: endometriotic stromal cells from ovarian ectopic sites of patient 3

source_name: OESC 3

value: patient 3


title: DON2531A115

tag: cell line

tag: macrophage batch

value: KOC

value: dNTPase knockout

value: standard media with LPS


title: DON2531A110

tag: macrophage samhd1

tag: macrophage culture time in hours

value: conditioned media


title: C3_Ctrl

source_name: Vero cells


title: endometriotic stromal cells from ovarian ectopic sites of patient 1

source_name: OESC 1

value: patient 1


title: S1_SV40


title: C2_Ctrl


title: DON2531A111

value: embryonic stem cell derived macrophage

value: WTA

value: wildtype

tag: macrophage culture media

value: conditioned media with LPS


title: DON2531A109


title: DON2531A108


title: DON2531A11


title: C1_Ctrl


title: DON2531A102


title: DON2531A103


title: DON2531A116


title: ∆luxO Mucus Replicate 1

city: Newark

first: E Fidelma

last: Boyd

state: DE

address: 118 Wolf Hall

institute: University of Delaware

description: Total RNA depleted for rRNA

data_processing:
Base calling and Q scoring was done using BCL2FASTQ version 1.8.4
Raw 51-base reads were filtered to remove adaptor only sequences and low quality reads using the FASTX Toolkit.
Filtered reads were aligned to the Vibrio parahaemolyticus RIMD2210633 genome (Refseq ID NC_004603.1 Chromosome 1 and NC_004605.1 Chromosome 2) using Burrows-Wheeler Aligner (BWA.aln) version 0.7.7. Gene annotations were obtained from Ensembl bacteria, Rfam, Bacterial Small Regulatory RNA database and RAST.
Number of reads aligning to each genomic position was calculated using Htseq version 0.6.1.
Differential expression analysis was performed on obtained read counts using DESeq2 version 1.4.5.
Genome_build: ASM19609v1

organism: Vibrio parahaemolyticus RIMD 2210633

source_name: bacterium

growth_protocol: Vibrio parahaemolyticus wild-type and mutant strains were grown for 4 h in LB 3% NaCl and then diluted 1:50 into M9 medium supplemented with mouse cecal mucus as the sole carbon source. In order to best mimic the limited oxygen in vivo conditions the cells were grown statically without any shaking. To determine expression patterns upon initial exposure to mucus, we examined early-exponential-phase cultures that were grown for 90 mins in the medium.

extract_protocol:
Total RNA was extracted from cells obtained by centrifugation at the end of 90 mins using Trizol (Invitrogen, Carlsbad, CA) according to manufacturer’s protocol. The RNA samples were then quantified using a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA). The samples were then treated with Turbo DNase (Invitrogen) according to manufacturer’s instructions. For each sample of the wild-type and mutant, RNA samples from two independent cultures were pooled together. Nanodrop quantifications were used to ensure equal representation of RNA from both biological replicates. Then, 3 μg of RNA was used for rRNA depletion using the Ribo-Zero rRNA removal kit for Gram-negative bacteria (Illumina).
Libraries for each sample were prepared from 100ng of rRNA-depleted-RNA using the Illumina TruSeq Stranded mRNA kit (Illumina) following standard manufacturer's protocol.

tag: strain

tag: genotype/variation

value: luxO mutant (VP2099)


title: ∆luxO Mucus Replicate 2

description: Total RNA depleted for rRNA


title: ∆luxO Mucus Replicate 3

description: Total RNA depleted for rRNA


title: DON2531A100


title: WT Mucus Replicate 2

description: Total RNA depleted for rRNA

value: Wild-type O3:K6 clinical isolate


title: DON2531A1

value: standard media


title: endometriotic stromal cells from ovarian ectopic sites of patient 2

source_name: OESC 2

value: patient 2

value: endometriosis

value: Ectopic endometriotic stroma :ovary

value: cell culture of endometriotic stromal cells


title: J01

city: Taian

first: Yuding

last: Wang

address: No. 61, Daizong Street

institute: Shandong Agricultural University

description: the longissimus dorsi (LD) muscle about 240 days after birth in Laiwu pigs

data_processing:
RRBS Sequencing of DNA
Bismark are used to mapping reads to reference genome and methylation calling
5mC analysis
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include chromosome, position, strand, count methylated, count unmethylated, C-context and trinucleotide context.

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
DNA was extracted from longissimus dorsi muscle samples (stored at −80°C) according to the TIANGEN TIANamp genomic gene Kit(DP304) instruction manual and  the same age pigs DNA were pooled.
DNA libraries were prepared for sequencing using standard RRBS protocols.

treatment_protocol: A total of 6 pure castrated male Laiwu pigs reared under similar environmental and feeding conditions were selected at two developments periods: 120 and 240 days of age and the same age pigs DNA were pooled.

tag: breed

value: Laiwu

tag: tissue

value: LD muscle

tag: age

value: 240 days old

value: wild type


title: J02

description: the longissimus dorsi (LD) muscle about 120 days after birth in Laiwu pigs

value: 120 days old

tag: genotype


title: plasmodium infection (PI)

city: Wenzhou

first: liyang

last: huang

institute: Wenzhou Medical College

description: plasmodium infection(PI)

data_processing:
illumina Hiseq2000
This experiment adopts the illumina Hiseq2000 sequencing platform single-ended 50 bp sequencing model for high-throughput sequencing samples
Original data needed and primers and remove the adaptor sequences, and pass by the length of the sequencing fragments bases of quality inspection and screening, finally choose sequencing fragments of reliable quality
Small RNA (sRNA) type (with unique) and quantity (in total), and the length of the small RNA do statistic, and in general, the length of the interval of 18 ~ 30 small RNA nt, length distribution can help us to determine the peak of small RNA species, such as micrornas focused on 21 or 22 nt, siRNA concentrated in 24 nt, piRNA focused on 30 nt
Small RNAs select read (clean data) of greater than 15 bp in length and less than 32 bp for subsequent analysis. Clean data refers to all of the above-mentioned filtering process to retain the sequencing sequence (the reads reads) data.
Genome_build: Anopheles gambiae, Aedes aegypti were used as a reference miRNAs database from the mirbase v.21
Supplementary_files_format_and_content: xlsx format and miRNA sequences and expresssion data

organism: Anopheles anthropophagus

source_name: midgut

growth_protocol: Anopheles anthropophagus (China wild type strain) was reared and maintained in humidified incubators at 26±1℃ on a 12 hour light:dark cycle as described previously .18~20g male ICR mice were used for mosquitoes blood feeding and Plasmodium infection experiments. 0.2mL stock solution of Plasmodium berghei ANKA strain were thawed and intraperitoneal (i.p) injected into ICR mice by using a 1.0 ml tuberculin syringe. When the gametocytes were confirmed, naive 4–5 days old female mosquitoes were fed on P. berghei–infected or uninfected ICR mice. Mosquitoes were kept at 26 ±1℃ until dissection.

extract_protocol:
Total RNAs were extracted from dissected tissue using mirVanaTMmiRNA Isolation Kit (Ambion). Quality and quantity of RNA was checked by using denaturalization agar gels and Du530 Spectrophotometer (Beckman, Gemany).
Libraries were prepared according to Illumina's instructions accompanying theRNA Sample Kit. Briefly, The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: Midguts dissection of female adults was performed 48 h post-blood feeding on P. berghei–infected or uninfected ICR mice . Adult female mosquitoes with 10% sugar feeding 48 h were collected as control sample. Dissections were performed on ice in RNAlater® Stabilization Solution (Ambion) and kept on ice. The midguts were dissected from the abdomen .

tag: group

value: plasmodium infection (PI)

value: midgut

tag: time

value: 48 hours


title: blood feeding (BF)

description: blooding feeding(BF)

value: blood feeding (BF)


title: sugar feeding (SF)

description: sugar feeding(SF)

value: sugar feeding (SF)


title: E18_20161004_Neurons_Sample_64

status: Public on Jan 12 2017

city: Pleasanton

first: Grace

last: Zheng

state: California

address: 7068 Koll Center Parkway, Suite # 401

institute: 10X Genomics Inc

description: Sample prepared 6 days after dissection, from the second E18 mouse

data_processing:
The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger).
Cell Ranger commands used to produce this aggregated dataset:
cellranger mrp (--cells=10000 …)
cellranger aggr --id=neuron_aggregation --csv=aggregator.csv --nosecondary
cellranger reanalyze --id=neuron_reanalyze --matrix=filtered_matrix.h5 --params=reanalyze.csv
Genome_build: mm10
Supplementary_files_format_and_content: bam: bam files of individual samples; mtx: aggregated count matrix of 133 samples in a hdf5 format (to conserve space). The instructions to read the matrix in hdf5 format can be found here, https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

source_name: E18 mouse brain cells

extract_protocol:
Cortex, hippocampus, and subventricular zone were purchased from BrainBits (C57EHCV). They were from 2 E18 C57BL/6 mice dissected on the same day, shipped overnight on ice, and stored at 4C until being prepared for scRNA-Seq. Brain tissues were dissociated following the Demonstrated Protocol for Mouse Embryonic Neural Tissue, https://support.10xgenomics.com/single-cell/sample-prep/doc/demonstrated-protocol-dissociation-of-mouse-embryonic-neural-tissue-for-single-cell-rna-sequencing
scRNA-Seq libraries were made following the User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry). 69 scRNA-Seq libraries were made from first mouse brain 2 days after the dissection. Another 64 scRNA-Seq libraries were made from second mouse brain 6 days after the dissection.
Each library was sequenced as follows: 26bp Read 1 (16bp Chromium barcode and 10bp UMI), 98bp Read 2 (transcript), and 8bp i7 sample barcode for each scRNA-Seq library. All the samples were sequenced on 11 Illumina Hiseq 4000 flow cells, and each sample was sequenced on multiple flow cells. Samples were downsampled and aggregated with approximately 18,500 reads per cell.

value: Cortex, hippocampus and subventricular zone

tag: developmental stage

tag: condition

value: Healthy


title: E18_20161004_Neurons_Sample_60


title: E18_20161004_Neurons_Sample_59


title: E18_20161004_Neurons_Sample_61


title: E18_20161004_Neurons_Sample_58


title: E18_20161004_Neurons_Sample_62


title: E18_20161004_Neurons_Sample_53


title: E18_20161004_Neurons_Sample_57


title: E18_20161004_Neurons_Sample_56


title: E18_20161004_Neurons_Sample_54


title: E18_20161004_Neurons_Sample_55


title: E18_20161004_Neurons_Sample_52


title: E18_20161004_Neurons_Sample_51


title: E18_20161004_Neurons_Sample_50


title: E18_20161004_Neurons_Sample_49


title: E18_20161004_Neurons_Sample_48


title: WT Mucus Replicate 1

description: Total RNA depleted for rRNA

value: Wild-type O3:K6 clinical isolate


title: E18_20161004_Neurons_Sample_44


title: E18_20161004_Neurons_Sample_47


title: E18_20161004_Neurons_Sample_45


title: E18_20161004_Neurons_Sample_43


title: E18_20161004_Neurons_Sample_46


title: E18_20161004_Neurons_Sample_63


title: E18_20161004_Neurons_Sample_40


title: E18_20161004_Neurons_Sample_38


title: E18_20161004_Neurons_Sample_39


title: E18_20161004_Neurons_Sample_42


title: E18_20161004_Neurons_Sample_41


title: E18_20161004_Neurons_Sample_36


title: E18_20161004_Neurons_Sample_37


title: E18_20161004_Neurons_Sample_34


title: E18_20161004_Neurons_Sample_31


title: E18_20161004_Neurons_Sample_30


title: E18_20161004_Neurons_Sample_32


title: E18_20161004_Neurons_Sample_29


title: E18_20161004_Neurons_Sample_33


title: E18_20161004_Neurons_Sample_27


title: E18_20161004_Neurons_Sample_28


title: E18_20161004_Neurons_Sample_26


title: E18_20161004_Neurons_Sample_24


title: E18_20161004_Neurons_Sample_23


title: E18_20161004_Neurons_Sample_22


title: E18_20161004_Neurons_Sample_20


title: E18_20161004_Neurons_Sample_25


title: E18_20161004_Neurons_Sample_14


title: E18_20161004_Neurons_Sample_17


title: E18_20161004_Neurons_Sample_16


title: E18_20161004_Neurons_Sample_15


title: E18_20161004_Neurons_Sample_35


title: E18_20161004_Neurons_Sample_21


title: E18_20161004_Neurons_Sample_13


title: E18_20161004_Neurons_Sample_19


title: E18_20161004_Neurons_Sample_18


title: E18_20161004_Neurons_Sample_08


title: E18_20161004_Neurons_Sample_10


title: E18_20161004_Neurons_Sample_12


title: E18_20161004_Neurons_Sample_11


title: E18_20161004_Neurons_Sample_03


title: E18_20161004_Neurons_Sample_05


title: E18_20161004_Neurons_Sample_07


title: E18_20161004_Neurons_Sample_09


title: E18_20161004_Neurons_Sample_02


title: E18_20160930_Neurons_Sample_71

description: Sample prepared 2 days after dissection, from the first E18 mouse


title: E18_20160930_Neurons_Sample_70


title: E18_20161004_Neurons_Sample_01


title: E18_20160930_Neurons_Sample_72


title: E18_20160930_Neurons_Sample_68


title: E18_20160930_Neurons_Sample_69


title: E18_20160930_Neurons_Sample_67


title: E18_20160930_Neurons_Sample_66


title: E18_20160930_Neurons_Sample_64


title: E18_20160930_Neurons_Sample_59


title: E18_20160930_Neurons_Sample_60


title: E18_20160930_Neurons_Sample_63


title: E18_20160930_Neurons_Sample_61


title: E18_20160930_Neurons_Sample_57


title: E18_20160930_Neurons_Sample_58


title: E18_20160930_Neurons_Sample_56


title: E18_20161004_Neurons_Sample_04


title: E18_20161004_Neurons_Sample_06


title: E18_20160930_Neurons_Sample_53


title: E18_20160930_Neurons_Sample_55


title: E18_20160930_Neurons_Sample_52


title: E18_20160930_Neurons_Sample_51


title: E18_20160930_Neurons_Sample_50


title: E18_20160930_Neurons_Sample_44


title: E18_20160930_Neurons_Sample_46


title: E18_20160930_Neurons_Sample_47


title: E18_20160930_Neurons_Sample_48


title: E18_20160930_Neurons_Sample_45


title: E18_20160930_Neurons_Sample_43


title: E18_20160930_Neurons_Sample_42


title: E18_20160930_Neurons_Sample_39


title: E18_20160930_Neurons_Sample_41


title: E18_20160930_Neurons_Sample_62


title: E18_20160930_Neurons_Sample_38


title: E18_20160930_Neurons_Sample_40


title: E18_20160930_Neurons_Sample_35


title: E18_20160930_Neurons_Sample_34


title: E18_20160930_Neurons_Sample_33


title: E18_20160930_Neurons_Sample_36


title: E18_20160930_Neurons_Sample_54


title: E18_20160930_Neurons_Sample_30


title: E18_20160930_Neurons_Sample_31


title: E18_20160930_Neurons_Sample_49


title: E18_20160930_Neurons_Sample_29


title: E18_20160930_Neurons_Sample_28


title: E18_20160930_Neurons_Sample_27


title: E18_20160930_Neurons_Sample_23


title: E18_20160930_Neurons_Sample_21


title: E18_20160930_Neurons_Sample_25


title: E18_20160930_Neurons_Sample_20


title: E18_20160930_Neurons_Sample_22


title: E18_20160930_Neurons_Sample_18


title: E18_20160930_Neurons_Sample_15


title: E18_20160930_Neurons_Sample_17


title: E18_20160930_Neurons_Sample_37


title: E18_20160930_Neurons_Sample_12


title: E18_20160930_Neurons_Sample_13


title: E18_20160930_Neurons_Sample_16


title: E18_20160930_Neurons_Sample_10


title: E18_20160930_Neurons_Sample_11


title: E18_20160930_Neurons_Sample_07


title: control endometrial stromal cells of patient 8

source_name: CESC 4

tag: individual

value: patient 8

tag: disease state

value: control

tag: sites

value: Endometrial stroma

value: cell culture of endometrial stromal cells


title: E18_20160930_Neurons_Sample_05


title: E18_20160930_Neurons_Sample_06


title: E18_20160930_Neurons_Sample_03


title: E18_20160930_Neurons_Sample_24


title: E18_20160930_Neurons_Sample_01


title: E18_20160930_Neurons_Sample_19


title: Control1

city: Stanford

first: Jared

last: Churko

state: CA

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

description:
Control
Sample name: Con1

data_processing:
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GR37 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.9
Genome_build: GR37
Supplementary_files_format_and_content: text file with RPKM values.

source_name: hiPSC-CM cell line_control

extract_protocol:
Qiagen RNAEasy Micro Kit
Ovation RNA-seq v2 kit

tag: cell type

value: hiPSC-CM

value: Control

tag: mutation


title: Control2

description:
Control
Sample name: Con2


title: Brugada line 2

description:
Brugada
Sample name: BrS2

source_name: hiPSC-CM cell line_Brugada_patient

value: Brugada Syndrome


title: E18_20160930_Neurons_Sample_02


title: Brugada line 1

description:
Brugada
Sample name: BrS1

value: SCN5A R620H and R811H


title: E18_20160930_Neurons_Sample_04


title: H9B_Mel3.b

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

country: Germany

institute: IZBI

description:
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt

data_processing:
Raw reads were processed using a custom script and aligned to a Bowtie2 (Langmead and Salzberg, 2012) indexed human genome (grch38 sourced from ENSEMBL) using TopHat (Trapnell et al., 2009) with default settings.
Transcript levels were quantified as fragments per kilobase of mapped reads (FPKM) generated by Cufflinks (Trapnell et al., 2010) using gencode protein coding genes (grch38 v22 Havana).
We excluded cells that did express neither of two housekeeping genes ACTB and GAPDH. 307 single cells remained for the transcriptome analysis.
Genome_build: grch38 sourced from ENSEMBL
Supplementary_files_format_and_content: FPKM values. The file GSE81383_data_melanoma_scRNAseq_BT_Mel.txt.gz contains the FPKM values for all samples. GSE81383_data_melanoma_scRNAseq_BT_2015-07-02.txt.gz contains the FPKM values for GSM2151479 - GSM2151570.

source_name: subcutaneous metastasis

growth_protocol: melanoma short-term culture Ma-Mel-123

extract_protocol:
Single melanoma cells from short-term cultures were captured on an integrated fluidic circuit RNA-seq chip (Fluidigm, Hamburg, Germany) using the Fluidigm C1 system. Cells were loaded onto the chip at a concentration of 200 cells/μL and imaged by phase-contrast. Cell capture, cell lysis, reverse transcription, and cDNA amplification were performed on the chip as described (Camp et al., 2015).
Illumina libraries were constructed using the Illumina Nextera XT DNA Sample Preparation kit using the protocol supplied by Fluidigm. Ninety-six libraries were pooled (3 µL each) and purified with SPRI beads. Library concentration and size distribution were assessed on an Agilent Bioanalyzer and with Qubit dsDNA HS Assay kits and a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Invitrogen, Darmstadt).  Each cell was paired-end sequenced (100 base reads) on an Illumina HiSeq 2500 to a depth of 2–5 million reads and base-calling, adaptor trimming, and de-multiplexing were performed as described (Renaud et al., 2013; Renaud et al., 2015).

value: skin (melanoma metastasis)

tag: culture

value: melanoma short-term culture Ma-Mel-93

tag: melanoma genetic conditions

value: BRAF wild type and NRAS G13R mutant


title: E18_20160930_Neurons_Sample_09

tag: strain


title: H5B_Mel3.b


title: H12B_Mel3.b


title: G8B_Mel3.b


title: G9B_Mel3.b


title: H6B_Mel3.b


title: H11B_Mel3.b


title: E18_20160930_Neurons_Sample_08


title: G5B_Mel3.b


title: G1B_Mel3.b


title: G6B_Mel3.b


title: G4B_Mel3.b


title: G3B_Mel3.b


title: G12B_Mel3.b


title: E18_20160930_Neurons_Sample_32


title: G10B_Mel3.b


title: H2B_Mel3.b


title: F6B_Mel3.b


title: F5B_Mel3.b


title: F3B_Mel3.b


title: F8B_Mel3.b


title: F10B_Mel3.b


title: E8B_Mel3.b


title: E9B_Mel3.b


title: E6B_Mel3.b


title: E5B_Mel3.b


title: E3B_Mel3.b


title: E2B_Mel3.b


title: E7B_Mel3.b


title: F4B_Mel3.b


title: E1B_Mel3.b


title: D8B_Mel3.b


title: D6B_Mel3.b


title: F11B_Mel3.b


title: D5B_Mel3.b


title: F7B_Mel3.b


title: D4B_Mel3.b


title: E12B_Mel3.b


title: D1B_Mel3.b


title: D12B_Mel3.b


title: D11B_Mel3.b


title: D10B_Mel3.b


title: C9B_Mel3.b


title: F2B_Mel3.b


title: C8B_Mel3.b


title: C7B_Mel3.b


title: C6B_Mel3.b


title: C2B_Mel3.b


title: C5B_Mel3.b


title: C1B_Mel3.b


title: C12B_Mel3.b


title: C10B_Mel3.b


title: C11B_Mel3.b


title: B7B_Mel3.b


title: B5B_Mel3.b


title: B8B_Mel3.b


title: D2B_Mel3.b


title: B4B_Mel3.b


title: B6B_Mel3.b


title: B2B_Mel3.b


title: B3B_Mel3.b


title: B1B_Mel3.b


title: B10B_Mel3.b


title: A8B_Mel3.b


title: C3B_Mel3.b


title: A7B_Mel3.b


title: A6B_Mel3.b


title: A5B_Mel3.b


title: B11B_Mel3.b


title: B12B_Mel3.b


title: A3B_Mel3.b


title: B9B_Mel3.b


title: A11B_Mel3.b


title: A12B_Mel3.b


title: A10B_Mel3.b


title: H8_Mel3.a

value: melanoma short-term culture Ma-Mel-108

value: BRAF V600E mutant and NRAS wild type


title: H7_Mel3.a


title: H3_Mel3.a


title: A4B_Mel3.b


title: D7B_Mel3.b


title: G9_Mel3.a


title: H1_Mel3.a


title: G7_Mel3.a


title: G3_Mel3.a


title: A9B_Mel3.b


title: G2_Mel3.a


title: G1_Mel3.a


title: F8_Mel3.a


title: A2B_Mel3.b


title: F9_Mel3.a


title: F1_Mel3.a


title: F7_Mel3.a


title: E8_Mel3.a


title: E9_Mel3.a


title: E1_Mel3.a


title: E7_Mel3.a


title: E3_Mel3.a


title: E2_Mel3.a


title: H2_Mel3.a


title: D8_Mel3.a


title: D9_Mel3.a


title: D2_Mel3.a


title: D7_Mel3.a


title: D3_Mel3.a


title: D1_Mel3.a


title: G8_Mel3.a


title: C9_Mel3.a


title: G5_Mel3.a


title: C2_Mel3.a


title: C1_Mel3.a


title: C3_Mel3.a


title: C8_Mel3.a


title: C7_Mel3.a


title: B9_Mel3.a


title: B8_Mel3.a


title: B7_Mel3.a


title: B4_Mel3.a


title: B10_Mel3.a


title: B1_Mel3.a


title: B2_Mel3.a


title: B3_Mel3.a


title: A9_Mel3.a


title: A8_Mel3.a


title: B11_Mel3.a


title: A6_Mel3.a


title: A4_Mel3.a


title: A2_Mel3.a


title: A11_Mel3.a


title: A12_Mel3.a


title: A5_Mel3.a


title: A10_Mel3.a


title: H3_Mel2

description:
replicat from H3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt

value: melanoma short-term culture Ma-Mel-123

value: double-negative for BRAF and NRAS mutations


title: H5_Mel2

description:
replicat from H5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H4_Mel2

description:
replicat from H4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H6_Mel2

description:
replicat from H6_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H8_Mel2

description:
replicat from H8_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H12_Mel2

description:
replicat from H12_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H2_Mel2

description:
replicat from H2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H11_Mel2

description:
replicat from H11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H1_Mel2

description:
replicat from H1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: G7_Mel2

description:
replicat from G7_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: G5_Mel2

description:
replicat from G5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B6_Mel3.a


title: G6_Mel2

description:
replicat from G6_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D11_Mel3.a


title: G4_Mel2

description:
replicat from G4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: G11_Mel2

description:
replicat from G11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: G1_Mel2

description:
replicat from G1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: G2_Mel2

description:
replicat from G2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F8_Mel2

description:
replicat from F8_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F7_Mel2

description:
replicat from F7_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F9_Mel2

description:
replicat from F9_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: G3_Mel2

description:
replicat from G3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F6_Mel2

description:
replicat from F6_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F4_Mel2

description:
replicat from F4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F3_Mel2

description:
replicat from F3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F2_Mel2

description:
replicat from F2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F5_Mel2

description:
replicat from F5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: H10_Mel2

description:
replicat from H10_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F12_Mel2

description:
replicat from F12_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E6_Mel2

description:
replicat from E6_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F1_Mel2

description:
replicat from F1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: F11_Mel2

description:
replicat from F11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E5_Mel2

description:
replicat from E5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E3_Mel2

description:
replicat from E3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E4_Mel2

description:
replicat from E4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E9_Mel2

description:
replicat from E9_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E11_Mel2

description:
replicat from E11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E2_Mel2

description:
replicat from E2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E1_Mel2

description:
replicat from E1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E12_Mel2

description:
replicat from E12_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D8_Mel2

description:
replicat from D8_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D6_Mel2

description:
replicat from D6_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: G10_Mel2

description:
replicat from G10_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: E10_Mel2

description:
replicat from E10_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D5_Mel2

description:
replicat from D5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D7_Mel2

description:
replicat from D7_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D2_Mel2

description:
replicat from D2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D10_Mel2

description:
replicat from D10_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D1_Mel2

description:
replicat from D1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C4_Mel2

description:
replicat from C4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C7_Mel2

description:
replicat from C7_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C3_Mel2

description:
replicat from C3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C11_Mel2

description:
replicat from C11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C10_Mel2

description:
replicat from C10_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C12_Mel2

description:
replicat from C12_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C1_Mel2

description:
replicat from C1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B8_Mel2

description:
replicat from B8_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B7_Mel2

description:
replicat from B7_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D9_Mel2

description:
replicat from D9_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C8_Mel2

description:
replicat from C8_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: C5_Mel2

description:
replicat from C5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B6_Mel2

description:
replicat from B6_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B5_Mel2

description:
replicat from B5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D3_Mel2

description:
replicat from D3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B2_Mel2

description:
replicat from B2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B3_Mel2

description:
replicat from B3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D12_Mel2

description:
replicat from D12_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B4_Mel2

description:
replicat from B4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D4_Mel2

description:
replicat from D4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A9_Mel2

description:
replicat from A9_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B11_Mel2

description:
replicat from B11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B12_Mel2

description:
replicat from B12_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A8_Mel2

description:
replicat from A8_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B10_Mel2

description:
replicat from B10_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: D11_Mel2

description:
replicat from D11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A7_Mel2

description:
replicat from A7_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A6_Mel2

description:
replicat from A6_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A5_Mel2

description:
replicat from A5_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: B1_Mel2

description:
replicat from B1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A3_Mel2

description:
replicat from A3_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A4_Mel2

description:
replicat from A4_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: NF2/Chr22_miRNA-seq [MN-64846]

city: New Haven

first: Akdes

last: Serin Harmanci

state: Connecticut

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University

data_processing:
Adapter sequences were trimmed using cutadapt. Reads shorter than 18 base pair and reads with quality less than 20 were filtered. Per base quality scores were assessed using FASTX tool. Adaptor trimmed reads were aligned to miRBase using mirDeep2 tool.
The set of known human miRNA precursors were downloaded from miRBase version 20.  We reported total read counts for 5p and 3p strands. Read counts for each sample were normalized to reads per million reads (RPM) and log2-transformed. Batch effect was corrected using ComBat in sva R package. We then performed unsupervised hierarchical clustering based on a Euclidean distance metric and complete linking. Differentially expressed miRNAs were identified using limma R package. An FDR threshold of 0.05 was used.
Genome_build: hg19
Supplementary_files_format_and_content: matrix

growth_protocol: Samples were excised during neurosugical procedures and frozen in OCT for later use. H&E slides were prepared for each sample to confirm tumor histology and assess tissue density. On the day of each experiment, sections were cut using a cryostat (20uM and immediately prepared for miRNA extraction.

extract_protocol:
10 to 15 frozen sections of each tumor block or dura sample were collected for each experiment. miRNA was extracted using the mirVANA miRNA isolation kit (Ambion, AM1560).
Samples were subjected to standard Illumina  library construction after assessment for material quality and quantity. Sequencing was performed on Illumina HiSeq instruments using 75 basepair, single-end reads and multiplexing 8 tumor samples per lane

treatment_protocol: All samples are untreated, primary specimens from brain tumor patients.

tag: tissue type

value: meningioma

tag: tumor grade

value: atypical

tag: mutation subtype


title: NF2/Chr22_miRNA-seq [MN-64760]


title: Hedgehog_miRNA-seq [MN-81172]

value: benign

value: Hedgehog


title: NF2/Chr22_miRNA-seq [MN-64705]


title: A2_Mel2

description:
replicat from A2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt

tag: tissue


title: NF2/Chr22_miRNA-seq [MN-64353]


title: NF2/Chr22_miRNA-seq [MN-64530]


title: A12_Mel2

description:
replicat from A12_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: A11_Mel2

description:
replicat from A11_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: POLR2A_miRNA-seq [MN-64273]


title: A1_Mel2

description:
replicat from A1_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt


title: RNAseq WT in vitro rep 1

city: New York

first: Ataman

last: Sendoel

address: York Avenue

institute: Rockefeller University

description: RNAseq in vitro

data_processing:
fastx_clipper (-a AGATCGGAAGAGCACACGTCT)( -l 20) and fastx_trimmer were used to clip adapter and trim (options as indicated)
bowtie2 to align to 45SpreRNA, norRNA reads were then used to align
tophat2 to align to mm10
Raw counts and rpkms for 5'UTR, ORF and 3'UTR were obtained using Plastid tools (Dunn, J.G. (2016). Plastid: a positional library for sequencing analysis. http://plastid.readthedocs.io)
Genome_build: mm10
Supplementary_files_format_and_content: .txt files, raw counts and rpkms.

source_name: Primary keratinocytes from P0 back skin

extract_protocol:
In vivo: CHX treatment, followed by dispase/CHX treatment to separate epidermis from dermis, trypsin/CHX to obtain single cell suspension.
Ribosome profiling protocol as described in Ingolia et al, Nature protocols, 2012.

value: R26-Sox2-IRES-eGFP fl/+

tag: age

value: Passage 10-15


title: RNAseq SOX2 in vitro rep 0

description: RNAseq in vitro

value: K14-Cre; R26-Sox2-IRES-eGFP fl/+


title: RNAseq SOX2 in vitro rep 1

description: RNAseq in vitro


title: NF2/Chr22_miRNA-seq [MN-64167]


title: Rib.prof. HrasG12V; Tgfbr2 KO, eIF2A KO clone 5A CHX rep 1

description:
Ribosome protected RNA fragments
Ribosome profiling in vitro

data_processing:
Library strategy: Ribo-Seq
fastx_clipper (-a AGATCGGAAGAGCACACGTCT)( -l 20) and fastx_trimmer were used to clip adapter and trim (options as indicated)
bowtie2 to align to 45SpreRNA, norRNA reads were then used to align
tophat2 to align to mm10
Raw counts and rpkms for 5'UTR, ORF and 3'UTR were obtained using Plastid tools (Dunn, J.G. (2016). Plastid: a positional library for sequencing analysis. http://plastid.readthedocs.io)
Genome_build: mm10
Supplementary_files_format_and_content: .txt files, raw counts and rpkms.

value: HrasG12V; Tgfbr2 fl/fl KO, eIF2A KO


title: RNAseq WT in vitro rep 0

description: RNAseq in vitro


title: Rib.prof. HrasG12V; Tgfbr2 KO, eIF2A KO clone 5A  CHX rep 0


title: Rib.prof. HrasG12V; Tgfbr2 KO, non-targeting sgRNA clone 4M CHX rep 1

value: HrasG12V; Tgfbr2 fl/fl KO; non-targeting sgRNA


title: Rib.prof. HrasG12V; Tgfbr2 KO, non-targeting sgRNA clone 4M CHX rep 0


title: NF2/Chr22_miRNA-seq [MN-64031]


title: MPNST-Doxycycline treated-rep1

city: Xiamen

first: Yingjia

last: Shen

state: Fujian

address: A316 Jingquan Building

department: Ecology

institute: Xiamen University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to human whole genome(GRCh38) using Tophat v2.0.3.
The number of reads falling in the exons of this meta-transcript were counted and normalized by DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized base mean values for each Sample.

molecule: polyA RNA

source_name: human malignant peripheral nerve sheathing tumors (MPNST) cell lines treated with Doxycycline

growth_protocol: Cells were grown in DMEM with 10% heat inactivated fetal bovine serum (FBS) and penicillin (100 IU/ml) and streptomycin (100 µg/ml). Cell cultures were carried out at 37oC in a humidified 5% CO2 atmosphere.

extract_protocol:
Tumor cells were frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Doxycycline treated (1 ug/ml)

value: tumor cells

tag: treatment

value: Doxycycline


title: MPNST-Doxycycline treated-rep3


title: MPNST-Doxycycline treated-rep2


title: NF2/Chr22_miRNA-seq [MN-63811]


title: Rib.prof. SOX2_invitro_Harringtonine_1

description:
Ribosome protected RNA fragments
Ribosome profiling in vitro
GSM2199599 and GSM2199600 are Harringtonine sample, which blocks ribosomes at translation initiation sites. These two samples are additional controls and supplied to have the complete set, but raw count data makes no sense here and processed data were never made (there are just start site reads, the height of the peaks has no meaning)


title: MPNST-untreated-rep3

source_name: human malignant peripheral nerve sheathing tumors (MPNST) cell lines

value: untreated


title: Rib.prof. WT_invitro_Harringtonine_1


title: Rib.prof. SOX2_invitro_nd_2


title: MPNST-untreated-rep2


title: Rib.prof. SOX2_invitro_CHX_2


title: NF2/Chr22_miRNA-seq [MN-63525]


title: Rib.prof. HrasG12V; Tgfbr2 KO nd

value: HrasG12V; Tgfbr2 fl/fl KO


title: MPNST-untreated-rep1


title: Rib.prof. SOX2_invitro_CHX_1


title: NF2/Chr22_miRNA-seq [MN-63711]


title: NF2/Chr22/SMARCB1_miRNA-seq [MN-64136]


title: C2_Mel2

description:
replicat from C2_mel
single cell
processed data file: data_melanoma_scRNAseq_BT_Mel.txt

value: skin (melanoma metastasis)


title: Rib.prof. SOX2_invitro_nd_1


title: NF2/Chr22_miRNA-seq [MN-63442]


title: Rib.prof. WT_invitro_nd_1


title: Rib.prof. WT_invitro_CHX_2


title: Rib.prof. HrasG12V; Tgfbr2 KO CHX


title: RNAseq SOX2 P4  in vivo rep 1

description: RNAseq in vivo

source_name: Mouse back skins


title: TRAF7/chr22_miRNA-seq [MN-63338]


title: Rib.prof. WT_invitro_CHX_1


title: RCH_MLL_InputDNA

first: Thomas

last: Milne

address: John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

data_processing:
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk; Rpkm tables (.txt) were generated using edgeR

source_name: Leukemia cell line (RCH-ACV)

growth_protocol: SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5; all other cell lines were grown in a similar manner in RPMI 1640.

extract_protocol:
ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040) or Ultra RNA Library Prep Master Mix Set (Part# E7530).

tag: cell line

value: Leukemia cell line; RCH-ACV

value: Paediatric pre B-cell line derived from cALL with t(1;19)(q23;p13) translocation


title: RCH_MLL_ChIPSeq


title: ML2_H3K79me2_InputDNA

source_name: Leukemia cell line (ML-2)

value: Leukemia cell line; ML-2

value: Adult monocytic cell line derived from AML M4 with t(6;11)(q27;q23) translocation


title: RNAseq WT P4  in vivo rep 1

description: RNAseq in vivo


title: NF2/Chr22_miRNA-seq [MN-62525]

value: meningioma

value: atypical


title: RNAseq SOX2 P4  in vivo rep 0

description: RNAseq in vivo


title: RNAseq WT P4  in vivo rep 0

description: RNAseq in vivo


title: ML2_H3K79me2_ChIPSeq

tag: chip antibody

value: H3K79me2 (Active Motif, 39143)


title: Rib.prof. SOX2 P4  in vivo rep 2

description:
Ribosome protected RNA fragments
Ribosome profiling in vivo


title: SEM_NascentRNASeq_Rep4

description: processed data file: SEM_nascent_rpkm_table.txt

source_name: Leukemia cell line (SEM)

value: Leukemia cell line; SEM

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: molecule subtype

value: nascent RNA


title: NF2/Chr22/SMARCB1_miRNA-seq [MN-62296]

value: benign


title: NF2/Chr22_miRNA-seq [MN-62292]


title: Rib.prof. SOX2 P4  in vivo rep 0

value: K14-Cre; R26-Sox2-IRES-eGFP fl/+


title: SEM_NascentRNASeq_Rep3


title: Rib.prof. WT P4  in vivo rep 2

value: R26-Sox2-IRES-eGFP fl/+


title: Rib.prof. WT_invitro_nd_2

value: Passage 10-15


title: Rib.prof. WT P4  in vivo rep 0


title: SEM_NascentRNASeq_Rep2


title: TRAF7/PIK3_miRNA-seq [MN-62677]


title: NF2/Chr22_miRNA-seq [MN-62287]


title: Rib.prof. WT P4  in vivo rep 1


title: NF2/Chr22_miRNA-seq [MN-62203]


title: SEM_NascentRNASeq_Rep1


title: SEM_LEO1_ChIPSeq


title: NF2/Chr22_miRNA-seq [MN-62113]


title: miR34a_KO_2

city: Padova

first: Davide

last: Risso

address: Via C. Battisti, 241

country: Italy

institute: University of Padova

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped to the Mouse reference genome (mm10) downloaded from Ensembl v. 77, using TopHat (v. 2.0.11)
Gene-level read counts were generated using featureCounts (v1.4.5) and Ensembl (v. 77) gene annotation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files contain gene-level read counts for each sample

source_name: induced Pluripotent Stem Cells

growth_protocol: Wildtype and miR-34a-knockout iPSCs were generated from primary mouse embryonic fibroblasts (MEFs) by somatic reprogramming. Primary MEFs were isolated from littermate-controlled E13.5 wild-type and miR-34a-knockout embryos from C57B6/J mouse strain, infected with retroviruses generated by pMX retroviral vectors that encoded mouse Oct4, Sox2 and Klf4 (Addgene, Cat. # 13366, 13367 and 13370), and cultured on irradiated MEF feeder in ES medium containing Knockout DMEM, 15% ES-grade FBS, 2 mM L-glutamine, 1x10-4M MEM non-essential amino acids, 1x10-4 M 2-mercaptoethanol and Penicillin. Subsequently, single iPSC-like colonies were individually picked and expanded on irradiated MEF feeders to establish a stable line. Three independent iPSC lines were generated for each genotype.

extract_protocol:
Total RNA was extracted from 3 pairs of wildtype and mir-34a-knockout iPSCs by Trizol and followed by a clean-up procedure for on-column DNase I treatment using RNeasy Mini Kit (Qiagen, Cat. # 74104).
Strand-specific, poly(A) selected RNA-seq libraries were prepared as previously described in Tan et al. (2013) [PMCID: PMC3530680]

tag: genotype


title: WT_1

value: wild-type


title: miR34a_KO_3


title: WT_2


title: SEM_PAF1_ChIPSeq


title: NF2/Chr22_miRNA-seq [MN-61624]


title: SEM_MED1_InputDNA


title: miR34a_KO_1


title: SEM_MED1_ChIPSeq


title: Rib.prof. SOX2 P4  in vivo rep 1


title: SEM_KDM2B_InputDNA


title: WT_3


title: SEM_H3K36me3_InputDNA


title: NF2/Chr22/SMARCB1_miRNA-seq [MN-56]


title: POLR2A_miRNA-seq [MN-60355]


title: SEM_KDM2B_ChIPSeq

value: KDM2B (gift from Rob Klose)


title: SEM_H3K36me3_ChIPSeq


title: NF2/Chr22_miRNA-seq [MN-47]


title: H12_mel

description:
single cell
processed data file: GSE81383_data_melanoma_scRNAseq_BT_2015-07-02.txt.gz, GSE81383_data_melanoma_scRNAseq_BT_Mel.txt.gz

data_processing:
Raw reads were processed using a custom script and aligned to a Bowtie2 (Langmead and Salzberg, 2012) indexed human genome (grch38 sourced from ENSEMBL) using TopHat (Trapnell et al., 2009) with default settings.
Transcript levels were quantified as fragments per kilobase of mapped reads (FPKM) generated by Cufflinks (Trapnell et al., 2010) using gencode protein coding genes (grch38 v22 Havana).
We excluded cells that did express neither of two housekeeping genes ACTB and GAPDH. Ninety-two single cells remained for the transcriptome analysis.
Genome_build: grch38 sourced from ENSEMBL
Supplementary_files_format_and_content: FPKM values. The file GSE81383_data_melanoma_scRNAseq_BT_Mel.txt.gz contains the FPKM values for all samples. GSE81383_data_melanoma_scRNAseq_BT_2015-07-02.txt.gz contains the FPKM values for GSM2151479 - GSM2151570.

value: skin (melanoma metastasis)

value: melanoma short-term culture Ma-Mel-123

value: double-negative for BRAF and NRAS mutations


title: H10_mel


title: H11_mel


title: NF2/Chr22_miRNA-seq [MN-61887]


title: POLR2A_miRNA-seq [MN-12]


title: TRAF7/PIK3_miRNA-seq [MN-61471]


title: Control SL71048

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar St

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale School of Medicine

data_processing:
Illumina Casava and bcl2fastq-1.8.3 was used for base calling
RNAseq reads were mapped to the hg19 genome assembly using Tophat version v2.0.6 allowing for multiple hits.
Cufflinks version 2.2.0 was used to calculate the FPKMs
Cuffdiff was used to compare FPKMs between groups and genes with a false discovery rate (FDR) adjusted p<0.05 were identified as differentially expressed genes (DEGs).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples except SL32681. this sample was excluded from the final analysis due to low reads number and low mapping rate. According to that raw files for SL32681 were not uploaded.

source_name: FFPE lung tissue

extract_protocol:
Five 10-µm slices of the whole lung tissue were cut from FFPE block, excess paraffin was trimmed and slices were treated twice with 1ml xylene for 30 min at 62°C, then washed twice with 100% ethanol. Total RNA was isolated by using MasterPure kit (Epicentre Biotechnologies). Ribosomal RNA was removed by using the RiboZero rRNA removal kit (Epicentre)
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol from 1ug of total RNA

tag: gender

value: M

value: lung


title: H5_mel


title: Control SL71049


title: H7_mel


title: Control SL71050

value: F


title: NF2/Chr22_miRNA-seq [MN-41]

value: meningioma


title: NF2/Chr22_miRNA-seq [MN-61134]

value: atypical


title: NF2/Chr22_miRNA-seq [MN-61027]


title: HP26695 CrppH -TEX +TAP

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

institute: University of Wuerzburg

data_processing:
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (READemption 0.4.2, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0-418 (READemption 0.4.2, Förstner et al., 2014)
Coverage calculation and normalization (READemption 0.4.2, Förstner et al., 2014)
Genome_build: NC_000915.1
Supplementary_files_format_and_content: wiggle

organism: Helicobacter pylori 26695

source_name: Helicobacter pylori 26695 cells

growth_protocol: H. pylori strains were grown on GC-agar (Oxoid) plates supplemented with 10% (vol/vol) donor horse serum (Biochrom AG), 1% (vol/vol) vitamin mix, 10 μg/ml vancoymcin, 5 μg/ml trimethoprim, and 1 μg/ml nystatin. For transformant selection and growth of mutant strains, 20 μg/ml kanamycin or 16 μg/ml chloramphenicol were added. For liquid cultures, 10 or 50 ml Brain Heart Infusion medium (BHI, Becton, Dickinson Company) supplemented with 10% (vol/vol) FBS (Biochrom AG) and 10 μg/ml vancoymcin, 5 μg/ml trimethoprim, and 1 μg/ml nystatin were inoculated with H. pylori from plate to a final OD600 of 0.02-0.05 and grown under agitation at 140 rpm in 25 cm³ or 75 cm³ cell culture flasks (PAA). Bacteria were grown at 37°C in a HERAcell 150i incubator (Thermo Scientific) in a microaerophilic environment (10% CO2, 5% O2, and 85% N2).

extract_protocol:
Frozen cell pellets were thawed on ice and re-suspended in lysis solution containing 600 µl of 0.5 mg/ml lysozyme in TE buffer (pH 8.0) and 60 µl 10% SDS. Bacterial cells were lysed by incubating the samples for 1–2 minutes at 65°C. Afterwards, total RNA was extracted using the hot-phenol method described previously (Sharma et al. 2010, Bloomberg 1990, EMBO J). DNaseI (Fermentas) treatment was performed on total RNA according to manufacturer’s instruction.
cDNA library preparation was performed by Vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/) in a strand-specific manner. In brief, the three RNA samples were split into three portions. One portion was treated with Terminator exonuclease (TEX) prior to the standard library preparation procedure described below to generate the +TEX/+TAP libraries. To this end, RNA was denatured for 2 min at 90˚C, cooled on ice for 5 min and treated with 1.5 U of Terminator Exonuclease (Epicentre) for 30 min at 30˚C. For the second portion the TAP treatment (see below) was omitted to generate the −TEX/−TAP libraries. The standard procedure without modifications was used to generate the –TEX/+TAP libraries from the third portion. Here, ~200 ng of RNA sample were poly(A)-tailed using 2.5 U E. coli poly(A) polymerase (NEB) for 5 min at 37°C. Then, the 5'PPP structures were removed using tobacco acid pyrophosphatase (TAP). TAP treatment was performed by incubating the samples with 5 U TAP for 15 min at 37˚C. Afterwards, an RNA adapter (5' Illumina sequencing adapter, 5' UUUCCCUACACGACGCUCUUCCGAUCU 3') was ligated to the 5’P of the TAP-treated, poly(A)-tailed RNA for 30 min at 25°C. First-strand cDNA was synthesized by using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (AffinityScript, Agilent) by incubation at 42°C for 20 min, ramp to 55°C followed by 55°C for 5 min. In a PCR-based amplification step using a high fidelity DNA polymerase (Herculase II Fusion DNA Polymerases, Agilent) the cDNA concentration was increased to 20-30 ng/μl (initial denaturation at 95°C for 2 min, 14-16 cycles 95°C for 20 sec and 68°C for 2 min). A library-specific barcode for multiplex sequencing was included as part of a 3' sequencing adapter. The TruSeq index primers for PCR amplification were used according to the instructions of Illumina. For all libraries the Agencourt AMPure XP kit (Beckman Coulter Genomics) was used to purify the DNA (1.8 x sample volume), and cDNA sizes were examined by capillary electrophoresis on a MultiNA microchip electrophoresis system (Shimadzu).

treatment_protocol: When the cultures reached mid-log phase (WT OD600 0.7; ΔrppH OD600 0.5; CrppH OD600 0.7), culture volumes of cells corresponding to a total amount of 4 OD600, were mixed with 0.2 volumes of stop-mix (95% EtOH and 5% phenol, V/V), frozen in liquid N2 and stored at −80°C until RNA extraction.

value: rppH complementation

tag: rna treatment

value: TAP treated


title: HP26695 CrppH -TEX -TAP

value: untreated


title: Control SL71047


title: H6_mel


title: HP26695 CrppH +TEX +TAP

value: TEX and TAP treated


title: HP26695 drppH -TEX +TAP

value: rppH deletion


title: Control SL32683


title: HP26695 WT +TEX +TAP

value: wild type


title: HP26695 drppH -TEX -TAP


title: H2_mel


title: HP26695 WT -TEX +TAP


title: IPF SL32680


title: HP26695 WT -TEX -TAP


title: IPF SL32679


title: H4_mel


title: 500 μg/l BDE47 treatment_miRNA

city: Shanghai

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

description: Sample name: 500

data_processing:
Illumina Casava1.7 software used for basecalling.
After obtained from the raw sequencing data, clean reads were mapped into reference zebrafish genome Zv10 assembly.
Trimmed mean of M-values of library size (TMM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: zv10
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample.

organism: Danio rerio

source_name: 6 dpf larvae

extract_protocol:
Zebrafish larvae were homogenized, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tuebingen

value: whole larvae

value: 6 day post fertilization


title: H1_mel

value: skin (melanoma metastasis)


title: IPF SL32677


title: s_DMSO vehicle_miRNA

description: Sample name: s


title: 5 μg/l BDE47 treatment_miRNA

description: Sample name: 5


title: G11_mel

value: melanoma short-term culture Ma-Mel-123


title: HP26695 drppH +TEX +TAP


title: c_Wildtype_miRNA

description: Sample name: c


title: G12_mel

value: double-negative for BRAF and NRAS mutations


title: G10_mel


title: IPF SL32674


title: IPF SL32671


title: G9_mel


title: MV411_MLL_InputDNA

city: Oxford

source_name: Leukemia cell line (MV4-11)

value: Leukemia cell line; MV4-11

tag: cell type

value: Paediatric monocytic cell line derived from AML M5 with t(4;11)(q21;q23) translocation


title: CCRF_MLL_InputDNA

source_name: Leukemia cell line (CCRF-CEM)

value: Leukemia cell line; CCRF-CEM

value: Paediatric immature T-cell line derived from ALL with t(5;14)(q35.1;q32.2)


title: IPF SL32670

value: F

value: lung


title: G6_mel


title: G8_mel


title: G7_mel


title: H3_mel


title: MV411_MLL_ChIPSeq


title: G5_mel


title: KOPN8_MLL_InputDNA

source_name: Leukemia cell line (KOPN-8)

value: Leukemia cell line; KOPN-8

value: Infant pre B-cell line derived from ALL with t(11;19)(q23;p13) translocation


title: G3_mel


title: OmpR_ChIPSeq

city: Boston

first: James

last: Galagan

state: MA

address: 44 Cummington Mall

department: Biomedical Engineering

institute: Boston University

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to GenBank ID U00096.2
Peak calling was done using SPAT
R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
Genome_build: U00096.2 (GenBank)
Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively

organism: Escherichia coli K-12

source_name: Culture cells

growth_protocol: Cells were grown in LB media with 1mM IPTG at 37 °C with shaking for 2 hours

extract_protocol:
For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
The appropriate protocols were performed using standard Illumina procedures

treatment_protocol: For total RNA extraction, cells were pelleted in 4 °C.

tag: transcription factor

value: OmpR

tag: antibody

value: anti-FLAG mAb

tag: antibody vendor/catalog#

value: Sigma/Cat. No. F1804


title: Nac_RNASeq

tag: strain

value: Nac


title: NtrC_ChIPSeq

value: NtrC


title: THP1_MLL_InputDNA

source_name: Leukemia cell line (THP-1)

value: Leukemia cell line; THP-1

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(p21;q23) translocation


title: G2_mel

source_name: subcutaneous metastasis

value: skin (melanoma metastasis)

tag: culture

value: melanoma short-term culture Ma-Mel-123

tag: melanoma genetic conditions


title: Nac_ChIPSeq


title: ML2_MLL_InputDNA

value: Leukemia cell line; ML-2

value: Adult monocytic cell line derived from AML M4 with t(6;11)(q27;q23) translocation


title: CCRF_MLL_ChIPSeq

value: Leukemia cell line; CCRF-CEM


title: THP1_MLL_ChIPSeq


title: SEM_Menin_InputDNA

value: Leukemia cell line; SEM

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: ML2_MLL_ChIPSeq

value: MLL1 (Bethyl, A300-086A)


title: F12_mel

value: double-negative for BRAF and NRAS mutations


title: F11_mel


title: F10_mel


title: SEM_Menin_ChIPSeq

value: Menin (Bethyl, A300-105A)


title: SEM_BRD4_InputDNA


title: G1_mel


title: SEM_BRD4_ChIPSeq


title: SEM_BioCAP_InputDNA


title: CsiR_ChIPSeq

value: CsiR


title: G4_mel


title: F9_mel


title: KOPN8_MLL_ChIPSeq

value: Leukemia cell line; KOPN-8

value: Infant pre B-cell line derived from ALL with t(11;19)(q23;p13) translocation


title: SEM_BioCAPseq


title: CsiR_RNASeq


title: F2_mel


title: F3_mel


title: F5_mel


title: F4_mel


title: F7_mel


title: E12_mel


title: E11_mel


title: F1_mel


title: pre-B acute lymphoblastic leukemia sample at relapse (LAX7R)

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: genomic DNA isolated from human pre-B ALL sample LAX7

data_processing:
Library strategy: ExomCapture-Seq
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All single-end, 50-bp-long reads were mapped to the reference human genome sequence, build NCBI37 (hg19), using BWA (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60). The variants SNVs and the indels were called against the human genome build NCBI37 (hg19) using GATK  with the default parameters (McKenna et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303).
Genome_build: hg19

source_name: pre-B acute lymphoblastic leukemia at relapse

growth_protocol: Leukemia cells from bone marrow biopsy of patients with pre-B ALL were xenografted into sublethally irradiated NOD/SCID mice via tail vein injection. After passaging, leukemia cells were harvested and cultured on OP9 stroma cells in Alpha Minimum Essential medium (Alpha-MEM, Invitrogen, Carlsbad, CA) without ribonucleotides and deoxyribonucleotides, supplemented with 20% fetal bovine serum, 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Genomic DNA was extracted from samples using the QIAamp DNA Mini kit (Qiagen). Exome capture was performed using  the Exome capture kit  Nimblegen Whole Exome Version 3. Enriched exome fragments were subjected to sequencing using HiSeq2000 (Illumina). Exomes were captured according to NimbleGne Whole Exome Capture protocol (Roche NimbleGen, USA). ExomCapture with the capture kit  Nimblegen Whole Exome Version 3, followed by high-throughput sequencing using Illumina HiSeq 2000.
Libraries were prepared using the Illumina DNA-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

tag: diagnosis

value: pre-B acute lymphoblastic leukemia


title: E10_mel

tag: tissue


title: F6_mel


title: SGC-0

city: Wuhan

first: Jing

state: Hubei

address: NO.1 Shizishan street, Hongshan district

institute: Huazhong Agricultural University

data_processing:
SOAPnuke 1.5.2 used for base-calling
reads were filtered by removing adapters, low quality reads and unknown bases
Clean reads were mapped to Galgal4 using Bowtie
Genes expression level are quantified by a software package: RSEM
Genome_build:  Galgal4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gallus gallus

source_name: pre-hierarchical granulosa cell

growth_protocol: cells were seeded in 6-well culture plate with M199 medium supplemented with 5% fetal bovine serum (FBS) and and incubated at 39°C and 5% CO2 in a humidified incubator

extract_protocol:
total RNA was extracted from transfected cells by TRIzol LS Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell were cultured overnight (18h) and were transfected with pcDNA3.1-FOXL2 or pcDNA3.1 using Lipofectamine 2000, respectively. 48h after transfection, cells were washed in PBS and were collected for RNA-seq analysis

value: chicken pre-hierarchical follicle (SYF)

tag: group

value: control

tag: age

value: 26 week


title: SGC-F

value: FOXL2 overexpression


title: BGC-0

source_name: pre-ovulatory granulosa cell

value: chicken pre-ovulatory follicle (F2-F4)


title: BGC-F


title: E5_mel

value: skin (melanoma metastasis)

value: melanoma short-term culture Ma-Mel-123


title: F8_mel


title: E8_mel


title: E9_mel


title: E6_mel


title: E1_mel


title: E7_mel


title: pre-B acute lymphoblastic leukemia sample at diagnosis (LAX7)

source_name: pre-B acute lymphoblastic leukemia at diagnosis


title: E3_mel


title: D11_mel


title: D12_mel


title: nGFP background control (Replicate 2)

city: Philadelphia

first: Daniel

last: Bose

state: PA

address: 3400 Civic Center Blvd., 9th floor

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: Background control data

data_processing:
3' adapter removal with cutadapt (v1.7.1), reads >15nt retained
mapped to mm10 genome using Bowtie 1.1 (-p 3 -v 2 -m 10 --best --strata)
filtered to remove any non T>C mismatches using in-house custom software
RNA binding site identification with PARalyzer v1.1 (requiring minimum read depth of 5 reads, a minimum of 1 T>C conversion and minimum cluster length of 15nt)
For downstream analyses with public data, genome co-ordinates were converted from mm10 to mm9 using the UCSC Genome Browser LiftOver tool.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files containing CBP PAR-CLIP read densities. Read counts were normalised per one million reads mapped (RPM).

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: Cells were passaged in DMEM + 10% FBS

extract_protocol:
CBP/p300 flox/flox MEFs or background control strains were incubated for 16h with 150uM 4-thiouridine (4-SU). Plates were washed with PBS before cells were cross-linked using 150mJ/cm2 365nM UV light with a stratalinker UV crosslinker (Stratagene). All subsequent stages of PAR-CLIP were carried out immediately to prevent degradation of cross-linked CBP. Cells were harvested by scraping in  PBS + 1mM EDTA and lysed by incubating for 10 minutes on ice with CLIP lysis buffer A (20mM Hepes KOH pH7.9, 150mM KCl, 5mM EDTA, 2% EMPIGEN, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 0.1% SDS, 2mM DTT) supplemented with Complete EDTA free protease inhibitor (Roche), Murine RNase inhibitor (NEB), Turbo DNase I (Ambion) and sonicated for 5x 30s cycles in a bioruptor (Diagenode). Cell lysate was cleared by centrifugation at 20000xg for 30 minutes. The cleared cell lysates were subjected to an initial partial RNAse digestion step using RNase/T1 cocktail (4000x) (Ambion) for 5 min at 21C to improve immunoprecipitation efficiency. Immunopreciptations were carried out using a depleting amount of anti-CBP antibody (Santa Cruz, sc-583) or anti-Flag M2 (Sigma, F1804) for 2 hours at 4C. Lysates were then subjected to a second, more stringent RNAse treatment using RNase A/T1 cocktail (10x) for 15min at 37C before recovering immunocomplexes for 30 minutes with BSA blocked Protein A dynabeads (Life Technologies). The digestion with higher RNase concentration was important for optimising transfer efficiency of the large (>250KDa) CBP-RNA complexes.  Beads were collected and washed twice with CLIP wash buffer (20mM Tris HCl pH 7.9 (4C), 400mM KCl, 5mM EDTA, 0.5mM EGTA, 2% EMPIGEN, 0.7% Na-deoxycholate, 0.5% N-lauroylsarcosine, 2M Urea, 2mM DTT, protease inhibitors) then IP50 buffer (20mM Tris HCl pH 7.9 (4C), 50mM KCl, 0.2mM EDTA, 10% Glycerol, 2mM DTT), before resuspending in 1x Turbo DNase buffer. CLIP wash buffer contains 2M Urea, which was important for removing non-specific RNA binding whilst retaining immunoprecipitated protein-RNA complexes. Contaminating DNA was removed by incubation with 2.5U Turbo DNase I for 30 minutes at 37C. Beads were washed with CLIP wash buffer and IP50 buffer. Cross-linked RNA complexes were dephosphorylated by incubating with Recombinant Shrimp Alkaline Phosphatase (rSAP, NEB) for 15 minutes at 37C, washing with Phosphatase wash buffer (20mM Tris HCl pH 7.9 (4C), 400mM KCl, 10mM EDTA, 10mM EGTA, 0.05% IGEPAL CA-630, 2mM DTT) then T4-PNK buffer (50mM Tris HCl pH 7.5 (RT), 50mM NaCl, 10mM MgCl2, 5mM DTT). Protein-RNA complexes were then labelled by incubating with 5U T4 PNK (NEB) with 10uCi g-32P-ATP for 15 minutes at 37C. Labelled material was washed again with CLIP wash buffer and IP50 before denaturing with LDS loading buffer and resolving on a 3-8% Tris-acetate gel. Gels were transferred to 0.2uM PVDF membrane for 12h at 40V, then exposed to autoradiography screens or x-ray film for 12-24h to image labelled RNA complexes. For sequencing experiments, labelled CBP-RNA bands (or control bands) were excised from the membrane and eluted by incubating with RNA elution buffer (Tris HCl pH8.0 (RT), 50mM NaCl, 1mM EDTA, 2mM CaCl2, 1% SDS) and Proteinase K (4mg/ml, Roche) for 30 minutes at 37C, then for 30 minutes at 55C with RNA elution buffer + 3.5M Urea and Proteinase K. RNA was then purified using acidic phenol:chloroform (Ambion) and ethanol precipitation.
Sequencing libraries for PAR-CLIP experiments were prepared using NEB next small RNA library set for Illumina sequencing (New England Biolabs) according to manufacturers instructions. Libraries were checked for quality by bioanalyzer before and after size selection by Pippin prep and were 50bp single-end sequenced on an Illumina NextSeq 500.

treatment_protocol: Cells were incubated with 4-thiouridine (4-SU) for 16h and irradiated with 150mJ/cm2 365nm UV.

value: CBP/p300 flox/flox

tag: transgene

value: nls-GFP

tag: tag

value: flag

tag: ip antibody

value: Flag M2 (mouse monoclonal), Sigma Aldrich F1804


title: Gal4-DBD background control (Replicate 1)

description: Background control data

value: yeast Gal4 DNA binding domain (Gal4-DBD)


title: D9_mel

value: double-negative for BRAF and NRAS mutations


title: D10_mel


title: CBP PAR-CLIP (Replicate 1)

description: Endogenous target PAR-CLIP data

value: CBP (C20, Rabbit polyclonal), Santa Cruz sc583


title: CBP PAR-CLIP (Replicate 2)

description: Endogenous target PAR-CLIP data


title: nGFP background control (Replicate 1)

description: Background control data


title: D7_mel


title: E4_mel


title: FBM_InputDNA

data_processing:
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk

source_name: Fetal bone marrow

growth_protocol: SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5

extract_protocol:
ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated (~200bp) and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040).

value: Mononuclear cells from second trimester human fetal bone marrow


title: CB_InputDNA

source_name: Cord blood

value: Mononuclear cells from full-term cord blood


title: D8_mel


title: PT_InputDNA

value: Presentation ALL patient sample engrafred in mice and harvested from spleen


title: D3_mel


title: Gal4-DBD background control (Replicate 2)

description: Background control data


title: D4_mel


title: D2_mel


title: D5_mel


title: CB_MLL_ChIPseq

tag: chip antibody

value: MLL1 (Bethyl, A300-086A)


title: PT_AF4_ChIPseq

value: AF4 (Abcam, ab31812)


title: PT_MLL_ChIPseq


title: SEM_siMLL-AF4_InputDNA

description: cells were treated with 300pmol MLL-AF4-specific siRNA

source_name: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: C10_mel


title: D1_mel


title: C9_mel


title: C12_mel


title: SEM_siMLL-AF4_MLL_ChIPseq


title: C8_mel


title: C7_mel


title: FBM_MLL_ChIPseq


title: D6_mel


title: SEM_siMLL-AF4_AF4_ChIPseq


title: SEM_siControl_InputDNA

description: cells were treated with 300pmol control siRNA


title: C6_mel


title: SEM_siControl_MLL_ChIPseq


title: SEM_MLL_Replicate_InputDNA


title: SEM_siControl_AF4_ChIPseq


title: C5_mel


title: SEM_MLL_Replicate_ChIPSeq


title: C4_mel


title: C3_mel


title: C1_mel


title: B12_mel


title: B11_mel


title: SEM_2umEPZ5676_Rep2

description: processed data file: EPZ5676_rpkm.txt

tag: cell line

value: Leukemia cell line; SEM

tag: treated with

value: 2µM EPZ-5676 for 7 days

tag: molecule subtype

value: nascent RNA


title: SEM_2umEPZ5676_Rep3

description: processed data file: EPZ5676_rpkm.txt

tag: cell type


title: SEM_1umEPZ5676_Rep3

description: processed data file: EPZ5676_rpkm.txt

value: 1µM EPZ-5676 for 7 days


title: SEM_1umEPZ5676_Rep2

description: processed data file: EPZ5676_rpkm.txt


title: SEM_1umEPZ5676_Rep1

description: processed data file: EPZ5676_rpkm.txt


title: B10_mel

value: skin (melanoma metastasis)

value: melanoma short-term culture Ma-Mel-123


title: B9_mel


title: SEM_05umEPZ5676_Rep3

description: processed data file: EPZ5676_rpkm.txt

value: 0.5µM EPZ-5676 for 7 days


title: SEM_05umEPZ5676_Rep2

description: processed data file: EPZ5676_rpkm.txt


title: B8_mel


title: SEM_0umEPZ5676_Rep3

description: processed data file: EPZ5676_rpkm.txt

value: DMSO for 7 days


title: SEM_0umEPZ5676_Rep2

description: processed data file: EPZ5676_rpkm.txt


title: SEM_05umEPZ5676_Rep1

description: processed data file: EPZ5676_rpkm.txt


title: B4_mel


title: SEM_0umEPZ5676_Rep1

description: processed data file: EPZ5676_rpkm.txt


title: B5_mel


title: B3_mel


title: C2_mel