title: SLX-14438_Input_none

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

description:
SLX-14438.D703_D503.HKN27BBXX
processed data file: CTCF_normalised_results.csv

data_processing:
alignement, bowtie2 (v2.3.2)
blacklist filtering, bedtools (v2.25.0)
peakcalling, macs2 (2.1.1.2016030)
normalisation, Brundle (1.0.0)
differintial bnding analysis, Diffbind (2.5.6)
Genome_build: hg19, mm9, dm3
Supplementary_files_format_and_content: csv; Fold-chage in ER binding normalised to H2av spike-in control

growth_protocol: MCF7 cells were grown in T175 flast in DEM + 10% FBS + Pen/Strep + Glutamine

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to the Thruplex DNA-seq Kit Manual

treatment_protocol: Treated samples were exposed to 100 nM Fulvesterant for 48 hours

value: mammary epithelial cells

tag: experiment number

tag: chip antibody

value: ER  (sc-543, Santa Cruz)

tag: control antibody

value: CTCF (3418 XP, CST)

tag: condition

tag: spike-in cell line

tag: spike-in organism

tag: replicate

value: Input


title: SLX-14438_Input_Fulvestrant

status: Public on Aug 22 2017

type: SRA

description:
SLX-14438.D702_D501.HKN27BBXX
processed data file: CTCF_normalised_results.csv

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: Fulvestrant


title: siCtl

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

country: USA

institute: PTC Therapeutics

library_source: transcriptomic

data_processing:
3’READS data were analyzed as described (Li et al. 2015). 3’READS reads were mapped to the human genome (hg19) using bowtie2 (local mode). Uniquely mapped reads (with MAPQ score > 10) that had at least two additional 5’ Ts not aligned to genome (presumably derived from the poly(A) tail) were named pA site supporting (PASS) reads and were used to calculate pA isoform expression. pA isoforms expressed below 5% of all isoforms of a gene were discarded.  Significantly regulated APA events were identified by the Significance Analysis of Alternative Polyadenylation (SAAP) method [Li et al., 2015].
Genome_build: hg19
Supplementary_files_format_and_content: 3READS.pA.read.counts.txt contains information of gene symbol, pA coordinates, read number of pAs in different 3'READS samples. "pA_type" is pA type based on location of a pA. "pAid" has information of chromosome, strand and coordinates (based on hg19).
Supplementary_files_format_and_content: .bw files are bigwig format files used for visualization of read profiles. ".p.bw" and ".m.bw" are for reads (polyA isoforms) on + and - strand, respectively. The height of the read is RPM (read per million PASS read) values.

molecule: total RNA

source_name: knockdown control

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was purified from control and siRNA-treated cells. RNA integrity was analyzed by using Agilent Bioanalyzer. Samples with an RNA integrity number (RIN) >9.0 were subjected to 3’READS analysis
Samples with an RNA integrity number (RIN) >9.0 were subjected to 3’READS analysis following the protocol described in Hoque et al. (2014). Briefly, after RNA fragmentation, poly(A)+ RNA fragments were captured on magnetic beads coated with a chimeric oligonucleotide (oligo CU5T45), which contained 45 thymidines at the 5’ portion and five uridines at the 3’ portion, and subjected to RNase H digestion, which removed the bulk of the poly(A) tail and eluted RNA from beads. Eluted RNA was ligated to 5’ and 3’ adapters followed by reverse transcription, PCR amplification, and deep sequencing on an Illumina HiSeq platform.

treatment_protocol: The siRNAs were transfected using DharmaFECT1 (GE Dharmacon) at 20 nM and maintained for 48, 72, or 96 h as indicated. To maintain high knockdown efficiency after 96 h, the siRNA transfection was repeated 48 h after the first transfection with half the amount of siRNA, and cells were harvested 48 h after the second transfection.

value: Hela

tag: transfection

value: siCtl

tag: library protocol


title: SLX-14438_3b_ERCTCF_none

description:
SLX-14438.D703_D504.HKN27BBXX
processed data file: CTCF_normalised_results.csv


title: 86049102N normal kidney RNA-seq

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
RNA-seq reads were aligned to the human genome (hg19) using TopHat2-2.0.12 [5] (default parameter and --library-type fr-firststrand) and only uniquely mapped reads were analysed.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files generated from uniquely mapped reads

source_name: adjacent normal kidney

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini kit.
RNAseq libraries were prepared using Illumina Tru-Seq RNA Sample Preparation v2 protocol, according to the manufacturer’s instructions. Briefly, poly-A RNAs were recovered from 1 µg of input total RNA using poly-T oligo conjugated magnetic beads. The recovered poly-A RNA was chemically fragmented and converted to SuperScript II and random primers. The second strand was synthesized using the Second Strand Master Mix. Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted to 11 pM and applied to an Illumina flow cell using the Illumina Cluster Station.

tag: individual

tag: disease state

value: ccRCC

tag: tissue

value: adjacent normal kidney


title: 86049102T ccRCC RNA-seq

source_name: ccRCC tumor

value: ccRCC tumor


title: SLX-14438_Ca_CTCF_Fulvestrant

description:
SLX-14438.D702_D503.HKN27BBXX
processed data file: CTCF_normalised_results.csv

value: CTCF


title: 77972083T ccRCC RNA-seq


title: SLX-14438_3a_ERCTCF_Fulvestrant

description:
SLX-14438.D703_D502.HKN27BBXX
processed data file: CTCF_normalised_results.csv


title: SLX-14438_2a_ERCTCF_Fulvestrant

description:
SLX-14438.D702_D504.HKN27BBXX
processed data file: CTCF_normalised_results.csv


title: SLX-14438_2b_ERCTCF_none

description:
SLX-14438.D702_D502.HKN27BBXX
processed data file: CTCF_normalised_results.csv


title: 77972083N normal kidney RNA-seq


title: 75416923T ccRCC RNA-seq


title: 74575859T ccRCC RNA-seq


title: SLX-14438_1b_ERCTCF_none

description:
SLX-14438.D701_D501.HKN27BBXX
processed data file: CTCF_normalised_results.csv


title: 70528835T ccRCC RNA-seq


title: 57398667T ccRCC RNA-seq


title: SLX-14229_Input_none

description:
SLX-14229.D703_D503.HJJL7BBXX
processed data file: CTCF_normalised_results.csv


title: SLX-14229_Ca_CTCF_Fulvestrant

description:
SLX-14229.D702_D503.HJJL7BBXX
processed data file: CTCF_normalised_results.csv


title: SLX-14229_Cb_CTCF_none

description:
SLX-14229.D701_D504.HJJL7BBXX
processed data file: CTCF_normalised_results.csv


title: 57398667N normal kidney RNA-seq


title: SLX-14438_Cb_CTCF_none

description:
SLX-14438.D701_D504.HKN27BBXX
processed data file: CTCF_normalised_results.csv


title: 40911432T ccRCC RNA-seq


title: SLX-14229_3b_ERCTCF_none

description:
SLX-14229.D703_D504.HJJL7BBXX
processed data file: CTCF_normalised_results.csv


title: 40911432N normal kidney RNA-seq


title: 20431713T ccRCC RNA-seq


title: 20431713N normal kidney RNA-seq


title: SLX-14229_2a_ERCTCF_Fulvestrant

description:
SLX-14229.D702_D504.HJJL7BBXX
processed data file: CTCF_normalised_results.csv


title: SLX-14229_2b_ERCTCF_none

description:
SLX-14229.D702_D502.HJJL7BBXX
processed data file: CTCF_normalised_results.csv


title: 17621953T ccRCC RNA-Seq


title: almt1-Pi+M

city: Irapuato

first: Luis

middle: Rafael

last: Herrera-Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Langebio

country: Mexico

institute: Cinvestav - Langebio

data_processing:
Basecalls for RNA-Seq were performed using illumina basecalling pipeline (SolexaPipeline 1.0). ShortRNA-Seq reads with 75-nt reads from each end generated by Illumina sequencing were aligned to the Arabidopsis thaliana reference genome reference genome sequences were downloaded from TAIR.
Alignment of RNA-Seq reads was performed using TopHat2. Count of RNA-Seq reads was performed using HTSeq-count.
Genome_build: TAIR 10
Supplementary_files_format_and_content: The count file has two columns that provide ID (Arabidopsis locus ID) and read number (the number of reads that were alligned to that locus).

organism: Arabidopsis thaliana

source_name: Root apex (2-3 mm)

growth_protocol: Briefly, seeds were grown 5 days after germination under high phosphate(1mM Pi, +Pi) or low phosphate (5µM, -Pi) conditions in petri dishes with 0.1X Modified MS media (1% w/v Sucrose, pH 5.7, and 1% w/v agar).

extract_protocol:
For RNA-Seq total RNA was isolated using the TRIZOL reagent (Invitrogen) according to the manufacturer's instructions.
For preparation of mRNA-Seq Libraries, total RNA was isolated from frozen root tip powder using the TRIzol® reagent (Invitrogen) according to the manufacturer’s instructions for isolation of total RNA from plant tissue. Non–strand-specific mRNA-seq libraries were generated from 5 μg of total RNA (Plant RNeasy kit) and prepared by using the TruSeq RNA Sample Prep kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Treatmens included Low Phosphate and Low Iron (Iron as FeSO4 was not added to the medium solution and 100 µM ferrozine (C20H12N4Na2O6S2; SIGMA) were added to chelate any Fe traces) and Malate Supplementation (-Pi medium supplemented with 1 mM L-malate (SIGMA) prior to pH adjustment).

tag: ecotype

tag: genotype

value: almt1 mutant

tag: phosphate treatment

value: Low Phosphate and Malate Supplementation

tag: duration of treatment

value: 5 days after germination

value: root tips (2-3 mm from the root apex)


title: SLX-14229_1a_ERCTCF_Fulvestrant

description:
SLX-14229.D701_D503.HJJL7BBXX
processed data file: CTCF_normalised_results.csv

tag: experiment number

tag: chip antibody


title: 17621953N normal kidney RNA-Seq


title: almt1-Pi

value: Low Phosphate


title: 75416923N normal kidney RNA-seq


title: SLX-14229_1b_ERCTCF_none

description:
SLX-14229.D701_D501.HJJL7BBXX
processed data file: CTCF_normalised_results.csv

tag: control antibody

tag: condition


title: 74575859N normal kidney RNA-seq


title: 70528835N normal kidney RNA-seq


title: almt1+Pi

value: High Phosphate


title: 12364284T ccRCC RNA-Seq


title: SLX-12998_Input_Fulvestrant

value: mammary epithelial cells

tag: spike-in cell line

tag: spike-in organism

value: mus musculus


title: SLX-14229_Input_Fulvestrant

description:
SLX-14229.D705_D501.HJJL7BBXX
processed data file: CTCF_normalised_results.csv

tag: cell line

value: ER  (sc-543, Santa Cruz)

value: CTCF (3418 XP, CST)

tag: replicate


title: stop1+Pi +M

value: stop1 mutant


title: SLX-12998_2_ER_none

tag: cell type


title: 786-O HIF2A siRNA RNA-seq

source_name: ccRCC cell line

growth_protocol: 786-O cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

treatment_protocol: 786-O cells stably expressing RC3 empty vector (EV) or wildtype VHL (VHL) were kindly provided by Dr. Michael Ohh (University of Toronto). 786-O cells were also treated with either non-targeting control or pooled siRNA against HIF2a (Dharmacon).

tag: treatment

value: HIF2A siRNA

tag: source


title: SLX-12998_Input_none

value: Input


title: 786-O NT RNA-seq

value: non-targeting control


title: SLX-14229_3a_ERCTCF_Fulvestrant

description:
SLX-14229.D703_D502.HJJL7BBXX
processed data file: CTCF_normalised_results.csv

value: Fulvestrant


title: SLX-12998_3_ER_none


title: stop1+Pi


title: Col-0 -Pi -Fe

value: wild type

value: Low Phosphate and Low Iron


title: 786-O VHL RNA-seq

value: wildtype VHL restoration


title: 786-O EV RNA-seq

value: empty vector


title: Col-0 -Pi

value: 5 days after germination


title: 3A RRBS

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

data_processing:
Fastq files aligned with bsmap 2.90 in RRBS mode using the following parameters: -g 1 -w 5 -D C-CGG -p 8 -R -s 12 -S 42 -u; methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z --ct-snp=no-action
use module bsratio of BSMAP-2.90 to compute the methylation ratio of single base level
Genome_build: hg19
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context, methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

source_name: HEK 293T

growth_protocol: ATCC-formulated Dulbecco's Modified Eagle's Medium and 10% fetal bovine serum

extract_protocol:
Extract DNA using Qiagen Allprep Micro kit.
Tru-Seq DNA sample prep kit

treatment_protocol: HEK293T cells were infected by dCas9-SunTag-DNMT3A for 30 days. We purified fluoscent-positive cells and performed RRBS.

value: HEK 293T

value: Human epithelial HEK 293T cells


title: SLX-12998_2_ER_Fulvestrant


title: SLX-14438_1a_ERCTCF_Fulvestrant

description:
SLX-14438.D701_D503.HKN27BBXX
processed data file: CTCF_normalised_results.csv


title: dCas9+3A+HOXA5 RRBS


title: SLX-12998_4_ER_none


title: SLX-12998_1_ER_Fulvestrant


title: dCas9+3A RRBS


title: Neg RRBS


title: SLX-8047_Input_None

description:
SLX-8047.D705_D507.C81G5ANXX
processed data file: H2av_normalised_results.csv

value: H2av (39715, ActiveMotif)

value: drosophila melanogaster


title: SLX-12998_3_ER_Fulvestrant

value: mammary epithelial cells

value: mus musculus


title: 12364284N normal kidney  RNA-Seq

tag: individual

tag: disease state

value: ccRCC

value: adjacent normal kidney


title: stop1-Pi

tag: ecotype

value: stop1 mutant

value: Low Phosphate

tag: tissue

value: root tips (2-3 mm from the root apex)


title: dCas9+3A+KLF4 RNA-seq

data_processing:
RNA-sequencing reads were mapped to hg19 using TopHat 2.0.10 pipleline. The gene expression values (FPKM) were caculated using cufflinks/2.2.1
Genome_build: Hg19
Supplementary_files_format_and_content: TXT files include gene name, chromosome:start-end, FPKM of genes.

extract_protocol:
Qiagen Rneasy Plus micro kit
Truseq stranded mRNA kit

treatment_protocol: HEK293T cells were infected by dCas9-SunTag-DNMT3A for 30 days. We purified fluoscent-positive cells and performed RNA-seq.


title: 3A RNA-seq


title: dCas9+3A+HOXA5 RNA-seq


title: SLX-8047_3b_ER_none

description:
SLX-8047.D705_D508.C81G5ANXX
processed data file: H2av_normalised_results.csv

value: ER  (sc-543, Santa Cruz)


title: SLX-8047_4b_ER_none

description:
SLX-8047.D704_D505.C81G5ANXX
processed data file: H2av_normalised_results.csv


title: SLX-8047_3a_ER_Fulvestrant

description:
SLX-8047.D706_D505.C81G5ANXX
processed data file: H2av_normalised_results.csv

value: Fulvestrant


title: Negative RNA-seq


title: Negative WGBS

description: library strategy: WGBS

data_processing:
use BSMAP-2.90 to align bisulfite-treated sequencing reads to the human genome hg19 of bisulfite treated data
use moabs to compute the methylation ratio of single base level
Genome_build: hg19
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context, methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

extract_protocol:
DNA extraction by Purelink extraction kit
bisulfite treated DNA was made into library with Illumina TruSeq DNA sample preparation kit


title: dCas9+3A+HOXA5 WGBS

description: library strategy: WGBS


title: Col-0 +Pi

tag: genotype

value: wild type

tag: phosphate treatment

value: High Phosphate


title: SLX-8047_2b_ER_none

description:
SLX-8047.D704_D506.C81G5ANXX
processed data file: H2av_normalised_results.csv

tag: experiment number


title: dCas9-3ACD+HOXA5_KLF4_BACH2_3 bisulfite sequencing

description: library strategy: Bisulfite-Seq (amplicons)

data_processing:
use BSMAP-2.90 to align bisulfite-treated sequencing reads to the human genome hg19 of bisulfite treated data
use module bsratio of BSMAP-2.90 to compute the methylation ratio of single base level
Genome_build: hg19
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context, methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

extract_protocol:
Extract DNA using Purelink DNA mini kit. Bisulfite conversion using Qiagen Epitect Bisulfite kit.
Nextera XT

treatment_protocol: For direct comparison (DC), constructs were delivered into HEK293T cells via Lipo2000 transfection (invitrogen). Cells were further cultured 48 hours and fluoscent-positive cells were purified using sorter. HEK293T cells were infected by dCas9-SunTag-DNMT3A for 30 days. We purified fluoscent-positive cells and performed BS-seq.


title: SLX-8047_1a_ER_Fulvestrant

description:
SLX-8047.D705_D506.C81G5ANXX
processed data file: H2av_normalised_results.csv

tag: chip antibody


title: SLX-8047_2a_ER_Fulvestrant

description:
SLX-8047.D704_D507.C81G5ANXX
processed data file: H2av_normalised_results.csv

tag: control antibody


title: dCas9-3ACD+HOXA5_KLF4_BACH2_2 bisulfite sequencing


title: SLX-8047_1b_ER_none

description:
SLX-8047.D706_D508.C81G5ANXX
processed data file: H2av_normalised_results.csv

tag: condition


title: SLX-12998_4_ER_Fulvestrant

tag: spike-in cell line


title: sG_sF_3

city: Xiamen

first: Lei

last: Zhang

state: Fujian

address: Xiang'an Nan Road

department: School of Life Sciences

country: China

institute: Xiamen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  TopHat v2.0.9.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene ,considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cells

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Cells were washed with PBS for twice, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with lentivirus for 24hrs, then changing medium. 72 hrs later, cells were harvest.


title: dCas9-3A+HOXA5_KLF4_BACH2_3 bisulfite sequencing


title: sF_3


title: Co


title: REV_MHH9604

city: Hannover

first: Michal

last: Koska

state: Deutschland

address: Feodor-Lynen-Straße 7

department: Molecular Bacteriology

country: Germany

institute: Twincore GmbH

data_processing:
RNA-seq reads were mapped to the PA14 reference genome (Genbank, NC_008463.1)  genome using the Stampy aligner with default settings.
SAMtools was utilized for sequence variation calling. The reads per gene (rpg) values of all genes were calculated from the SAM output files.
Differential expression was estimated using the R library DESeq
Supplementary_files_format_and_content: The processed files in TXT format include gene names and their recovered read counts for each sample

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa planktonic culture

growth_protocol: The clinical isolates had been grown under standard conditions (LB broth; 37°C) and harvested in RNAprotect (Qiagen) at an optical density at 600 nm (OD600) of 2 before the transcriptome sequencing (RNA-seq) was performed.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Whole-transcriptome sequencing was performed by the use of a custom-made protocol with barcoded RNA libraries to enable pooled sequencing of several samples (for details see Dötsch et al., 2012. The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing)

treatment_protocol: small-colony variant isolates were cultured in 10 ml of LB broth at 37 °C and when turbidity was visible, a 100 µl aliquot was again inoculated into 10 ml of LB broth. At the same time, an aliquot was spread on Columbia blood agar and examined for the occurrence of revertants exhibiting larger surface colonies. This process was repeated until a stable revertant was generated (1-2 weeks).

tag: strain

value: revertant


title: YFP-high fraction

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Drive, 2179 CIEMAS

department: Biostatistics and Bioinformatics

institute: Duke University

description: Sample 5 (S5)

data_processing:
Illumina Casava 1.8.2 software used for basecalling; Illumina bcl2fastq Conversion Software v2.18 was then used to convert bcl files to fastq format. The quality score encoding is in +Phred 33.
Sequenced reads were filtered for rRNA using SortMeRNA 2.0 (with default parameters) and trimmed for adaptor sequences using Trimmomatic 0.36 (with parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:32)
HISAT2 (version 2.0.3) was used to align the reads to human genome hg19
HTSeq (version 0.6.0) was used to obtain readcounts for each gene (under "-m union" mode); GTF file used was obtained from PrimerSeq repository (http://primerseq.sourceforge.net/gtf.html)
The raw counts for each gene were converted to TPM (transcripts per million) values. For this, the mean fragment length were computed using PicardTools "ComputeInsertSizeMetrics" function.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Counts and TPM values for each sample

source_name: U2OS pTRIPZ-YFP-ER-E2F1

growth_protocol: Cells were grown in DMEM with 8% fetal bovine serum and Pen/strep

extract_protocol:
Cells from different YFP fractions were sorted by flow cytometry. RNA was isolated using Qiagen RNAeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 500 ng/ml doxycycline for 48 hours followed by addition of 90 nM OHT for an additional 20 hours.

tag: cell line

value: U2OS pTRIPZ-YFP-ER-E2F1

value: osteosarcoma

tag: fraction

value: YFP-high fraction


title: SLX-8047_4a_ER_Fulvestrant

description:
SLX-8047.D706_D507.C81G5ANXX
processed data file: H2av_normalised_results.csv

tag: cell type

value: H2av (39715, ActiveMotif)

tag: spike-in organism

tag: replicate


title: dCas9+3A RNA-seq

value: HEK 293T

value: Human epithelial HEK 293T cells


title: dCas9-3A+HOXA5_KLF4_BACH2_2 bisulfite sequencing


title: dCas9-3A+HOXA5_KLF4_BACH2_1 bisulfite sequencing


title: REV_MHH8607


title: YFP-medium fraction

description: Sample 4 (S4)

value: YFP-medium fraction


title: YFP-low fraction

description: Sample 3 (S3)

value: YFP-low fraction


title: dCas9+3A+HOXA5_KLF4_BACH2_1 bisulfite sequencing


title: dCas9+3A+HOXA5_KLF4_BACH2_3 bisulfite sequencing


title: dCas9+3A+HOXA5_KLF4_BACH2_2  bisulfite sequencing


title: REV_MHH9536


title: parental

description: Sample 1 (S1)

value: parental


title: dCas9-3ACD_DC bisulfite sequencing


title: dCas9-3ACD+HOXA5_KLF4_BACH2_1 bisulfite sequencing


title: dCas9+3A+KLF4 bisulfite sequencing


title: Neg_DC bisulfite sequencing


title: dCas9+3A_DC bisulfite sequencing


title: SLX-12998_1_ER_none

value: mammary epithelial cells

value: mus musculus


title: dCas9+3A+HOXA5 bisulfite sequencing


title: dCas9+3A bisulfite sequencing


title: Input 50-125 kDa

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Library strategy: eCLIP-seq
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding; column 4 contains -log10(p-value) and column 5 contains log2(fold-enrichment) in eCLIP versus paired size-matched input
Supplementary_files_format_and_content: bw format

growth_protocol: 293T cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, cells were crosslinked with UV (254 nm, 400 mJ/cm2). Cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen.

tag: antibody


title: 3A bisulfite sequencing


title: Input 25-100 kDa


title: Input 125-200 kDa


title: Negative bisulfite sequencing


title: V5-only 150-225 kDa

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog#

tag: antibody lot#


title: Input 175-250 kDa


title: V5-only 50-125 kDa


title: V5-only 75-150 kDa


title: dCas9-3A_DC bisulfite sequencing


title: TLBR4

city: Bethesda

first: Jing

last: Chen

state: MD

address: 10 center drive

institute: NEI

description: No additional information.

data_processing:
RNA-Seq Analysis
Calculation Method: The mapping of paired-end reads and the extraction of putative single nucleotide variants (SNVs) were performed. In brief, paired-end reads were mapped to the RNA sequences in the RefSeq database (NCBI building 37) using the Burrows-Wheeler Aligner (BWA) software with default parameters. Reads that failed to map to RefSeq were mapped to RNA sequences in the Ensemble database. The remaining unmapped reads were mapped to the human genome assembly (NCBI building 37). Mutant SNV calls were declared if more than two reads were mutated and the ratio of mutant reads versus total coverage was >20%. SNVs that corresponded to single nucleotide polymorphisms in the dbSNP database (build #132), the 1000 Genomes database (May 2011 release), and the NHLBI GO Exome Sequencing Project (ESP) database (ESP5400 December 2011 release) were excluded.
Genome_build: hg19

extract_protocol:
RNeasy Kit
Other: Total RNA was extracted using the RNeasy kit (QIAGEN).
Libraries were generated with the TruSeq RNA Sample Prep Kit-v2 (Illumina) according to the manufacturer's instructions.

tag: disease state

value: ALK- anaplastic large cell lymphoma (ALCL)


title: TLBR2

description: No additional information.


title: DL40


title: TLBR3

description: No additional information.


title: Input 75-150 kDa


title: V5-only 25-100 kDa


title: V5-only 125-200 kDa


title: V5-only 100-175 kDa


title: TLBR1

description: No additional information.


title: YFP-negative fraction

description: Sample 2 (S2)

value: YFP-negative fraction


title: FE-PD

description: No additional information.

source_name: FE-PD

value: FE-PD


title: Mac-2B

description: No additional information.


title: V5-only 175-250 kDa


title: Mac-2A

description: No additional information.


title: FLAG-only 75-150 kDa

value: FLAG

value: Sigma


title: Input 100-175 kDa


title: FLAG-only 150-225 kDa


title: Mac-1

description: No additional information.


title: FLAG-only 125-200 kDa


title: FLAG-only 25-100 kDa


title: SM13_MM8

city: Boston

first: Chia-Jen

last: Liu

state: MA

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Exosomal microRNAs were extracted from the serum of a patient with multiple myeloma

data_processing:
The BCL files were demultiplexed using CASAVA 1.8.2 (Illumina) into FASTQ files.
Raw sequencing reads were then analyzed using miRDeep2 to quantify known small RNA species.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited csv files include read counts and normalized values for each sample.

source_name: Serum

extract_protocol:
Total RNA was extracted from exosome pellets using the miRNeasy Micro Kit (Qiagen)
Small RNA libraries were prepared and amplified using the NEBNext small RNA Library Prep Set (New England BioLabs). Amplified libraries were resolved on a 10% polyacrylamide gel for size selection. The 140 to 160 nucleotide bands corresponding to adapter-ligated constructs derived from the 21 to 40 nucleotide RNA fragments were excised and recovered in a DNA elution buffer. The average size distribution of each library was determined using Agilent Bioanalyzer with High Sensitivity Chip Kit (Agilent) and quantified on ABI 7900HT Fast RT-PCR instrument using the KAPA Library Quantification kit (Kapa Biosystems). Each library was adjusted to final concentration of 2 nM, pooled and sequenced on an Illumina HiSeq 2000 sequencer for single-read 50 cycles.

tag: group

value: Multiple myeloma patient


title: SM15_MM10


title: FLAG-only 100-175 kDa


title: SM16_MM11


title: Input 150-225 kDa


title: SM11_MM6


title: SM12_MM7


title: SM10_MM5


title: SM9_MM4


title: DGCR8 wt-eCLIP input


title: FLAG-only 175-250 kDa


title: DGCR8 FLAG-eCLIP


title: DGCR8 FLAG-eCLIP input


title: SM8_MM3


title: LIN28 V5-eCLIP input


title: DGCR8 wt-eCLIP


title: LIN28 wt-eCLIP


title: SM4_N4

description: Exosomal microRNAs were extracted from the serum of a healthy adult

value: Healthy adult


title: LIN28 wt-eCLIP input


title: LIN28 V5-eCLIP


title: SM6_MM1


title: SM7_MM2


title: FLAG-only 50-125 kDa


title: RBFOX2 V5-eCLIP input


title: SM2_N2


title: SM3_N3


title: RBFOX2 V5-eCLIP


title: RBFOX2 wt-eCLIP


title: SM1_N1


title: PATU-ishME3-Dox+1

city: Houston

first: Jennifer

last: Wang

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Sequenced reads were mapped to hg19 genome using the Spliced Transcripts Alignment to a Reference (STAR) software tool
The HTSeq software tool was used to calculate the read count for each transcript
The Limma R package was used for assessment of transcript abundance measurements and doing differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes transcript abundance measurements (read count) for each sample

source_name: PDAC cell line_xenograph_tumor_on-dox

extract_protocol:
RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using the standard Illumina protocols

tag: tissue

value: PDAC xenograft tumor

value: PATU


title: PATU-ishME3-Dox+2


title: PATU-ishME3-Dox-3

source_name: PDAC cell line_xenograft_tumor_off-dox


title: FMR1 FLAG-eCLIP


title: FMR1 wt-eCLIP

value: MBL


title: PATU-ishME3-Dox-1


title: FMR1 FLAG-eCLIP input


title: FMR1 wt-eCLIP input


title: SM5_N5


title: HNRNPC V5-eCLIP isoform 2


title: HNRNPC wt-eCLIP

value: HNRNPC


title: MES sample 2  (MiSeq TEsR sequencing)

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

description:
Targeted enrichemnt sequencing of small RNAs
processed data file:
Count_all_miRNAs_snoRNAs_rRNAs_snRNAs.txt

data_processing:
Samples and corresponding barcodes are split by the build-in MiSeq Illumina pipeline. Adapter sequence was removed using a Python package cutadapt (Martin,M. 2011. DOI: http://dx.doi.org/10.14806/ej.17.1.2011), with the adapter sequence AGATCGGAAGAGC. The adapter-removed reads were mapped to the reference sequence (mm10) using bwa/0.7.12 with bwa mem option or bowtie2.2.6 with local alignment option. The output files are in SAM format.  The SAM files were converted to BAM files using samtools/1.2.1 . The BAM files were then filtered for Unique mapped reads using samtools/1.2.1 with –q10 option. The enriched expression level of the target was calculated using coveragebed utility in the bedtools/2.25.0 package. Normalization and analysis of read count data were performed using R/3.2.2.
Genome_build: mm10
Supplementary_files_format_and_content: Mapped read counts and base-pair coverage (tab separated files)

organism: Mus musculus

source_name: MES sample

growth_protocol:
MESs: mouse ESCs  (B6G-2) from the RIKEN BioResource Center
Culture media were changed daily, and cells were passaged every 2–3 days.
Cells were negative for mycoplasma contaminations.
MEF cells were grown in DMEM + 10% serum + glutamine. MES cells were grown under feeder-free conditions in mouse ESC medium containing DMEM (Wako), 1,000 U/ml leukemia inhibitory factor (LIF; Millipore), 15% FBS (Gibco), 2.4 mM L-glutamine (Invitrogen), 0.1 mM non-essential amino acids (NEAA; Invitrogen), 0.1 mM 2-mercaptoethanol (Gibco), 50 U/ml penicillin and 50 μg/ml streptomycin (Gibco).

extract_protocol:
The RNA was prepared by the mirVana microRNA Isolation Kit (Ambion) according to the manufacturer’s instructions (with or without the small RNA enrichment step). Before TEsR capture, 2.5 µg purified total RNA sample was treated to remove ribosomal RNAs by using Ribo-Zero Gold rRNA removal method (Epicentre).
The step-by-step protocol is presented in our protocol paper (manuscript under review). Briefly, we developed a powerful method, termed Target-Enrichment of small RNAs (TEsR), that enables researchers to answer the above questions by reliably detecting and quantifying multiple forms of sRNAs, including rare sRNAs. To allow full-length sequencing of mature sRNAs and their precursors, TEsR circumvents two common processes that exclude longer forms of sRNAs, namely size selection (by gel, bead, or columns) and PCR amplification by random primers. In TEsR, linkers are ligated to each of the two ends of the full-length sRNA molecules, allowing strand information to be maintained and thus enabling the detection of both sense and antisense sRNAs. In order to minimize undesired ligations, TEsR uses amine-blocked linkers to block 3’-ends and pre-adenylated DNA linkers that show high reactivity with 3’-end of RNA. Optimal use of ligases was tested for high RNA-DNA and RNA-RNA ligation specificity and efficiency. To capture also the significant proportion of sRNAs that are capped, as it is the case for many small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), tRNA, and miRNA, a 5’-cap removal step is applied before ligating the 5’-RNA linker to the RNA. Both the initial stringent denaturing conditions and the immediate mixing with an excess of hybridization probes, ensure the removal and prevent the reformation of sRNA secondary structures. After linker ligation, TEsR amplifies all ligated sRNAs by PCR, specifically captures targeted molecules by hybridization, and then wash-removes PCR products from abundant and/or irrelevant RNA species.
Targeted small RNAs were captured by in-solution hybridization and sequenced at a ultra-deep level.

treatment_protocol: We used TRF2 conditional knock out mouse embryonic fibroblasts, Cre recombinase (Rosa26-CreERT2) inducible by 4-hydroxytamoxifen (4OHT) at 0.6 uM for 48 hours as described in Rossiello et al. (Nature Communications, 2017).

value: Mouse embryonic stem cells

tag: treatment group

value: No induction for TRF2 uncapping

tag: molecule subtype

value: small RNA


title: HNRNPC V5-eCLIP isoform 1


title: PATU-ishME3-Dox-2


title: HNRNPC wt-eCLIP input


title: N1het_TercWT_2

city: San Francisco

first: Christina

last: Theodoris

state: California

address: 1650 Owens Street

institute: Gladstone Institutes, University of California, San Francisco

description: aortic valve RNA-seq

data_processing:
Sequencing quality was assessed with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed using Fastq-mcf (http://code.google.com/p/ea-utils)
Reads were aligned to the mm9 (Mus musculus assembly July 2007) transcriptome and genome using Tophat (Kim et al., 2013)
Unmapped (-F 4) and low-quality reads with MAPQ score below 30 (-q 30) were removed using Samtools (Li et al., 2009)
Duplicate reads were removed using Picard MarkDuplicates (http://broadinstitute.github.io/picard)
USeq (Nix et al., 2008) was used to normalize raw read counts, calculate FPKM (fragment per kb per million reads mapped), and analyze differential expression using the negative binomial test with FDR correction 10%
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file containing Ensembl ID, gene name, average FPKM in each genotype, and binary indicator for whether gene was significantly dysregulated in the indicated comparison (1=significantly dysregulated)

source_name: aortic valve

extract_protocol:
Hearts were washed with PBS, and three AV leaflets were harvested by micro-dissection from each of four N1WT/mTRWT, four N1+/-/mTRWT, three N1WT/mTRG2, and four N1+/-/mTRG2 mice. Leaflets were incubated in collagenase for 20 minutes at 37 °C to dissociate cells, and RNA was isolated using the Qiagen RNeasy Micro Kit.
cDNA was prepared with the NuGen Ovation RNA-seq System V2 Kit. Total RNA was reverse transcribed to synthesize the first-strand cDNA using a combination of random hexamers and a poly-T chimeric primer. The RNA template was then partially degraded by heating, and the second-strand cDNA was synthesized using DNA polymerase. The double-stranded DNA was then amplified using single primer isothermal amplification (SPIA). In this linear cDNA amplification process, RNase H degraded RNA in DNA/RNA heteroduplex at the 5′-end of the double-stranded DNA, after which the SPIA primer bound to the cDNA and the polymerase started replication at the 3′-end of the primer by displacement of the existing forward strand. Random hexamers were then used to amplify the second-strand cDNA linearly. Finally, libraries from the SPIA-amplified cDNA were made using the NuGen Ovation Ultralow DR Kit. The mRNA-seq libraries were analyzed by Agilent Bioanalyzer and quantified using an Illumina Library Quantification Kit (KAPA Biosystems). Four mRNA-seq libraries were pooled per lane of paired-end 100 bp sequencing on an Illumina HiSeq 2500 instrument.

tag: genotype

tag: age

value: 2 months


title: MEF induced sample 2 (MiSeq TEsR sequencing)

source_name: MEF induced

growth_protocol:
MEFs, a gift from Eros Lazzerini Denchi (The Scripps Research Institute, La Jolla, USA), were grown in DMEM supplemented with 10% fetal bovine serum and 1% glutamine
Cells were passaged every 2–3 days
Cells were negative for mycoplasma contaminations.
MEF cells were grown in DMEM + 10% serum + glutamine. MES cells were grown under feeder-free conditions in mouse ESC medium containing DMEM (Wako), 1,000 U/ml leukemia inhibitory factor (LIF; Millipore), 15% FBS (Gibco), 2.4 mM L-glutamine (Invitrogen), 0.1 mM non-essential amino acids (NEAA; Invitrogen), 0.1 mM 2-mercaptoethanol (Gibco), 50 U/ml penicillin and 50 μg/ml streptomycin (Gibco).

value: Mouse embryonic fibroblast

value: Induction for TRF2 uncapping


title: RBFOX2 wt-eCLIP input


title: MEF uninduced sample 2  (MiSeq TEsR sequencing)

source_name: MEF uninduced


title: MES sample 1  (MiSeq TEsR sequencing)


title: MEF uninduced sample 1  (MiSeq TEsR sequencing)


title: MEF induced sample 1 (MiSeq TEsR sequencing)


title: KO-DSS RNASeq rep1

city: shanghai

first: Yongfeng

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

description: KO DSS-1

data_processing:
Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
FPKM  method is used in calculated expression level
Genome_build: hg19

source_name: DSS treated colon

growth_protocol: no treatment

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

treatment_protocol: mice were treated with 2% DSS for 3 day and isolated the colon epethelial cell

tag: cell typr

value: primary colon epithelial cell

value: colon


title: KO-DSS RNASeq rep2

description: KO DSS-2


title: PATU-ishME3-Dox-4

tag: cell line


title: WT-DSS RNASeq rep1

description: control DSS-1

value: wild type


title: Hypoxia+MitoQ-NPs [P]

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

institute: Cardiff University

description: polyA-enriched total RNA

data_processing:
For each sample, the data from both lanes were pooled before running the analysis pipeline. Alignment of the sequencing reads was performed via TopHat using the rat reference genome Rnor_6.0 (GenBank Assembly ID GCA_000001895.4). HTSeq was used to generate read counts from the resulting BAM files.
We used RUVSeq to adjust read counts in order to mitigate unwanted variation unrelated to treatment groups. Using these counts as input, differential gene expression analysis was performed using edgeR.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: CSV files containing fold change and p values after each RUVSeq normalisation step (UQ, k1, k2, k3, k4) for every detected Ensembl ID and gene name. Processed data files are provided for every possible comparison between the four groups.

organism: Rattus norvegicus

source_name: Frontal cortex

growth_protocol: Three-month-old female Sprague-Dawley rats (Charles River, Wilmington, MA) were maintained on ad libitum standard rat chow and tap water in a 10:14-h light-dark cycle and acclimatized before breeding. All animal procedures were approved by the University of Alberta Health Sciences Animal Policy and Welfare Committee, in accordance with the Canadian Council on Animal Care guidelines. All efforts were made to minimise suffering and the number of animals used.

extract_protocol:
RNA was extracted from 50 mg of fetal frontal cortex tissue at GD20 using the Qiagen RNeasy Mini kit (Qiagen). RNA quality and integrity was confirmed on the 2100 Bioanalyzer.
Libraries were prepared using the TruSeq Stranded mRNA Linrary Preparation Kit from Illumina.

treatment_protocol: Day 0 of pregnancy was determined by sperm in a vaginal smear. On gestational day (GD) 15 of pregnancy the rats were injected intravenously with saline (vehicle control) or 125 μM MitoQ-NPs and exposed for the next 6 days to 21% (Normoxia) or 11% oxygen (Hypoxia) in an A-Chamber (BioSpherix, USA). Rats were sacrificed at GD20 and the foetal brains were collected flash-frozen.

tag: embryonic age

tag: strain

value: Sprague-Dawley

tag: Sex

value: Male

value: foetal frontal cortex

tag: maternal oxygen concentration

tag: maternal injection

value: MitoQ-NPs


title: Hypoxia+Saline [O]

description: polyA-enriched total RNA

value: Saline


title: Hypoxia+Saline [K]

description: polyA-enriched total RNA


title: Normoxia+MitoQ-NPs [J]

description: polyA-enriched total RNA


title: Hypoxia+MitoQ-NPs [H]

description: polyA-enriched total RNA


title: Normoxia+MitoQ-NPs [N]

description: polyA-enriched total RNA


title: Normoxia+Saline [M]

description: polyA-enriched total RNA


title: Normoxia+MitoQ-NPs [F]

description: polyA-enriched total RNA


title: Normoxia+Saline [E]

description: polyA-enriched total RNA


title: Normoxia+Saline [I]

description: polyA-enriched total RNA


title: Normoxia+MitoQ-NPs [B]

description: polyA-enriched total RNA


title: Hypoxia+Saline [G]

description: polyA-enriched total RNA


title: Normoxia+Saline [A]

description: polyA-enriched total RNA


title: WT-DSS RNASeq rep2

description: control DSS-2


title: Hypoxia+MitoQ-NPs [D]

description: polyA-enriched total RNA


title: Hypoxia+Saline [C]

description: polyA-enriched total RNA


title: J6

status: Public on Aug 21 2017

city: Edmonton

first: Ou

state: AB

address: 410 Agriculture/Forestry Centre, University of Alberta

department: AFNS

country: Canada

institute: University of Alberta

data_processing:
Alignment to genome with Tophat2
Alignment output piped to Ht-seq-count for read counting
Reads mapped were normalized into reads per million
Differential analysis was performed using edgeR
Functional anlaysis with Ingenuity Pathway Anlaysis
Genome_build: umd3.1
Supplementary_files_format_and_content: [.txt] file content is normalized expressional abundance for genes expressed in each tissue of each animal

organism: Bos taurus

source_name: Spirla colon tissue

extract_protocol:
Two 2 cm2 biopsies of each tissue were collected from each animal and immediately flash frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered gut tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina truseq_stranded_total_rna_sample_preparation kit

treatment_protocol: Gut tissues collected from cattle with two phenotypes, one is negative for E. coli O157, one is shedding > 104 CFU E. coli O157/g of feces

tag: individual

tag: phenotype

value: positive for E. coli 0157

value: Spiral colon


title: J7

source_name: Descending colon tissue

value: Descending colon


title: I6


title: J3

source_name: Proximal jejunum tissue

value: Proximal jejunum


title: J1

source_name: Duodenum tissue

value: Duodenum


title: J2

source_name: Cecum tissue

value: Cecum


title: I7


title: I3


title: Hypoxia+MitoQ-NPs [L]

description: polyA-enriched total RNA


title: I2


title: I5

source_name: Distal jejunum tissue

value: Distal jejunum


title: H6


title: H7


title: H5


title: H2


title: H3


title: EXOSC3_patient

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

data_processing:
91 Mio FASTQ reads were aligned to the human reference sequence (GRCh37.75) with the STAR 2.4.0.1 aligner.
Resulting BAM files were investigated and normalized with the CUFFLINKS 2.2.1. pipeline (CUFFLINKS>CUFFMERGE>CUFFQUANT>CUFFNORM).
As the quantitative measure for gene abundance we used the FPKM value (fragments per kilobase of transcript per million mapped reads), which is calculated by the CUFFQUANT module of the CUFFLINKS software.
In order to render the highly different absolute FPKM expression levels comparable on the same graph, we provide the z-score for each gene, which is calculated using the mean and the SD of the 6 controls according to z-scorepatient = (mean(FPKM)controls – FPKMpatient)/SD(FPKM)controls.
Genome_build: Homo sapiens GRCh37.75
Supplementary_files_format_and_content: FPKM

source_name: quadiceps muscle of EXOSC3 patient

extract_protocol:
fresh muscle biopsy, flash frozen in liquid nitrogen, TRIzol extraction of RNA
BGISEQ-500 RNA-seq, single end 50 bp, unstranded

tag: mutation

tag: gender

value: male


title: H1


title: G7


title: G5


title: G6


title: G3


title: G2


title: G1


title: F7


title: F5


title: F6


title: F3


title: E3

value: negative for E. coli O157


title: I1


title: F2


title: E2


title: F1


title: E1


title: E6


title: E5


title: D7


title: E7


title: D3


title: D5


title: D2


title: D1


title: D6


title: C7


title: C3


title: C6


title: C2


title: C1


title: B3


title: B6


title: B7


title: B1


title: B5


title: A6


title: A5


title: A7


title: A3


title: A2


title: A1


title: KO1

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build NCBIM37.v65) using RSEM v1.20 and Bowtie2 v0.12.7.
Data were normalized using TMM method from limma Bioconductor package
Genome_build: NCBIM37.v65
Supplementary_files_format_and_content: NormCounts.txt. Tab separated text file

molecule: polyA RNA

source_name: mouse embryonic heart

growth_protocol: Ctcf fl/+; Nkx2.5-Cre x Ctcf fl/fl crosses. Embryonic hearts (control, doble heterozygous and Ctcf KO) were taken at 10.5dpc, taking the day in which the plug was found as 0.5dpc.

extract_protocol:
Pulled hearts samples were smashed and polyA RNA was extracted with trizol and cleaned with a Quiagen column
RNA libraries were prepared for sequencing using standard RNA TrueSeq kit from Illumina

treatment_protocol: No treament

tag: developmental stage

value: heart

value: Ctcf fl/fl; Nkx2.5-Cre/+

value: mix


title: KO2

tag: tissue


title: KO3


title: J5


title: HET3

value: Ctcf fl/+; Nkx2.5-Cre/+


title: HET1


title: HET2


title: C5


title: HEK293T_G3BP2_replicate1_PAR-CLIP-seq

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

description: processed data file: G3BP2_processed.xlsx

data_processing:
library strategy: PAR-CLIP-seq
All samples were sequenced using an Illumina Hiseq2000 with single end 50-bp read length. The adapters were trimmed by using the FASTX-Toolkit2.
PAR-CLIP data: Deep sequencing data were mapped to Human genome version hg38 using Tophat version 2.03 without any gaps and allowed for at most two mismatches. PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings.
RNA-seq data: RNA-Seq libraries were quantified with kallisto version 0.43.0 (Bray et al., 2016) by pseudoallignment to the RefSeq transcript database downloaded at 28-06-2016. Absolute transcript concentrations per cell were computed by linear-fitting the RNA spike-in TPM values to attomoles. RNA half-life measures were calculated as described in Wang et al. (Wang et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: PAR-CLIP data is in Excel tables of each experiment with all bound genes and associated peak locations. RNA-Seq data is in tab delimited files with per gene: readcounts, transcripts per million, and transcript copynumber per cell.

growth_protocol: HeLa and HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo) supplemented with 10% Fetal bovine serum (FBS, Gibco), 1X Penicillin/Streptomycin (15140-122, Thermo) and 1 mM glutamine (Invitrogen).

extract_protocol:
RNA was extracted using Qiagen RNA miniprep kit.
For RNA-seq experiment,  RNA was purified and ERCC spike-in was added. rRNA was depleted using RiboZero kit. Library was prepared using in-house protocols.
For PAR-CLIP experiment, RNA was purified and the purified bound RNA was dissolved in 12 µl RNase-free water, of which 6 µl was subjected to small RNA library preparation with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (E7300S, NEB).

treatment_protocol: For RNA-seq experiment, G3BP1 and METTl3 were knocked down by transfecting siRNAs (Origene). Transcription was inhibited by  ActinomycinD and samples were collected at predetermined intervels.  For PAR-CLIP experiment,  five 15-cm were transfected with Flag-tagged G3BP1 or G3BP2 plasmid at 80% confluency. After another 6 hours, the media was changed and 200 µM 4SU was added. After 14 hours, the media was aspirated and the cells were washed twice with PBS for each plate. The plates were kept on ice, and crosslinking was carried out using 0.15 J/cm2 365nm Ultraviolet light. 2 ml PBS was added and the cells were collected using a cell lifter.

tag: cell line background

tag: par-clip antibody

value: Anti-FLAG antibodies


title: WT1

tag: genotype

value: Ctcf fl/fl


title: HNRNPC V5-eCLIP isoform 2 input

tag: antibody


title: HEK293T_G3BP2_replicate2_PAR-CLIP-seq


title: WT2


title: HeLa_METTL3KD-6h_RNA-seq to determine mRNA half-lives

description: processed data file: quantification_g3bp1KdMettl3Kd.txt

data_processing:
All samples were sequenced using an Illumina Hiseq2000 with single end 50-bp read length. The adapters were trimmed by using the FASTX-Toolkit2.
PAR-CLIP data: Deep sequencing data were mapped to Human genome version hg38 using Tophat version 2.03 without any gaps and allowed for at most two mismatches. PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings.
RNA-seq data: RNA-Seq libraries were quantified with kallisto version 0.43.0 (Bray et al., 2016) by pseudoallignment to the RefSeq transcript database downloaded at 28-06-2016. Absolute transcript concentrations per cell were computed by linear-fitting the RNA spike-in TPM values to attomoles. RNA half-life measures were calculated as described in Wang et al. (Wang et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: PAR-CLIP data is in Excel tables of each experiment with all bound genes and associated peak locations. RNA-Seq data is in tab delimited files with per gene: readcounts, transcripts per million, and transcript copynumber per cell.

value: HeLa

tag: genotype/variation

value: METTL3 knockdown

tag: time point

value: 6h after ActinomycinD


title: B2


title: HNRNPC V5-eCLIP isoform 1 input

tag: cell line


title: HeLa_METTL3KD-3h_RNA-seq to determine mRNA half-lives

value: 3h after ActinomycinD


title: HeLa_METTL3KD-0h_RNA-seq to determine mRNA half-lives

value: 0h after ActinomycinD


title: HeLa_G3BP1OE_oe_6h_RNA-seq to determine mRNA half-lives

description: processed data file: quantification_g3bp1KdG3bp1Oe.txt

value: G3BP1 overexpression


title: HeLa_G3BP1OE_oe_3h_RNA-seq to determine mRNA half-lives


title: HeLa_G3BP1OE_oe_0h_RNA-seq to determine mRNA half-lives


title: HeLa_G3BP1OE_con_3h_RNA-seq to determine mRNA half-lives

value: FLAG control overexpression


title: HeLa_G3BP1OE_con_6h_RNA-seq to determine mRNA half-lives


title: HeLa_G3BP1OE_con_0h_RNA-seq to determine mRNA half-lives


title: HeLa_G3BP1KD_kd_6h_RNA-seq to determine mRNA half-lives

value: G3BP1 knockdown


title: HeLa_G3BP1KD_kd_3h_RNA-seq to determine mRNA half-lives


title: HeLa_G3BP1KD_con_6h_RNA-seq to determine mRNA half-lives

value: scrambled control knockdown


title: HeLa_G3BP1-METTL3KD-6h_RNA-seq to determine mRNA half-lives

value: G3BP1 knockdown + METTL3 knockdown


title: HeLa_G3BP1KD_con_0h_RNA-seq to determine mRNA half-lives


title: HeLa_G3BP1KD_con_3h_RNA-seq to determine mRNA half-lives


title: WT3

tag: strain


title: HEK293T_G3BP1_replicate2_PAR-CLIP-seq

description: processed data file: G3BP1_processed.xlsx


title: HeLa_G3BP1KD_kd_0h_RNA-seq to determine mRNA half-lives


title: HEK293T_G3BP1_replicate1_PAR-CLIP-seq


title: HeLa_G3BP1-METTL3KD-3h_RNA-seq to determine mRNA half-lives


title: HeLa_Con-3h_RNA-seq to determine mRNA half-lives


title: HeLa_Con-0h_RNA-seq to determine mRNA half-lives


title: HeLa_G3BP1-METTL3KD-0h_RNA-seq to determine mRNA half-lives


title: HeLa_Con-6h_RNA-seq to determine mRNA half-lives


title: Tumor at diagnosis. Patient p56

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

country: Austria

institute: Children's Cancer Research Institute

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
T56d

data_processing:
RNA-seq reads were mapped with GSNAP v2014-12- 28 [20147302] (“-- maxsearch=100 -- npaths=1 -- max-mismatches=1 --novelsplicing=0 “) to human reference genome build GRCh37. Known SNPs and splice sites were extracted from dbSNP build 138 and Ensembl GRCh37 build 75, respectively.
DESeq2-normalized fragments per million (FPM), log2 scale
Genome_build: hg19
Supplementary_files_format_and_content: DESeq expression matrix (log2)

source_name: Tumor

extract_protocol:
miRNeasy Micro Kit
30 ng of total RNA was used for cDNA synthesis following the NEBNext® UltraT RNA Library Prep Kit for Illumina® protocol (New England BioLabs). From the point when cDNA was synthesized, the library was completed in an automated way at the EMBL Genomics Core Facility (Heidelberg, Germany) following the manufacture's protocol.

tag: cell type

value: Tumor cells from the primary tumor


title: MNCs at relapse. Patient p33

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M33r

source_name: Non-tumor mononuclear cells (MNCs)

value: DTCs-depleted bone marrow (MNCs)


title: MNCs at relapse. Patient p34

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M34r


title: MNCs at relapse. Patient p24

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M24r


title: MNCs at relapse. Patient p23

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M23r


title: MNCs at relapse. Patient p13

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M13r


title: MNCs at relapse. Patient p22

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M22r


title: MNCs at diagnosis. Patient p60

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M60d


title: MNCs at relapse. Patient p15

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M15r


title: MNCs at relapse. Patient p11

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M11r


title: MNCs at relapse. Patient p20

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M20r


title: MNCs at relapse. Patient p21

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M21r


title: MNCs at relapse. Patient p10

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M10r


title: MNCs at relapse. Patient p08

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M08r


title: MNCs at relapse. Patient p12

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M12r


title: MNCs at relapse. Patient p07

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M07r


title: MKN7_wt_H3K9me3

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
For FAIRE-seq, Illumina CASAVA1.8.2 software was used for basecalling and demultiplexing.
FAIRE-seq reads were aligned to hg19 reference human genome, using ELAND (Illumina mapping program)
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
FAIRE-seq libraries were prepared according to Illumina's instructions. ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: Gastric cancer cell line

tag: infected with

value: none (control)

tag: chip antibody

value: H3K9me3_ChIP (abcam, ab8898, lot GR232099-3)


title: MKN7_EB1_H3K27me3

data_processing:
For ChIP-seq (K4me3, K27ac), Illumina CASAVA1.8.2 software was used for basecalling and demultiplexing.
For ChIP-seq (K4me3, K27ac), ChIP-seq reads were aligned to hg19 reference human genome, using ELAND (Illumina mapping program)
For H3K27me3 ChIP-seq, BCL2FASTQ version1.8.4 software was used for basecalling.
For H3K27me3 ChIP-seq, ChIP-seq reads were aligned to hg19 reference human genome, using bowtie.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared according to Illumina's instructions.

value: EBV


title: DTCs at diagnosis. Patient p37

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D37d

source_name: Disseminated tumor cells (DTCs)

value: Bone marrow derived DTCs


title: DTCs at diagnosis. Patient p39

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D39d


title: MKN7_wt_H3K27me3


title: MKN7_EB1_H3K4me1

value: epstein-barr virus (EBV)

value: H3K4me1_ChIP (abcam, ab8895, lot GR114265-2)


title: DTCs at diagnosis. Patient p42

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D42d


title: DTCs at diagnosis. Patient p61

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D61d


title: DTCs at diagnosis. Patient p43

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D43d


title: MKN7_EB1_H3K9me3


title: DTCs at relapse. Patient p33

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D33r


title: DTCs at diagnosis. Patient p31

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D31d


title: DTCs at diagnosis. Patient p30

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D30d


title: DTCs at diagnosis. Patient p28

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D28d


title: DTCs at relapse. Patient p26

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D26r


title: DTCs at diagnosis. Patient p27

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D27d


title: DTCs at relapse. Patient p25

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D25r


title: DTCs at relapse. Patient p22

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D22r


title: DTCs at relapse. Patient p24

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D24r


title: DTCs at relapse. Patient p20

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D20r


title: DTCs at relapse. Patient p18

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D18r


title: DTCs at relapse. Patient p17

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D17r


title: MKN7_wt_H3K4me1


title: DTCs at diagnosis. Patient p36

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D36d


title: DTCs at relapse. Patient p21

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D21r


title: DTCs at diagnosis. Patient p40

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D40d


title: DTCs at relapse. Patient p15

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D15r


title: DTCs at diagnosis. Patient p35

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D35d


title: DTCs at relapse. Patient p10

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D10r


title: DTCs at relapse. Patient p11

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D11r


title: DTCs at relapse. Patient p14

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D14r


title: DTCs at relapse. Patient p16

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D16r


title: DTCs at diagnosis. Patient p10

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D10d


title: DTCs at diagnosis. Patient p33

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D33d


title: DTCs at relapse. Patient p08

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D08r


title: DTCs at diagnosis. Patient p08

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D08d


title: Ikk2 2h

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

institute: Genome Institute of Singapore

description: 2 hours postfertilization

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were uniquely mapped to Zv9 genome with ensembl-annotation 71 using tophat v2.0.9
Mapped reads fragments per kilobase of transcript per million (FPKM) was calculated and normalized using cuffdiff (Cufflinks v2.1.1) with default parameters.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish Ikk2 mutants were obtained using zinc-finger nuclease-mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2.

extract_protocol:
Embryos were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment.

value: AB

value: whole embryo


title: Ikk2 4h

description: 4 hours postfertilization


title: DTCs at relapse. Patient p23

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D23r


title: WT 4h

description: 4 hours postfertilization

value: wild type


title: DTCs at diagnosis. Patient p05

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D05d


title: DTCs at diagnosis. Patient p06

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D06d


title: DTCs at relapse, without enrichment. Patient p07

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D07r2


title: DTCs at relapse. Patient p07

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D07r


title: RNAseq on shDouble Rep4

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

data_processing:
Kallisto was used to quantitate transcript expression levels using GRCh38 reference with the following paramters --single -l 200 -s 50 -b 50
tximport was used to aggregate count data per gene using Kallisto output.
DESeq2 was used for differential expression analysis with an FDR of 0.05 and no explicit fold change cut off
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files of count data for each sample;
count_matrix.csv: csv of raw count data from tximport
brg_all.csv: csv of log2 fold changes for shBRG
brm_all.csv: csv of log2 fold changes for shBRM
double_all.csv: csv of log2 fold changes for shDouble

source_name: HepG2_shBRG1 + shBRM

growth_protocol: HepG2 cellls were purchased from ATCC and grown in DMEM + 10%FCS + penicillin and streptomycin

extract_protocol:
RNA was extracted using direct-zol kit (Zymo) form cells resuspended in Trizol.
Kapa mRNA-seq

treatment_protocol: shRNA treatments were carried out by infecting cells with lentivirus in the presence of 8ug/mL polybrene, followed by selection with puromycin and harvested 5 days post transduction

value: liver cancer cell line

tag: tranduced with

value: shBRG1 + shBRM


title: RNAseq on shBrg1 Rep4


title: RNAseq on shNS Rep4

value: shNS


title: RNAseq on shDouble Rep3


title: WT 2h

description: 2 hours postfertilization


title: 3-plus-RRBS-39

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were quality and adapter trimmed using Trim Galore with RRBS option.
The trimmed reads were aligned to the human and mouse genomes (build hg19/GRCh37 and mm10/GRCm38, respectively) using Bismark aligner.
Methylation calls were performed by Bismark.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: bismark coverage report (tab-delimited): <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: Hematopoietic progenitor cell

growth_protocol: Human cell lines were grown in RPMI media with 10-20% FBS, mouse progenitors were cultured in Optimem media supplemented with 10%FBS and SCF, IL3 and IL6 cytokines

extract_protocol:
DNA was isolated by proteinase K digestion, phenol chloroform extraction and ethanol precipitation
Bisulfite sequencing libraries were prepared using the TruMethyl-Seq Kit from CEGX following standard Illumina protocols

treatment_protocol: Human cell lines were treated with vitamin C in culture for 0, 12 and 72hrs. Mouse progenitors were treated with 1ug/ml Doxycycline to turn off Tet2 shRNA expression for 14 days

value: Mouse hematopoietic progenitor

tag: time

tag: dox

value: plus


title: 3-minus-RRBS-39

value: minus


title: 7-plus-RRBS-39


title: 14-minus-RRBS-46


title: RNAseq on shBrg1 Rep3


title: 10-plus-RRBS-46


title: DTCs at diagnosis. Patient p01

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D01d


title: RNAseq on shNS Rep3


title: DTCs at relapse. Patient p06

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D06r


title: DTCs at diagnosis. Patient p04

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D04d


title: DTCs at relapse. Patient p12

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D12r


title: DTCs at diagnosis. Patient p03

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D03d


title: 7-plus-RRBS-46


title: 7-minus-RRBS-46


title: 3-plus-RRBS-46


title: RNAseq on shBrg1 Rep2


title: 3-minus-RRBS-46


title: R-14-plus-39

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human and mouse genomes (build hg19/GRCh37 and mm10/GRCm38, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

extract_protocol:
RNA was isolated from cells according to the RNeasy Qiagen Kit protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cancer type


title: RNAseq on shDouble Rep1


title: 7-minus-RRBS-39


title: RNAseq on shBrm Rep3

value: shBrrm


title: DTCs at diagnosis. Patient p02

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D02d


title: 14-plus-RRBS-39


title: 10-plus-RRBS-39


title: RNAseq on shDouble Rep2


title: 14-minus-RRBS-39


title: RNAseq on shBrg1 Rep1


title: 14-plus-RRBS-46


title: 10-minus-RRBS-46


title: R-10-minus-46


title: 10-minus-RRBS-39


title: R-14-plus-46


title: R-14-minus-46


title: RNAseq on shNS Rep2


title: RNAseq on shBrm Rep1


title: R-10-plus-46


title: R-10-minus-39


title: R-14-minus-39


title: R-07-plus-46


title: DTCs at diagnosis. Patient p07

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
D07d


title: RNAseq on shBrm Rep2


title: R-10-plus-39


title: RNAseq on shNS Rep1


title: H3K27ac CHIP-seq in shNS Rep2

data_processing:
Align bowtie2 --sensitive
samtools rmdup
samtools merge
bamCoverage --binSize 30 --extendReads 150 --normalizeUsingRPKM --centerReads
macs2 callpeak -q 0.01 -keep-dup all --nomodel --extsize 150 -g hs --broad
peaks were filtered against blacklist (ENCODE) using bedtools
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files = Reads per million
Supplementary_files_format_and_content: peaks are annotated against gencode v24 for nearest gene

source_name: HepG2_H3K27ac CHIP-seq in shNS

extract_protocol:
Cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees prior to processing for ChIP using protocol from Raab et al 2015.
Kapa DNA hyperpep kit

treatment_protocol: cells were transfected with shRNA targeting BRG1 in the presence of 8ug/mL polybrene, and grown in 2ug/mL puromycin and harvested 7 days after transduction.

value: Histone H3K27ac antibody (pAb)

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot #


title: Input sequencing from shNS rep1

source_name: HepG2_Input sequencing from shNS


title: R-07-minus-46


title: R-07-minus-39


title: Input sequencing from shNS rep2


title: H3K27ac CHIP-seq in shBRG1 Rep1

source_name: HepG2_H3K27ac CHIP-seq in shBRG1


title: Input sequencing from shBRG1 rep2

source_name: HepG2_Input sequencing from shBRG1


title: Input sequencing from shBRG1 rep1


title: R-07-plus-39


title: H3K27ac CHIP-seq in shNS Rep1


title: H3K27ac CHIP-seq in shBRG1 Rep2


title: R-03-plus-46


title: BRM CHIP-seq in shNS Rep1

source_name: HepG2_BRM CHIP-seq in shNS

value: BRM (D9E8B) XP® Rabbit mAb

value: Cell Signaling

value: Lot 2


title: BRM CHIP-seq in shNS Rep2


title: R-03-minus-46


title: BRM CHIP-seq in shBRG1 Rep2

source_name: HepG2_BRM CHIP-seq in shBRG1


title: ChIP input, t=5h

first: Antonina

last: Hafner

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

data_processing:
ChIP-Seq: Alignment done with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6
genome build: hg19
processed data files format and content: bedGraph.gz

growth_protocol: MCF7 and MCF7 p53sh cells were grown in RPMI+10%FBS

extract_protocol:
For ChIP-Seq, cells were crosslinked in 1% formaldehyde and quenched with glycine after 5min, and collected by scraping after washes in PBS+ protease inhibitors.
ChIP seq libraries were prepared using Nugen Ovation Ultralow Library V2 systems kit

treatment_protocol: Cells were either untreated (t=0h timepoints), treated with 10Gy gamma irradiation and collected at corresponding timepoints (t= xh); or treated with 10Gy gamma irradiation following 3 additions of Nutlin 3a (Sigma) according to the protocol described in Purvis et al. 2012 (PMID:23452846)

tag: passage

value: between 4-14 for all experiments


title: MKN7_EB1_FAIRE

value: Gastric cancer cell line

value: epstein-barr virus (EBV)


title: BRG1 CHIP-seq in shNS Rep2

source_name: HepG2_BRG1 CHIP-seq in shNS

value: Anti-BRG1 antibody

value: Abcam


title: R-03-plus-39


title: MKN7_EB1_H3K4me3

value: EBV


title: BRM CHIP-seq in shBRG1 Rep1

value: liver cancer cell line


title: R-03-minus-39


title: MKN7_wt_H3K27ac

value: none (control)


title: BRG1 CHIP-seq in shNS Rep1

value: shNS


title: ChIP input, t=7.5h


title: ChIP input, t=2.5h


title: MKN7_wt_H3K4me3


title: ChIP input, t=0h


title: MKN7_wt_FAIRE


title: H3K27ac ChIP-Seq, t=7.5h

value: Abcam ab4729


title: BRG1 CHIP-seq in shBRG1 Rep2

source_name: HepG2_BRG1 CHIP-seq in shBRG1


title: BM3_Neutrophiles

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

description:
Gene expression data from FACS-purified neutrophiles
The FASTQ files containing sequencing results are in Illumina 1.8+ format, as opposed to the Illumina 1.5+ (proprietary) format.  Meaning they use Sanger quality values (Q + 33), not Illumina quality values (Q + 64)

data_processing:
QA & Trimming: QA was performed using FastQC, low quality bases (Phred below 20) and Illumina adapters were trimmed from paired end reads using Trimmomatic v 0.33
Alignment: Resulting reads (on average 85 x 10^6 per sample) were aligned to the human reference genome GRCh38 release 23 (GENCODE) using STAR version 2.4. Alignment quality statistics and count matrices were computed using HTSeq by mapping the reads to the exons of GENCODE.V23.
Genome_build: GENCODE GRCh38 release 23
Supplementary_files_format_and_content: The processed count data is uploaded as a single .csv file that includes the raw counts for all 9 samples in form of a matrix

source_name: neutrophiles purified from bone marrow

growth_protocol: Different successive stages of terminal granulocytic differentiation (myeloblasts, promyelocytes, metamyelocytes and neutrophils) from healthy human bone marrow were separated and collected by fluorescence-activated cell sorting (FACS) using the following cell type specific markers: CD10-APC, CD11b-APC-Cy7, CD34-PE-Cy7, CD45-PerCP, CD117-PE (Becton Dickinson Biosciences, San Jose, CA, USA) and CD36-FITC (Beckman Coulter, Marseille, France).

extract_protocol:
Total RNA was isolated from cells using Trizol (Invitrogen, Breda, The Netherlands) and stored at -80°C. The RNA quality was verified on an Agilent TapeStation.
Libraries were generated using the TruSeq Stranded Total RNA LT (with Ribo-Zero Gold) kit from Illumina and sequenced on an Illumina HiSeq at the Stanford Sequencing Service Center, CA, USA.

tag: tissue

value: neutrophiles purified from bone marrow

tag: facs


title: BRG1 CHIP-seq in shBRG1 Rep1


title: H3K27ac ChIP-Seq, t=5h

tag: antibody


title: H3K27ac ChIP-Seq, t=0h


title: BM3_Pro_Blasts

description:
Gene expression data from FACS-purified promyelocytes and blasts
The FASTQ files containing sequencing results are in Illumina 1.8+ format, as opposed to the Illumina 1.5+ (proprietary) format.  Meaning they use Sanger quality values (Q + 33), not Illumina quality values (Q + 64)

source_name: blasts and promyelocytes purified from bone marrow


title: p53 ChIP-Seq, t=7.5h, IR 10Gy+Nutlin

value: X-DO1, Santa Cruz sc-126 X


title: BM3_Metamyelocytes

description:
Gene expression data from FACS-purified metamyelocytes
The FASTQ files containing sequencing results are in Illumina 1.8+ format, as opposed to the Illumina 1.5+ (proprietary) format.  Meaning they use Sanger quality values (Q + 33), not Illumina quality values (Q + 64)

source_name: metamyelocytes purified from bone marrow


title: BM2_Promyelocytes

description:
Gene expression data from FACS-purified promyelocytes
The FASTQ files containing sequencing results are in Illumina 1.8+ format, as opposed to the Illumina 1.5+ (proprietary) format.  Meaning they use Sanger quality values (Q + 33), not Illumina quality values (Q + 64)

source_name: promyelocytes purified from bone marrow

value: promyelocytes purified from bone marrow


title: H3K27ac ChIP-Seq, t=2.5h


title: MKN7_EB1_H3K27ac


title: TET_TNF_Batch5_425_13601

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: RNA extracted from immortalized N/TERT-2G keratinocytes

data_processing:
Sequence reads were aligned to the human reference genome (NCBI build 37) using Bowtie and splice junctions were identified using TopHat with default settings.
Read counts were estimated for each gene using an in-house python script (see Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, et al. 2014. Transcriptome analysis of psoriasis in a large case-control Sample: RNA-Seq rovides insights into disease mechanisms. J Invest Dermatol 134:1828-1838)
Expression values were expressed as the number of reads per kilobase per million mapped reads (RPKM).
Genome_build: NCBI build 37
Supplementary_files_format_and_content: Processed data includes raw read counts and RPKM values for all human genes (NCBI build 37) and each sample (.txt files).

source_name: keratinocyte

growth_protocol: N/TERT-TR-shTRAF3IP2 cells were generated by transfecting N/TERT-TR cells with a lentivirus expressing an shRNA (targeting sequence 5’-GCCAGATGCTTGTGTATCCTC-3’) mapping to the 3’ untranslated region of the TRAF3IP2 gene (NM_147686 and NM_001164281 encoding TRAF3IP2 isoforms 2 and 3, respectively). N/TERT-TR-shTRAF3IP2 cells were grown in complete keratinocyte serum-free medium (KSFM, Life Technologies, Carlsbad, CA) adjusted to 0.4 mM CaCl2, with feedings every two days. Cells were plated at 8,000 cells/cm2. Cells were then grown for seven days, at which point they were confluent.

extract_protocol:
Total RNA was isolated using the RNeasy plus isolation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.  An Agilent Bioanalzyer (Agilent Technologies, Santa Clara, CA) was used to assess RNA quality and quantity.
Polyadenylated RNA was purified and used to prepare complementary DNA libraries for high throughput sequencing using the Illumina mRNA-Seq kit according to the manufacturer’s protocol (Illumina, San Diego, CA). Sequencing of fragmented complementary cDNA was performed using the Illumina Genome Analyzer Iix

treatment_protocol: TRAF3IP2 shRNA expression was induced by addition of Tet (1µg/ml) to the medium the day after seeding. Cells were stimulated with IL-17 and/or TNF. Recombinant human IL-17A and TNF were purchased from R&D Systems (Minneapolis, MN).

tag: batch id

tag: tetracycline

value: TET(+)

tag: treatment

value: TNF


title: TET_CTL_Batch5_425_13599

value: control


title: BM2_Metamyelocytes

value: metamyelocytes purified from bone marrow


title: CTL_IL17TNF_Batch5_425_13598

value: TET(-)


title: TET_IL17TNF_Batch5_425_13602


title: CTL_TNF_Batch5_425_13597


title: p53 ChIP-Seq, t=7.5h, IR 10Gy

city: Boston

value: between 4-14 for all experiments

tag: cell line


title: p53 ChIP-Seq, t=5h, IR 10Gy


title: CTL_CTL_Batch5_425_13595


title: p53 ChIP-Seq, t=1h, IR 10Gy


title: BM2_Blasts

description:
Gene expression data from FACS-purified blasts
The FASTQ files containing sequencing results are in Illumina 1.8+ format, as opposed to the Illumina 1.5+ (proprietary) format.  Meaning they use Sanger quality values (Q + 33), not Illumina quality values (Q + 64)

source_name: blasts purified from bone marrow

value: blasts purified from bone marrow


title: CTL_IL17_Batch5_425_13596


title: p53 ChIP-Seq, t=0h


title: p53 ChIP-Seq, t=4h, IR 10Gy


title: BM1_Neutrophiles


title: p53 ChIP-Seq, t=2.5h, IR 10Gy


title: BM1_Metamyelocytes


title: BM1_Blasts


title: MAF1_macrophage2

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

institute: Stanford University

description:
ChIP-seq macrophage biological replicate 2
Processed data file: MAF1_peak_edgeR.txt

data_processing:
Biological replicates and experimental conditions (-PMA; +PMA) were sequenced together on an Illumina HiSeq2000 (paired-end, 100) for each individual experiment type (RNA-seq, ChIP-seq, PRO-seq), and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed ChIP and ATAC sequencing reads were mapped to the hg19 genome using Bowtie v 2.2.4, duplicate reads were removed by Picard tools v. 1.92 and mitochondrial reads filtered before peak-calling using MACS2 v. 2.1.0.
Alignment of sequencing reads to the current hg19 annotation of human tRNA genes (gtRNAdb; (Chan and Lowe 2009; Chan and Lowe 2016)) included the upstream and downstream 100 nt flanking genomic regions.
Genome_build: hg19
Supplementary_files_format_and_content: tDNA count files were generated by extracting reads over tRNA genes (100nt flanking) and non-tRNA genes and normalized counts determined by DESeq; ATAC and ChIP peaks were determined using MACS2 v. 2.1.0. Changes in chromatin accessibility and histone occupancy were determined by differential read count analyses (EdgeR) over merged peak lists for each factor

source_name: THP-1 cells, + PMA exposure, MAF1 ChIP

growth_protocol: THP-1 cells were obtained from ATCC (Lot # 62454382) and grown for multiple passages in T-75 flasks between 2-8 x 105 cells/mL in growth medium containing RPMI-1640 (Corning), 10% fetal bovine serum, and 1% penicillin streptomycin.

extract_protocol:
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 x 10^6 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 minutes. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 minutes of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1x RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 seconds on, 60 seconds off; 15 additional cycles on a Bioruptor sonicator: 30 seconds on, 30 seconds off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled Dynabead protein G (ThermoFisher) magnetic beads. Anti-histone H3 (acetyl K27) antibody was obtained from Abcam (ab4729), POLR3D antibody was obtained from abcam (ab86786; Lot# GR267691-1). 3-5 ug of antibody per ChIP was coupled to 18 uL beads and rotated overnight with sheared chromatin at 40 C. Beads were then washed 5x in ChIP wash buffer (Santa Cruz), 1x in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65C overnight, followed by digestion of RNA (30 min RNase incubation at 37C) and digestion of protein (30 min proteinase K incubation at 45C). ChIP DNA was then purified on a minElute column (Qiagen)
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For differentiation of THP-1 cells, non-adherent cells were diluted to 2 x 10^5 cells/mL and grown overnight, and a final concentration of 100 nM PMA was added the following morning. THP-1 derived macrophages were collected after 72 hr exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 minutes followed by cell wash in phosphate buffer saline (PBS) buffer.

tag: pma exposure

value: 72 hr PMA exposure

tag: cell type

value: derived macrophages

value: anti-MAF1 (Santa Cruz sc-365312 lot # G1411)