title: MEL-R

city: Madrid

first: Dora

middle: B

last: Krimer

address: Ramiro de Maeztu 9

department: Cell and Molecular Biology

country: Spain

institute: National Spanish Research Council (CSIC)

data_processing:
UniVec Build 6.0 database was used to detect Illumina sequence adapters and trimmed.
Then, mapped to mouse cDNA Ensembl (NCBIM37.67.cdna, 30-04-2012) using BWA, Release 0.6.1 with parameters aln -t -o 2 -e 2 -1 30 -k 3
RNA-seq differential expression analysis was performed following the protocol from Trapnell C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols (2012), Vol.7 (3), 562-578.
Normalized units were in Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM).
The software versions used were TopHat v2.0.1 and Cufflinks v2.0.0
Genome_build: mouse NCBI genome build 37.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: erythroleukemia cells

growth_protocol: MEL-DS19 and MEL-R cells were culture in DMEM supplemented with 10% FBS and 100 units/ml penicillin and streptomycin. MEL-R were cultured in the presence of 5mM HMBA

extract_protocol:
Total RNA was isolated from 1 x 107 cells using the Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell differentiation was induced by exposing logarithmically growing cell cultures to 5 mM of HMBA

tag: strain background

value: MEL-R

value: HMA-resistant erythtoleukemia cells


title: MEL DS19

status: Public on Dec 31 2016

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

value: MEL DS19

tag: cell type

value: erythroleukemia cells


title: pDC CpGP_donor 3

city: Nijmegen

first: Till

middle: Sebastian Manuel

last: Mathan

state: Gelderland

address: Geert Grooteplein 26-28

department: Tumor Immunology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: pDC CpGP_donor 3

data_processing:
Illumina RTA 1.13.48 and OLB-1.9.4 software used for basecalling.
As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean  data). The procedure include following steps:1. Remove reads with adaptor sequences.2. Remove reads in which the percentage of unknown bases (N) is greater than 10%.3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality,
Allignment (SOAPaligner/SOAP2): Sequencing data produced by Illumina HiSeqTM 2000 was aligned to HG19 using SOAPaligner/soap2 Version2.21t with parameter -m 0 -x 1000 -s 40 -l 32 -v 5 -r 2 -p 3
To convert raw read counts to CPM values while normalizing for library sizes, we used the R packages 'limma' (version 3.28.20) and 'edgeR' (version 3.14.0) on R version 3.3.1. The following code was used, with the matrix of read counts contained in 'x': cpm(calcNormFactors(DGEList(x)))
Genome_build: hg19
Supplementary_files_format_and_content: 1) "Mathan et al. RNAseq data raw values" contains the raw reads before the normalization step.  2) "Mathan et al. Processed RNAseq data CPM values" contains the reads after the normalization step to counts/million reads)

organism: Homo sapiens

source_name: Blood

extract_protocol:
CD1c+ mDCs and pDCs were isolated from blood by magnetic-activated cell sorting (FACS). Total RNA was isolated using Trizol. The quality of the isolated RNA (concentration, RIN, 28S/18S and size) was determined by Agilent 2100 Bioanalyzer.
RNA libraries were prepared according to the TruSeq RNA Sample Prep Kit v2 (Illumina)

treatment_protocol: CD1c+ mDCs were treated o/n with GM-CSF, pRNA or without a stimulus. pDCs were treated overnight with IL-3 and the following day with following stimuli for 6 hours: FSME, pRNA, CpGP and only IL-3. pDC unstimulated describes the condition, that RNA was extracted from freshly isolated pDCs without an incubation time.

tag: health condition

value: Healthy Volunteer

tag: tissue

value: Blood

tag: isolation method

value: MACS


title: RNA-Seq_NON_ALL03_IN_TEM_IL5

city: La Jolla

first: Alessandro

last: Sette

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Allergy and Immunology

description:
PolyAtail selected messenger RNA
Smart seq 2 cDNA amplification

data_processing:
Illumina filtering
Alignment with TopHat
DUST scores were calculated with PRINSEQ Lite (v 0.20.3)
Low-complexity reads (DUST > 4) were removed from the BAM files
Generation of SAM files with SAMtools
Obtention of read counts with htseq-count using "union" option
Removing absent features (zero counts in all samples)
Raw counts were imported to R/Bioconductor package DESeq2 to identify differentially expressed genes among samples
DESeq2 normalizes counts by dividing each column of the count table (samples) by the size factor of this column. The size factor is calculated by dividing the samples by geometric means of the genes.
P-values for differential expression are calculated using binomial test for differences between the base means of two conditions.
These p-values are then adjusted for multiple test correction using Benjamini Hochberg algorithm to control the false discovery rate.
We considered genes differentially expressed between two groups of samples when the DESeq2 analysis resulted in an adjusted P-value of <0.05 and the fold-change in gene expression was 2-fold.
Genome_build: UCSC hg19

source_name: Blood PBMCs

growth_protocol: Cells were cultured for less than 18 hours in RPMI1640 supplemented with 5% human AB serum in 24 well plates at a density of 4x106/ml and incubated at 37˚C

extract_protocol:
IFNγ or IL5 cytokine producing cells were captured using a cytokine secretion assay according to manufacturers’ instructions  (Miltenyi Biotech, Germany). Briefly cells were harvested, washed and labeled with 20 μl of anti-IFNγ/CD45- or anti-IL5/CD45- antibody conjugates (Miltenyi Biotech). After cytokine capture, cells were stained with 20 μl/107 cells of PE-labeled detection antibody and co-stained with a combination of antibodies (Anti-CD3, -CD4, -CD45RA and –CCR7) to allow further separation of cells into effector memory (TEM; CD45RA-CCR7-), and central memory (TCM; CD45RA-CCR7+)  by FACS sorting (FACS ARIA BD-Bioscience). Cells were sorted directly in 750ul Trizol LS. To maximize the cell lysis, samples were votexed every 5 minutes for 15 seconds.Total RNA was purified from the different sorted populations using a miRNAeasy kit (Qiagen, USA) as described as recommended by manufacturer. Purified total RNA (0.2–5ng) was amplified following the smart-seq2 protocol (Picelli et al. Nature methods, Vol10 (11), pp1096-98).
1 ng of amplified cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina, San Diego, USA).
Single-end 50bp length reads RNA-seq using the HiSeq2500 sequencer (Illumina, San Diego, USA)

treatment_protocol: 4 million/ml PBMCs from 5 allergic and 6 non-allergic individuals were stimulated in vitro for 3 hours with 2.5 μg/ml of a Tymothy Grass Allergen immunodominant peptides pool (see paper).

value: IL5 secreting memory effector CD4 Tcells - CD3+ CD4+ CD45RA- CCR7- IFNG+

tag: patient phenotype

value: Timothy Grass Non Allergic

tag: seasonality

value: Blood draw during of Timothy Grass pollen season


title: camta1/2/3/sid2 ZT12 rep3

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

description: Plants grown at 22⁰C on soil under a photoperiod of 12 h for 21 days, sampled at ZT12

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to the Arabidopsis reference genome (TAIR10) using Tophat version 1.4.1 in default mode with minimum and maxmum intron lengths being set to 10 and 15,000 bp, respectively. The transcript abundance (FPKM) was estimated using Cufflinks (version 2.1.1). Cuffdiff was run using default parameters with inputs of the TAIR10 genome and transcript annotations.
Genome_build: TAIR v10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: aerial part

growth_protocol: Plants were grown on soil at 22⁰C under a 12 h photoperiod with 100-120 μmol m-2 s-1 light intensity. all samples were collected at ZT12

extract_protocol:
RNA was extracted using the RNeasy plant mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: entire aerial part

tag: age

value: 21 days after germination

tag: ecotype

tag: genotype

value: camta1/2/3/sid2 mutant


title: WT ZT12 rep2

value: wild type


title: camta1/2/3/sid2 ZT12 rep2


title: pDC pRNA_donor 2

description: pDC pRNA_donor 2


title: pDC FSME_donor 3

description: pDC FSME_donor 3


title: pDC FSME_donor 1

description: pDC FSME_donor 1


title: RNA-Seq_ALL01_OUT_TEM_NEG

value: memory effector CD4 Tcells - CD3+ CD4+ CD45RA- CCR7- IFNG+

value: Timothy Grass Allergic

value: Blood draw out of Timothy Grass pollen season


title: camta1/2/3/sid2 ZT12 rep1


title: pDC pRNA_donor 1

description: pDC pRNA_donor 1


title: mDC GM-CSF_donor 3

description: mDC GM-CSF_donor 3


title: WT ZT12 rep3


title: pDC IL3_donor 3

description: pDC IL3_donor 3


title: pDC FSME_donor 2

description: pDC FSME_donor 2


title: mDC GM-CSF_donor 2

description: mDC GM-CSF_donor 2


title: WT ZT12 rep1


title: pDC IL3_donor 2

description: pDC IL3_donor 2


title: pDC CpGP_donor 2

description: pDC CpGP_donor 2


title: pDC IL3_donor 1

description: pDC IL3_donor 1


title: mDC GM-CSF_donor 1

description: mDC GM-CSF_donor 1


title: pDC unstimulated_donor 1

description: pDC unstimulated_donor 1


title: mDC pRNA_donor 1

description: mDC pRNA_donor 1


title: mDC pRNA_donor 2

description: mDC pRNA_donor 2


title: pDC unstimulated_donor 3

description: pDC unstimulated_donor 3


title: pDC unstimulated_donor 2

description: pDC unstimulated_donor 2


title: mDC unstimulated_donor 2

description: mDC unstimulated_donor 2


title: HT1080 NET47 LaminB1-Dam

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: HT1080 NET47 LaminB1-Dam

library_source: genomic

data_processing:
Basecalls and quality filtering performed by BGI according to their standard procedures
Clean reads were aligned to the human hg19 genome using the Burrows-Wheeler aligner bwa mem. Mitochondrial sequences (a common contaminant in these experiments) and unaligned reads were filtered out.
Reads were counted per DpnI fragment (genomic sequence flanked by GATC motifs), and log2(ratio LaminB1/dam) measurements were obtained for undifferentiated and differentiated samples. The log2 ratios were then normalised using quantile normalisation (Bioconductor Limma package) and converted to bigwig format for visualisation purposes.
To identify LADs, we used a circular binary segmentation algorithm (CBS) from the R/Bioconductor package 'DNAcopy' (Venkatraman E. Seshan and Adam Olshen (). DNAcopy: DNA copy number data analysis. R package version 1.44.0) using default parameters. Positive signal segments identified by the CBS algorithm were merged if closer than 5Kb, and then any regions smaller than 15Kb were removed.
IP and PI regions between conditions were then identified by the differences in mean intensity {log2(LaminB1/Dam)} values for each of the segments identified by CBS. Segments where the signal difference was 2-fold or higher when both positive and at least one above a threshold of 0.5, or where the signal was negative in one condition and positive in the other, were highlighted and merged when closer than 5Kb into differential regions (DRs). Regions smaller than 15Kb were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: smooth_100_wt.bw contains the DamID LaminB1/Dam profile for untreated HT1080 cells, per DpnI fragment, quantile normalised, smoothened in 100-fragment windows with a 1-fragment shift
Supplementary_files_format_and_content: smooth_100_n29.bw contains the DamID LaminB1/Dam profile for HT1080-NET29 cells, per DpnI fragment, quantile normalised, smoothened in 100-fragment windows with a 1-fragment shift
Supplementary_files_format_and_content: smooth_100_n39.bw contains the DamID LaminB1/Dam profile for HT1080-NET39 cells, per DpnI fragment, quantile normalised, smoothened in 100-fragment windows with a 1-fragment shift
Supplementary_files_format_and_content: smooth_100_n47.bw contains the DamID LaminB1/Dam profile for HT1080-NET47 cells, per DpnI fragment, quantile normalised, smoothened in 100-fragment windows with a 1-fragment shift
Supplementary_files_format_and_content: LADs_wt_15cut_sm100.bed contains LAD regions for HT1080
Supplementary_files_format_and_content: LADs_n29_15cut_sm100.bed contains LAD regions for HT1080-NET29
Supplementary_files_format_and_content: LADs_n39_15cut_sm100.bed contains LAD regions for HT1080-NET39
Supplementary_files_format_and_content: LADs_n47_15cut_sm100.bed contains LAD regions for HT1080-NET47
Supplementary_files_format_and_content: DR_wt_n29.bed differential regions representing a loss of peripheral association after NET29 expression (PI), compared to untreated HT1080 cells
Supplementary_files_format_and_content: DR_n29_wt.bed differential regions representing a gain of peripheral association after NET29 expression (IP), compared to untreated HT1080 cells
Supplementary_files_format_and_content: DR_wt_n39.bed differential regions representing a loss of peripheral association after NET39 expression (PI), compared to untreated HT1080 cells
Supplementary_files_format_and_content: DR_n39_wt.bed differential regions representing a gain of peripheral association after NET39 expression (IP), compared to untreated HT1080 cells
Supplementary_files_format_and_content: DR_wt_n47.bed differential regions representing a loss of peripheral association after NET47 expression (PI), compared to untreated HT1080 cells
Supplementary_files_format_and_content: DR_n47_wt.bed differential regions representing a gain of peripheral association after NET47 expression (IP), compared to untreated HT1080 cells

molecule: genomic DNA

source_name: fibroblast

growth_protocol: HT1080 fibroblasts were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Genomic DNA was extracted using Qiagen DNA-Easy kit, following manufacturer's instructions.
DamID enrichment protocol: Dam-methylated genomic DNA was enriched using the standard protocol as described by Vogel et al. (2007) Nature Protocols 2:1467-1478. It involves digesting gDNA with DpnI enzyme, which cuts at non-Adenine-methylated GATC motifs.
Libraries were prepared by Beijing Genomics Institute (BGI) to Illumina's specifications

treatment_protocol:
Stable cell lines expressing a NET-GFP fusion were obtained after transfection and subsequent selection/maintenance with 500ug/ml Geneticin. Correct localisation was verified by FISH.
DamID protocol: Lentivirus encoding the control Dam, or LaminB1-Dam fusion, was used to transduce HT1080 cells. Transduction was allowed for 24h, and then the medium refreshed. At 72h post-transduction genomic DNA was extracted.

tag: treatment

value: NET47 overexpression

tag: damid


title: HT1080 NET39 Dam control

description: HT1080 NET39 Dam control

value: NET39 overexpression

value: Dam


title: mDC unstimulated_donor 1

description: mDC unstimulated_donor 1


title: HT1080 NET47 Dam control

description: HT1080 NET47 Dam control


title: HT1080 NET39 LaminB1-Dam

description: HT1080 NET39 LaminB1-Dam


title: mDC unstimulated_donor 3

description: mDC unstimulated_donor 3


title: mDC pRNA_donor 3

description: mDC pRNA_donor 3


title: HT1080 NET29 LaminB1-Dam

description: HT1080 NET29 LaminB1-Dam

value: NET29 overexpression


title: pDC pRNA_donor 3

description: pDC pRNA_donor 3

value: Healthy Volunteer


title: DAC+GSK343_2 (MCF7)

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description:
derived from metastatic site: pleural effusion
Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in two fastq files from each sample to hg19, generating one BAM file per sample
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM and fold change of each condition compared to control, only keep genes with at least one read in one of the samples
export fold change of each inhibitor vs. control into a text file, then import all the fold changes into one excel file
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first 30 columns are the RPKMs of the individual samples. The following columns are the fold change and FDR of the triplicates of each condition compared against the triplicates of control samples

source_name: MCF7 breast cancer cell line

growth_protocol: MCF7 cell line was cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: Cells were treated daily with 100nM decitabine (5-aza-CdR, Sigma), 10uM S2101 (Millipore), 1uM UNC0638 (Sigma), and 1uM GSK343 (Sigma) for 96 hours, or 20nM depsipeptide (Romidepsin, Sigma) was added for 24 hours

value: mammary gland, breast

value: breast cancer cell line MCF7

tag: er status

value: positive

tag: gender

value: female


title: RB_2_RNA-seq

city: Cambridge

first: Kelvin

last: Zhang

state: Massachusetts

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

data_processing:
First we filtered out raw reads with low quality and reads containing adapters.
Next, filtered raw reads (pair-end, 100 bp in length) were mapped to the Homo sapiens reference genome (UCSC hg19) with the gapped aligner Tophat.
The UCSC hg19 gene model was used as the reference genome annotation
The raw read counts were generated by htseq-count. Expression levels were quantified using FPKM units (Fragments Per Kilobase of exon per Million reads mapped) using customized scripts written in Perl.
Genome_build: hg19
Supplementary_files_format_and_content: a txt file contains RPKMs of all samples

source_name: sorted cells lymph node

extract_protocol:
fresh tissue was obtained from a patient's bladder tumor and lymph nodes and dissociated into single cells.  The single cells were either sorted or processed as unsorted.  RNA was isolated for library preparation.
24 RNA libraries were prepared for sequencing using standard Illumina protocols

tag: surface markers


title: HT1080 untreated Dam control

description: HT1080 untreated Dam control

value: untreated


title: EB_2_RNA-seq

source_name: sorted cells tumor


title: LB_2_RNA-seq


title: DB_2_RNA-seq


title: BB_2_RNA-seq


title: HT1080 untreated LaminB1-Dam

description: HT1080 untreated LaminB1-Dam


title: Jurkat_RNA-seq

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
Sequenced reads were aligned to hg19 human genome using STAR 2.4.0i (Dobin A, et al. 2013) with parameters outFilterMatchNminOverLread set to 0.80 and outFilterMultimapNmax set to 1
Genome_build: hg19
Supplementary_files_format_and_content: A BEDGRAPH RNA-seq coverage across the entire genome was calculated by Bedtools genomecov. The bedgraph file was converted into bigwig file.

source_name: Jurkat cell

growth_protocol: Jurkat cells were cultured in RPMI- 1640 medium supplemented with 10% FBS at 37 °C and 5% CO2

extract_protocol:
After 24hours, Jurkat cell pellet was collected and total RNA was extracted  using qiazol and purified using the miRNeasy Isolation Kit (Qiagen)  according to the manufacturer's instructions
RNA samples were first digested with Dnase I to remove possible DNA contaminants and Poly (A) containing mRNA were then purified from total RNA using Poly (T) oligo attached magnetic beads. The purified Poly (A) mRNA were then fragmented using covaris and first strand cDNA was synthesized using random hexamers. This was followed by second strand cDNA synthesis and purification of the cDNA. The cDNA was then subjected to end-repair and 3' adenylated before adaptors were ligated to the 3'adenylated ends. The products were then purified on TAE-agarose gel and PCR amplification was carried out to enrich the cDNA templates. The library was then validated using Agilent Bio-analyzer and ABI StepOnePlus Real-Time PCR System.

treatment_protocol: 10 million Jurkat cells were counted and cultured in 30ml of RPMI-1640 medium supplemented with 10% FBS at 37 °C and 5% CO2 for 24hours in a T75 flask

value: Jurkat


title: R_2_RNA-seq

source_name: lymph node

value: not sorted


title: L_2_RNA-seq


title: D_2_RNA-seq

source_name: bladder tumor


title: AB_2_RNA-seq


title: E_2_RNA-seq


title: HT1080 NET29 Dam control

description: HT1080 NET29 Dam control


title: A_2_RNA-seq


title: B_2_RNA-seq


title: myc

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

description: Myc ChiP-seq after VEGF stimulation for 0h

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using bowtie2 with the following configurations: -p 8 -M 1
ChiP-seq Peaks were called using MACS with the following setting: -f BAM -g 2.45e9, and differential peaks were calculated using bdgdiff module in MACS.
The reads density was calculated using Homer and displayed in tag heat map using JAVA Tree.
RNA-seq reads were aligned to the hg19-ERCC genome assembly (contains hg19 and ERCC sequences ) using tophat2 with the following configurations: -p 4.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell, Cole, et al. , Nature protocols 7.3 (2012): 562-578. In short, cufflinks was used for transcript assembly, cuffmerge for assemblies merge, cuffdiff for differnetial analysis and CummeRbund for the following analysis.
Genome_build: hg19

source_name: Human Endothlial cell line

growth_protocol: Primary HUVEC cells purchased from Lonza  within 3-6 passages were grown  in EBM2+1% FBS or EGM2 medium (Lonza)

extract_protocol:
ChiP-seq: Chromatin DNA was extracted from sonicated nuclei and further selectively accumulated by ChiP-specific antibody.  RNA-seq: total RNA were purified by Qiagen RNeasy column.
Illumina multiplex library protocol for ChiP-seq and mRNA seq of VEGF stimualtion is as described (Bing Zhang, et al. , 2013,Genome Res. 2013 Jun;23(6):917-27); Spike-in mRNA-seq protocol followed ScriptSeq v2 RNA-seq kit (Illumina)

treatment_protocol: 50ng/ml VEGFa was used to treat serum-starved HUVEC cells. For modified RNA experiments, 0.5ug/ml modified RNA expressing GFP and ETS1 was used. For siRNA experiment, 10ng/ml siRNA was used.

value: Primary Human Umbilical Vein Endothelial Cells

tag: passages

tag: antibody

value: myc, Santa Cruz sc-764 X


title: LB_1_RNA-seq


title: RNAPII-input

description: ChIP-seq input


title: RNA-modGFP

description: RNA-seq data of modGFP OE in HUVEC


title: EB_1_RNA-seq


title: DB_1_RNA-seq


title: AB_1_RNA-seq


title: R_1_RNA-seq


title: H3K27ac

description: H3K27ac  ChiP-seq after VEGF stimulation for 0h

value: H3K27me3, Millipore 17-622


title: D_1_RNA-seq


title: H3K36me3

description: H3K36me3  ChiP-seq after VEGF stimulation for 0h

value: H3K36me3, Abcam ab9050


title: L_1_RNA-seq


title: H3K4me3

description: H3K4me3 ChiP-seq after VEGF stimulation for 0h

value: H3K4me3, Active motif  39159


title: H3K4me1

description: H3K4me1 ChiP-seq after VEGF stimulation for 0h

value: H3K4me1, Abcam ab8895


title: A_1_RNA-seq


title: B_1_RNA-seq


title: H3K4me2

description: H3K4me2 ChiP-seq after VEGF stimulation for 0h

value: H3K4me2, abcam  ab32356


title: H3K27me3

description: H3K27me3 ChiP-seq after VEGF stimulation for 0h

value: H3K27ac, Abcam ab4729


title: RNAPII-siCTR

description: RNAPII ChiP-seq on CTR siRNA KD

value: RNAPII,  EMD Millipore 05-623B


title: E_1_RNA-seq


title: RNAPII-modETS1

description: RNAPII ChiP-seq on modETS1 OE


title: RNAPII-siETS1

description: RNAPII ChiP-seq on ETS1 siRNA KD


title: RB_1_RNA-seq


title: RNAPII-modGFP

description: RNAPII ChiP-seq on modGFP OE


title: BB_1_RNA-seq


title: RNA-modETS1

description: RNA-seq data of modETS1 OE in HUVEC


title: ETS1-modETS1

description: ETS1 ChiP-seq on modETS1 OE

value: ETS1, Santa-Cruz sc-111X


title: ETS1-modGFP

description: ETS1 ChiP-seq on modGFP OE


title: Huh1 ODC1siRNA

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence, then mapped to hg19 Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bam2rpkm v.0.06 from the University of Liverpool. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

source_name: Hepatocellular carcinoma cell line

extract_protocol:
Total 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

value: Liver

value: Hepatocellular carcinoma cell line

tag: cell line

tag: sirna

value: ODC1 siRNA treated


title: ETS1-12hour

description: ETS1 ChiP-seq after VEGF stimulation for 12hour

tag: cell type


title: Huh1 NCsiRNA

tag: tissue

value: Negative control siRNA treated


title: Huh7 NCsiRNA


title: ETS1-1hour

description: ETS1 ChiP-seq after VEGF stimulation for 1hour


title: Huh7 ODC1siRNA


title: ETS1-4hour

description: ETS1 ChiP-seq after VEGF stimulation for 4hour


title: Brd4-modGFP

description: Brd4 ChiP-seq on modGFP OE

value: Brd4, Bethyl Laboratories, A301-985A50


title: ETS1-0hour

description: ETS1 ChiP-seq after VEGF stimulation for 0hour


title: 786-O lincRNA KD by siRNA2

city: Stanford

first: Xue

last: Gong

institute: Stanford University

data_processing:
mapping by Tophat v2.0.0 using default parameters
quantilifcation by Cufflinks v2.0.2 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Kidney

growth_protocol: A498 were grown at 37°C in DMEM medium with L-glutamate, supplemented with 10% (vol/vol) fetal bovine serum and 1X Pen/Strep; 786-O were grown at 37°C in RPMI-1640 medium with L-glutamate, supplemented with 10% (vol/vol) fetal bovine serum and 1X Pen/Strep.

extract_protocol:
Total RNA was extracted by Qiagen RNAeasy Mini
Barcoded cDNA libraries were then prepared from total RNA using the Illumina TruSeq RNAseq kit

treatment_protocol: For transfection, 10,000 cells per 6-well plate well were seeded and transfected using Lipofectamine 2000 (Life Technologies) following the manufacturer’s protocol. All siRNAs were On-TARGETplus pools purchased from Dharmacon/GE Healthcare and transfected at a final siRNA concentration of 50nM for 16 hr.

tag: transfection

value: lincRNA KD

tag: tumor type

value: ccRCC

value: Kidney


title: A498 lincRNA KD by siRNA2


title: 786-O NTC rep1

value: non-target control


title: Brd4-modETS1

description: Brd4 ChiP-seq on modETS1 OE

value: Primary Human Umbilical Vein Endothelial Cells


title: iWAT, GRO-seq, Rev-erb alpha KO

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Low quality bases, tailing polyA, and adapter sequences were trimmed using cutadapt. Trimmed reads were then mapped to the mouse reference genome (mm9) and any reads mapped to highly abundant RNA such as rRNA, snoRNA, etc were removed before downstream process. Remaining reads were extended to 150bp for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: Read-per-million (RPM) normalized stack-height profile in bigWig format

source_name: Inguinal white adipose tissue

extract_protocol:
The nuclear run-on assay was performed as previously described (Core et al., 2008; Step et al., 2014; Wang et al., 2011). Nuclei extraction: Mouse tissues were harvested at Zeitgeber Time 10 and washed with cold swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In). Nuclear extract was prepared by dounce homogenization in cold swelling buffer and filtered using the cell strainer (100 µm, BD Biosciences). Lysate was centrifuged at 400g for 10 min, then resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% Igepal) and incubated on ice for 5 min. Nuclei were washed twice with lysis buffer, and resuspended in freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA). Nuclear Run-On (NRO): Nuclei were mixed with an equal volume of run-on buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 200 U/ml Superase-In, 1% Sarkosyl, 500 μM ATP, GTP and Br-UTP, 2 μM CTP) and incubated for 5 min at 30°C. Nuclear RNA was extracted with Trizol (Invitrogen) and treated with DNase (Ambion). RNA was hydrolyzed using fragmentation reagents (Ambion) for 13 min at 70°C and purified through a Micro Bio-Spin Column P-30 (Bio-Rad). RNA was treated with T4 polynucleotide kinase (New England Biolabs) for 1h at 37°C, then with an additional T4 polynucleotide kinase for 1h more, and inactivated for 5 min at 75°C. NRO-RNA immuno-precipitation: Anti-BrdU agarose beads (Santa Cruz) were rotated for 1h in blocking buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20, 0.1% PVP, and 0.1% BSA). Then NRO-RNA was rotated with beads for 1h, followed by washes twice in binding buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20), twice in low salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20, 138 mM NaCl), and twice in TET buffer (TE pH 7.4, 0.05% Tween-20). BrdU-labeled RNA was eluted from the beads four times for 10 min with 100 μl elution buffer pre-heated to 42°C. RNA was precipitated by adding 300 mM NaCl, 1 µl of glycogen and 2.5 volumes of ethanol and incubated overnight at -20°C. RNA was resuspended in water (with 1 U/µl Superase-In and 0.05% Tween-20), denatured for 3 min at 65°C, and treated with poly(A)-polymerase (New England Biolabs) for 30 min at 37°C.
Synthesis of cDNA from RNA was performed as described previously (Wang et al., 2011) using oNTI223 primer (5′-/5Phos/GA TCG TCG GAC TGT AGA ACT CT/idSp/CAA GCA GAA GAC GGC ATA CGA TTT TTT TTT TTT TTT TTT TTV N-3′) where the “5Phos” indicates 5′ phosphorylation, “idSp” indicates the abasic dSpacer furan, and “VN” indicates degenerate nucleotides. The reaction was treated with exonuclease I (Fermentas) for 15 min at 37°C, followed by 100 mM NaOH for 20 min at 98°C, and neutralized with 100 mM HCl. cDNA was denatured at 70°C for 3 min, and run on 10% TBE-urea gel, then products from 105-400 nucleotides size were excised and eluted from shredded gel pieces for 4h in TE + 0.1% Tween and precipitated by adding 1 µl of glycogen, 300 mM NaCl and 2 volumes of ethanol and incubated overnight at -20°C. cDNA was resuspended into circularization reaction and circularized with CircLigase (Epicentre) for 1 hour at 60°C, denatured for 10 min at 80°C, and relinearized by adding relinearization mix (25 mM KCl, 500 µM DTT) and APE I (15U; New England Biolabs). Linearized DNA was amplified by PCR using Phusion Hot Start II Kit, according to manufacturer’s instructions. The oligonucleotide primers oNTI200 (5′-CAA GCA GAA GAC GGC ATA-3′) and oNTI201 (5′-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC G-3′) were used for amplification. The PCR product was run on a 10% TBE gel and products from 150-305 nucleotides size were eluted from shredded gel pieces for 4h in TE + 0.1% Tween + 150 mM NaCl and purified using ChIP DNA Clean and Concentrator Kit (Genesee Scientific). Libraries were sequenced on an Illumina HiSeq2000 with sequencing primer 5′-CGA CAG GTT CAG AGT TCT ACA GTC CGA CGA TC-3′.

value: Inguinal white adipose tissue

tag: genotype/variation

value: Rev-erb alpha KO

tag: strain


title: 786-O lincRNA KD by siRNA1


title: A498 NTC rep1


title: eWAT, GRO-seq, Wildtype

description: nascent RNA

source_name: Epididymal white adipose tissue

value: Epididymal white adipose tissue

value: Wildtype


title: eWAT, GRO-seq, Rev-erb alpha KO

description: nascent RNA


title: iWAT, GRO-seq, Wildtype

description: nascent RNA


title: A498 NTC rep2


title: BAT, GRO-seq, Wildtype

description: nascent RNA

source_name: Browm adipose tissue

value: Browm adipose tissue


title: Sample_5-RD-dux4_no-dox_18hr_expt16

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Removed reads with at least one "N" in the sequence from the raw FASTQ files.
Aligned the FASTQ files onto hg38 using tophat-2.0.12 and bowtie2-2.2.3.
Counted gene hits using Bioconductor's summerizeOverlaps() function with "Intersection-Strict" mode.
Transcripts of genes are collected from the basic gencode v22 available on UCSC genome browser.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 instance yield by DESeq2 comparing dux to non-dux samples and saved in both rda and CSV format.

molecule: polyA RNA

source_name: Human RD rhabdomyosarcome cells containing a doxycyline-inducible DUX4 transgene

growth_protocol: RD-DUX4i cells were grown in DMEM (Gibco) supplemented with 10% FBS (Hyclone) 1% penicillin/streptomycin (Gibco) and 2.0 μg/ml puromycin (Sigma).

extract_protocol:
RNA was isolated using TRIzol reagent (ThermoFisher Scientific) according to manufacturer’s instructions.
Illumina TruSeq libraries were prepared with 500 ng total RNA per sample and using the standard library preparation protocol.

treatment_protocol: DUX4 transgene was induced with 1.0 μg/ml of doxycycline hyclate (Sigma).

value: rhabdomyosarcoma

value: -Doxycycline

tag: experiment number


title: Sample_4-RD-dux4_with-dox_16hr_expt14

value: +Doxycycline


title: Sample_6-RD-dux4_with-dox_18hr_expt16


title: CBAP-down-4

city: Taipei

first: Yun-Jung

last: Chiang

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description:
KG2
CBAP knockout-2

data_processing:
Basecalls performed using CASAVA version 1.8
Sequences were aligned to the version 19 of human genome (hg19) using Bowtie/Tophat (default settings; version 2.0) .
Cuffdiff module of Cufflinks was used to estimate FPKM (fragments per kilobase of exon model per million mapped fragments) and differentially express transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: text file format of FPKM for each sample

source_name: Human T-acute lymphoblastic leukemia cell line: Jurkat_CBAP knockout

growth_protocol: cells were cultured according to the instructions of ATCC

extract_protocol:
Whole RNA was extracted from cells using RNeasy Mini Kit (Qiagen, Venlo) according to the manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: method for knockdown or knockout

value: Jurkat

value: T-acute lymphoblastic leukemia


title: 786-O NTC rep2


title: BAT, GRO-seq, Rev-erb alpha KO

description: nascent RNA


title: BAT, Rev-erb alpha ChIP-seq, Rev-erb alpha KO / Thermoneutral / 5pm

data_processing:
Deep sequencing was carried out by the Functional Genomics Core (J. Schug and K. Kaestner) of the Penn Institute for Diabetes, Obesity, and Metabolism using illumina HiSeq 2000 and sequences were obtained using the Solexa Analysis Pipeline. Sequencing reads mapped to the mouse genome (UCSC mm9) using Bowtie. BigWig files for RPM-normalized stack-height profiles were generated using bedtools and SRA tool kit.
Genome_build: mm9
Supplementary_files_format_and_content: Read-per-million (RPM) normalized stack-height profile in bigWig format

source_name: Brown adipose tissue

extract_protocol:
Murine BAT was collected immediately after euthanasia. It was quickly minced and cross-linked in 1% formaldehyde for 20 min, followed by quenching with 1/20 volume of 2.5 M glycine solution and two washes with ice-cold PBS. Chromatin fragmentation was performed by sonication in ChIP SDS lysis buffer (50 mM HEPES, 1% SDS, 10 mM EDTA, pH 7.5) using probe sonication. Proteins were immunoprecipitated in ChIP dilution buffer (50 mM HEPES, 155 mM NaCl, 1.1% Triton X-100, 0.11% sodium-deoxycholate, complete protease inhibitor tablet, pH 7.5). Crosslinking was reversed overnight at 65 °C in elution buffer (50 mM Tris-HCL, 10 mM EDTA, 1% SDS, pH 8.0) and DNA was isolated using phenol/chloroform/isoamyl alcohol. Precipitated DNA was analysed by quantitative PCR.
ChIP DNA was prepared for sequencing according to the amplification protocol provided by Illumina.

value: Brown adipose tissue

tag: time

tag: genotype

tag: temperature

tag: chip antibody

value: Rev-erb alpha (Cell Signaling, catalog number CS2124, rabbit antibody)


title: CBAP-down-1

description:
C17
CBAP knockdown-1

source_name: Human T-acute lymphoblastic leukemia cell line: Jurkat_CBAP knockdown

value: shRNA


title: Sample_1-RD-dux4_no-dox_16hr_expt11

tag: treatment


title: A498 lincRNA KD by siRNA1

value: lincRNA KD

value: ccRCC


title: BAT, Rev-erb alpha ChIP-seq, WT / Thermoneutral / 5pm

value: WT


title: BAT, Rev-erb alpha ChIP-seq, WT / 4C / 5pm


title: C2-8

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
Forward and reverse raw reads separated by 12 barcodes were received from our core facility
Analysis was performed using the Tuxedo suite of programs including tophat for read mapping, cufflinks for transcript assembly and cuffdiff for transcript abundance comparisons
Following the Tuxedo pipeline the output was further processed using the R Bioconductor package CummeRbund
Genome_build: GRCh37/hg19

source_name: Human embryonic Kidney derived cell line

growth_protocol: human embryonic kidney cell line (HEK293; ATCC #CRL-1573) was cultured using standard protocols. Cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen #11965-084) with 10% fetal bovine serum (Sigma #12003C).

extract_protocol:
RNeasy Mini Kit (Qiagen #74104).
RiboMinus™ technology (ThermoFisher Scientific) was used to deplete ribosomal RNA. Illumina’s TruSeq RNA v2 protocol was used to generate libraries

treatment_protocol: no treatment

tag: modifications

value: CRISPR/Cas9 targetted - unmodified

tag: dinucleotide length


title: CBAP-up-4

description:
CBAP-KO cell reconstituted with CBAP gene
KC2
CBAP-reconstituted-2

source_name: Human T-acute lymphoblastic leukemia cell line: Jurkat_CBAP-KO cell reconstituted with CBAP gene

tag: cell line


title: CBAP-up-3

description:
CBAP-KO cell reconstituted with CBAP gene
KC1
CBAP-reconstituted-1


title: C2-7

value: Human embryonic Kidney derived cell line


title: CBAP-up-2

description:
C11
sh-Ctrl-2

source_name: Human T-acute lymphoblastic leukemia cell line: Jurkat_control_sh


title: CBAP-up-1

description:
C1
sh-Ctrl-1


title: C2-6


title: C2-5


title: Myelin 24 Months Rep1

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

description: RNA-Seq

data_processing:
For all the sequenced samples  reads were aligned to Mouse genome (mm9) using TopHat with default parameters.  For RNASeq data the aligned reads were then provided as an input to HTSeq_count utility from HTSeq package. The raw read count files obtained from HTSeq-count were then processed for differential expression using DESeq package. The raw read counts were normalized for library size differences using estimateSizeFactors function from DESeq package.
Genome_build: mm9
Supplementary_files_format_and_content: normalized read count

source_name: Myelin

extract_protocol:
RNA extraction protocol not provided.
Library construction protocol not provided.

treatment_protocol: A light-weight membrane fraction enriched for myelin was purified from mouse brains as described (Jahn, O., et al., Myelin proteome analysis: methods and implications for the myelin cytoskeleton. Neuromethods, 2013) . Male c57Bl6/N mice from the breeding colony of the Max Planck Institute of Experimental Medicine (MPIEM, Göttingen, Germany) were used. For immunoblot and qRT-PCR, mice were 75 days old.

value: brain

tag: tissue compartment

value: Myelin

tag: age

value: 24 months


title: Myelin 24 Months Rep2

description: RNA-Seq

tag: tissue


title: Sample_3-RD-dux4_no-dox_16hr_expt14

tag: cell type


title: C2-4


title: CBAP-down-2

description:
C29
CBAP knockdown-2


title: Sample_2-RD-dux4_with-dox_16hr_expt11


title: C2-2


title: PTL_6 [CHB_SPNALT]

city: Zhenjiang

first: youwen

last: tan

address: Danjianmen 300

institute: the third hospital of zhenjiang affiliated Jiangsu University

data_processing:
The raw sequences were processed using the Illumina pipeline program. After masking of adaptor sequences and removal of contaminated reads, the clean reads were filtered for miRNA prediction with the software package ACGT101-miR-v4.2 (LC Sciences, Houston, Texas, USA) and subsequently analyzed according to (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248653/). Secondary structure prediction of individual miRNAs was performed by Mfold software (Version 2.38; http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form) using the default folding conditions.
Genome_build: GRCh37.p13

extract_protocol:
The supernatant serum was stored at -80°C until analysis.
Total RNA was isolated using LCS TRK1001 miRNeasy kit
The libraries were constructed from total RNA using the Illumina® Truseq Small RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.
The quantity and purity of total RNAs were monitored using a NanoDrop® ND-1000 spectrophotometer
The integrity of total RNAs was analyzed using an Agilent 2100 Bioanalyzer system and RNA 6000 Nano LabChip Kit

tag: subject status

value: chronic hepatitis B (CHB) patients

tag: sample group

value: CHB patients presenting persistently normal alanine aminotransferase with significant histological features (SPNALT)

value: venous blood


title: Myelin 6 MonthsRep3

description: RNA-Seq

tag: strain

value: 6 months


title: PTL_4 [CHB_NSPNALT]

value: CHB patients presenting persistently normal alanine aminotransferase with no significant histological features (NSPNALT)


title: PTL_2 [control]

value: healthy controls


title: C2-3


title: Myelin P75 Rep3

description: RNA-Seq


title: Myelin P75 Rep2

description: RNA-Seq


title: Myelin 24 MonthsRep3

description: RNA-Seq


title: Myelin P75 Rep1

description: RNA-Seq


title: Myelin P18 Rep3

description: RNA-Seq


title: RAFLS from RA before therapy, AP treated replicate 1

city: Shanghai

first: Christine

last: Nardini

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology

description:
Gene expression data from RA rats after 18 days AP treatment
RA1_AP+
APP_1

data_processing:
Base calling was done with OLB (v1.9.4) and the raw sequences and quality scores (Phred64) were obtained in fastq format.
Low quality reads were filtered from the raw data to obtain high quality reads. The filtered reads include: 1) reads with adapter sequences, 2) reads in which the percentage of unknown bases (N) is greater than 10%, 3) reads in which more than 50% bases whose quality value <= 5. This step was done by the company.
The clean reads were aligned to rat genome UCSC rn4 (downloaded from iGENOME http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn )with the aligner bowtie2 (2.1.0). Parameters: bowtie2 -N 1 -p 30 -x rn4 -U clean_data.fq.gz -S align.sam
The aligned reads were quantified by HTseq (0.5.4p3) using the UCSC rn4 annotation (GTF file downloaded from iGENOME). Parameters: htseq-count -m intersection-nonempty -s no -a 0 -t exon -i transcript_id
The raw read counts were normalized to CPM (count per million) by the R package edgR v3.4.2.
Genome_build: UCSC rn4
Supplementary_files_format_and_content: The transcriptomic expression was summarized in a tab delimited matrix: the rows are REFSEQ_ID, the columns A-H are annotations for each ID, and columns I-Q are the expression (CPM) of respective sample.

organism: Rattus norvegicus

source_name: RA Synovial Fibroblasts Like cells

growth_protocol: RA Synovial Fibroblasts Like cells extracted from synovium tissue were grown in 75cm2 tissue colture flasks and maintained in a 37ºC, 5% CO2-95% O2 atmosphere.

extract_protocol:
Once  in vitro cultures ended, cells were harvested enzimatically with trypsin (Pierce) treatment, collected by centrifuged and resuspended in RNA Later before  -80ºC storage. Total RNA was then extracted and purified using Trizol Reagent (Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 6000. Nano Kit  (Cat#5067-1511, Agilent Technologies).
The total RNA samples were first treated with Dnase I to degrade any possible DNA contamination. Then the mRNA was enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments (~200bp). Then the first strand of cDNA was sythesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3'-end single nucleotide A addtion was then performed. Finally sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR system were used to qualify and quantify the sample library.

treatment_protocol: RAFLS cuture were divided in three groups and mantained in different conditions, i.e. medium additioned with fetal bovine serum (FBS), blood serum from AP treated animals (AP+), blood serum from untreated animals (AP-)

value: Wistar rat

tag: disease state

value: rheumatoid arthritis

value: acupuncture

tag: gender

value: female

value: rat synovium fibroblast


title: Myelin P18 Rep2

description: RNA-Seq

value: WT


title: RAFLS from RA before therapy, standard condition replicate 1

description:
Gene expression data from RA rats before therapy, cultivated in standard condition (FBS)
RA1_FBS
FBS_1

value: control


title: Myelin P18 Rep1

description: RNA-Seq


title: RAFLS from RA before therapy, untreated replicate 1

description:
Gene expression data from healthy rats before therapy
RA1_AP-
APM_1

value: untreated


title: RAFLS from RA before therapy, standard condition replicate 2

description:
Gene expression data from RA rats before therapy, cultivated in standard condition (FBS)
RA2_FBS
FBS_2


title: muscle tissue 1 from RA PLA treated after 34 days, replicate 2

description: gene expression data from RA rats after 34 days PLA treatment

data_processing:
Base calling was performed using CASAVA version 1.8.2 and the raw sequences and quality scores (Phred33) were obtained in fastq format.
Raw reads were trimmed and filtered by cutadapt (1.2.1): reads beginning with the 5' adapter were discarded and the trailing 7' adapters were trimmed (maximum mismatch rate 0.1, match times 1, minimum overlapping length 5 for 7' adapter and 10 for 5' adapter, and low quality ends (Phred score < 30) were trimmed. Finally reads shorter than 25bp were removed.
Filtered reads were aligned to rat genome UCSC rn4 (downloaded from iGENOME http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn) by bowtie2 2.1.0 (one mismatch allowed, other parameters by default). Parameters: bowtie2 -N 1 -p 30 -x rn4 -U filtered.fastq -S align.sam
The aligned reads were quantified by HTseq (0.5.4p3) using the UCSC rn4 annotation (GTF file downloaded from iGENOME). Parameters: htseq-count -m intersection-nonempty -s no -a 0 -t exon -i transcript_id
The raw read counts were normalized to CPM (counts per million) by the R package edgeR v3.4.2.
Genome_build: UCSC rn4
Supplementary_files_format_and_content: The transcriptomic expression was summarized in a tab delimited matrix: the rows are REFSEQ_ID, the columns A-H are annotations for each ID, and columns I-R are the expression (CPM) of respective sample.

source_name: muscle tissue from RA PLA treated after 34 days, replicate 2

growth_protocol: Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC.

extract_protocol:
Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies).
The qualified RNA samples were sent to Illumina Sequencing Services of Partner Institute for Computational Biology Omics Core. The cDNA library was constructed for sequencing as described in Illumina TruSeq™ RNA sample preparation v2 guide (Catalog # RS-930-1021). Sequencing was performed on the Illumina HiSeq 2000.

treatment_protocol: Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction.

value: Wistar

value: Sub-epidermidis muscle tissue


title: Myelin 6 Months Rep2

description: RNA-Seq

value: brain

value: Myelin


title: muscle tissue 1 from RA PLA treated after 34 days, replicate 1

source_name: muscle tissue from RA PLA treated after 34 days, replicate 1


title: Myelin 6 Months Rep1

description: RNA-Seq


title: muscle tissue 1 from RA AP treated after 34 days, replicate 1

description: gene expression data from RA rats after 34 days AP treatment

source_name: muscle tissue from RA AP treated after 34 days, replicate 1


title: Disuse serum 2

city: Scarsdale

first: Brandon

last: Milholland

state: New York

address: 119B Montgomery Avenue

institute: Albert Einstein College of Medicine

data_processing:
Adapters were trimmed using QUART.
Sequences from each of the samples were aligned to the known mm10 miRNAs present in version 20 of mirBase, version 0.12.7 of bowtie.
Genome_build: miRBase 20
Supplementary_files_format_and_content: csv file containing read counts for each sample

source_name: serum

extract_protocol:
For tissue samples, total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.For serum samples, total RNA was purified from 300 ul of serum samples using the miRNeasy serum/plasma kit (Qiagen) according to the manufacturer’s instructions.
2μg of total RNA from each tissue samples and 10 ng of total RNA from each serum samples were used for small RNA cDNA library preparation (26). Using Illumina TruSeq Small RNA sample preparation kit, barcoded 3'-adapters and 5’-adapters were ligated to RNA in each sample. Synthesized cDNA amplified up to 15 cycles using indexes for multiplexing. Amplified DNAs were selected by the excision (145-160bp) on 10% TBE polyacrylamide gel and purified.

value: disuse-induced atrophy model

tag: rna source

value: serum


title: Disuse serum 3

value: 6 months


title: muscle tissue 1 from RA PLA treated after 1 hour, replicate 2

description: gene expression data from RA rats after 1 hour PLA treatment

source_name: muscle tissue from RA PLA treated after 1 hour, replicate 2


title: Disuse serum 4


title: Old serum 4

value: 24 months


title: muscle tissue 1 from RA AP treated after 34 days, replicate 2

source_name: muscle tissue from RA AP treated after 34 days, replicate 2


title: Disuse serum 1


title: muscle tissue 1 from RA AP treated after 1 hour, replicate 1

description: gene expression data from RA rats after 1 hour AP treatment

source_name: muscle tissue from RA AP treated after 1 hour, replicate 1


title: muscle tissue 1 from RA AP treated after 1 hour, replicate 2

source_name: muscle tissue from RA AP treated after 1 hour, replicate 2


title: RAFLS from RA before therapy, untreated replicate 2

description:
Gene expression data from healthy rats before therapy
RA2_AP-
APM_2


title: muscle tissue 1 from RA PLA treated after 1 hour, replicate 1

source_name: muscle tissue from RA PLA treated after 1 hour, replicate 1


title: Old serum 3


title: Old serum 2


title: RAFLS from RA before therapy, AP treated replicate 2

description:
Gene expression data from RA rats after 18 days AP treatment
RA2_AP+
APP_2


title: Young serum 4


title: Young serum 5


title: Disuse serum 5


title: muscle tissue 1 from RA before therapy, replicate 1

description: gene expression data from RA rats before therapy

source_name: muscle tissue from RA before therapy, replicate 1


title: Young serum 1


title: muscle tissue 1 from RA before therapy, replicate 2

source_name: muscle tissue from RA before therapy, replicate 2


title: Young serum 3


title: Disuse muscle 4

source_name: tibialis anterior muscle

value: tibialis anterior muscle


title: Disuse muscle 3


title: Disuse muscle 2


title: Old muscle 5


title: Old muscle 1


title: Old muscle 4


title: Old muscle 3


title: Old muscle 2


title: Young muscle 5


title: Young muscle 1


title: bmp7_minus_d7 RNA-seq

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

data_processing:
ChIP-seq reads were aligned to the mm9 genome using bowtie 2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-seq data sets were aligned to the mouse genome (mm9) using TopHat.
The mapped reads were further quantified as fragments per kilobase of transcript per million mapped reads (FPKM) based on the RefSeq database using the Cufflinks program
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited wig files counted by the number of reads falling into 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each RNA-seq Sample

source_name: C3H10T1/2 cells

growth_protocol: Growth medium: DMEM (high glucose), 10% FBS, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% FBS, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3; Differentiation medium (d2-d7): DMEM (high glucose), 10% FBS, PenStrep, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3. Before differentiation cells were seeded at 70% confluency (d-3).

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufactorer's instructions and treated with DnaseI
RNA-seq libraries were generated by BGI following their standard procedure: mRNAs is enriched by using the oligo (dT) magnetic beads. By using the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp), then the first strand cDNA synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and poly (A) addition. Finally, sequencing adapters are ligated to the fragments. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification._x0000__x0000__x0000_

value: mesenchymal stem cell

tag: chip-antibody

tag: day of differentiation


title: Young muscle 4


title: Old serum 1


title: bmp7_minus_d2 RNA-seq

value: day 2


title: Young muscle 2


title: bmp7_minus_d0 RNA-seq

value: day 0


title: Disuse muscle 1


title: bmp7_minus_6h RNA-seq

value: day 0, 6h


title: Young muscle 3


title: Young serum 2


title: Disuse muscle 5


title: wa_d7 RNA-seq

source_name: 3T3-L1 cells

growth_protocol: Growth medium: DMEM (high glucose), 10% BCS, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% FBS, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin; Differentiation medium (d2-d7): DMEM (high glucose), 10% FBS, PenStrep, 0.12ug/ml Insulin. Before differentiation cells were seeded at 70% confluency (d-4).

value: Swiss albino

value: preadipocyte cell


title: bmp7_minus_d-3 RNA-seq

value: day -3


title: wa_6h RNA-seq


title: wa_d2 RNA-seq


title: wa_d0 RNA-seq


title: ba_d7 RNA-seq rep2

growth_protocol: Growth medium: DMEM (high glucose), 10% Fetalclone III serum, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3; Differentiation medium (d2-d7): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3. Before differentiation cells were seeded at 70% confluency and growth medium was supplemented with 8.3nM human recombinant BMP7 for 3 days.


title: wa_d-4 RNA-seq

value: day -4


title: ba_d2 RNA-seq rep2


title: ba_d-3 RNA-seq rep2


title: ba_d0 RNA-seq rep2


title: ba_d7 RNA-seq rep1


title: ba_6h RNA-seq rep2


title: ba_d2 RNA-seq rep1


title: ba_6h RNA-seq rep1

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufactorer's instructions and treated with DnaseI
RNA-seq libraries were generated by BGI following their standard procedure: mRNAs is enriched by using the oligo (dT) magnetic beads. By using the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and poly (A) addition. Finally, sequencing adapters are ligated to the fragments. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification.


title: ba_d7_six1


title: ba_d-3 RNA-seq rep1


title: ba_d0 RNA-seq rep1


title: ba_d7_pparg


title: ba_d7_k9ac


title: ba_d2_k9ac


title: ba_d0_k9ac


title: ba_6h_k9ac


title: ba_d-3_k9ac


title: ba_d7_k4m1


title: ba_d2_k4m1


title: ba_d0_k4m1


title: ba_d7_k27m3


title: wa_d-2 RNA-seq

value: day -2


title: ba_d-3_k4m1


title: ba_d0_k27m3


title: ba_6h_k27m3


title: ba_d-3_k27m3


title: ba_d2_k4m3


title: ba_d7_k4m3


title: ba_6h_k4m3


title: ba_d0_k4m3


title: ba_d7_k27ac


title: ba_d2_k27ac


title: ba_d0_k27ac


title: ba_6h_k27ac


title: ba_d-3_k27ac


title: ba_d-3_k4m3


title: ba_6h_input


title: ba_d7_input


title: ba_d-3_input

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication with a Bioruptor UCD-300 (Diagenode) to obtain fragments 200–800 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. ChIP DNA was quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
ChIP-seq libraries were generated following the procedue described in "TELP, a sensitive and versatile library construction method for next-generation sequencing" by Peng X, Wu J, Brunmeir R, Kim SY, Zhang Q, Ding C, Han W, Xie W, Xu F., published in Nucleic Acids Res. 2015 Mar 31;43(6):e35. doi: 10.1093/nar/gku818. Epub 2014 Sep 15.


title: ba_d2_input


title: ba_d2_k27m3


title: ba_6h_k4m1


title: Tnonmet-shControl (2)

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

description: Cell line derived from non-metastatic primary lung adenocarcinoma

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: Non-metastatic primary tumor derived cell line

growth_protocol: Cell lines were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
Total RNA was isolated using using RNAqueous® Total RNA Isolation Kit from Life Technologies.
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.
RNA-seq (single end 45mer reads)

treatment_protocol: Tnonmet cell lines were infected with retroviruses and lentiviruses that express shRNAs against Nkx2-1, Foxa2, and Cdx2, or against luciferase as a control.

value: shControl

tag: genotype


title: Tnonmet-shControl (1)

tag: treatment

value: Cell line derived from non-metastatic primary lung adenocarcinoma


title: Tmet (1)

description: Cell line derived from metastatic primary lung adenocarcinoma

source_name: Metastatic primary tumor derived cell line


title: Tnonmet-shNkx2-1/Foxa2/Cdx2 (1)


title: Tnonmet-shNkx2-1/Foxa2/Cdx2 (2)


title: Tmet (2)

value: Cell line derived from metastatic primary lung adenocarcinoma


title: ba_d0_input


title: Tnonmet-shNkx2-1 (2)


title: Tnonmet-shNkx2-1 (1)


title: NPC_RNA_1

city: Heidelberg

first: Jan-Philipp

last: Mallm

address: Im Neuenheimer Feld 267

country: Germany

institute: DKFZ

description: total RNA

data_processing:
alignment to the mouse genome assembly mm9 with bowtie
read extension by fragment size
read normalization using input and IgG control according to the manuscript
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: Neural progenitor cells

growth_protocol: mESC were maintained in PowerStem EsPro1 supplemented with LIF on gelatine.

extract_protocol:
For each sample, 1 x 10^6 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). For histone modifications, chromatin was sheared by sonication to mononucleosomal fragments. Total RNA was extracted using Trizol. Prior to library preparation, RNA was digested with DNaseI.
Libraries were prepared according to Illumina standard protocols with external barcodes for ChIP-seq. RNA-seq libraries were generated with the Encore RNA-seq kit by Nugen.

treatment_protocol: mESC were depleted from LIF for four days in STEMPan medium (Pan Biotech) in suspension flasks. Then, 5 µM retinoic acid was added for four days, then the cells were plated on matrigel in NSC medium (PAA) for four additional days.

value: ES-derived neural progenitor cells

tag: antibody


title: NPC_H3K4me1_1

description: ChIP DNA

value: ab8895, abcam


title: NPC_H3K9ac_1

description: ChIP DNA

value: ab4441, abcam


title: NPC_RNA_3

description: total RNA


title: NPC_H3K27me3_2

description: ChIP DNA

value: ab6002, abcam


title: NPC_RNA_4

description: total RNA


title: NPC_H3K4me1_2

description: ChIP DNA


title: NPC_H3K4me3_1

description: ChIP DNA

value: ab8580, abcam


title: NPC_H3K4me3_2

description: ChIP DNA


title: NPC_H3K27ac_2

description: ChIP DNA

value: ab4729, abcam


title: NPC_RNA_2

description: total RNA


title: ESC_RNA_4

description: total RNA

source_name: Embryonic stem cells

value: Embryonic stem cells E3.5


title: NPC_H3K27me3_1

description: ChIP DNA


title: NPC_IgG_1

description: ChIP DNA


title: NPC_H3K27ac_1

description: ChIP DNA


title: NPC_IgG_2

description: ChIP DNA


title: ESC_RNA_3

description: total RNA


title: ESC_RNA_2

description: total RNA


title: ESC_RNA_1

description: total RNA


title: ESC_H3K36me3_2

description: ChIP DNA

value: ab9050, abcam


title: ESC_H3K9me3_1

description: ChIP DNA

value: ab8898, abcam


title: ESC_H3K9me3_2

description: ChIP DNA


title: ESC_H3K4me3_1

description: ChIP DNA


title: ESC_H3K4me1_1

description: ChIP DNA


title: ESC_H3K4me1_2

description: ChIP DNA


title: CBAP-down-3

description:
KG1
CBAP knockout-1

source_name: Human T-acute lymphoblastic leukemia cell line: Jurkat_CBAP knockout

tag: method for knockdown or knockout

value: Jurkat

value: T-acute lymphoblastic leukemia


title: NPC_H3K9ac_2

description: ChIP DNA


title: Sample_HOXA9-FLAG

city: Madrid

first: Ana

last: Del Rio

state: Madrid

address: Calle Melchor Fernandez Almagro 3

institute: CNIO

data_processing:
Samples were sequenced in a Genome Analyzer IIx (GA2, Illumina) single 40-base read run.
Alignment to the human sequence assembly (GRCh37/hg19, Feb 2009) was performed using BWA with default settings, permitting alignments with 1 mismatch in 40 base reads.
Peak detection was performed using MACS 2.020 following the developer’s technical recommendations (p-value cutoff for peak detection = 10-5). Significant ChIP-seq peaks were established at FDR ≤ 5%.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: wig files with alignments, bed files with peaks provided by MACS

source_name: HEK293FT cell line expressing HOXA9-FLAG

growth_protocol: HEK293FT cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Invitrogen)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the antibody.
Libraries were constructed using the ChIP-seq sample preparation kit (Illumina, San Diego, California, USA)

tag: cell line

tag: tag

value: FLAG

value: embryonal kidney

tag: chip antibody

value: Monoclonal ANTI-FLAG® M2 (SIGMA ALDRICH, F3165, lot-SLBG5311 )


title: ESC_H3K27ac_1

description: ChIP DNA


title: Input_NUP98

source_name: HEK293FT cell line


title: ESC_H3K9ac_2

description: ChIP DNA


title: ChIP_NUP98

source_name: HEK293FT cell line expressing NUP98-FLAG


title: ESC_H3K27me3_2

description: ChIP DNA


title: ESC_H3K27ac_2

description: ChIP DNA


title: ESC_IgG_2

description: ChIP DNA


title: ESC_H3K9ac_1

description: ChIP DNA


title: ESC_IgG_3

description: ChIP DNA


title: ESC_H3K4me3_2

description: ChIP DNA


title: ESC_IgG_1

description: ChIP DNA


title: ESC_IgG_4

description: ChIP DNA


title: CLOCK_ChIPSeq_NIH3T3_34h

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

description:
Chromatin
Processed data file: CLOCK_NIH3T3_filtered_withannot.bed

data_processing:
The obtained fastq raw sequence files were mapped to the mm9 genome using Bowtie allowing for three mismatches, but only one hit on the genome (Langmead et al., 2009). Mapped reads files were handled and manipulated using SAMtools (Li et al., 2009). Peaks were called using the MACS algorithm (Zhang et al., 2008; shift = 75, bandwidth = 150, genome size = 2.4 Gb) providing the input sample as background and deconvolved to find the center of the peak and a more refined binding site using custom scripts (Rey et al., 2011). These scripts were also used to quantify peaks and annotate binding sites to the closest Ensembl TSS (Curwen et al., 2004). This pipeline has been turned into an automated web-based station (http://htsstation.epfl.ch (David et al., 2014)), that was used for analysis of the 18-38h after-Dex time courses of anti-BMAL1 and anti-CLOCK ChIP-seq samples in NIH3T3 cells.
For anti-BMAL1 and anti-CLOCK ChIP-seq data binding sites were refiltered after obtaining the initial list of peaks, using custom criteria that take into account not only the area of the detected binding site but also the individual chromatin environment as assessed by including 20 background regions 1 kb up- and downstream of the peak.
1) ChIP signal needs to be three-fold enriched over input.
2) The site has to have higher tag density +2SD (standard deviations) than the mean of the neighboring regions.
3) The site has to have higher enrichment over input than the mean of the neighboring regions +2SD.
The binding sites in BED format were handled and manipulated using BEDTools (Quinlan and Hall, 2010). Quantification of the signal at binding sites was performed with a script based on the code provided by Rey et al., 2011, which counts tags mapped to the genome in a given window (usually ±250bp around the center of the binding site as determined by deconvolution) and normalized to total number of tags.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Wig: enrichment score over input; Bed: chromosome, start, end, closest gene symbol (if present in file), distance to TSS (if present in file).

source_name: NIH3T3 cells, 34h, CLOCK ChIP

growth_protocol:
NIH3T3 fibroblasts were kept in DMEM high glucose medium (Life Technologies) supplemented with 1% Penicilling/Streptomycin/Glutamate (PGS; Sigma Aldrich) solution and 10% fetal calf serum (FCS, Sigma Aldrich). They were split using trypsin (Tryple Express, Life Technologies) as detaching and dissociation agent as necessary depending on experimental conditions or when reaching confluency. For synchronization with dexamethasone (Dex; Sigma Aldrich), cells were incubated for 30 minutes with 100 nM Dex solution (stock 100µM in ethanol), then washed once with PBS and supplied with fresh medium.
Mice: C57/BL6, 12-14 wk-old, 12h/12h LD, food ad libitum.

extract_protocol:
Anti-BMAL1 and anti-CLOCK antibodies were kindly provided by Prof. Michael Brunner (University of Heidelberg). For chromatin preparation, medium of two confluent 15 cm dishes (approximately 10,000,000 cells each) per timepoint was removed, 6 ml PBS+1% fresh formaldehyde were added and cells were placed for 5' at 37°C in the incubator. Cells were washed twice with ice cold PBS and the reaction was stopped with 1.5 ml stop solution (125 mM glycine or 100 mM Tris pH 9.4, 10 mM DTT). Cells were scraped off the dish, transfered to 2 ml tubes, kept on ice for 15', then at 30°C for 15' and vortexed. Lysates were spun down 1' at 2500 rpm, 4°C, supernatant was removed. 500 µl sol II (10 mM EDTA, 1 mM EGTA, 10 mM HEPES pH 6.8, 0.25% Tx-100) were added, tubes were vortexed to resuspend and spun down 5' at 2500 rpm, 4°C. Supernatant was removed, 500 µl solIII (1mM EDTA, 1mM EGTA, 10 mM HEPES pH 6.8, 200 mM NaCl) were added. Tubes were vortexed to resuspend, spun down 5' at 2500 rpm, 4°C and supernatant was removed.
The nuclei from the two plates per sample were united in 300 µl nuclei resuspension buffer (22 mM Tris pH 7.4, 165 mM NaCl, 2.2 mM EDTA) + 1% SDS and sonicated 20 min (30" on/off cycles) in a Bioruptor ultrasonicator 4°C water bath (Diagenode) to obtain a fragment size of approx. 250 bp. Chromatin was diluted in 2700 µl chromatin dilution buffer (20 mM Tris pH 7.4, 150 mM NaCl, 2 mM EDTA, 1.1% Tx-100) and aliquoted (500 µl per IP + 5 µl Input).
To submit DNA purified from ChIP samples for sequencing, we pooled several IPs to collect 10ng of DNA. We precipitated the DNA using standard sodium acetate precipitation to resuspend it in a small volume and measured the amount of DNA on a Qubit 2.0 fluorometer (Life Technologies). Sample DNA as well as input DNA as control were submitted for Illumina deep sequencing at the Lausanne Genomic Facility (University of Lausanne).
A total of 5-10 ng DNA were used for the preparation of the library. Libraries for ultra-high-throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

treatment_protocol: NIH3T3 cells were synchronized by dexamethasone.

value: dexamethasone synchronized

tag: time post-dex synchronization

value: anti-CLOCK


title: CLOCK_ChIPSeq_NIH3T3_38h

source_name: NIH3T3 cells, 38h, CLOCK ChIP


title: Input_NIH3T3_18h-38h_timecourse_pooled

description: Chromatin

source_name: NIH3T3 cells, input


title: CLOCK_ChIPSeq_liver_pooled

description:
Chromatin
Processed data file: CLOCK_Liver_sites.bed

source_name: Liver, CLOCK ChIP

tag: strain/background

tag: tissue

value: liver

tag: age


title: CLOCK_ChIPSeq_NIH3T3_30h

source_name: NIH3T3 cells, 30h, CLOCK ChIP


title: CLOCK_ChIPSeq_NIH3T3_26h

source_name: NIH3T3 cells, 26h, CLOCK ChIP


title: ESC_input_2

description: genomic DNA

tag: cell type

tag: strain


title: ESC_input_1

description: genomic DNA


title: CLOCK_ChIPSeq_NIH3T3_18h

source_name: NIH3T3 cells, 18h, CLOCK ChIP


title: Sample_NUP98-HOXA9-FLAG

source_name: HEK293FT cell line expressing NUP98-HOXA9-FLAG


title: Sample_pool_input_NUP98-HOXA9_HOXA9


title: KO 3

city: Berlin

first: Sebastian

last: Schafer

state: Deutschland

address: Robert-Roessle-Str. 10

department: Experimental Genetics

institute: MDC Berlin

data_processing:
Reads were then mapped against the reference genome GRCh37 with TopHat 1.4.1 (Trapnell et al 2009)  using standard parameters. The gene annotation of the Ensembl database was supplied to the pipeline to align reads across known as well as predicted splice junctions.
We then tested for differential exon usage with DEXSeq (Anders et al 2012) between 3 biological replicates each of CD2BP2-/- and CD2BP2+/+ podocytes. Exon counts are supplied as processed data.DEXSeq scored disjunct exonic parts using a negative binomial test based on exon count data. We defined an exonic part to be differentially spliced if DEXSeq assigned an FDR < 0.05 and the delta PSI (percent spliced in) value was >0.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: Read counts for exonic parts in a tab delimited text file. File contains gtf-like information followed by read counts, covered bases, total bases per exon and percentage of exon covered.

source_name: Podocytes

growth_protocol: A mouse genomic CD2BP2 clone was used for construction of the targeting vector. A 7.5 kb fragment containing the seven exons of CD2BP2 flanked by HindIII sites was subcloned into pZERO plasmid. The 3’loxP site was inserted downstream of exon 3. Subsequently a 5´-homology arm and the 3’-homology were inserted in pPNT-frt3 up- and downstream of the neomycin resistance gene respectively and the 5’loxP site. The resulting targeting vector was linearized with FseI and transfected into R1/E murine ES cells. Homologous recombination was identified in ES cells by Southern blotting as depicted in the targeting strategy (suppl. Figure 1) and verified by sequencing of genomic DNA and cDNA. ES cells were injected into C57BL/6 morulae. Resulting germline chimeras were interbred with a FLPO deleter strain to eliminate the neomycin resistance gene. Details about primers, probes and PCR-based genotyping are described in S1.

extract_protocol:
Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).
RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.

treatment_protocol: 6-10 weeks old CD2BP2flox/flox MxCre+ mice and littermate controls were treated with 300 μg poly (I:C) intra peritoneal. BMMs were isolated from femur and tibia and cultured in DMEM with 10% FCS, 4 mM L-Glutamine, 1 mM Sodium Pyruvate, 50 U/ml of penicillin, 50µg/ml streptomycin, 1 % nonessential amino acids and 1 μg/μL M-CSF as previously described (Knobeloch et al., 2005). After differentiation, cells were harvested and subject to protein or RNA extraction.

tag: genetic background

value: Podocytes

value: CD2BP2 Knockout


title: KO 2


title: Input_NIH3T3_12h20h

description: Chromatin


title: ESC_H3K27me3_1

description: ChIP DNA


title: ESC_H3K36me3_1

description: ChIP DNA


title: BMAL1_ChIPSeq_NIH3T3_30h

description:
Chromatin
Processed data file: BMAL1_20h_NIH3T3_Stringent_peaks_all_withannotation.bed

source_name: NIH3T3 cells, 30h, BMAL1 ChIP


title: BMAL1_ChIPSeq_NIH3T3_38h

source_name: NIH3T3 cells, 38h, BMAL1 ChIP


title: WT Control 1

value: Wildtype


title: WT Control 2


title: RNA_PolII_ChIPSeq_NIH3T3_20h

description:
Chromatin
Processed data file: PolII_20h_vs_Input.wig.gz

source_name: NIH3T3 cells, 20h, RNA PolII ChIP

value: anti-RNA PolII


title: BMAL1_ChIPSeq_NIH3T3_26h

source_name: NIH3T3 cells, 26h, BMAL1 ChIP


title: BMAL1_ChIPSeq_NIH3T3_18h

source_name: NIH3T3 cells, 18h, BMAL1 ChIP


title: BMAL1_ChIPSeq_NIH3T3_22h

source_name: NIH3T3 cells, 22h, BMAL1 ChIP


title: BMAL1_ChIPSeq_NIH3T3_20h

source_name: NIH3T3 cells, 20h, BMAL1 ChIP


title: Foxo1-0hours-ChIPseq

city: Barcelona

first: Chris

last: van Oevelen

state: Catalunya

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

institute: Centre for Genomic Regulation (CRG)

data_processing:
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files, which were subsequently aligned to the mouse genome (mm9) using either the Illumina Eland alignment tool or Bowtie (cmd: bowtie -n 0 -l 28 -m 1 mm9 INPUT OUTPUT, Langmead et al, 2009, PMID: 19261174) without mismatches. Aligned sequences were further filtered to remove identical sequence tags and sequence tags that do not align uniquely to the mouse genome
To detect regions enriched for factor  binding relative to background, we used HOMER (http://biowhat.ucsd.edu/homer/ngs/index.html) (Heinz et al, 2010, PMID: 23064439) with the peak localization/shape option set to region and the style option set to factor.
Genome_build: mm9
Supplementary_files_format_and_content: USCS bed format: chr start end strand

source_name: Haftl pre-B cells

growth_protocol: C10 cells were grown in RPMI 1640 without phenol red (Lonza) supplemented with 10% charcoal/dextran-treated FBS (Hyclone) and 50 μM 2-mercaptoethanol (GIBCO), incubated at 37°C in 5% CO2

extract_protocol: ChIP experiments were performed as described previously (van Oevelen et al, 2008, PMID:20956564). DNA libraries of C/EBPa and C/EBPb enriched chromatin fragments were prepared using Illumina's reagents and instructions. All other libraries were prepared according to manufacturer’s instructions with some modifications (Asp et al, 2011, PMID: 21551099). All libraries were sequenced on the Illumina 2AAIIx sequencer except C/EBPa and PU.1 libraries generated 10, 30 and 60 minutes post induction and pax5 (0 hours) and Foxo1 (0 hours) that were sequenced using the Illumina Hiseq2000 sequencer.

treatment_protocol: C10 cells were induced by the addition 100 nM of β-estradiol (Calbiochem) and grown with 10 nM of IL-3 and CSF-1 (Peprotech). Control cells were treated with 0.1% ethanol (solvent)

value: haftl derived C10 cells

tag: time after induction

value: 0 hours


title: Expt4_FU5-13_DE_el_41

city: La Jolla

first: Gene

last: Yeo

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

institute: UCSD

data_processing:
Demultiplexing: Reads were demultiplexed based on the presence of the gene-specific primer at the beginning of R2, and a random-mer was extracted off of the beginning of R1.
Read trimming: Reads were trimmed at the 3' end using the cutadapt program, with options "--discard-untrimmed flag -a Gene_Specific_Primer"
Tail counting: Non-PCR duplicate reads were counted by summing reads with the same sequence that did not have the same randommer sequence as any other read. Counts were performed for unique only (hamming distance > 0), as well as randommers at least 1 nt apart (hamming distance >1)
Genome_build: Analysis was done on raw reads without genome mapping
Supplementary_files_format_and_content: Processed files are tab-delimited files, with each line containing the sample ID, trimmed sequence, total number of observed reads for that sequence,  number of non-PCR duplicate reads for that sequence (hamming distance > 0), and number of non-PCR duplciate reads for that sequence (hamming distance > 1)

source_name: HEK 293

extract_protocol:
One 10 cm dish of stable cell lines expressing FLAG-TOE1 variants was transfected twice with 20 nM siRNA targeting either luciferase or the 3’UTR of TOE1 using siLentFect (Bio-Rad) according to the manufacturer’s recommendations 72 h and 24 h before harvest. At ~50% confluency, cells were induced for 24 hours with tetracycline at 1 ng/ml. Cells were harvested in PBS and lysed in isotonic lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% Triton X-100, 1 mM PMSF, 2 μg/mL aprotinin, 2 μg/mL leupeptin, 0.1 μg/ml yeast total RNA, 80 U/mL RNaseOUT (Invitrogen)) for 10 minutes on ice. Lysates were cleared at 20K x g for 15 min at 4°C. FLAG peptide was added to 1 μg/ml and lysates were incubated for 2 h with Anti-FLAG M2 beads (Sigma) at 4°C. Beads were then washed 8 times with NET2 (10 mM Tris, pH 7.5, 150 mM NaCl, 0.1% Triton X-100). One-fifth of the beads were eluted in protein loading buffer, and four-fifths of the beads were resuspended in Trizol (Life Technologies). RNA was extracted according to manufacturer’s protocol.
RNA adapters containing bar-codes and 10-11 nucleotide randomers were ligated to the 3’ ends of total and eluted RNA with T4 RNA ligase (NEB) at 16°C for 16 hours. Ligated RNA samples were treated with RQ1 RNase-free DNase (Promega) for 30 minutes at 37°C and extracted with PCA (Affymetrix). cDNA was generated from AR-17 primer with Superscript III (Life Technologies). 3’ ends were amplified by Q5 High-Fidelity DNA Polymerase (NEB) first, using snRNA gene-specific primers and AR-17, and then with primers D501 and D702 (Illumina). Libraries were purified on AMPure XP magnetic beads (Beckman), and validated by 2200 Tape Station Instrument (Agilent). Libraries were pooled at 4 nM, denatured with NaOH and diluted in HT1 buffer (Illumina) to 7 pM before sequencing with MiSeq Reagent Kit V2 Nano configuration (Illumina).

value: HEK 293

tag: sirna

tag: rip antibody

value: Mouse anti-FLAG (Sigma)

value: DEaddback

value: NNNNNNNNNNCT


title: Mnase-3hours-Mnaseseq

description: Sample 48

data_processing:
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files, which were subsequently aligned to the mouse genome (mm9) using either the Illumina Eland alignment tool or Bowtie (cmd: bowtie -n 0 -l 28 -m 1 mm9 INPUT OUTPUT, Langmead et al, 2009, PMID: 19261174) without mismatches. Aligned sequences were further filtered to remove identical sequence tags and sequence tags that do not align uniquely to the mouse genome
Genome_build: mm9
Supplementary_files_format_and_content: USCS bed format: chr start end strand

extract_protocol: Nucleosome positioning was determined by a modification of published method (Cappabianca et al, 1999, PMID: 10804530) .DNA libraries mononucleosomes were prepared using Illumina's reagents and instructions. All libraries were sequenced on the Illumina Hiseq2000 sequencer.

tag: cell line source

value: HAFTL (pre-B cells)

value: 3 hours

tag: molecule subtype

value: mononucleosomal genomic DNA


title: Mnase-24hours-Mnaseseq

description: Sample 50

value: 24 hours


title: ZF.GFP.High

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing:
Reads were aligned to the zebrafish genome (v9) using tophat
Gene expression levels were calculated using Htseq-count based on Ensembl gene annotations
Gene expression levels were next normalized across samples using quantile normalization
Only genes with at least 40 reads in at least one sample were included in the analysis
Prior to quantile normalization, genes with less than 20 counts were set to 20.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample.

organism: Danio rerio

source_name: 5 dpf larvae_hair cell

extract_protocol:
DirectZol (Zymo)
TruSeq

treatment_protocol: cells obtained by cell sorting

tag: genotype/variation

value: 5 day post fertilization (dpf) larvae

value: hair cells (GFP positive)


title: Expt4_FU5-11_DE_tot_41

value: NNNNNNNNNNNCT


title: ZF.GFP.Low

source_name: 5 dpf larvae_non-hair cell

value: non-hair cells (GFP negative)


title: Expt4_FU5-12_WT_el_41

value: WTaddback


title: KO 1

value: Podocytes

tag: genotype

value: CD2BP2 Knockout


title: Expt4_FU5-09_siC_tot_41

tag: cell line

value: FLAG


title: Expt4_FU5-08_siLuc_tot_41

value: siControl

value: FLAGonly-siLuc


title: Expt9_FU5-07_NPC_1603U4

source_name: NPC derived from primary fibroblasts

value: NPC derived from primary fibroblasts


title: Expt4_FU5-10_WT_tot_41

value: HEK 293


title: Expt9_FU5-05_NPC_1603A3


title: RNA_PolII_ChIPSeq_NIH3T3_12h

description:
Chromatin
Processed data file: PolII_12h_vs_Input.wig.gz

source_name: NIH3T3 cells, 12h, RNA PolII ChIP

tag: treatment

value: dexamethasone synchronized

value: anti-RNA PolII


title: WT Control 3

value: Wildtype


title: BMAL1_ChIPSeq_NIH3T3_12h

source_name: NIH3T3 cells, 12h, BMAL1 ChIP

tag: chip antibody


title: Expt9_FU5-06_NPC_1603U3


title: Expt9_FU5-04_NPC_1603A1

value: NNNNNNNNNNCT


title: Pax5-0hours-ChIPseq

value: haftl derived C10 cells

value: 0 hours


title: Expt9_FU2-05_NPC_1603U4


title: Expt9_FU2-04_NPC_1603U3


title: Expt9_FU5-03_NPC__ATCC


title: Expt9_FU2-02_NPC_1603A1


title: Expt9_FU1V68-04_NPC_1603U3


title: Expt9_FU2-01_NPC__ATCC


title: Expt9_FU1V68-05_NPC_1603U4


title: Expt9_FU1V68-02_NPC_1603A1


title: Expt9_FU1V68-01_NPC__ATCC


title: Expt9_FU2-03_NPC_1603A3


title: Expt9_FU1V68-03_NPC_1603A3


title: Expt7_FU1-Vs-16_E220_tot_40

description: TOE1 expression induced at 1 ng/mL tetracycline

value: E220 addback- siCaf1z


title: Expt7_FU1-Vs-15_V173_tot_40

value: V173 addback- siCaf1z

value: NNNNNNNNNNNCT


title: Expt7_FU1-Vs-14_F148_tot_40

value: F148 addback- siCaf1z


title: Expt7_FU1-Vs-13_A103_tot_40

value: A103 addback - siCaf1z


title: Expt7_FU1-Vs-07_DE_tot_40


title: V72-3

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

data_processing:
Base-calling and adapter sequence removal were done at BGI-Shenzhen
Strand-specific sequencing reads for each cultivar were quality checked using FASTQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and mapped to the potato reference genome (Genome assembly: PGSC_DM_v4.03; http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml) using TopHat2 (version 2.0.13)
Transcript assembly was performed using Cufflinks (version 2.2.1)
Coding Potential Calculator (CPC) was used to differentiate candidate lncRNA transcripts from mRNAs
HTSeq-count was used to make read counts mapped to lncRNA transcripts and DeSeq2 was used to determine the differential expression with a false discovery rate threshold of 10%
Genome_build: PGSC_DM_v4.03

organism: Solanum tuberosum

source_name: stem tissues

growth_protocol: Potato tubers were grown in the greenhouse under standard conditions (22 to 26 °C, 16 h light/ 8 h dark photoperiod and 70% relative humidity)

extract_protocol:
Total RNA was extracted from potato stems using the QIAGEN RNeasy plant mini kit (Qiagen) including DNAse treatment (Qiagen)
The construction of whole transcriptome libraries and sequencing were carried out at the Beijing Genomics Institute (BGI-Shenzhen, China).  cDNA libraries were sequenced using standard Illumina protocols for strand-specific and normal RNA-seq.

treatment_protocol: Stem inoculations were done as previously described in (Kubheka et al 2013), except that we used wild-type P. carotovorum subsp. brasiliense strain 1692 for the inoculations and inoculated plants were assessed and sampled at 0, 6, 12, 24, and 72 hours post inoculation (hpi) in triplicates (three plants were pooled together for each biological replicate)

value: stem

tag: cultivar

value: Valor

tag: phenotype

value: susceptible

tag: inoculant

value: Pectobacterium carotovorum subsp brasiliense 1692


title: Expt7_FU1-Vs-22_WT_tot_40


title: Expt7_FU1-Vs-21_siC_tot_40

value: FLAG


title: V24-3

tag: tissue


title: V72-1


title: Expt7_FU1-Vs-20_siL_tot_40

value: HEK 293

value: siControl


title: V24-1


title: Expt6_FU1-Vs-06_DE_el__42_EDTA

description: post-IP activity assay

value: Mouse anti-FLAG (Sigma)

value: DEaddback


title: V12-3


title: Expt6_FU1-Vs-04_DE_el_42_trizol

description: post-IP activity assay


title: V24-2


title: Expt6_FU1-Vs-05_DE_el__42_Mg

description: post-IP activity assay

value: NNNNNNNNNNCT


title: Expt6_FU1-Vs-03_WT_el_42_EDTA

description: post-IP activity assay

value: WTaddback


title: Expt6_FU1-Vs-02_WT_el_42_Mg

description: post-IP activity assay


title: V12-1


title: V6-2


title: Expt6_FU1-Vs-12_DE_tot_42

description: post-IP activity assay


title: V6-3


title: V12-2


title: V6-1


title: VC-3

value: control


title: Expt6_FU1-Vs-10_siC_tot_42

description: post-IP activity assay


title: Expt6_FU1-Vs-11_WT_tot_42

description: post-IP activity assay


title: Expt6_FU1-Vs-09_siL_tot_42

description: post-IP activity assay

value: FLAGonly-siLuc


title: V72-2


title: VC-1


title: Expt4_FU4-05_WTrip_rip41


title: Expt4_FU4-06_DErip_rip41


title: B72-3

value: tolerant


title: Expt4_FU4-03_WTtot_rip41

value: NNNNNNNNNNNCT


title: Expt4_FU4-02_siCaf1ztot_rip41


title: Expt4_FU4-04_DEtot_rip41


title: B24-2


title: B72-1


title: B24-3


title: B72-2


title: Expt4_FU4-01_siLUCtot_rip41


title: Expt4_elu-U6-DEaddback


title: Expt6_FU1-Vs-01_WT_el_42_trizol

description: post-IP activity assay


title: B24-1


title: Expt4_input-U6-FLAGonly-siLuc


title: Expt4_input-U6-DEaddback-siCaf1z


title: B12-3


title: B12-2


title: Expt4_input-U6-WTaddback-siCaf1z


title: B6-2


title: B12-1


title: Expt4_elu-U6-Wtaddback


title: VC-2


title: Expt3_elu-U6-DEaddback


title: Expt3_input-U6-DEaddback-siCaf1z


title: B6-3


title: B6-1


title: BC-1


title: Expt2_FU5-10_siCaf_totalrip35


title: Expt3_input-U6-FLAGonly-siCaf1z


title: Expt2_FU5-09_siLuc_totalrip35


title: BC-2


title: Expt3_input-U6-WTaddback-siCaf1z


title: Expt8_PATFIB_U5_4128A

source_name: Primary Fibroblast

tag: cell type

value: Primary Fibroblast


title: Expt8_PATFIB_U5_ATCC


title: Expt8_PATFIB_U2_4128U


title: Expt8_PATFIB_U5_1603U


title: Expt4_input-U6-FLAGonly-siCaf1z


title: Expt3_input-U6-FLAGonly-siLuc


title: Expt8_PATFIB_U2_1603U


title: BC-3


title: Expt8_PATFIB_U5_4128U


title: Expt8_PATFIB_U5_1603A


title: Expt8_PATFIB_U5_4127A


title: Expt5_FU1-Vs-16_a103_tot

description: TOE1 expression induced to be roughly equal to endogenous levels

value: A103 addback - siCaf1z


title: Expt8_PATFIB_U2_4128A


title: Expt8_PATFIB_U2_ATCC


title: Expt8_PATFIB_U2_1603A


title: Expt8_PATFIB_U2_4127A


title: Expt5_FU1-Vs-13_siC_tot


title: Expt5_FU1-Vs-19_e220_tot

value: E220 addback- siCaf1z


title: Expt5_FU1-Vs-17_f148_tot

value: F148 addback- siCaf1z


title: Expt5_FU1-Vs-06_f148_rip

value: F148 addback


title: Expt5_FU1-Vs-14_wt_tot


title: Expt5_FU1-Vs-03_wt_rip


title: Expt5_FU1-Vs-04_de_rip


title: Expt5_FU1-Vs-02_E220_rip

value: E220 addback


title: Expt4_input-U5-FLAGonly-Caf1z

value: FLAG


title: Expt5_FU1-Vs-01_V173_rip

value: HEK 293

value: V173 addback


title: Expt8_PATFIB_U1_4128A


title: Expt8_PATFIB_U1_4128U


title: Expt8_PATFIB_U1_1603U


title: Expt4_input-U5-FLAGonly-siLuc


title: Expt8_PATFIB_U1_4127A


title: Expt5_FU1-Vs-18_v173_tot

value: V173 addback- siCaf1z


title: Expt8_PATFIB_U1_1603A


title: E2A-48hours-ChIPseq

value: haftl derived C10 cells

value: 48 hours


title: E2A-12hours-ChIPseq

value: 12 hours


title: E2A-3hours-ChIPseq

value: 3 hours


title: E2A-24hours-ChIPseq

value: 24 hours


title: Expt5_FU1-Vs-12_siL_tot

value: siControl

value: NNNNNNNNNNCT


title: Expt3_elu-U5-WTaddback

value: Mouse anti-FLAG (Sigma)

value: WTaddback