title: MDX_5

city: Bern

first: Jean-Sebastien

last: ROUGIER

address: Bühlstrasse 28

department: IBMM

institute: University of Bern

description:
comparaison_RNA_expression.xls
counts_length_TPM all_conditions.xls

data_processing:
The quality of the reads was assessed using fastqc v.0.11.2
Ribosomal RNA was removed by mapping the reads with Bowtie2 v. 2.2.1 to a collection of rRNA sequences (NR_003279.1, NR_003278.3 and NR_003280.2) downloaded from NCBI
The remaining reads were mapped to the Mus musculus reference genome (GRCm38.83) with Tophat v.2.0.13
The number of reads overlapping with each gene were counted with htseq-count v.0.6.1
Differential gene expression between the conditions was tested with the Bioconductor package DESeq2 v. 1.10.1

source_name: Ventricular cardiomyocytes

extract_protocol:
Adult ventricular cardiomyocytes were isolated by enzymatic digestion on a Langendorff sytem. Right after isolation, total RNA was extracted with an FFPE Clear RNAready kit (AmpTec, Germany), which included a DNase treatment step. Then, RNA quality was assessed with Qubit and Bioanalyzer, and RNA quantity was checked with Qubit.
Libraries were constructed with 1 ug RNA using the TruSeq Stranded Total RNA protocol, and either poly-A selection (WT samples) or Ribo-Zero Gold depletion (Illumina) (CASK, SAP97, MDX samples). Library molecules with inserts <300 basepairs (bp) were removed to allow sequencing of long non-coding RNA (lncRNA) (for CASK, SAP97, MDX).

value: Mixed, 3x backcrossed on C57Bl/6J

tag: age (weeks)

value: MDX -/-


title: MDX_4

status: Public on Aug 22 2017

type: SRA

country: Switzerland

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype


title: A-498 wt VHL input rep2

city: Singapore

first: Xiaosai

last: Yao

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

country: Singapore

institute: Genome Institute of Singapore

library_source: genomic

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
H3K27ac and H3K4me1 ChIP-seq were called with CCAT whereas H3K27me3 ChIP-seq were called with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks are in bed format, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"

molecule: genomic DNA

organism: Homo sapiens

source_name: ccRCC cell line

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

extract_protocol:
One million cells were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed 3 times with TBSE buffer.  Pelleted cells were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). Sonicated DNA was normalized for each pair of cells with and without wildtype VHL before immuno-precipitation. The total volume of immunoprecipitation was 1 ml and the amount of antibody used was 2 µg. The input DNA was precleared with protein G Dynabeads (Life Technologies) for 1 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 3 times with cold wash buffer.
Whole-genome-amplification was performed on ChIP DNA and input using the WGA4 kit (Sigma-Aldrich).  The amplified DNA was used with NEBNext ChIP-Seq library prep reagent set.

treatment_protocol: 786-O cells stably expressing RC3 empty vector (VHL-) or wildtype VHL (VHL+) were kindly provided by Dr. Michael Ohh (University of Toronto). Whole-genome H3K27ac ChIP-seq was performed on these two isogenic cell lines.

tag: histone

value: Input

tag: chip antibody

tag: source


title: 12364284 empty vector H3K4me1 ChIP-seq rep1

value: H3K4me1 (ab8895, Abcam)

value: Patient derived ccRCC cell line


title: A-498 wt VHL H3K27ac ChIP-seq rep2

value: H3K27ac (ab4729, Abcam)


title: 12364284 empty vector H3K27ac ChIP-seq rep1


title: 40911432 wt VHL input rep2


title: MDX_3


title: A-498 empty vector input rep2


title: 40911432 wt VHL H3K27ac ChIP-seq rep1


title: MDX_2


title: MDX_1


title: A-498 wt VHL H3K27ac ChIP-seq rep1


title: A-498 wt VHL input rep1


title: A-498 empty vector H3K27ac ChIP-seq rep2


title: 12364284 empty vector H3K27me3 ChIP-seq rep2

value: H3K27me3 (07-449, Millipore)


title: A-498 empty vector input rep1


title: MDX_Ct5

value: Mixed 3x backcrossed on C57Bl/6

value: wild type


title: MDX_Ct4


title: A-498 empty vector H3K27ac ChIP-seq rep1


title: MDX_Ct3


title: 786-O wt VHL H3K27ac ChIP-seq rep2


title: 786-O wt VHL H3K4me1 ChIP-seq rep2


title: 786-O wt VHL H3K27me3 ChIP-seq rep2


title: 786-O wt VHL input rep2


title: 786-O empty vector input rep2


title: 786-O empty vector H3K27me3 ChIP-seq rep2


title: 786-O wt VHL input rep1


title: MDX_Ct1


title: 786-O empty vector H3K4me1 ChIP-seq rep2


title: SAP_KO2

value: Mixed

value: MHC-Cre + SAP97 fl/fl


title: SAP_KO3


title: 786-O empty vector H3K27ac ChIP-seq rep2


title: 786-O wt VHL H3K27me3 ChIP-seq rep1


title: 786-O wt VHL H3K27ac ChIP-seq rep1


title: 786-O wt VHL H3K4me1 ChIP-seq rep1


title: 786-O empty vector input rep1


title: SAP_KO1


title: 786-O empty vector H3K27me3 ChIP-seq rep1


title: SAP_Ct3

value: SAP97 fl/fl


title: SAP_Ct2


title: 786-O empty vector H3K27ac ChIP-seq rep1


title: UPF1_4

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

country: USA

institute: University of Rochester

data_processing:
bcltofastq-1.8.4
miRge (strict) "--diff-isomirs --adapter illumina --species human" changed isoMir alignment parameter from "-n 2" to "-n 0"
cutAdapt-1.12
bowtie-1.2
Genome_build: miRge human miRNA annotation (mirBase v21)
Supplementary_files_format_and_content: text file includes raw expression counts

source_name: T24_UPF1 siRNA

growth_protocol: T24 cells were propagated in RPMI-1640 (Gibco)

extract_protocol:
Small RNA-enriched fractions were purified from cell pellets using miRNeasy and RNeasy MinElute Cleanup Kits (Qiagen).
cDNA libraries were generated using the TruSeq Small RNA library preparation protocol (Illumina). After addition of the TruSeq 3' adapter (5' adenylated) using truncated T4 RNA ligase II (New England Biolabs) and, subsequently, the 5' adapter using T4 RNA ligase I (New England Biolabs), RNA was reverse-transcribed using a 3' adapter-specific primer. The resulting cDNA was then amplified using 12 cycles of PCR, a universal forward primer and a reverse primer, the latter harboring a bar code. cDNA libraries were purified using the Pippin Prep system (Sage Sicence) and quantified first using an Agilent Bioanalyzer and subsequently using qPCR. Barcoded libraries were mixed at equimolar concentrations and analyzed by single-end 50-nt sequencings using an Illumina HISeq2500v4 sequencer (Illumina).

treatment_protocol: Transfection with 50nM siRNA using RNAiMax (ThermoFisher)

tag: cell line

tag: cell type

value: human urinary bladder cancer cells

tag: treated with

value: UPF1 siRNA

tag: molecule subtype

value: RNA fractions enriched in < 200-nt RNAs


title: UPF1_5


title: SAP_Ct1


title: CASK_KO3

value: MHC-Cre + CASK fl/fl


title: UPF1_2


title: MDX_Ct2


title: UPF1_1


title: TSN_3

source_name: T24_TSN siRNA

value: TSN siRNA


title: TSN_4


title: CASK_KO2


title: CASK_KO1


title: TSN_2


title: TSN_1


title: CASK_Ct3

value: MHC-Cre


title: Ctl_5

source_name: T24_Control siRNA

value: Control siRNA


title: Ctl_3


title: 786-O empty vector H3K4me1 ChIP-seq rep1


title: Ctl_1


title: Ctl_4


title: Ctl_2


title: CASK_Ct2


title: CASK_Ct1


title: RNASeq SECIS2 deletion3

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

data_processing:
Sequence reads were trimmed of adapter sequences using Hannon lab Fastx toolkit
rRNA sequences were removed using bowtie alignments to mouse 43SrRNA
RefSeq FASTA sequences were obtained from the UCSC genome browser (mm9). These FASTA files were reduced to a single entry for each mRNA corresponding to the longest isoform. Uniquely aligning sequences, allowing for 2 mismatches, were identified using the Bowtie sequence aligner. A-sites of ribosome footprints on Selenoprotein P were predicted based off meta-analysis offset of footprints relative to all AUG initiation codons.
Normalization of A-site counts= (raw RPF A-site Cts/RPF million mapped reads)/(Selenop RNA reads/RNA million mapped reads)
Genome_build: mm9
Supplementary_files_format_and_content: Selenop Asite raw count and normalized count across Selenoprotein p

molecule: polyA RNA

source_name: Liver

extract_protocol:
Total RNA was isolated by bead beating for ribosome profiling in polysome buffer or qiazol for total RNA isolation.
RNA-Seq: Liver total RNA was isolated. rRNA was removed using Ribo-Zero (Illumina), fragmented, size selected (20-40nts) and libraries prepared using Illumina TruSeq small RNA preparation kit. Sequencing was done using the Illumina HiSeq2000 instrument.

treatment_protocol: Mice were fed standard chow prior to euthanasia and harvesting of liver tissue

tag: diet

value: Standard Chow

tag: tissue

value: liver


title: nascentRNA_24335_JQ1_10_2

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

data_processing:
Reads were aligned to the human reference genome (GRCh38 assembly) using Bowtie (version 0.12.5), retaining only uniquely mapped reads.
Smoothed enrichment profiles were generated using the SPP package (Kharchenko et al. 2008), using smoothing bandwidth of 5kb.
Genome_build: GRCh38
Supplementary_files_format_and_content: tdf files were generated by converting wig files using igvtools

growth_protocol: 293TRex, TC-797 (31), and BICR6 (Hypopharyngeal squamous cell carcinoma (32) were maintained in Dulbecco Modified Eagle medium (DMEM) (Invitrogen) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, S10350, Atlanta Biologicals), 1% pen-strep and 1X GlutaMAX (Invitrogen). NMC cells 24335 (ZNF532-NUT) were initially established in OCMI-E media (33) (purchased from Live Tumor Culture Core, University of Miami, http://sylvester.org/shared-resources/Live-Tumor-Culture-Core). 797TRex and 293TRex derivatives, which contain a single genomic FRT recombination site, and constitutively express tetracycline repressor (TR), were created as described (2) and maintained as above with blasticidin (Invitrogen) and zeocin (Invitrogen). 797TRex, 293TRex and /N- and C- BioTAP-BRD4-NUT lines were generated as described previously (2-3), and maintained in blasticidin and hygromycin (Sigma). Stable 797TRex and BICR6 ZNF532-BioTAP lines were generated by lentiviral transduction using the following vectors: N-BioTAP and C-BioTAP pHAGE-CMV-TET-ZNF532 (details on vectors and constructs will be provided upon request) followed by selection with puromycin.

extract_protocol:
The main steps of BioTAP-XL procedure: harvesting cells, formaldehyde cross-linking, chromatin preparation, affinity purification, input and IP protein recovery were performed as described (12, 36). Cross-linked chromatin for ChIP-seq experiments using antibodies against proteins and histone modifications was prepared from 5 × 10(8) 24335 (ZNF532-NUT) NMC cells as described (36). Nascent RNA was purified as described (3). Each RNA library was constructed from 50 ng of nascent RNA following the manufacturer’s instructions (NEBNext Ultra directional RNA library prep kit, New England BioLabs)
ChIP-seq library preparation were performed as described (Alekseyenko et al. 2015). RNA library was constructed from 50 ng of nascent RNA following the manufacturer’s instructions (NEBNext Ultra directional RNA library prep kit, New England BioLabs)

treatment_protocol: BioTAP-XL procedure and mass spectrometric data analysis:7.5 × 108 cells grown as monolayer cultures in 150mm dishes (50 plates total) were used for BioTAP-XL purification. Tetracycline was added (1 μg/mL) to 60-70% confluent culture to induce transcription of the N- or C-BioTAP tagged BRD4-NUT cDNA for 24h or for 4d in the case of ZNF532 cDNA. Recovery and analysis of nascent RNA: 4 × 106 ZNF532-NUT 24335 cells were grown in 100 mm dishes. Cells were split into two T-25 flasks and JQ1 (10uM final concentration) or DMSO were added to the media. After 4 hours, cells were harvested and nascent RNA was purified as described (3). Each RNA library was constructed from 50 ng of nascent RNA following the manufacturer’s instructions (NEBNext Ultra directional RNA library prep kit, New England BioLabs)

value: NMC

tag: agent

value: 10uM JQ1 for 4hours


title: UPF1_3


title: nascentRNA_24335_JQ1_10_1


title: RNASeq SECIS2 deletion2


title: nascentRNA_24335_JQ1_0_2

value: DMSO for 4hours


title: nascentRNA_24335_JQ1_0_1


title: TSN_5


title: IP_ZNF532_24335_1

value: ZNF532 (anti-ZNF532, 10ul  Bethyl Laboratories, cat. no. A305-442A


title: IP_ZNF532_24335_2


title: RNASeq SECIS2 WT3


title: RNASeq SECIS2 deletion1


title: IP_p300_24335_1

value: P300 (anti-P300 , 10 ul, Bethyl, catalog no. A300-358A)


title: RNASeq SECIS2 WT2


title: IP_p300_24335_2


title: IP_NUT_24335_2

value: NUT (anti-NUT, 15 ul per IP; Cell Signaling, catalog no. 3625)


title: IP_H3K9me2_24335_2

value: H3K9me2 (anti-H3K9me2,  5 ul per IP, Abcam, catalog no. ab1220)


title: IP_H3K27me3_24335_2

value: H3K27me3 ( anti-H3K27me3, 10 ul per IP, Cell Signaling, catalog no. 9733)


title: IP_H3K27me3_24335_1


title: IP_H3K9me2_24335_1


title: IP_H3K27ac_24335_2

value: H3K27ac (anti-H3K27ac , 10 ul per IP, Active Motif, catalog no. 39133)


title: IP_H3K27ac_24335_1


title: Ribosome Profiling SECIS2 deletion2

data_processing:
Library strategy: Ribosome profiling
Sequence reads were trimmed of adapter sequences using Hannon lab Fastx toolkit
rRNA sequences were removed using bowtie alignments to mouse 43SrRNA
RefSeq FASTA sequences were obtained from the UCSC genome browser (mm9). These FASTA files were reduced to a single entry for each mRNA corresponding to the longest isoform. Uniquely aligning sequences, allowing for 2 mismatches, were identified using the Bowtie sequence aligner. A-sites of ribosome footprints on Selenoprotein P were predicted based off meta-analysis offset of footprints relative to all AUG initiation codons.
Normalization of A-site counts= (raw RPF A-site Cts/RPF million mapped reads)/(Selenop RNA reads/RNA million mapped reads)
Genome_build: mm9
Supplementary_files_format_and_content: Selenop Asite raw count and normalized count across Selenoprotein p

extract_protocol:
Total RNA was isolated by bead beating for ribosome profiling in polysome buffer or qiazol for total RNA isolation.
Ribosome Profiling: Liver tissue was homogenized, and crude polysomes digested with RNase1, isolated by centrifugation through sucrose, and ribosome footprints (~30nts) size purified by denaturing polyacrylamide gel electrophoresis. Libraries were constructed using illumina TruSeq Small RNA Sample Preparation kit. Sequencing was done using the Illumina HiSeq2000 instrument


title: Ribosome Profiling SECIS2 deletion3


title: IP_BRD4_24335_2

value: BRD4 short and long forms (anti-BRD4-SL , against short and long isoforms of BRD4, 5 ul per IP, Bethyl, catalog no. A301-985A)


title: IP_BRD4_24335_1


title: Ribosome Profiling SECIS2 deletion1


title: Ribosome Profiling SECIS2 WT1


title: Ribosome Profiling SECIS2 WT2


title: Input_24335_1


title: Input_24335_2


title: Ribosome Profiling SECIS2 WT3


title: RNASeq SECIS1 WT3


title: RNASeq SECIS1 WT2


title: IP_NUT_24335_1


title: RNASeq SECIS2 WT1


title: RNASeq SECIS1 deletion3


title: SJSA, Genomewide, Nutlin treated, replicate 3

city: Aurora

first: Ahwan

last: Pandey

state: CO

department: Pharmacology

institute: University of Colorado Anschutz Medical Center

description:
shRNA cassette
SJSA_GW_Nutlin3
GW_counts.tab.gz

data_processing:
Library strategy: shRNA-seq
Basecalls performed using bcl2fastq_v1.8.4 with the following options (--mismatches 1 fastq-cluster-count 0 )
Samples were demultiplex using fastx_barcode_splitter in fastx_0.0.13.2 allowing 2 mismatches
FASTQC v0.11.2 was used to determine sequence quality
Seqeunces were trimmed using fastx_trimmer in fastx_0.0.13.2 with the following options (-Q33 -f 22 -l 42)
Trimmed sequences were mapped with Bowtie2 v2.2.3 using the following options (--phred33 --end-to-end --very-sensitive-local)
Genome_build: hg19 (BROAD Human TRC version 1/1.5/2)
Supplementary_files_format_and_content: Tab delimited text files containing raw shRNA counts for each sample

source_name: SJSA, Genomewide, Nutlin treated

growth_protocol: SJSA cells were cultivated in RPMI with 10% FBS. After transduction with shRNA libraries, cells were incubated with selection media. After this period cells were plated at equal densities and cultivated for 24 hours.

extract_protocol:
DNeasy Kit from Qiagen
Custom; shRNA amplicon
After recovery, 5x10e6 cells were harvested and gDNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany). The shRNA cassettes were isolated from genomic DNA with a first PCR reaction using the following primers: pLKO ForHTm primer (GGGCCTATTTCCCATGATTCCTTC), and Rev-pLKO.1 (CCAAAGTGGATCTCTGCTGTCCC). After verification of a single PCR product at 497 bp size, PCR reactions were pooled and cleaned up with QIAquick PCR Purification Kit (Qiagen). Next, 1microg of the resulting DNA was digested with XhoI overnight at 37C (for ligation of barcode linkers to allow multiplex sequencing), gel excised and the appropriate band was isolated using QIAquick Gel Extraction Kit (Qiagen). Selected barcode linkers were added to ligation reactions with 100 ng of the purified XhoI fragment. Ligations were performed overnight at 16C and run on 2% TAE agarose gel. The resulting ligation product was excised from the gel and purified as before. A second PCR was performed for addition of Illumina adapters with PCR2 primers (PCR2 Fwd: CAAGCAGAAGACGGCATACGATGGAAAGGACGAAACACCGG, PCR2 rev: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT). These PCR reactions were run again on a 2% TAE agarose gel, and the appropriate final product was excised and purified as above. Before sequencing, we assessed the purity and quantity of our sequencing libraries with the Bioanalyzer High Sensitivity DNA Kit (Agilent), and confirmed the presence of only one DNA fragment.

treatment_protocol: Cells were treated with either 0.2% DMSO or 10 microM Nutlin for 48 hours. After the treatment, cells were washed three times with PBS, and provided with regular cultivation media. Nutlin-treated cells were allowed to grow and repopulate the plate until ~80% confluency, while DMSO-treated cells were split accordingly as needed. Once reached the appropriate density, cells were harvested and re-plated for second round of treatment with either DMSO or Nutlin. After 48 hours, cells were washed with PBS and allowed to recover and grow back to ~80% confluency in drug-free media.

value: Osteosarcoma Cell Line SJSA

tag: screen

value: Genomewide

tag: treatment

value: Nutlin


title: SJSA, p53 Target, Nutlin treated, replicate 2

description:
shRNA cassette
SJSA_p53T_Nutlin2
p53T_counts.tab.gz

source_name: SJSA, p53 Target, Nutlin treated

value: p53 Target


title: SJSA, p53 Target, Nutlin treated, replicate 1

description:
shRNA cassette
SJSA_p53T_Nutlin1
p53T_counts.tab.gz


title: SJSA, Genomewide, Nutlin treated, replicate 2

description:
shRNA cassette
SJSA_GW_Nutlin2
GW_counts.tab.gz


title: SJSA, p53 Target, DMSO treated, replicate 1

description:
shRNA cassette
SJSA_p53T_DMSO1
p53T_counts.tab.gz

source_name: SJSA, p53 Target, DMSO treated

value: DMSO


title: SJSA, p53 Target, DMSO treated, replicate 3

description:
shRNA cassette
SJSA_p53T_DMSO3
p53T_counts.tab.gz


title: SJSA, Genomewide, Nutlin treated, replicate 1

description:
shRNA cassette
SJSA_GW_Nutlin1
GW_counts.tab.gz


title: SJSA, p53 Target, Nutlin treated, replicate 3

description:
shRNA cassette
SJSA_p53T_Nutlin3
p53T_counts.tab.gz


title: SJSA, p53 Target, DMSO treated, replicate 2

description:
shRNA cassette
SJSA_p53T_DMSO2
p53T_counts.tab.gz


title: SJSA, Genomewide, DMSO treated, replicate 3

description:
shRNA cassette
SJSA_GW_DMSO3
GW_counts.tab.gz

source_name: SJSA, Genomewide, DMSO treated


title: RNASeq SECIS1 deletion1

value: Standard Chow


title: SJSA, Genomewide, DMSO treated, replicate 1

description:
shRNA cassette
SJSA_GW_DMSO1
GW_counts.tab.gz


title: SJSA, Genomewide, DMSO treated, replicate 2

description:
shRNA cassette
SJSA_GW_DMSO2
GW_counts.tab.gz


title: SJSA, GRO-Seq, Nutlin treated, replicate 2

description:
nuclear RNA from Nutlin treated SJSA cells
SN4
SD1.SD3.SN2.SN4_keep_duplicates.tab.gz
SN2SN4.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
SN2SN4.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw

data_processing:
FASTQC v0.11.2 was used to determine sequence quality
fastqc-mcf from ea-utils (v1.1.2) was used to detect and remove sequencing adapters, detect limited skewing at the ends of reads and clip, detect poor quality at the ends of reads and clip, detect Ns and remove from ends, remove reads with CASAVA “Y” flag (purity filtering) and discard sequences that were too short after all of the above (< 30bp)
Reads were then mapped to the reference human genome (GRCh37/hg19) using Bowtie2 (bowtie2-2.2.3, --sensitive –-end-to-end)
Reads were then filtered to remove low quality mapped reads (MAPQ < 10) and non-unique reads were removed by SAMtools (0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts for each sample
Supplementary_files_format_and_content: Normalized bigwig files using deeptools 2.2.2 (--binSize=1 --minMappingQuality 10 –normalizeUsingRPKM). Replicates were added.

molecule: nuclear RNA

source_name: SJSA, Nutlin treated

growth_protocol: All cell lines were plated 24 hours prior to treatment.

extract_protocol:
RNA was extracted using TRI reagent, according to manufacturer's instructions.
Custom

treatment_protocol: 1 hour of 10 microM Nutlin or 0.2% DMSO.

tag: batch


title: Ribosome Profiling SECIS1 WT3

value: liver


title: SJSA, GRO-Seq, DMSO treated, replicate 2

description:
nuclear RNA from DMSO treated SJSA cells
SD3
SD1.SD3.SN2.SN4_keep_duplicates.tab.gz
SD1SD3.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
SD1SD3.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw

source_name: SJSA, DMSO treated


title: SJSA, GRO-Seq, DMSO treated, replicate 1

description:
nuclear RNA from DMSO treated SJSA cells
SD1
SD1.SD3.SN2.SN4_keep_duplicates.tab.gz
SD1SD3.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
SD1SD3.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw


title: MCF7, GRO-Seq, Nutlin treated, replicate 2

description:
nuclear RNA from Nutlin treated MCF7 cells
MN2
MD1.MD2.MN1.MN2_keep_duplicates.tab.gz
MN1MN2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
MN1MN2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw

source_name: MCF7, Nutlin treated

value: Breast Carcinoma Cell Line MCF7


title: MCF7, GRO-Seq, Nutlin treated, replicate 1

description:
nuclear RNA from Nutlin treated MCF7 cells
MN1
MD1.MD2.MN1.MN2_keep_duplicates.tab.gz
MN1MN2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
MN1MN2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw


title: Ribosome Profiling SECIS1 WT2


title: Ribosome Profiling SECIS1 WT1


title: MCF7, GRO-Seq, DMSO treated, replicate 1

description:
nuclear RNA from DMSO treated MCF7 cells
MD1
MD1.MD2.MN1.MN2_keep_duplicates.tab.gz
MD1MD2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
MD1MD2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw

source_name: MCF7, DMSO treated


title: MCF7, GRO-Seq, DMSO treated, replicate 2

description:
nuclear RNA from DMSO treated MCF7 cells
MD2
MD1.MD2.MN1.MN2_keep_duplicates.tab.gz
MD1MD2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
MD1MD2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw


title: HCT116, GRO-Seq, Nutlin treated, replicate 2

description:
nuclear RNA from Nutlin treated HCT116 cells
HN2
HD1.HD2.HN1.HN2_keep_duplicates.tab.gz
HN1HN2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
HN1HN2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw

source_name: HCT116, Nutlin treated

value: Colorectal Adenocarcinoma Cell Line HCT116


title: Ribosome Profiling SECIS1 deletion3


title: RNASeq SECIS1 WT1


title: HCT116, GRO-Seq, Nutlin treated, replicate 1

description:
nuclear RNA from Nutlin treated HCT116 cells
HN1
HD1.HD2.HN1.HN2_keep_duplicates.tab.gz
HN1HN2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
HN1HN2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw


title: Ribosome Profiling SECIS1 deletion2


title: RNASeq SECIS1 deletion2


title: HCT116, GRO-Seq, DMSO treated, replicate 2

description:
nuclear RNA from DMSO treated HCT116 cells
HD2
HD1.HD2.HN1.HN2_keep_duplicates.tab.gz
HD1HD2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
HD1HD2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw

source_name: HCT116, DMSO treated


title: Ribosome Profiling H19:H391


title: SJSA, GRO-Seq, Nutlin treated, replicate 1

description:
nuclear RNA from Nutlin treated SJSA cells
SN2
SD1.SD3.SN2.SN4_keep_duplicates.tab.gz
SN2SN4.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
SN2SN4.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw


title: LATS1/2;YAPTAZ-ECKO4

city: Irvine

first: Hosung

last: Bae

state: CA

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Lung endothelial cells (Lung ECs)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: FACS sorted Lung ECs

tag: age

value: VE-cadherin-CreERT2 Lats1f/f Lats2 f/f;Yapf/f TAZf/f


title: MCF7, ChIP-Seq, Nutlin treated

description:
p53 ChIP-seq of Nutlin-treated MCF7 cells
MN

data_processing:
FASTQC v0.11.2 was used to determine sequence quality
Low quality reads were removed (phred < 10, ea-utils_1.1.2, http://code.google.com/p/ea-utils)
Reads were then mapped to the reference human genome (GRCh37/hg19) using Bowtie2 (bowtie2-2.2.3, --sensitive –-end-to-end)
Reads were then filtered to remove low quality mapped reads (MAPQ < 10) and non-unique reads were removed by SAMtools (0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Genome_build: hg19
Supplementary_files_format_and_content: Normalized bigwig files using deeptools 2.2.2 (--binSize=1 --minMappingQuality 10 –normalizeUsingRPKM). Replicates were added.

extract_protocol:
Custom
Illumina TruSeq ChIP Library Preparation Kit

treatment_protocol: 12 hours of 10 microM Nutlin or 0.2% DMSO.

value: p53 (DO1) (Calbiochem, catalog# OP43-100mg, lot# 2635181)


title: MCF7, ChIP-Seq, Input

description:
MCF7 input
MDI

source_name: MCF7, Input

value: Input


title: HCT116, ChIP-Seq, Input

description:
HCT116 input
HDI

source_name: HCT116, Input


title: HCT116, ChIP-Seq, DMSO treated

description:
p53 ChIP-seq of DMSO-treated HCT116 cells
HD


title: SJSA, ChIP-Seq, DMSO treated

description:
p53 ChIP-seq of DMSO-treated SJSA cells
SD


title: MCF7, ChIP-Seq, DMSO treated

description:
p53 ChIP-seq of DMSO-treated MCF7 cells
MD


title: SJSA, ChIP-Seq, Input

description:
SJSA input
SDI

source_name: SJSA, Input


title: LATS1/2;YAPTAZ-ECKO3


title: SJSA, ChIP-Seq, Nutlin treated

description:
p53 ChIP-seq of Nutlin-treated SJSA cells
SN


title: 786-O P300 ChIP-seq

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicates removed by rmdup were used in the subsequent analysis.
Significant peaks were called using MACS2 (q-value < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: bed format for ucsc genome browser, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"

source_name: ccRCC cell line

extract_protocol:
For each transcription factor, ~3x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 1.5 ml and the amount of antibody used was 15 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 6 times with wash buffer at room temperature.
Amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB)

tag: transcription factor

value: P300 (sc-585, Santa Cruz)


title: HCT116, ChIP-Seq, Nutlin treated

description:
p53 ChIP-seq of Nutlin-treated HCT116 cells
HN


title: 57398667N Input

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
Significant peaks were called using CCAT (p-value < 0.05).
Genome_build: hg19
Supplementary_files_format_and_content: bed format for ucsc genome browser, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "fold change"

source_name: adjacent normal kidney tissue

extract_protocol:
Approximately 5 mg flesh frozen tissues were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed 3 times with TBSE buffer.  Pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). The total volume of immunoprecipitation was 1 ml and the amount of antibody used was 2 µg. The input DNA was precleared with protein G Dynabeads (Life Technologies) for 1 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 3 times with cold wash buffer.
Whole-genome-amplification was performed on ChIP DNA and input using the WGA4 kit (Sigma-Aldrich).  The amplified DNA was used with NEBNext ChIP-Seq library prep reagent set.


title: LATS1/2;YAPTAZ-ECKO1

tag: strain


title: 786-O NFkb ChIP-seq

value: NFkB

value: NFĸB p65 (sc-372, Santa Cruz)


title: 57398667N H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: 786-O ETS1 ChIP-seq


title: Pol II_siMed23A_ChIPSeq (UV)

city: Shanghai

first: Min

last: Xia

address: 320 YueYang Road

country: China

institute: SIBCB

description: 23a_pol2_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following configurations: -v1, -best, -strata, -k2, and -m1.
peaks were called using MACS by P-value threshold of 10-5.
called peaks were annotated using R package ChIPpeakAnno and the average ChIP-seq intensity between 2 kb upstream of TSS and 2 kb downstream of TSS was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS; Scores represent ChIP intensity.

source_name: Melanoma cell line

growth_protocol: Cells are culturing in DMEM with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
ChIP DNA was prepared for DNA library using ChIP-seq Sample Prep Kit (illumina).

value: Pol II: Santa Cruz, sc-899


title: 786-O C-Jun ChIP-seq

value: C-Jun

value: c-Jun (sc-1694, Santa Cruz)


title: LATS1/2-ECKO4

tag: genotype

value: VE-cadherin-CreERT2 Lats1f/f Lats2 f/f


title: 57398667T Input

source_name: ccRCC tumor tissue

tag: histone


title: siMed23B_input (UV)

description: 23b_input_UV_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz

tag: chip antibody


title: HCT116, GRO-Seq, DMSO treated, replicate 1

description:
nuclear RNA from DMSO treated HCT116 cells
HD1
HD1.HD2.HN1.HN2_keep_duplicates.tab.gz
HD1HD2.mapped.no-rgid.sorted.filtered.fw.bs1.RPKMnorm.bw
HD1HD2.mapped.no-rgid.sorted.filtered.rev.bs1.RPKMnorm.bw

value: DMSO


title: LATS1/2-ECKO3


title: 786-O Input

tag: source


title: LATS1/2-ECKO2


title: H3K27ac_siMed23A_ChIPSeq (no UV)

description: 23a_k27_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz

value: H3K27ac: Abcam, ab4729


title: LATS1/2;YAPTAZ-ECKO2


title: 77972083N Input


title: Lung WT2

value: wild type


title: 77972083T Input


title: Lung WT3


title: 77972083T H3K27ac ChIP-seq


title: 77972083N H3K27ac ChIP-seq


title: 17621953N input


title: Lung WT1


title: miRNA_wt_p27

city: Bethesda

first: Jianguo

last: Fan

state: MD

address: 6 Center Drive Rm 108A

institute: National Eye Institute

data_processing:
Differential mRNA expression between miR183C knockout mice and agematched C57bl6/J control mice was quantified by RNA-seq data analysis using the Tuxedo package (i.e. the Tophat-Cufflinks pipeline) on the NIH Biowulf high performance computing platform.
Alignment was performed by use of Tophat version 2.1.1 (Bowtie2) and the mouse10 reference genome (NCBI) with standard parameters. Cufflinks version 2.2.1 was used to assemble the transcriptomes and CuffDiff was used to quantify the levels of gene expression in Reads Per Kilobase of transcript per Million mapped reads (RPKM).
False discovery rate (FDR) value of less than or equal to 0.1 was used as the criteria for “significant” differentially regulated genes.
Output files from Cuffdif was uploaded as the processed data files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene, "1" refers to wild type and "2" refers to miR183 Cluster KO.

source_name: Retina

growth_protocol: DNA-free total RNA was prepared from a pool of retinas from 5 miR183CKO/KO or age-matched C57bl6/J control mice, by use of PureLink RNA Mini Kit and TRIzol Reagent (Life Technologies)

extract_protocol:
RNA integrity was evaluated by 2100 Bioanalyzer (Agilent Technologies) with RIN no less than 7. RNA-seq was performed by NIH Intramural Sequencing Center (Bethesda, MD).
One paired end index library from each  polyA(+)-selected RNA samples was prepared. Six samples were pooled and loaded on 2 lane(s) of Illumina HiSeq 2000 Sequencer, and run as paired end index 100 base reads with a total of 40 million base read pairs per sample.
Differential mRNA expression between miR183C knockout mice and agematched C57bl6/J control mice was quantified by RNA-seq data analysis using the Tuxedo package (i.e. the Tophat-Cufflinks pipeline) on the NIH Biowulf high performance computing platform.

treatment_protocol: and on-column DNase treatment with PureLink Dnase (Life Technologies) according to manufacturer’s instructions.

value: retina

value: post natal day 27


title: miRNA_ko_p27

value: miR183 Cluster KO


title: 17621953N H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: miRNA_ko_p11

value: post natal day 11


title: YAPTAZ-ECKO4

source_name: Brain endothelial cells (Brain ECs)

value: FACS sorted Brain ECs

value: VE-cadherin-CreERT2 Yapf/f Tazf/f


title: 17621953N H3K4me3 ChIP-seq

value: H3K4me3 (07-473, Millipore)


title: YAPTAZ-ECKO3


title: Pol II_siMed23A_ChIPSeq (no UV)

description: 23a_pol2_no_treat_chr(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,M,X,Y).wig.gz


title: YAPTAZ-ECKO2


title: 17621953T input

value: Input


title: 17621953N H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: 17621953T H3K27ac ChIP-seq


title: 57398667T H3K27ac ChIP-seq


title: YAPTAZ-ECKO1


title: WT4


title: 17621953T H3K4me1 ChIP-seq


title: LATS1/2-ECKO1

value: FACS sorted Lung ECs


title: miRNA_wt_p11


title: miRNA_ko_p5

value: post natal day 5


title: WT3


title: Lung WT4


title: miRNA_wt_p5


title: WT1


title: WT2


title: 70528835N input


title: 70528835N H3K27ac ChIP-seq


title: 17621953T H3K4me3 ChIP-seq


title: input DNA

city: shanghai

first: Yongfeng

last: Liu

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

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

data_processing:
Sequence Analysis: The 75-nt sequence reads generated by Illumina sequencing (using NextSeq  500) are mapped to the genome using the BWA algorithm with default settings. Alignment  information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter,  align with no more than 2 mismatches, and map uniquely to the genome are used in the  subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are  removed.
Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the  end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-  ends to a length of 150-250 bp, depending on the average fragment length in the size selected  library (normally 200 bp). To identify the density of fragments (extended tags) along the genome,  the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peak Finding:The generic term “Interval” is used to describe genomic regions with local  enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end  coordinate. MACS is  used  to identify the binding sites of transcription factors that bind to discrete sites.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: DSS treated colon

growth_protocol: no treatment

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

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

tag: cell typr

value: primary colon epithelial cell

value: colon


title: KDR+HPC_TUMOR_REP3

city: New York

first: Yujie

last: Huang

state: NY

address: 510E 70st Street

department: Neurological Surgery

institute: Weill Cornell Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.

source_name: late stage GL261 tumor mice

extract_protocol:
HPCs were isolated by flowcytometer, and total RNAwere extracted by invitrogen microRNA isolation kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: cell type

value: Lin-ckit+sca- cells

tag: tumor stage


title: KDR+HPC_TUMOR_REP1


title: KDR-HPC_TUMOR_REP4


title: KDR-HPC_TUMOR_REP3


title: 70528835T input


title: 70528835N H3K4me3 ChIP-seq


title: KDR-HPC_TUMOR_REP2


title: 70528835N H3K4me1 ChIP-seq


title: EZH2 ChIPSeq

value: EZH2 Active Motif, cat # 3990


title: SJSA, total RNA, Nutlin treated, replicate 2

description:
total RNA from Nutlin treated wt SJSA cells
S1603_SJSA_nutlin2
SJSA_nutlin.bs1.forward.deeptools.normalized.bigwig
SJSA_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

data_processing:
Signal processing, base-calling and removal of barcode and adapter sequences was carried out automatically by the Torrent Suite Software (Life Technologies)
FASTQC v0.11.2 was used to determine sequence quality
fastx-trimmer from the fastx_0.0.13.2 toolkit was used to trim reads to 150bp
fastx-clipper from the fastx_0.0.13.2 toolkit was used to remove reads shorter than 30bp
Alignment to the Human genome (hg19/GRCh37) was carried out using GSNAP (gsnap_2015-06-12) with a mismatch setting of 3%
Reads were then filtered to remove low quality mapped reads (MAPQ < 10) and non-unique reads were removed by SAMtools (0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Raw count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene --mode=intersection-nonempty)
Normalized bigwig files using deeptools 2.2.2 (--binSize=1 --minMappingQuality 10 –normalizeUsingRPKM). Replicates were added.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts for each sample
Supplementary_files_format_and_content: Normalized bigwig files

source_name: SJSA, Nutlin treated

extract_protocol:
RNA was extracted using TRI reagent, according to manufacturer's instructions. Total RNA quality was assessed using Bioanalyzer RNA Pico chips (Agilent). PolyA RNA was purified from 15 g of total RNA using the Dynabeads mRNA Direct micro kit (Life Technologies) according to the manufacturer’s instructions.
Libraries for Ion Torrent sequencing were prepared using the Ion Total RNAseq v2 kit (Life Technologies), according to the manufacturer’s instructions.

tag: cell line

value: Osteosarcoma Cell Line SJSA

tag: p53 status

value: wt

value: Nutlin


title: SJSA, total RNA, Nutlin treated, replicate 1

description:
total RNA from Nutlin treated wt SJSA cells
S1591_SJSA_nutlin1
SJSA_nutlin.bs1.forward.deeptools.normalized.bigwig
SJSA_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: KDR-HPC_TUMOR_REP1

tag: tissue


title: SJSA, total RNA, DMSO treated, replicate 2

description:
total RNA from DMSO treated wt SJSA cells
S1602_SJSA_dmso2
SJSA_dmso.bs1.forward.deeptools.normalized.bigwig
SJSA_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

source_name: SJSA, DMSO treated

value: DMSO


title: SJSA, total RNA, DMSO treated, replicate 1

description:
total RNA from DMSO treated wt SJSA cells
S1590_SJSA_dmso1
SJSA_dmso.bs1.forward.deeptools.normalized.bigwig
SJSA_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: 70528835T H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: 70528835T H3K4me3 ChIP-seq


title: HPC_NAIVE_REP3

source_name: non tumor mice


title: MCF7, total RNA, Nutlin treated, replicate 2

description:
total RNA from Nutlin treated wt MCF7 cells
S1619_MCF7_nutlin2
MCF7_nutlin.bs1.forward.deeptools.normalized.bigwig
MCF7_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

source_name: MCF7, Nutlin treated

value: Breast Carcinoma Cell Line MCF7


title: HPC_NAIVE_REP2


title: MCF7, total RNA, Nutlin treated, replicate 1

description:
total RNA from Nutlin treated wt MCF7 cells
S1587_MCF7_nutlin1
MCF7_nutlin.bs1.forward.deeptools.normalized.bigwig
MCF7_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: 75416923N input


title: KDR+HPC_TUMOR_REP2


title: 75416923N H3K27ac ChIP-seq


title: HPC_NAIVE_REP1


title: MCF7, total RNA, DMSO treated, replicate 2

description:
total RNA from DMSO treated wt MCF7 cells
S1618_MCF7_dmso2
MCF7_dmso.bs1.forward.deeptools.normalized.bigwig
MCF7_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

source_name: MCF7, DMSO treated


title: 75416923N H3K4me1 ChIP-seq


title: MCF7, total RNA, DMSO treated, replicate 1

description:
total RNA from DMSO treated wt MCF7 cells
S1586_MCF7_dmso1
MCF7_dmso.bs1.forward.deeptools.normalized.bigwig
MCF7_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: 70528835T H3K27ac ChIP-seq


title: wt HCT116, total RNA, Nutlin treated, replicate 1

description:
total RNA from Nutlin treated wt HCT116 cells
S1562_wtHCT_nutlin1
wtHCT_nutlin.bs1.forward.deeptools.normalized.bigwig
wtHCT_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

source_name: wt HCT116, Nutlin treated

value: Colorectal Adenocarcinoma Cell Line HCT116


title: 75416923T H3K27ac ChIP-seq


title: 75416923T input


title: 75416923T H3K4me1 ChIP-seq


title: 86049102N Input


title: p53ko HCT116, total RNA, Nutlin treated, replicate 1

description:
total RNA from Nutlin treated p53KO HCT116 cells
S1563_koHCT_nutlin1
koHCT_nutlin.bs1.forward.deeptools.normalized.bigwig
koHCT_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

source_name: p53ko HCT116, Nutlin treated

value: KO


title: wt HCT116, total RNA, DMSO treated, replicate 1

description:
total RNA from DMSO treated wt HCT116 cells
S1556_wtHCT_dmso1
wtHCT_dmso.bs1.forward.deeptools.normalized.bigwig
wtHCT_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

source_name: wt HCT116, DMSO treated


title: wt HCT116, total RNA, DMSO treated, replicate 2

description:
total RNA from DMSO treated wt HCT116 cells
S1564_wtHCT_dmso2
wtHCT_dmso.bs1.forward.deeptools.normalized.bigwig
wtHCT_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: 86049102N H3K27ac ChIP-seq


title: 86049102N H3K4me1 ChIP-seq


title: p53ko HCT116, total RNA, DMSO treated, replicate 2

description:
total RNA from DMSO treated p53KO HCT116 cells
S1565_koHCT_dmso2
koHCT_dmso.bs1.forward.deeptools.normalized.bigwig
koHCT_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz

source_name: p53ko HCT116, DMSO treated


title: SJSA, polysomal RNA, Nutlin treated, replicate 2

description:
polysomal RNA from Nutlin treated SJSA cells
SN_pol3
SN_pol.bs1.forward.deeptools.normalized.bigwig
SN_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz

extract_protocol:
Polysomal fractions were separated on linear sucrose gradient by ultracentrifugation. RNA was purified using phenol/chloroform extraction. RNA quality was assessed using Bioanalyzer RNA Pico chips (Agilent). PolyA RNA was purified from 15 g of total RNA using the Dynabeads mRNA Direct micro kit (Life Technologies) according to the manufacturer’s instructions.
Libraries for Ion Torrent sequencing were prepared using the Ion Total RNAseq v2 kit (Life Technologies), according to the manufacturer’s instructions.


title: 86049102N H3K4me3 ChIP-seq

value: H3K4me3 (07-473, Millipore)


title: shCtl_2

city: Montreal

first: Ariane

last: Pelletier

state: QC

address: 110 Avenue Des Pins Ouest

country: Canada

institute: IRCM

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for low quality reads and adapter sequences with Trimmomatic, then mapped to mm10 whole genome using TopHat 2.0.13
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using first featureCounts to count the reads, and then DESeq2 to normalize the reads and compute the fold changes, p-values and adusted p-values between the shCdGAP samples and the shCtl samples.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing the FPKM values for each sample as well as the fold change, p-value and adjusted p-value between the shCdGAP samples and the shCtl samples.

source_name: Mammary tumor explants

growth_protocol: Mammary tumor explants cells were kept in culture in DMEM 10% FBS 1%PS 10ug/ml Insulin (Sigma), 600ug/ml G418. The cells were routinely passaged at a confluency of approximately 70% on cell culture-treated plates.

extract_protocol:
RNA was harvested from cells using Trizol Reagent and RNeasy columns (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: NMuMG-derived Neu-NT shCTL mammary tumor explants

value: Neu-NT shCON


title: shCtl_3


title: p53ko HCT116, total RNA, DMSO treated, replicate 1

description:
total RNA from DMSO treated p53KO HCT116 cells
S1557_koHCT_dmso1
koHCT_dmso.bs1.forward.deeptools.normalized.bigwig
koHCT_dmso.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: 86049102T Input

value: Input


title: shCtl_1


title: SJSA, polysomal RNA, Nutlin treated, replicate 1

description:
polysomal RNA from Nutlin treated SJSA cells
SN_pol2
SN_pol.bs1.forward.deeptools.normalized.bigwig
SN_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: 86049102T H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: shCdGAP_3

value: Neu-NT shCdGAP


title: SJSA, polysomal RNA, DMSO treated, replicate 2

description:
polysomal RNA from DMSO treated SJSA cells
SD_pol3
SD_pol.bs1.forward.deeptools.normalized.bigwig
SD_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: wt HCT116, total RNA, Nutlin treated, replicate 2

description:
total RNA from Nutlin treated wt HCT116 cells
S1570_wtHCT_nutlin2
wtHCT_nutlin.bs1.forward.deeptools.normalized.bigwig
wtHCT_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: shCdGAP_2


title: 86049102T H3K4me1 ChIP-seq


title: SJSA, polysomal RNA, DMSO treated, replicate 1

description:
polysomal RNA from DMSO treated SJSA cells
SD_pol2
SD_pol.bs1.forward.deeptools.normalized.bigwig
SD_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: p53ko HCT116, total RNA, Nutlin treated, replicate 2

description:
total RNA from Nutlin treated p53KO HCT116 cells
S1571_koHCT_nutlin2
koHCT_nutlin.bs1.forward.deeptools.normalized.bigwig
koHCT_nutlin.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts.tab.gz


title: 75416923T H3K4me3 ChIP-seq


title: 86049102T H3K4me3 ChIP-seq


title: shCdGAP_1


title: MCF7, polysomal RNA, Nutlin treated, replicate 2

description:
polysomal RNA from Nutlin treated MCF7 cells
MN_pol2
MN_pol.bs1.forward.deeptools.normalized.bigwig
MN_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: MCF7, polysomal RNA, DMSO treated, replicate 2

description:
polysomal RNA from DMSO treated MCF7 cells
MD_pol2
MD_pol.bs1.forward.deeptools.normalized.bigwig
MD_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: 40911432N H3K27ac ChIP-seq

source_name: adjacent normal kidney tissue


title: 40911432N H3K4me1 ChIP-seq


title: MCF7, polysomal RNA, DMSO treated, replicate 1

description:
polysomal RNA from DMSO treated MCF7 cells
MD_pol1
MD_pol.bs1.forward.deeptools.normalized.bigwig
MD_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: 40911432T Input


title: HCT116, polysomal RNA, Nutlin treated, replicate 2

description:
polysomal RNA from Nutlin treated HCT116 cells
HN_pol2
HN_pol.bs1.forward.deeptools.normalized.bigwig
HN_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz

source_name: HCT116, Nutlin treated


title: 40911432N H3K4me3 ChIP-seq


title: 40911432T H3K27ac ChIP-seq

source_name: ccRCC tumor tissue


title: HCT116, polysomal RNA, DMSO treated, replicate 2

description:
polysomal RNA from DMSO treated HCT116 cells
HD_pol2
HD_pol.bs1.forward.deeptools.normalized.bigwig
HD_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz

source_name: HCT116, DMSO treated


title: VE_E12_5_K27ac_FC_2

city: Vienna, Austria

first: Daniel

last: Andergassen

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM Research Center for  Molecular Medicine of the  Austrian Academy of Sciences

description: mixed (1 litter pooled)

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.3.1z12). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
STAR alignment of ChIP-seq data was conducted with different parameters to disable spliced reads, i.e. a maximum intron size of 1, and prevent soft clipping by enforcing end-to-end alignment (--alignEndsType EndToEnd). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1).
Based on the alignment efficiency for each sample we took the number of reads from the unaligned FASTQ file required to obtain 15 million aligned reads for RNA-seq and 20Mio for H3K27ac, then realigned these reads and performed all subsequent analysis on this data. The first reads were used from the unaligned FASTQ files. (see Supplemental table).
The Single Nucleotide Polymorphism (SNP) annotation file was created from a VCF file containing SNP variant data of 18 mouse strains, downloaded from the Sanger institute. SNP information for the strains CAST/EiJ and FVB/NJ were extracted and converted to the required browser extensible data (BED) format using a custom script that is available together with Allelome.PRO. Note that the name field in this file contains SNP information. Only homozygous high quality SNPs were used.
To define allelic expression using the Allelome.PRO pipeline, we downloaded the RefSeq annotation from the UCSC genome browser (mm10) on July 15th 2015 and removed transcripts with gene body length less than 100bp. To annotate the regions not covered by RefSeq we merged the reads from the 4 replicates (2x FVBxCAST and 2x CASTxFVB) for each tissue using SAMtools (version 1.2) and used Cufflinks (version 2.2.1) to perform a reference based assembly for each tissue (version 2.2.1). Next we used Cuffmerge to merge the assemblies from each tissue together with the RefSeq annotation (-g RefSeq.gtf). Next we discarded transcripts overlapping RefSeq in sense orientation and single exon transcripts. The final annotation consists of 23521 RefSeq genes (20743 protein-coding (NM) and 2778 NR non-coding) and 6290 assembled genes (XLOC) outside of the RefSeq annotation. Sliding windows were used to define allelic ChIP-seq (4Kb sliding windows for H3K27ac and H3K4me3 and 20kb sliding window for H3K27me3).
Defining allelic RNA-seq and ChIP-seq: Allele-specific expression and histone modification enrichment was detected from RNA-seq and ChIP-seq data as previously described using the Allelome.PRO program (Andergassen et al. 2015). Allelome.PRO settings for RNA-seq and H3K4me3: FDR 1%, allelic-ratio cut off 0.7, minread 2, annotation as described above. Allelome.PRO settings for H3K27ac & H3K27me3: FDR 1%, allelic-ratio cut off 0.7, minread 1, annotation as described above.
Defining XCI escapers: Allelome.PRO was run using a false discovery rate (FDR) of 1%, an allelic-ratio cut off of 0.6 and the minread parameter was set to 2. To increase the stringency in defining escapers, genes categorized as BAE in tissues with skewed or imprinted XCI (strain biased for CAST or maternal expression), but have as strain/imprinted score towards the CAST/MAT allele in all 4 replicates and an allelic-ratio above the ratio cutoff (0.6) were excluded from the analysis. Such cases can happen for lowly expressed genes, which are just below the FDR cutoff in one or more replicates.
genome build: mm10
processed data files format and content: tab-delimited text files include the Allelom.PRO output for RNA-seq and Chip-seq

source_name: Visceral yolk sac endoderm

growth_protocol: After reciprocal mating (CASTxFVB and FVBxCAST), 22 mouse tissues (x4 replicates) from individual females (XX), males (XY) or pooled litters (XY/XX)) were microdissected from pluripotent (1), embryonic (4), extra-embryonic (5), neo natal (2), adult (8) or from lactating females (2) (E3.5: embryonic stem cells (ESCs) (XY); E9.5: Visceral yolk sac endoderm (VE) (XY/XX); E12.5: liver (XY/XX), VE (XY/XX), Placenta (XX); E16.5: Brain, liver, heart, VE, Placenta (XX); 3 days postnatal: Brain, tongue (XX); adult: Brain, liver, heart, lung, spleen, thymus, leg muscle, virgin mammary glands (XX); lactating female: Brain, mammary glands (XX)). Male ESCs were isolated according to Bryja et al. 2006 and adapted to 2i media (Ying et al. 2003 and Ying et al. 2008). VE was isolated from visceral yolk sac according to Hudson et al. 2011. Mammary gland isolation was performed according to Joshi et al. 2010

extract_protocol:
Total RNA and DNA were extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion).
RNA-seq: DNaseI treated (DNA-FreeTM Ambion) total RNA (1-3 µg) was depleted for Ribosomal RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre) or enriched for polyA containing mRNA (Illumina). Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified as described in Sultan et al. 2012 for strand-specific sequencing. ChIP-seq: Native ChIP was conducted as described in Regha et al. 2007. ChIP-seq libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina).

value: Visceral yolk sac endoderm

value: FVB/NJxCAST/EiJ


title: VE_E12_5_K27ac_FC_1

description: mixed (1 litter pooled)


title: VE_E12_5_K27ac_CF_1

description: mixed (1 litter pooled)

value: CAST/EiJxFVB/NJ


title: Li_E12_5_K27ac_FC_2

description: mixed (1 litter pooled)

source_name: Liver

value: Liver


title: VE_E12_5_K27ac_CF_2

description: mixed (1 litter pooled)


title: Li_E12_5_K27ac_FC_1

description: mixed (1 litter pooled)


title: HCT116, polysomal RNA, DMSO treated, replicate 1

description:
polysomal RNA from DMSO treated HCT116 cells
HD_pol1
HD_pol.bs1.forward.deeptools.normalized.bigwig
HD_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: 40911432T H3K4me3 ChIP-seq


title: 40911432T H3K4me1 ChIP-seq


title: 40911432N Input


title: 12364284T H3K4me3 ChIP-seq


title: MCF7, polysomal RNA, Nutlin treated, replicate 1

description:
polysomal RNA from Nutlin treated MCF7 cells
MN_pol1
MN_pol.bs1.forward.deeptools.normalized.bigwig
MN_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz


title: Patient 4, CRIg Low

city: Brisbane

first: Katharine

last: Irvine

address: 306 Carmody Rd

country: Australia

institute: Institute for Molecular Bioscience

data_processing:
Basecalling: Illumina RTA v2.4.6
bcl to fastq conversion, including trimmming of adapters: Illumina bcl2fastq2 v2.1.4
Mapping: STAR v2.3.0e
Read counts per gene: htseq-count (HTSeq-0.6.1), with Illumina iGenomes UCSC hg19 annotation
Genome_build: UCSC hg19
Supplementary_files_format_and_content: .txt file reports read counts per gene

source_name: Ascites fluid macrophage

extract_protocol:
TRIZOL
TruSeq Ribo-Zero GOLD RNA Library Preparation Kit

tag: individual

value: Patient 4

value: Ascites fluid macrophage

tag: crig expression

value: Low

tag: cd14 expression

value: positive


title: 12364284T H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: aLi_E12_5_K4m3_FC_2

description: female (1 individual)

value: adult (8 weeks)


title: Patient 3, CRIg Low

value: Patient 3


title: 12364284T H3K27ac ChIP-seq


title: aLi_E12_5_K4m3_CF_2

description: female (1 individual)


title: Patient 2, CRIg Low

value: Patient 2


title: HCT116, polysomal RNA, Nutlin treated, replicate 1

description:
polysomal RNA from Nutlin treated HCT116 cells
HN_pol1
HN_pol.bs1.forward.deeptools.normalized.bigwig
HN_pol.bs1.reverse.deeptools.normalized.bigwig
HTSeq_intersection-nonempty_counts_polysomal_only.tab.gz

value: Colorectal Adenocarcinoma Cell Line HCT116

tag: treatment

value: Nutlin

tag: batch


title: aLi_E12_5_K4m3_CF_1

description: female (1 individual)

tag: age


title: 75416923N H3K4me3 ChIP-seq

value: H3K4me3 (07-473, Millipore)


title: 12364284T Input

value: Input


title: Patient 1, CRIg Low

value: Patient 1


title: Li_E12_5_K27ac_CF_2

description: mixed (1 litter pooled)

tag: strain


title: Patient 6, CRIg Low

value: Patient 6


title: 12364284N H3K4me3 ChIP-seq


title: 12364284N H3K4me1 ChIP-seq


title: 12364284N H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: Patient 5, CRIg Hi

value: Patient 5

value: High


title: Pl_E12_5_K4m3_CF_2

description: female (1 individual)

source_name: Placenta

value: Placenta

value: CAST/EiJxFVB/NJ


title: Pl_E12_5_K4m3_FC_1

description: female (1 individual)

value: FVB/NJxCAST/EiJ


title: 12364284N Input


title: Patient 5, CRIg Low

value: Ascites fluid macrophage

value: Low

value: positive


title: Pl_E12_5_K4m3_CF_1

description: female (1 individual)


title: Li_E12_5_K27ac_CF_1

description: mixed (1 litter pooled)

value: Liver


title: Patient 4, CRIg Hi

value: Patient 4


title: Patient 6, CRIg Hi


title: aLi_E12_5_K4m3_FC_1

description: female (1 individual)

value: adult (8 weeks)


title: 74575859T H3K4me3 ChIP-seq


title: VE_E12_5_K4m3_FC_2

description: mixed (1 litter pooled)

value: Visceral yolk sac endoderm


title: VE_E12_5_K4m3_FC_1

description: mixed (1 litter pooled)


title: VE_E12_5_K4m3_CF_2

description: mixed (1 litter pooled)


title: Patient 3, CRIg Hi

value: Patient 3


title: 74575859T H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: Patient 2, CRIg Hi

value: Patient 2


title: Patient 1, CRIg Hi

value: Patient 1


title: Li_E12_5_K4m3_FC_2

description: mixed (1 litter pooled)


title: 74575859T Input

value: Input


title: 74575859N H3K4me3 ChIP-seq

value: H3K4me3 (07-473, Millipore)


title: Li_E12_5_K4m3_FC_1

description: mixed (1 litter pooled)


title: 74575859N H3K4me1 ChIP-seq


title: Li_E12_5_K4m3_CF_2

description: mixed (1 litter pooled)


title: Li_E12_5_K4m3_CF_1

description: mixed (1 litter pooled)


title: 74575859N H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: 74575859N Input


title: 20431713T H3K4me3 ChIP-seq


title: 20431713T H3K27ac ChIP-seq


title: aLM_CF_2

description: female (1 individual)

source_name: Leg Muscle

value: Leg Muscle


title: 20431713T Input


title: 20431713N H3K4me1 ChIP-seq


title: aLM_FC_1

description: female (1 individual)


title: 20431713N H3K27ac ChIP-seq


title: aLM_CF_1

description: female (1 individual)

value: CAST/EiJxFVB/NJ


title: aTh_FC_1

description: female (1 individual)

source_name: Thymus

value: Thymus

value: FVB/NJxCAST/EiJ


title: 20431713T H3K4me1 ChIP-seq


title: 74575859T H3K27ac ChIP-seq


title: 20431713N Input


title: VE_E12_5_K4m3_CF_1

description: mixed (1 litter pooled)


title: aTh_CF_1

description: female (1 individual)


title: aTh_CF_2

description: female (1 individual)


title: 20431713N H3K4me3 ChIP-seq


title: aSp_FC_1

description: female (1 individual)

source_name: Spleen

value: Spleen


title: aTh_FC_2

description: female (1 individual)


title: aSp_FC_2

description: female (1 individual)


title: PCS-400 Input

source_name: normal primary renal proximal tubule epithelial cells

growth_protocol: All ccRCC cells (786-O, A498 and tumor-derived cell lines) were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). HK-2 and PCS400 were grown in Renal Epithelial Cell Basal Medium (ATCC). Cells were maintained in a 5% CO2-humidified incubator at 37°C. In order to derive cell lines from primary tumors, ccRCC primary tumor tissues were disassociated by collagenase. Dissociated cells were maintained in RPMI with 10% FBS. At 80-90% confluency, the cells were passaged at 1:3 ratio. The cultured cells were considered to be successfully immortalized after 60 passages.

extract_protocol:
One million cells  were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed 3 times with TBSE buffer.  Pelleted cells were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). The total volume of immunoprecipitation was 1 ml and the amount of antibody used was 2 µg. The input DNA was precleared with protein G Dynabeads (Life Technologies) for 1 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 3 times with cold wash buffer.
Whole-genome-amplification was performed on ChIP DNA and input using the WGA4 kit (Sigma-Aldrich).  The amplified DNA was used with NEBNext ChIP-Seq library prep reagent set.


title: PCS-400 H3K27ac ChIP-seq


title: aSp_CF_2

description: female (1 individual)


title: aSp_CF_1

description: female (1 individual)


title: PCS-400 H3K4me1 ChIP-seq


title: aLM_FC_2

description: female (1 individual)


title: PCS-400 H3K4me3 ChIP-seq


title: HK-2 Input

source_name: normal immortalized renal proximal tubule epithelial cells

value: HK-2 (ATCC CRL-2190)


title: aHe_FC_2

description: female (1 individual)

source_name: Heart

value: Heart


title: aHe_FC_1

description: female (1 individual)


title: HK-2 H3K4me1 ChIP-seq


title: aHe_CF_2

description: female (1 individual)


title: HK-2 H3K4me3 ChIP-seq


title: aLi_FC_2

description: female (1 individual)

value: Liver


title: HK-2 H3K27ac ChIP-seq


title: A-498 Input

source_name: ccRCC cell line

value: A498 (ATCC HTB-44)


title: A-498 H3K4me1 ChIP-seq


title: aLi_FC_1

description: female (1 individual)

value: adult (8 weeks)


title: aLi_CF_2

description: female (1 individual)


title: aBr_FC_2

description: female (1 individual)

source_name: Brain

value: Brain


title: A-498 H3K4me3 ChIP-seq


title: aLi_CF_1

description: female (1 individual)


title: 786-O H3K27ac ChIP-seq


title: A-498 H3K27ac ChIP-seq


title: aBr_FC_1

description: female (1 individual)


title: 786-O Input rep2


title: 786-O H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: Pl_E16_5_FC_2

description: female (1 individual)

value: Placenta


title: aBr_CF_1

description: female (1 individual)


title: 786-O H3K4me3 ChIP-seq


title: Pl_E16_5_FC_1

description: female (1 individual)


title: 74575859 Input

value: in house derived


title: aBr_CF_2

description: female (1 individual)


title: 74575859 H3K27ac ChIP-seq


title: Pl_E16_5_CF_1

description: female (1 individual)


title: aHe_CF_1

description: female (1 individual)


title: Pl_E16_5_CF_2

description: female (1 individual)


title: Pl_E12_5_FC_2

description: female (1 individual)


title: MEF induced HiSeq sample 2 (HiSeq TruSeq sRNA sequencing)

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

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

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

description:
Standard TruSeq small RNA sequencing
processed data file:
Control_SRhi10132_count_all_miRNAs_snoRNAs_rRNAs_snRNAs.txt

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

source_name: MEF HiSeq sample

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

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

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

value: Mouse embryonic fibroblast

tag: treatment group

value: Induction for TRF2 uncapping

tag: molecule subtype

value: small RNA


title: Pl_E12_5_FC_1

description: female (1 individual)


title: 74575859 H3K4me3 ChIP-seq

tag: histone

tag: chip antibody

value: H3K4me3 (07-473, Millipore)


title: Carotid artery from RBP7 knock-out treated with Rosiglitazone, replicate 4

city: Iowa City

first: Henry

last: Keen

state: IA

institute: University of Iowa

description:
Sample name: 21_RBP7_KO_ROSI
Processed data file: all.TPM.txt.gz

data_processing:
The quality of the sequence reads was assessed using the FastQC program.
Paired-end reads (100-bp) were then aligned to the mouse transcriptome (UCSC known genes, genome build mm10, Dec. 2011) with the Kallisto program.
Differential expression was assessed using the sleuth program and a p-value less than 0.01 was used to filter genes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all.TPM.txt: Tab-delimited text file of TPM (Transcripts Per Million) values.

source_name: carotid artery, RBP7 knock-out, Rosiglitazone

extract_protocol:
Total RNA from carotid artery was extracted using the Trizol method and purified using the Qiagen RNeasy column. A DNase digestion was performed to remove genomic DNA.
Indexed sequencing libraries were generated from total RNA according to the manufacturer's (Illumina) suggested protocol.

treatment_protocol: Mice were treated with either Rosliglitazone (ROSI, 10 uM) or vehicle DMSO (CONT) for 24 hrs.

tag: strain/background

tag: genotype/variation

value: RBP7 knock-out

tag: Sex

value: Male

value: Carotid artery

value: Rosiglitazone


title: MEF induced HiSeq sample 1 (HiSeq TruSeq sRNA sequencing)

tag: cell type


title: 20431713 H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)

tag: source


title: Carotid artery from RBP7 knock-out treated with Rosiglitazone, replicate 3

description:
Sample name: 18_RBP7_KO_ROSI
Processed data file: all.TPM.txt.gz

tag: tissue


title: 20431713 Input

value: Input


title: 786-O Input rep1


title: Carotid artery from RBP7 knock-out treated with Rosiglitazone, replicate 2

description:
Sample name: 04_RBP7_KO_ROSI
Processed data file: all.TPM.txt.gz


title: Carotid artery from RBP7 knock-out treated with Rosiglitazone, replicate 1

description:
Sample name: 02_RBP7_KO_ROSI
Processed data file: all.TPM.txt.gz


title: Pl_E12_5_CF_1

description: female (1 individual)

value: CAST/EiJxFVB/NJ


title: 20431713 H3K4me1 ChIP-seq


title: VE_E16_5_FC_2

description: female (1 individual)

value: Visceral yolk sac endoderm

value: FVB/NJxCAST/EiJ


title: VE_E16_5_FC_1

description: female (1 individual)


title: 20431713 H3K4me3 ChIP-seq


title: Carotid artery from RBP7 knock-out treated with DMSO, replicate 4

description:
Sample name: 20_RBP7_KO_CONT
Processed data file: all.TPM.txt.gz

source_name: carotid artery, RBP7 knock-out, DMSO

value: DMSO


title: 12364284 Input


title: Carotid artery from RBP7 knock-out treated with DMSO, replicate 3

description:
Sample name: 19_RBP7_KO_CONT
Processed data file: all.TPM.txt.gz


title: 74575859 H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: 12364284 H3K27ac ChIP-seq


title: VE_E16_5_CF_1

description: female (1 individual)


title: Carotid artery from RBP7 knock-out treated with DMSO, replicate 1

description:
Sample name: 03_RBP7_KO_CONT
Processed data file: all.TPM.txt.gz


title: 12364284 H3K4me1 ChIP-seq


title: Carotid artery from RBP7 wild-type treated with Rosiglitazone, replicate 3

description:
Sample name: 10_RBP7_WT_ROSI
Processed data file: all.TPM.txt.gz

source_name: carotid artery, RBP7 wild-type, Rosiglitazone

value: RBP7 wild-type


title: VE_E12_5_FC_1

description: mixed (1 litter pooled)


title: Pl_E12_5_CF_2

description: female (1 individual)

value: Placenta


title: 12364284 H3K4me3 ChIP-seq

value: in house derived


title: 40911432 H3K27ac ChIP-seq


title: VE_E12_5_FC_2

description: mixed (1 litter pooled)


title: VE_E12_5_CF_2

description: mixed (1 litter pooled)


title: Carotid artery from RBP7 wild-type treated with Rosiglitazone, replicate 2

description:
Sample name: 08_RBP7_WT_ROSI
Processed data file: all.TPM.txt.gz


title: VE_E12_5_CF_1

description: mixed (1 litter pooled)


title: 40911432 Input rep2


title: Carotid artery from RBP7 wild-type treated with Rosiglitazone, replicate 1

description:
Sample name: 06_RBP7_WT_ROSI
Processed data file: all.TPM.txt.gz


title: 40911432 Input rep1


title: 40911432 H3K4me1 ChIP-seq


title: 40911432 H3K4me3 ChIP-seq


title: VE_E9_5_FC_1

description: mixed (1 litter pooled)


title: VE_E9_5_FC_2

description: mixed (1 litter pooled)


title: VE_E16_5_CF_2

description: female (1 individual)


title: VE_E9_5_CF_2

description: mixed (1 litter pooled)


title: Carotid artery from RBP7 wild-type treated with DMSO, replicate 2

description:
Sample name: 09_RBP7_WT_CONT
Processed data file: all.TPM.txt.gz

source_name: carotid artery, RBP7 wild-type, DMSO


title: Carotid artery from RBP7 wild-type treated with DMSO, replicate 3

description:
Sample name: 11_RBP7_WT_CONT
Processed data file: all.TPM.txt.gz


title: Carotid artery from RBP7 wild-type treated with DMSO, replicate 1

description:
Sample name: 07_RBP7_WT_CONT
Processed data file: all.TPM.txt.gz


title: VE_E9_5_CF_1

description: mixed (1 litter pooled)

source_name: Visceral yolk sac endoderm


title: Carotid artery from RBP7 knock-out treated with DMSO, replicate 2

description:
Sample name: 05_RBP7_KO_CONT
Processed data file: all.TPM.txt.gz


title: 86049102 H3K27ac ChIP-seq


title: D648T

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

data_processing:
tophat -g 1 --no-novel-juncs --no-novel-indels -G $gtf --transcriptome-index $transcriptome --b2-sensitive $index $reads
Counts of reads on genes were computed using HTseq-count v0.6.1 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: The .txt files contain read counts on genes

source_name: Primary tumor tissue from mouse lacking hepatic Kap1 expression through a conditional AlbCre system

extract_protocol:
Total RNA from cell lines was isolated using the Qiagen miRNeasy Kit
TruSeq stranded RNA sample preparation kit (Illumina).

treatment_protocol: Mice weref HFD-fed for 27 weeks prior to sacrifice

value: Tumor Sample

tag: transgenes

tag: time point

value: sacrificed at 35 wo after HFD-fed for 27 weeks


title: 86049102 Input rep2


title: He_E16_5_FC_1

description: female (1 individual)

source_name: embronic Heart

value: embronic Heart


title: 86049102 H3K4me1 ChIP-seq


title: D580L

source_name: Liver tissue from mouse lacking hepatic Kap1 expression through a conditional AlbCre system

value: Liver Tissue


title: D648L


title: He_E16_5_CF_2

description: female (1 individual)


title: He_E16_5_CF_1

description: female (1 individual)


title: 86049102 H3K4me3 ChIP-seq

value: H3K4me3 (07-473, Millipore)


title: D647L

source_name: Liver Tissue from transgenic mouse expressing AlbCre transgene

value: TgAlbCre


title: Br_E16_5_FC_1

description: female (1 individual)

source_name: embronic Brain

value: embronic Brain


title: Br_E16_5_FC_2

description: female (1 individual)


title: D577L


title: Input ChIP-Seq

city: San Francisco

first: Kelly

last: Nissen

address: 600 16th Street

institute: UCSF

data_processing:
ChIP-Seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence. Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Genome_build: Sequence and feature files for S. pombe were obtained from the Pombase.org. ASM294v1.16
Supplementary_files_format_and_content: bedGraphs

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: Overnight cultures were grown in YES5 at 30°C, allowed to saturate, and then diluted to 0.1 OD600 in 100mL. The 100mL cultures were then grown in YES5 at 30°C to between 0.5–0.8 OD600 prior to formaldehyde crosslinking.

extract_protocol:
100mL cultures grown to between 0.5–0.8 OD600 were crosslinked with 1% formaldehyde (Sigma) for 15 minutes, and then quenched for 5 minutes with 125mM glycine (Sigma). Crosslinked cells were isolated by centrifugation and washed twice with 4°C TBS. Pellets were aliquoted into 50 OD600 units of cells, flash frozen in liquid nitrogen and stored at -80°C. Aliquots were thawed on ice and resuspended in 1 mL ChIP lysis buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 1x EDTA-free Complete protease inhibitor (PI; Roche) Protease inhibitors (2mM PMSF, 20μg/mL leupeptin, 20μg/mL pepstatin, 20μg/mL aprotonin, 20μg/mL antipain). Lysate was generated using a Mini-Beadbeater (Biospec Products) for 8 cycles of 1.5 minutes beadbeating followed by 2 minutes on ice after each cycle. DNA was isolated by centrifugation. DNA was sheared in a Bioruptor waterbath sonicator (Diagenode) with 6 cycles on high (10 min total, 30 sec ON, 1 min OFF). After sonication, cell debris was removed by centrifugation and the supernatant was brought up to 1mL in ChIP lysis buffer. 100μL of the lysate was then removed and saved as an input. 10ug of antibody against M2 FLAG (F3165, Sigma) was added to the remaining 900μL of lysate and this reaction was incubated for 2 hours at 4°C. Prior to addition, 30μL of packed Protein G DYNAbeads (Invitrogen) were washed for 5 minutes each at 4°C: twice with 1mL TBS and then twice in 1mL ChIP lysis buffer, and then resuspended in 100μL ChIP lysis buffer. This 100μL of washed beads was add to the reaction and incubated for 2 hours at 4°C for immunoprecipitation. Beads were then washed for 5 minutes each at 4°C: twice with 1mL ChIP lysis buffer, twice with 1mL high salt ChIP lysis buffer (ChIP lysis buffer with 500mM NaCl), and once with TE at room temperature. Crosslinking was reversed in 1% SDS at 65°C overnight in the presence of Proteinase K (30μL of 20mg/mL). SDS was removed from DNA using NucleoSpin Gel Clean-up Columns with 1250μL NTB (Macherey-Nagel).
ChIP DNA libraries were prepared using End-It DNA End Repair Kit followed by A-tailing using Klenow fragment (NEB), ligation to Illumina adaptors using Rapid T4 DNA Ligase (Enzymatics), PCR amplification for 15 cycles, and size selection between 200-350bp

value: Wild-type; pht1-3xFLAG; gift from S. Grewal used in Zofall et al. 2009

tag: genotype

tag: media


title: H2A.Z ChIP-Seq


title: H1 KD Input rep2

city: Bronx

first: Travis

middle: J

last: Bernardo

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: Crosslinked, Sheared DNA

data_processing:
Illumina HiSeq2500 system used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the dm3 whole genome using bowtie
UR regions were identified using a custom bash/R script. Aligned reads in the control knockdown (pooled from both replicates as BAM files following alignment) were scanned along 5-kb windows, and regions were designated as under-replicated if 20 consecutive windows fell below the average per-chromosome read count.
Normalized reads for each UR region were calculated (for both control and H1 knockdown) as the total aligned reads per million divided by the length of the UR domain (in kb) identified in the control knockdown sample. Fold change was then calculated as reads per million per kb (H1 knockdown) divided by reads per million per kb (control knockdown).
Genome_build: dm3/BDGP5.3
Supplementary_files_format_and_content: tab-delimited BED file containing identified under-replicated domains in the pINT-Nau/+; Tub-GAL4/+ genotype

organism: Drosophila melanogaster

source_name: Salivary Gland

growth_protocol: Larvae were reared on a standard corn meal, sugar, and yeast medium with Tegosept at 29°C, and collected during the L3 wandering stage

extract_protocol:
Freshly dissected salivary glands were crosslinked, nuclei were sonicated to shear DNA at an average size of 200 bp, and DNA was purified using a QiaQuick PCR Purification Kit.
Sequencing libraries were prepared using the Illumina TruSeq ChIP Sample Prep Kit following the manufacturer's protocol.

value: salivary gland

value: pINT-H15M/+; Tub-GAL4/+


title: Naut KD Input rep2

description: Crosslinked, Sheared DNA

value: pINT-Nau/+; Tub-GAL4/+


title: H1 KD Input rep1

description: Crosslinked, Sheared DNA


title: Br_E16_5_CF_1

description: female (1 individual)

value: CAST/EiJxFVB/NJ


title: Br_E16_5_CF_2

description: female (1 individual)


title: Naut KD Input rep1

description: Crosslinked, Sheared DNA


title: He_E16_5_FC_2

description: female (1 individual)

value: FVB/NJxCAST/EiJ


title: Li_E16_5_FC_1

description: female (1 individual)

source_name: embronic Liver

value: embronic Liver


title: N1het_TercG2_2

first: Christina

last: Theodoris

state: California

address: 1650 Owens Street

institute: Gladstone Institutes, University of California, San Francisco

description: aortic valve RNA-seq

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

source_name: aortic valve

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

value: 2 months


title: N1het_TercG2_3

description: aortic valve RNA-seq


title: N1het_TercG2_4

description: aortic valve RNA-seq


title: N1het_TercG2_1

description: aortic valve RNA-seq


title: WT_TercG2_3

description: aortic valve RNA-seq


title: 86049102 Input rep1

city: Singapore

first: Xiaosai

last: Yao

institute: Genome Institute of Singapore

source_name: ccRCC cell line

value: Input


title: D580T

tag: batch


title: Li_E16_5_CF_2

description: female (1 individual)

tag: age


title: WT_TercG2_1

description: aortic valve RNA-seq

tag: strain


title: Li_E12_5_FC_2

description: mixed (1 litter pooled)


title: Li_E16_5_CF_1

description: female (1 individual)


title: Li_E12_5_FC_1

description: mixed (1 litter pooled)


title: N1het_TercWT_4

description: aortic valve RNA-seq


title: N1het_TercWT_3

description: aortic valve RNA-seq


title: Li_E16_5_FC_2

description: female (1 individual)


title: N1het_TercWT_1

description: aortic valve RNA-seq


title: Li_E12_5_CF_2

description: mixed (1 litter pooled)


title: WT_TercWT_4

description: aortic valve RNA-seq


title: ESC_FC_2

description: male (1 individual)

source_name: embronic stem cells

value: embronic stem cells

tag: passages


title: ESC_FC_1

description: male (1 individual)


title: WT_TercWT_3

description: aortic valve RNA-seq


title: WT_TercWT_1

description: aortic valve RNA-seq


title: WT_TercWT_2

description: aortic valve RNA-seq


title: Pl_E12_5_K27ac_CF_2

description: female (1 individual)

source_name: Placenta

value: Placenta


title: Pl_E12_5_K27ac_FC_1

description: female (1 individual)


title: lfMG_K4m3_FC_1

description: female (1 individual)

source_name: Mammary gland (during lactation)

value: Mammary gland (during lactation)

value: adult (12 weeks) - 3 days post natal


title: Pl_E12_5_K27ac_CF_1

description: female (1 individual)


title: ESC_CF_1

description: male (1 individual)


title: WT_TercG2_2

description: aortic valve RNA-seq


title: Li_E12_5_CF_1

description: mixed (1 litter pooled)


title: Pl_E12_5_CR_2

description: male (1 individual)

value: CASTxR2<delta> (R2<delta>=Airn promoter deletion, FVB background)


title: Pl_E12_5_WT_1

description: male (1 individual)


title: Pl_E12_5_CR_3

description: female (1 individual)


title: Pl_E12_5_WT_2

description: female (1 individual)


title: ESC_CF_2

description: male (1 individual)


title: To_3dpn_K4m3_FC_1

description: female (1 individual)

source_name: Tongue

value: Tongue

value: 3days post natal


title: De_E12_5_C_3

description: female (1 individual)

source_name: Decidua

value: Decidua

value: CAST/EiJ


title: De_E12_5_C_2

description: female (1 individual)


title: Pl_E12_5_CR_1

description: female (1 individual)


title: lfBr_FC_2

description: female (1 individual)

source_name: Brain (during lactation)

value: Brain (during lactation)


title: lfBr_FC_1

description: female (1 individual)


title: lfBr_CF_2

description: female (1 individual)


title: E2_U6-F T4

city: Houston

first: Boyi

last: Gan

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
The raw reads in FASTQ format were aligned to the reference genome, hg19, using MOSAIK alignment software. MOSAIK implemented Smith-Waterman algorithm to perform gapped alignment.
The overlaps between aligned reads and annotated genes, genecode.v15, were counted using HTSeq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). The reads mapped to both strands were counted. The gene counts were normalized using the scaling factor method. If the number of overlapped read of any given gene is less than one per million total mapped read for all samples, this gene was excluded from further analysis.
A negative binomial generalized linear model was _t to each gene expression and the Wald test was performed to compare the expressions between U6-F vs. U6-EV cell lines. The Benjamini-Hochberg method was used to control false discovery rate (FDR).
Genome_build: hg19
Supplementary_files_format_and_content: text file and normalized read counts

source_name: U6-F T4

growth_protocol: cells were grow in normal cultureing media with 25mM Glucose for 0,4,8 hr

extract_protocol: mRNA is extracted using Trizol

treatment_protocol: cells were grow in cultureing media without Glucose  for 0,4,8 hr

tag: cell line

value: FLAG-BAP

value: T4; no glucose in the growth medium for 4hr


title: lfBr_CF_1

description: female (1 individual)

value: CAST/EiJxFVB/NJ


title: F2_U6-F T8

source_name: U6-F T8

value: T8; no glucose in the growth medium for 8hr


title: F1_U6-F T8


title: lfMG_FC_2

description: female (1 individual)

value: FVB/NJxCAST/EiJ


title: Pl_E12_5_WT_3

description: male (1 individual)


title: D2_U6-F T0

source_name: U6-F T0

value: T0; regular growth medium for 8 h


title: E1_U6-F T4


title: lfMG_CF_1

description: female (1 individual)


title: D1_U6-F T0


title: vMG_FC_2

description: female (1 individual)

source_name: Mammary gland

value: Mammary gland (virgin)

value: adult (8 weeks)


title: vMG_CF_1

description: female (1 individual)


title: vMG_FC_1

description: female (1 individual)


title: lfMG_FC_1

description: female (1 individual)


title: B2_U6-EV T4

source_name: U6-EV T4

value: Empty-vector


title: B1_U6-EV T4


title: vMG_CF_2

description: female (1 individual)


title: C2_U6-EV T8

source_name: U6-EV T8


title: aLu_FC_2

description: female (1 individual)

source_name: Lung

value: Lung


title: C1_U6-EV T8


title: aLu_FC_1

description: female (1 individual)


title: A1_U6-EV T0

source_name: U6-EV T0


title: A2_U6-EV T0


title: aLu_CF_2

description: female (1 individual)


title: De_E12_5_C_1

description: female (1 individual)


title: aLu_CF_1

description: female (1 individual)


title: Br_3dpn_FC_2

description: female (1 individual)

source_name: Brain

value: Brain


title: Br_3dpn_FC_1

description: female (1 individual)


title: lfMG_CF_2

description: female (1 individual)

value: Mammary gland (during lactation)

value: adult (12 weeks) - 3 days post natal


title: Br_3dpn_CF_1

description: female (1 individual)

value: 3days post natal


title: Br_3dpn_CF_2

description: female (1 individual)


title: To_3dpn_FC_2

description: female (1 individual)

value: Tongue


title: To_3dpn_FC_1

description: female (1 individual)


title: To_3dpn_CF_2

description: female (1 individual)


title: To_3dpn_CF_1

description: female (1 individual)


title: siZCCHC8

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

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

source_name: ZCCHC8 knockdown

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

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

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

value: Hela

tag: transfection

tag: library protocol


title: siRBM7

source_name: RBM7 knockdown


title: siMtr4

source_name: Mtr4 knockdown