title: Spt16dsRNA_b_Rpb3_ip_Rep1

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
RNA-seq reads were aligned to UCSC genome dm6 with STAR version 2.5.2b, with default settings, using Ensembl 84 gene models.
ChIPseq reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. Reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM).
For PROseq, adapter 5′-TGGAATTCTCGGGTGCCAAGG-3′ was removed. Reads were trimmed up to 36 bp. Reads with length less than 15 bp after trimming were removed. After reverse-complement, reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. The last basepair of the reads were used to generate bigWig files and downstream analysis.
Genome_build: dm6, Ensembl 84
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

source_name: S2 cells

extract_protocol:
For ChIP-seq, Briefly Drosophila S2 cells were crosslinked with 1% formaldehyde for 20 min at room temperature, after which crosslinking was quenched in 0.125 M glycine. Isolated nuclei were sonicated using  Misonix 3000 Sonicator, and the supernatant used for  immunoprecipitation with the indicated antibody. ChIP-seq libraries were then sequenced on the Illumina HiSeq 2500 platform. For RNA-seq,  total RNA was extracted using the QIAGEN RNeasy mini kit. Libraries were then prepared using the Illumina TruSeq Standard mRNA LT sample prep kit, and sequenced on the Illumina HiSeq 2500 platform. For PRO-seq, nuclei was first isolated from S2 Cells, followed by run on and biotin enrichment. biotinylated transcripts were then cloned using 5' and 3' RNA adaptors. Cloned transcripts were then reverse transcribed, PCR amplified, and sequenced on the Illumina Nextseq 500 platform. For ChIP nexus, briefly, Cells were cross-linked in 1.0% formaldehyde, lysed and sonicated using the Bioruptor Pico. Sheared chromatin was used in immunoprecipitation with the indicated antibodies. While the DNA is still bound to the antibodies, the DNA ends were repaired, dA-tailed, and ligated to adapters with single 3'-T overhangs and 5’ overhangs. Cloned fragments were blunted by Klenow 3’-5’ exo-polymerase followed by end-trimming using T4 DNA polymerase. The blunt end DNA was digested with λ-exonuclease followed by RecJf. Single stranded DNA products were then eluted, reverse cross-linked and purified. Purified DNA was then circularized using Circligase, and linearized using BamH1 after addition of an oligonucleotide complementary to the BamHI restriction site. Linearized single stranded DNA was then PCR-amplified using adaptor sequences. Libraries were then gel purified and sequenced on the Illumina NextSeq 500 platform.
ChIP-seq libararies were prepared using the KAPA HTP Library Prep Kit for Illumina and Bioo Scientific NEXTflex DNA barcodes. Libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies), a Caliper LabChip GX (Perkin Elmer) and a Qubit fluorometer (Life Technologies).  Post amplification size selection was performed on all libraries using the SPRIselect system (Beckman Coulter).  Libraries were re-quantified, normalized, pooled and sequenced on an Illumina HiSeq 2500 instrument as 50-bp single reads using HiSeq Control Software 2.2.58.
RNA-seq libraries were generated from 1ug of high quality total RNA, as assessed using the Bioanalyzer (Agilent). For samples in the RNAseq_1 series, libraries were made according to the manufacturer’s directions using the TruSeq Stranded mRNA LT Sample Prep Kit – set A (Illumina, Cat. No. RS-122-2101) kit. For samples in the RNAseq_2 series, libraries were made according to the manufacturer’s directions using the TruSeq Stranded mRNA LT Sample Prep Kit - set A and B (Illumina, Cat. No. RS-122-2101 and RS-122-2102) kit. The resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 50 bp single reads on the Illumina HiSeq 2500 instrument.
PRO-seq libraries were generated essentially as described in Mahat et al (2016), Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc. 11, 1455-76.   doi: 10.1038/nprot.2016.086.  Primers RPI4, RPI5, RPI6 and RPI7 were used to barcode cDNAs from eGFPdsRNA_rep1 (Non-targeting control, replicate 1), eGFPdsRNA_rep2(Non-targeting control, replicate 2), SSRP1kda1 (SSRP1 dsRNA mediated knockdown, replicate 1), and SSRP1kda2 (SSRP1 dsRNA mediated knockdown, replicate 2) respectively.
ChIP-nexus libraries: DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products.

treatment_protocol: Drosophila S2 Cells were treated with SSRP1 dsRNA and Spt16 dsRNA to knockdown SSRP1 and Spt16 respectively. S2 cells were treated with eGFP dsRNA as a non-targeting control.

tag: treatment

value: Spt16 dsRNA

tag: antibody

value: Rpb3 (Gift from Zeitlinger Lab)


title: Spt16dsRNA_b_Rpb3_ip_Rep2

status: Public on Jun 14 2019

type: SRA

city: KANSAS CITY

first: Joan

middle: W

last: Conaway

state: Missouri

country: USA

institute: Stowers Institute for Medical Research

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured in Schneider’s media (GIBCO #21720) supplemented with 10% heat-inactivated fetal bovine serum (PAA #A15-701) at 25°C


title: Spt16dsRNA_a_Rpb3_ip_Rep2


title: SSRP1dsRNA_b_Rpb3_ip_Rep1

value: SSRP1 dsRNA


title: SSRP1dsRNA_b_Rpb3_ip_Rep2


title: Spt16dsRNA_a_Rpb3_ip_Rep1


title: Hand2as+/+_rep5 8-wk

city: Beijing

first: Xue

last: Han

address: Zhongguancun North Street

department: School of Medicine

country: China

institute: Tsinghua University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA
All RNA-Seq data were mapped to the mouse reference genome (mm9) using TopHat (version 2.0.11). For samples E11.5 hearts and E16.5 ventricles of Hand2asF, reads were assigned to their transcribed strand (Tophat parameter “--library-type=fr-firststrand”).
FPKM was calculated by Cufflink version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for control (heterozygous or wildtype) and homozygous Hand2as KO mice heart tissues

molecule: polyA RNA

organism: Mus musculus

source_name: 8-wk cardiomyocytes

growth_protocol: All animal experiments were conducted in accordance of institutional guidelines for animal welfare and approved by the Institutional Animal Care and Use Committee (IACUC) at Tsinghua University.

extract_protocol:
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

tag: strain

tag: tissue

value: heart

tag: developmental stage

value: 8 weeks

tag: genotype


title: Hand2asD/+_rep1 8-wk


title: Hand2as+/+_rep2 8-wk


title: Hand2as+/+_rep1 8-wk


title: Hand2as+/+_rep3 8-wk


title: SSRP1dsRNA_a_Rpb3_ip_Rep2


title: SSRP1dsRNA_a_Rpb3_ip_Rep1


title: eGFPdsRNA_Rpb3_ip_Rep2

value: eGFPdsRNA


title: eGFPdsRNA_RNAseq_Rep2

description: poly-A Stranded RNA-Seq

data_processing:
Reads demultiplexed and evaluated for quality
Alignment of reads with STAR (version 2.6.1) to combined genome of hg38 and dm6 with parameter `--quantMode GeneCounts`.
Raw gene counts were imported into edgeR for DGE analysis. The RUVg function in the RUVSeq method was applied to normalize to spike-in (hg38) (Risso, D., Ngai, J., Speed, T.P., and Dudoit, S. (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotech 32, 896-902, https://www.nature.com/articles/nbt.2931; Risso, D. RUVSeq: Remove unwanted variation from RNA-Seq data. https://www.bioconductor.org/packages/RUVSeq)
Table exported from edgeR containing gene values for fold-change, FDR, and FPKM.
Genome_build: dm6 (primary), hg38 (spike-in)
Supplementary_files_format_and_content: Raw gene counts output by STAR and final output table from edgeR

source_name: eGFP (non-targeting control)

extract_protocol:
At the end of the 4-day knockdown, Drosophila S2 cells were harvested. Human HEK293T cells were added to the harvested S2 cells (0.8x10e6 human cells / 15x10e6 S2 cells) as spike-in control.  Each Pool of S2 and HEK293T cells was washed twice using 1 X PBS. Total RNA was extracted using the QIAGEN RNeasy mini kit. Libraries were prepared using the Illumina TruSeq Standard mRNA LT sample prep kit and sequenced on the Illumina HiSeq 2500 platform.
RNA-seq libraries were generated from 1ug of high quality total RNA, as assessed using the Bioanalyzer (Agilent). Libraries were made according to the manufacturer’s directions using the TruSeq Stranded mRNA LT Sample Prep Kit – set A (Illumina, Cat. No. RS-122-2101) kit. The resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 50 bp single reads on the Illumina HiSeq 2500 instrument.

treatment_protocol: Drosophila S2 Cells were treated with SSRP1 dsRNA and Spt16 dsRNA to knockdown SSRP1 and Spt16 respectively. S2 cells were treated with eGFP dsRNA as a non-targeting control. Spt16dsRNA_a and Spt16dsRNA_b are two ~400 bp dsRNAs that target non-overlapping regions of the Spt16 mRNA, and SSRP1dsRNA_a and SSRP1dsRNA_b are two ~400 bp dsRNAs that target non-overlapping regions of the SSRP1 mRNA.  Rep1 and Rep2 are biological replicates (independent cultures, independent treatments, independent RNA extractions and libraries).

tag: cell line

tag: knockdown

value: eGFP (non-targeting control)

tag: spike-in cells

value: Human HEK293T cells


title: Hand2asD/+_rep2 8-wk


title: Hand2as+/+_rep4 8-wk


title: eGFPdsRNA_Rpb3_ip_Rep1


title: Spt16dsRNA_a_Rpb3_in_Rep2


title: Spt16dsRNA_b_Rpb3_in_Rep1


title: SSRP1dsRNA_b_Rpb3_in_Rep2


title: eGFPdsRNA_Rpb3_in_Rep1


title: SSRP1dsRNA_a_Rpb3_in_Rep2


title: SSRP1dsRNA_a_Rpb3_in_Rep1


title: Spt16dsRNA_b_Spt16_ip_Rep2

value: Spt16 (Custom made)


title: Spt16dsRNA_b_Spt16_ip_Rep1


title: Spt16dsRNA_a_Spt16_ip_Rep2


title: Spt16dsRNA_a_Spt16_ip_Rep1


title: eGFPdsRNA_Spt16_ip_Rep2


title: Spt16dsRNA_b_Rpb3_in_Rep2


title: SSRP1dsRNA_b_SSRP1_ip_Rep1

value: SSRP1 (Custom made)


title: SSRP1dsRNA_b_SSRP1_ip_Rep2


title: SSRP1dsRNA_a_SSRP1_ip_Rep2


title: Spt16dsRNA_a_Rpb3_in_Rep1


title: eGFPdsRNA_Spt16_ip_Rep1


title: SSRP1dsRNA_a_SSRP1_ip_Rep1


title: eGFPdsRNA_Rpb3_in_Rep2


title: RNA from bulk cells of organoids, within 6 mo in culture, 7 d after last passage, with Forskolin and Fgf1, replicate 1

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: RNA from bulk cells of organoids, within 6 months in culture, 7 days after last passage, with Forskolin and Fgf1, replicate 1

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the total number of reads for every transcript.
Genome_build: mm10
Supplementary_files_format_and_content: *Epi_org*.csv: Comma separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the GeneID and primer number of the sample. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

molecule: total RNA

source_name: skin

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq2 technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: passages

tag: source

value: cells from cultured organoids


title: RNA from bulk cells of organoids, within 6 mo in culture, 7 d after last passage, with Forskolin and Fgf1, replicate 5

description: RNA from bulk cells of organoids, within 6 months in culture, 7 days after last passage, with Forskolin and Fgf1, replicate 5


title: RNA from bulk cells of organoids, within 6 mo in culture, 7 d after last passage, with Forskolin and Fgf1, replicate 6

description: RNA from bulk cells of organoids, within 6 months in culture, 7 days after last passage, with Forskolin and Fgf1, replicate 6


title: RNA from cells sorted from the interfollicular epidermis for Itga6+Sca1+, replicate 1

value: sorted cells from tissue


title: eGFPdsRNA_SSRP1_ip_Rep2


title: RNA from bulk cells of organoids, within 6 mo in culture, 7 d after last passage, with Forskolin and Fgf1, replicate 4

description: RNA from bulk cells of organoids, within 6 months in culture, 7 days after last passage, with Forskolin and Fgf1, replicate 4


title: eGFPdsRNA_IgG_ip_Rep2

value: IgG (Santa Cruz, Cat# sc-2027)


title: RNA from bulk cells of organoids, within 6 mo in culture, 7 d after last passage, with Forskolin and Fgf1, replicate 2

description: RNA from bulk cells of organoids, within 6 months in culture, 7 days after last passage, with Forskolin and Fgf1, replicate 2


title: eGFPdsRNA_SSRP1_ip_Rep1


title: Spt16dsRNA_b_Spt16_input_Rep2


title: HSCD0_rep1

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

data_processing:
All samples were sequenced on a NextSeq 500 sequencing system with the following run parameters:
26 cycles for read 1, 98 cycles for read 2, 8 cycles for index 1. Binary sequencing data were converted to the fastq format
Then the CellRanger analysis pipeline (v2.0.0) from 10x Genomics was used with standard parameters in order to
(1) align the reads for each sample and count them for each gene and each cell with cellranger count
(2) merge all in vitro HSC samples (Sample 1 to 4) to make one expression matrix for all of them
The other samples are provided in the non merged version.
Cell names ending with 1 to 4 in the invitro HSC expression matrix corresponds to sample 1 to sample 4 respectively
Genome_build: mm10 (preprocessed release 84 downloaded from the website of 10x Genomics)
Supplementary_files_format_and_content: 7 expression matrices, one for the in vitro HSC and one for each of the other samples.

growth_protocol: Resting hepatic stellate cells were isolated from untreated C57BL6/J mice. Actiated myofibroblasts were isolated from mice that received 0.5 ml/kg bodyweight CCl4 IP for 3 weeks

extract_protocol:
total liver cells were isolated by collagenase digestion, follwed by FACS purification for living UV autoflorescent hepatic stellate cells, which were either used as controls or subjected to in vitro differentiation
activated hepatic stellate cells were also isolated by collagenase digestion and FACS purified as living CD45- and CD31- cells
in both cases 50.000 cells were then resuspended in cold PBS + 0.1 % BSA and subjected to 10x single cell library generation according to manufacturers protocol
cDNA

treatment_protocol: in vitro differentiated myofibroblasts were cultivated in DMEM + 10 % FCS + 1% P/S for up to 9 days without additional stimuli

tag: age of donors

value: 11 weeks

value: untreated HSC

tag: cell type

value: UV Autofluorescence high


title: CD45nCD31n_rep4

value: 3 weeks CCl4 IP


title: HSCD0_rep2


title: CD45nCD31n_rep3


title: Spt16dsRNA_b_Spt16_input_Rep1

value: Spt16 dsRNA


title: RNA from bulk cells of organoids, within 6 mo in culture, 7 d after last passage, with Forskolin and Fgf1, replicate 3

description: RNA from bulk cells of organoids, within 6 months in culture, 7 days after last passage, with Forskolin and Fgf1, replicate 3


title: RNA from cells sorted from the interfollicular epidermis for Itga6+Sca1+, replicate 3


title: Spt16dsRNA_a_Spt16_input_Rep2


title: RNA from cells sorted from the interfollicular epidermis for Itga6+Sca1+, replicate 2


title: CD45nCD31n_rep1


title: Spt16dsRNA_a_Spt16_input_Rep1


title: State 2 (Nanog low, Sox2 high) Replicate E small RNA-Seq

city: Cambridge

first: Salil

last: Garg

state: Massachusetts

department: Biology

institute: Koch Institute for Integrative Cancer Research

description: small RNA-seq

data_processing:
Paired end read alignment using STAR v.2.4.1d
RSEM v1.2.30 transcriptomic feature counts against GencodeM15 GTF feature file (without miRbase v21 annotations (RNA-seq) or with miRbase v21 annotations (small RNA-seq))
Ebseq (RSEM v1.2.30 native) multitest for differential expression analysis
Genome_build: murine mm10 (GRCm38)
Supplementary_files_format_and_content: ESCStates_GencodeM15_Combinedreps_clip_Ebseq_results_withFC.txt: Ebseq conditional means and pattern PPDE measurements for RNA-sequencing data
Supplementary_files_format_and_content: ESC_StateExpression_GencodeM15mirBase_sRNAseq_results.txt: Ebseq conditional means and fold changes pattern PPDE measurements for small RNA-sequencing data

source_name: Embryonic Stem Cells

growth_protocol: 10% FBS + Leukemia Inhibitory Factor (LIF)

extract_protocol:
Cell states were separated by flow cytometric sorting, followed by total RNA isolation (Trizol), DNAse treatment, and quality assessment (BioAnalyzer)
rRNA-depleted RNA-sequencing:  Libraries were prepared according to manufacturer's instructions (KAPA HyperPrep with RiboErase HMR, kit KK8561).  In brief, samples were treated with capture oligos followed by rRNA depletion, DNase digestion, RNA fragmented, followed by 1st Strand synthesis and 2nd Strand Synthesis with dUTP incorporation, adapter ligation, and 11 cycles of PCR amplification including barcoding.  The final libraries were QC checked by electrophoresis and qPCR for colony forming units prior to pooling and loading on an Illumina FlowCell (NextSeq 500, 150 bp PE reads).  small RNA (miRNA) sequencing:  Libraries were prepared according to the manufacturer's instructions (NEB small RNA sequencing kit, E7300S).  In brief, samples were treated by 3' adaptor ligation, primer hybridization, 5' adaptor ligation, cDNA synthesis, 13 cycles of pcr amplification followed by library cleanup and QC assessment as above prior to pooling and loading on an Illumina FlowCell (HiSeq2000 1 lane, 40 bp SE reads).

tag: cell state

value: State 2 (Nanog low, Sox2 high)

tag: replicate

value: Replicate E


title: Total Population Replicate E small RNA-Seq

description: small RNA-seq

value: Total Population


title: State 1 (Nanog high, Sox2 high) Replicate E small RNA-Seq

description: small RNA-seq

value: State 1 (Nanog high, Sox2 high)


title: Total Population Replicate D small RNA-Seq

description: small RNA-seq

value: Replicate D


title: State 3 (Nanog low, Sox2 low) Replicate E small RNA-Seq

description: small RNA-seq

value: State 3 (Nanog low, Sox2 low)


title: State 2 (Nanog low, Sox2 high) Replicate D small RNA-Seq

description: small RNA-seq


title: eGFPdsRNA_Spt16_input_Rep1

value: eGFPdsRNA


title: eGFPdsRNA_IgG_ip_Rep1


title: HSC_d9

description: processed data file: HSCinvitro_d1_d3_d7_d9.csv

value: in vitro activation for 9 days

value: in vitro HSC d9


title: eGFPdsRNA_Spt16_input_Rep2

value: Spt16 (Custom made)


title: Total Population Replicate C RNA-Seq

description: rRNA-depleted RNA-seq

value: Replicate C


title: State 1 (Nanog high, Sox2 high) Replicate D small RNA-Seq

description: small RNA-seq


title: SSRP1dsRNA_b_SSRP1_input_Rep2

value: SSRP1 dsRNA

value: SSRP1 (Custom made)


title: State 2 (Nanog low, Sox2 high) Replicate C RNA-Seq

description: rRNA-depleted RNA-seq


title: State 3 (Nanog low, Sox2 low) Replicate C RNA-Seq

description: rRNA-depleted RNA-seq


title: CD45nCD31n_rep2

value: 11 weeks


title: State 1 (Nanog high, Sox2 high) Replicate C RNA-Seq

description: rRNA-depleted RNA-seq


title: SSRP1dsRNA_b_SSRP1_input_Rep1


title: HSC_d1

value: in vitro activation for 1 day

value: in vitro HSC d1


title: SSRP1dsRNA_a_SSRP1_input_Rep2


title: Total Population Replicate B RNA-Seq

description: rRNA-depleted RNA-seq

value: Replicate B


title: State 1 (Nanog high, Sox2 high) Replicate B RNA-Seq

description: rRNA-depleted RNA-seq


title: moDC2_3w

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

country: United Kingdom

institute: UCL

data_processing:
Sequencing was carried out on Illumina NextSeq 500 by UCL Genomics (at the Institute of Child Health, ICH UCL)
Alignment and mapping of all libraries were performed using TopHat Alignment, version 1.0.0, and Cufflinks Assembly & DE, version 2.0.0 (BaseSpace, Illumina, USA).
Raw expression counts per gene were calculated using the Cufflinks Assembly & DE, version 2.0.0 (BaseSpace, Illumina, USA), employing a geometric library normalisation method and a fragment bias correction algorithm.
Data normalisation was carried out using DESeq2 software from Bioconductor
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 normalised expression data

source_name: Dermal monocytes

extract_protocol:
RNA yield, quality and integrity were evaluated using the RNA 6000 Pico kit on an Agilent 2100 Bioanalyser (Agilent Technologies, USA). Only samples with a RNA Integrity Number (RIN) above 8.0 were included in the study. RNA was extracted using the RNeasy Micro Kit (QIAGEN, USA) following the manufacturer’s protocol.
cDNA amplification from total RNA was performed using the SMART-seq® v4 Ultra® Low Input RNA Kit (Clontech, USA). Paired-end sequencing libraries were prepared from the amplified cDNA according to the Nextera® XT DNA library prep protocol (43 bp reads, approx. 23 million reads/sample), and sequenced using an Illumina NextSeq 500 (Illumina, USA).

treatment_protocol: Recipient male C57BL/6 mice were irradiated and received female C57BL/6 bone marrow with polyclonal CD4 T cells and anti-male TCR transgenic (Matahari) T cells. At different time points post-transplant, myeloid cell populations were sorted from the epidermis, dermis and blood for analysis by RNAseq.

value: FACS sorted myeloid cell population

tag: donor genotype

value: C57BL/6 mice (female)

tag: recipient genotype

value: C57BL/6 mice (male)


title: HSC_d7

tag: treatment

value: in vitro activation for 7 days

value: in vitro HSC d7


title: SSRP1dsRNA_a_SSRP1_input_Rep1

tag: antibody


title: HSC_d3

tag: strain

value: in vitro activation for 3 days

value: in vitro HSC d3


title: State 2 (Nanog low, Sox2 high) Replicate B RNA-Seq

description: rRNA-depleted RNA-seq

value: State 2 (Nanog low, Sox2 high)


title: HLC3_3w

source_name: Host eLC

tag: tissue


title: moDC1_3w


title: eGFPdsRNA_SSRP1_input_Rep2

value: eGFPdsRNA


title: eGFPdsRNA_SSRP1_input_Rep1


title: State 2 (Nanog low, Sox2 high) Replicate A RNA-Seq

description: rRNA-depleted RNA-seq

value: Replicate A


title: State 1 (Nanog high, Sox2 high) Replicate A RNA-Seq

description: rRNA-depleted RNA-seq

value: State 1 (Nanog high, Sox2 high)


title: State 3 (Nanog low, Sox2 low) Replicate A RNA-Seq

description: rRNA-depleted RNA-seq

value: State 3 (Nanog low, Sox2 low)


title: State 3 (Nanog low, Sox2 low) Replicate D small RNA-Seq

description: small RNA-seq

value: Replicate D


title: moDC3_3w


title: Total Population Replicate A RNA-Seq

description: rRNA-depleted RNA-seq

value: Total Population


title: State 3 (Nanog low, Sox2 low) Replicate B RNA-Seq

description: rRNA-depleted RNA-seq


title: HLC1_3w


title: eGFPdsRNA_IgG_input_Rep2

value: IgG (Santa Cruz, Cat# sc-2027)


title: Pol2_8h_FLOX

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile -fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Removing duplicate reads: samtools rmdup -sS bamfile
Transcription factors (MYC, Pol2) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam --mfold=7,30 -g mm -p 0.00001
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

source_name: Pol2_FLOX_primary B-cells

growth_protocol: Naïve mouse B-cells were isolated from the spleen of 7-10 weeks old wild type or c-mycf/f mice with the B-cell isolation kit (MACS Miltenyi Biotec Cat. no. 130-090-862). After purification, naïve B cells were incubated for 1h at 37°C with recombinant Tat-Cre protein (50 mg/ml) in optimem + 1% fetal bovine serum in order to induce deletion of the c-mycf/f allele. Cells were washed with PBS and then grown in B cell medium composed of DMEM medium (Dulbecco’s Modified Eagle Medium) and IMDM medium (Iscove’s Modified Dulbecco’s Medium) in a 1:1 ratio and additionated of 10% fetal calf serum (FCS) (Globefarm Ltd, Cranleigh, UK), 2 mM L-glutamine (Invitrogen Life Technologies, Paisley, UK), 1% non-essential amino acids (NEAA), 1% penicillin/streptomycin and 25 mM β-mercaptoethanol.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection with AMPure beads and PCR with index primers.

treatment_protocol: 12h after seeding, B cells were stimulated with lipopolysaccharide LPS (50 mg/ml; SIGMA L6237) to induce cell activation where indicated.

tag: strain background

tag: genotype/variation

value: c-myc FLOX/FLOX

tag: age

value: 7-10 weeks

value: spleen

value: primary naive mouse B-cells

value: LPS (50 ug/ml) 8h

tag: chip antibody

value: RNAPII (Santa Cruz sc899)


title: Pol2_4h_FLOX

value: LPS (50 ug/ml) 4h


title: eGFPdsRNA_IgG_input_Rep1


title: input_pol2_FLOX

source_name: input_pol2_FLOX _primary B-cells

value: untreated


title: Dpre3_3w

source_name: EpCAM+ cells

value: FACS sorted myeloid cell population

value: C57BL/6 mice (female)

value: C57BL/6 mice (male)


title: Pol2_0h_FLOX


title: Pol2_8h_WT

source_name: Pol2_WT_primary B-cells

value: WT


title: Spt16dsRNA_b_H3K4me3_ip_Rep2

value: Spt16 dsRNA

value: H3K4me3 (Abcam, Cat# ab8580)


title: Spt16dsRNA_b_H3K4me3_ip_Rep1


title: Dpre2_3w


title: Pol2_0h_WT


title: Dpre1_3w


title: input_pol2_WT

source_name: input_pol2_WT_primary B-cells


title: Pol2_4h_WT


title: HLC2_3w


title: Myc_8h_WT

source_name: Myc_WT_primary B-cells

value: c-Myc N262 (Santa Cruz sc764)


title: DLC4_3w

source_name: Donor LC 3 weeks


title: Spt16dsRNA_a_H3K4me3_ip_Rep1


title: Myc_4h_WT


title: Myc_0h_WT


title: Myc_2h_WT

value: LPS (50 ug/ml) 2h


title: DLC2_3w


title: FLOX_8h_rep4_RNA-seq

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: txt file reporting the eRPKM, log2FC and padj from DESEq2 output

source_name: Primary B-cells

growth_protocol: Naïve mouse B-cells were isolated from the spleen of 7–10 weeks old wild type or c-mycf/f mice with the B-cell isolation kit (MACS Miltenyi Biotec Cat. no. 130-090-862). After purification, naïve B cells were incubated for 1h at 37°C with recombinant Tat-Cre protein (50 mg/ml) in optimem + 1% fetal bovine serum in order to induce deletion of the c-mycf/f allele. Cells were washed with PBS and then grown in B cell medium composed of DMEM medium (Dulbecco’s Modified Eagle Medium) and IMDM medium (Iscove’s Modified Dulbecco’s Medium) in a 1:1 ratio and additionated of 10% fetal calf serum (FCS) (Globefarm Ltd, Cranleigh, UK), 2 mM L-glutamine (Invitrogen Life Technologies, Paisley, UK), 1% non-essential amino acids (NEAA), 1% penicillin/streptomycin and 25 mM β-mercaptoethanol.

extract_protocol:
Total RNA was purified onto RNeasy columns (Qiagen) and treated on-column with DNase (Qiagen).
Libraries for RNA-Seq were then prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads).


title: input_Myc_WT

source_name: input_Myc_WT_primary B-cells


title: SSRP1dsRNA_b_H3K4me3_ip_Rep2

value: SSRP1 dsRNA


title: DLC3_3w


title: FLOX_8h_rep3_RNA-seq

value: c-myc FLOX/FLOX


title: FLOX_8h_rep2_RNA-seq

value: 7-10 weeks


title: Bmono2_3w

source_name: Blood monocytes


title: DLC1_3w


title: SSRP1dsRNA_a_H3K4me3_ip_Rep1

source_name: S2 cells


title: SSRP1dsRNA_a_H3K4me3_ip_Rep2


title: Spt16dsRNA_a_H3K4me3_ip_Rep2


title: FLOX_8h_rep1_RNA-seq

value: spleen


title: WT_8h_rep2_RNA-seq

value: primary naive mouse B-cells


title: WT_8h_rep4_RNA-seq

value: LPS (50 ug/ml) 8h


title: Bmono1_3w


title: eGFPdsRNA_H3K4me3_ip_Rep2

value: eGFPdsRNA


title: NLC3_10w

source_name: Embryo-derived (eLC)


title: eGFPdsRNA_H3K4me3_ip_Rep1


title: WT_8h_rep1_RNA-seq


title: FLOX_4h_rep4_RNA-seq

value: LPS (50 ug/ml) 4h


title: SSRP1dsRNA_b_H3K4me3_ip_Rep1


title: FLOX_4h_rep3_RNA-seq


title: NLC2_10w


title: NLC1_10w


title: FLOX_4h_rep1_RNA-seq


title: WT_4h_rep4_RNA-seq


title: DLC3_10w

source_name: Donor LC 10 weeks


title: Spt16dsRNA_b_H3K4me3_input_Rep1


title: WT_4h_rep3_RNA-seq


title: WT_8h_rep3_RNA-seq


title: Spt16dsRNA_a_H3K4me3_input_Rep2


title: FLOX_4h_rep2_RNA-seq


title: WT_4h_rep2_RNA-seq


title: WT_4h_rep1_RNA-seq


title: DLC2_10w


title: Spt16dsRNA_a_H3K4me3_input_Rep1


title: FLOX_2h_rep4_RNA-seq


title: DLC1_10w


title: FLOX_2h_rep2_RNA-seq


title: FLOX_2h_rep3_RNA-seq


title: FLOX_2h_rep1_RNA-seq


title: SSRP1dsRNA_b_H3K4me3_input_Rep2


title: WT_2h_rep3_RNA-seq


title: SSRP1dsRNA_b_H3K4me3_input_Rep1


title: WT_2h_rep2_RNA-seq


title: 16-101_CD11b

data_processing:
Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa (version 0.7.10-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases 8 bases (except 18-105_CD271, where the length is 6 bases) representing the unique molecular identifier followed by 8 correspond to the cell specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification.
Genome_build: hg19
Supplementary_files_format_and_content: *.csv: semicolon separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

organism: Homo sapiens

source_name: Extracted RNA from CD11b isolated by MACS from the adult human subventricular zone using CD11b antibody, library 13

extract_protocol:
RNA extraction was performed with QIAGen miRNAeasy mini kit in combination with DNAse treatment according to the manufacturers instruction.
RNA was processed using the previously described Celseq2 technique adapted for bulk sequencing. In brief, reverse transcription and second strand synthesis were performed in seperate tubes; libraries were pooled for in vitro transcription based RNA amplification. Libraries were generate using Truseq small RNA primer (rpi) library primers, Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: CD11b from the adult human subventricular zone


title: 16-016_CD11b

source_name: Extracted RNA from CD11b isolated by MACS from the adult human subventricular zone using CD11b antibody, library 15


title: Spt16dsRNA_b_H3K4me3_input_Rep2


title: SSRP1dsRNA_a_H3K4me3_input_Rep2


title: WT_2h_rep4_RNA-seq


title: 16-090_CD11b

source_name: Extracted RNA from CD11b isolated by MACS from the adult human subventricular zone using CD11b antibody, library 12


title: FLOX_0_rep5_RNA-seq

value: untreated


title: FLOX_0_rep6_RNA-seq


title: 16-084_CD11b

source_name: Extracted RNA from CD11b isolated by MACS from the adult human subventricular zone using CD11b antibody, library 11


title: WT_2h_rep1_RNA-seq


title: FLOX_0_rep4_RNA-seq


title: SSRP1dsRNA_b_Rpb3_in_Rep1

value: Rpb3 (Gift from Zeitlinger Lab)


title: eGFPdsRNA_H3K4me3_input_Rep2


title: FLOX_0_rep3_RNA-seq


title: 16-116_CD11b

source_name: Extracted RNA from CD11b isolated by MACS from the adult human subventricular zone using CD11b antibody, library 10


title: FLOX_0_rep1_RNA-seq


title: SSRP1dsRNA_a_H3K4me3_input_Rep1


title: WT_0_rep5_RNA-seq


title: WT_0_rep6_RNA-seq


title: Spt16dsRNA_b_H3_ip_Rep2

value: H3 (Abcam, Cat# ab1791)


title: WT_0_rep4_RNA-seq

value: WT


title: WT_0_rep3_RNA-seq


title: Spt16dsRNA_b_H3_ip_Rep1

value: Spt16 dsRNA


title: WT_0_rep2_RNA-seq


title: 16-116_SVZ

source_name: Extracted RNA from SVZ homogenate dissociated from the adult human brain, library 5


title: 16-102_SVZ

source_name: Extracted RNA from SVZ homogenate dissociated from the adult human brain, library 4


title: WT_0_rep1_RNA-seq


title: Spt16dsRNA_a_H3_ip_Rep2


title: input_week4_Het-CKO

city: Irvine

first: Yumei

last: Li

state: CA

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

data_processing:
The sequencing adaptors were filtered and reads with low quality (average quality <20 or fraction of bases with quality less than 20  >0.5 or fraction of N bases >0.1) were filtered.
High-quality reads were aligned to mm10 mouse genome using bwa (v0.7.13-r1126) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 20 were kept.
Reads were further analyzed by DANPOS2 (v2.2.2) with parameters -c 10000000 --extend 74.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for H2BGFP ChIP-seq were generated using DANPOS2. Scores represented nucleosome occupancy measured by ChIP signals subtract input.

source_name: mixed heart samples of WT and CKO

growth_protocol: Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory animal care. The Dox was mixed with water and was fed to the mice according to experimental requirement.

extract_protocol:
The cardiomyocytes were isolated from the adult mice heart according to previous protocol, and the cardiomyocytes were fixed and then lysed. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP library preparation Kit (NEBE7370). Briefly, DNA was end-repaired. The blunt, phosphorylated ends were treated with TA ligase Master mix and NEBNext Adaptor for Illumina. After adaptor ligation, DNA was PCR amplified with Illumina primers for 15 cycles. The DNA library was purified and the size of DNA fragments was selected by AMPure XP beads. The libraries were then sent to be sequenced.

value: heart

value: isolated adult ventricular cardiomyocytes

tag: developmental stage

value: adult

tag: genotype

value: WT;CKO

value: No


title: 16-102_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 7

value: NSC from the adult human subventricular zone


title: Spt16dsRNA_a_H3_ip_Rep1


title: input_week0_Het-CKO


title: H2BGFP_week4_CKO_rep2

description: input: input_week4_Het-CKO

source_name: heart

value: cardiac conditional EED knockout


title: FLOX_0_rep2_RNA-seq

value: c-myc FLOX/FLOX

value: 7-10 weeks

value: spleen

value: primary naive mouse B-cells


title: eGFPdsRNA_H3K4me3_input_Rep1

value: eGFPdsRNA

value: H3K4me3 (Abcam, Cat# ab8580)


title: SSRP1dsRNA_b_H3_ip_Rep2

value: SSRP1 dsRNA


title: H2BGFP_week4_CKO_rep1

description: input: input_week4_Het-CKO


title: 16-101_SVZ

source_name: Extracted RNA from SVZ homogenate dissociated from the adult human brain, library 3


title: 15-087_CD11b

source_name: Extracted RNA from CD11b isolated by MACS from the adult human subventricular zone using CD11b antibody, library 7

value: CD11b from the adult human subventricular zone


title: H2BGFP_week4_Het_rep2

description: input: input_week4_Het-CKO

value: WT


title: H2BGFP_week0_CKO

description: input: input_week0_Het-CKO


title: H2BGFP_week4_Het_rep1

description: input: input_week4_Het-CKO


title: 16-101_CD271


title: H2BGFP_week0_Het_rep1

description: input: input_week0_Het-CKO


title: 18-105_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 9


title: SSRP1dsRNA_b_H3_ip_Rep1

value: H3 (Abcam, Cat# ab1791)


title: input_WT2

value: heart


title: H2BGFP_week0_Het_rep2

description: input: input_week0_Het-CKO

value: isolated adult ventricular cardiomyocytes


title: SSRP1dsRNA_a_H3_ip_Rep2


title: SSRP1dsRNA_a_H3_ip_Rep1


title: 16-098_SVZ

source_name: Extracted RNA from SVZ homogenate dissociated from the adult human brain, library 2


title: input_WT1

value: adult


title: 16-098_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 6


title: H3_WT

description: input: input_WT1

value: H3 (Abcam, ab1791)


title: H2BGFP_week6_WT

description: input: input_WT1


title: H2BGFP_week8_WT

description: input: input_WT1


title: 16-090_SVZ

source_name: Extracted RNA from SVZ homogenate dissociated from the adult human brain, library 1


title: eGFPdsRNA_H3_ip_Rep2

source_name: S2 cells


title: H2BGFP_week4_WT_rep3

description: input: input_WT2


title: eGFPdsRNA_H3_ip_Rep1


title: 16-084_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 5


title: Spt16dsRNA_b_H3_input_Rep2

value: Spt16 dsRNA


title: H2BGFP_week4_WT_rep1

description: input: input_WT1


title: Spt16dsRNA_b_H3_input_Rep1


title: 16-016_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 4

value: NSC from the adult human subventricular zone


title: H2BGFP_week2_WT_rep2

description: input: input_WT1

data_processing:
The sequencing adaptors were filtered and reads with low quality (average quality <20 or fraction of bases with quality less than 20  >0.5 or fraction of N bases >0.1) were filtered.
High-quality reads were aligned to mm10 mouse genome using bwa (v0.7.13-r1126) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 20 were kept.
Reads were further analyzed by DANPOS2 (v2.2.2) with parameters -c 10000000 --extend 74.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for H2BGFP ChIP-seq were generated using DANPOS2. Scores represented nucleosome occupancy measured by ChIP signals subtract input; bigWig files for BRG1 and CHD4 ChIP-seq were generated using deepTools. Scores represented signals with total reads normalized to 10 M.


title: H2BGFP_week4_WT_rep2

description: input: input_WT2


title: 15-093_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 3


title: H2BGFP_week2_WT_rep1

description: input: input_WT1


title: Spt16dsRNA_a_H3_input_Rep2


title: H2BGFP_week1_WT_rep1

description: input: input_WT1


title: 15-018_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 1


title: 15-033_CD271

source_name: Extracted RNA from NSC isolated by MACS from the adult human subventricular zone using CD271 antibody, library 2


title: Spt16dsRNA_a_H3_input_Rep1


title: H2BGFP_week0_WT_rep2

description: input: input_WT2


title: SSRP1dsRNA_b_H3_input_Rep2


title: SSRP1dsRNA_b_H3_input_Rep1


title: SSRP1dsRNA_a_H3_input_Rep1


title: PS04Thio-1

city: Wroclaw

first: Marcin

middle: Jan

last: Szafran

address: Joliot-Curie 14A

department: Faculty of Biotechnology

country: Poland

institute: University of Wroclaw

description: TopA_overexpression Replicate 1

data_processing:
Paired-end 76-bp reads were  mapped against the S. coelicolor chromosome and fold changes of gene transcription  was calculated using Rockhopper software version 2.0.3 (McClure et al., 2013)
To calculate the fold change in gene transcription, normalized gene expression (normalization by the upper quartile of gene expression) of the wild type strain under control conditions was divided by normalized gene expression under particular experimental conditions.
The log2 value of the fold change was calculated. The transcripts with a log2 value between -1.5 and 1.5 were eliminated from subsequent analyses.
Genome_build: Streptomyces coelicolor A3(2)
Supplementary_files_format_and_content: txt files were generated using Rockhopper software version 2.0.3
Supplementary_files_format_and_content: M145_PS04.txt:differential gene transcription M145 versus non-induced PS04
Supplementary_files_format_and_content: M145_PS04Thio.txt:differential gene transcription M145 versus induced PS04
Supplementary_files_format_and_content: M145_Mi145Novob.txt:differential gene transcription M145 versus M145 treated with novobiocin

organism: Streptomyces coelicolor

source_name: vegetative hyphae

growth_protocol: medium: liquid YEME/TSB; 30 mL, 18 hours of growth, 30C, 180 rpm. PS04 strain was indcuded with thiostrepton [1 µg/mL]. To indcude rapid chromosome relaxation M145 strain was treated with novobiocion [10 µg/mL] for 10 min before harvesting the culture.

extract_protocol:
Mycelia were collected by centrifugation, frozen and stored at -70°C for subsequent RNA isolation. RNA was isolated using the procedure described previously by Moody et al. (Moody et al., 2013), digested with TURBO DNase I (Invitrogen, USA) and checked for chromosomal DNA contamination using PCR.
RNA libraries were prepared for sequencing using standard Illumina protocols (NEBNext Ultra II Directional RNA Library Prep Kit)

treatment_protocol: PS04 strain was indcuded with thiostrepton [1 µg/mL] for long-term decrease of DNA supercoiling. To induce the rapid chromosome relaxation, M145 strain was treated with novobiocin [10 µg/mL] for 10 min before harvesting the culture.

tag: supercoiling state

value: long-term decreased DNA supercoiling


title: PS04-2

description: TopA_depletion Replicate 2

value: long-term increased DNA supercoiling


title: PS04-4

description: TopA_depletion Replicate 4


title: PS04-3

description: TopA_depletion Replicate 3


title: PS04Thio-3

description: TopA_overexpression Replicate 3


title: PS04Thio-2

description: TopA_overexpression Replicate 2


title: PS04-1

description: TopA_depletion Replicate 1


title: M145Novob-2

description: novo10 Replicate 2

value: short-term and rapid chromosome relaxation


title: H2BGFP_week1_WT_rep2

description: input: input_WT1


title: eGFPdsRNA_H3_input_Rep2


title: M145Novob-1

description: novo10 Replicate 1


title: M145-4

description: wildtype Replicate 4

value: wild type DNA supercoiling


title: eGFPdsRNA_H3_input_Rep1


title: M145-3

description: wildtype Replicate 3


title: H2BGFP_week0_WT_rep1

description: input: input_WT2


title: M145-1

description: wildtype Replicate 1


title: M145-2

description: wildtype Replicate 2


title: Hand2asF/F_E11.5_scRNA-seq

description: processed data: Single-cell mRNA profiling_ Hand2as KO embryonic hearts.txt

data_processing:
Sequencing data analyses including sample demultiplexing, barcode processing and single-cell 3′ gene counting were done by the Cell Ranger Single-Cell Software Suite (http://software.10xgenomics.com/single-cell/overview/welcome)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for Hand2as+/+ and Hand2asF/F embyonic hearts

source_name: E11.5 heart

extract_protocol:
E11.5 hearts of wild type and Hand2asF/F from heterozygotes intercrosses were subjected for Single-cell RNA-seq. We harvested six embryonic hearts for each genotype. Embryonic hearts were trypsinized (0.25%, 5min, 37℃) individually, and subjected for Fluorescence-activated cell sorting (FACS) after 7-Aminoactinomycin D (AAT Bioquest, 17501) staining for collection of living single cells.
Single cells from six embryonic hearts were combined as a single sample for 10X Genomics Single Cell 3’ library construction (10X Genomics, PN-120237). The RNA libraries were constructed by following the manufacture recommended procedure to get ~5,000 cells barcoded per sample.


title: AGO CLIP, individual 6

city: New York

first: Mariko

last: Kobayashi

state: NY

address: 1230 York Avenue

department: Molecular Neuro-Oncology

institute: Rockefeller University

data_processing:
All fastq processing done using fastqx_toolkit-0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/).  Sequencing reads were filtered for quality reads (min:0-6:20,mean:7-50:20), collapsed exact sequences, trimmed 5' degenerate linker, demultiplexed and trimmed 4nt barcode sequence, and clipped 3' adapter sequence (GTGTCAGTCACTTCCAGCGG).
Processed fastq files were aligned to human reference genome using novoalign (Novocraft Technologies) applying iterative 3'trimming and retaining only single-hit reads.
Due to low complexity of sequencing reads, data from individual 1-3 (pool_1) and individual 4-6 (pool_2) were pooled.  Aligned reads from pool_1 and pool_2 were combined with pooled aligned reads from published human AGO CLIP data (GSE52084) (Boudreau et al., 2014), representing 11 individual replicates + 2 pooled samples, totaling 13.  Peak calling strategy using CLIP Toolkit command tag2peak.pl was used, applying FDR cut-off of <0.01 over background.  Genomic coordinates for each peak were constructed with standard width of 80nt (+/- 40nt from peak midpoint).  Robust peaks were defined by peak height of 50 (PH50) and biological complexity of 7 (BC7), meaning each peak was represented by at least 50 independent reads made up of reads from 7 out of 13 replicates.   Complete protocol detailed in referenced publication
Genome_build: hg19
Supplementary_files_format_and_content: Counts of each BC7, PH50 peak (23,662), hg19 genomic location, Boudreau et al., 2014's data of 11 patients, pool1, pool2, strand info

source_name: postmortem BA9

extract_protocol:
Argonaute IP, alkaline phosphatase treatment, polynucleotide kinase (PNK) radiolabeling, addition of pre-adenylated 3’ linker, SDS-PAGE, and nitrocellulose transfer and extraction performed.   AGO:RNA complexes excised out of nitrocellulose membrane, followed by proteinase K digestion of AGO protein.
AGO-CLIP footprints were cloned using the Br-dU incorporation and bead-capture strategy.  Barcoded reverse transcription (RT) primers, allowing multiplexing of 3 samples per Hiseq (Illumina) run,50 base pair single-end reads.

value: motor cortex (BA9)

tag: Sex

value: F

tag: postmortem interval

tag: storage (months)

tag: ago

value: rna complex:Pooled high molecular weight AGO:RNA complexes ~130-150kDa

tag: biological replicate

value: replicate 6

tag: informatic pool

value: pool 2


title: WI38_RASOIS_144H_siRNA_RELA_2_REP2

type: RNA

city: Paris Cedex 15

first: Oliver

last: Bischof

address: 28 rue du Docteur Roux

department: Cell Biology & Infection

country: France

institute: Institut Pasteur

hyb_protocol: Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing:
Raw Affymetrix HTA 2.0 array intensity data were analyzed using open-source Bioconductor packages on R. All the data were normalized all together using the robust multi-array average normalization approach implemented in the oligo package (Carvalho and Irizarry, 2010). Internal control probe sets were removed and average expression deciles over all treatment and time points. Probes whose average expression was lower than the 4th expression decile were removed for subsequent analyses.
To remove sources of experimental variation and consider batch effects, data were finally corrected with the sva package. Principal component analysis and bi-clustering based on Pearson’s correlation and Ward’s aggregation criterion were used to confirm consistency between biological replicates and experimental conditions at each step of the pre-processing.

label: biotin

source_name: WI38, RASOIS, 144H, siRNA RELA

label_protocol: Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.

growth_protocol: WI-38 expressing a 4OHT-inducible ER:RAS fusion gene were cultured in DMEM with 4.5g/L glucose and 10% FBS at 37˚C in the presence of 10% CO2 and 3% O2.

extract_protocol: RNA was extracted using the QIAGEN RNAeasy Plus kit according to the manufacturer's instructions.

treatment_protocol: Oncogenic RAS-induced senescence was initiated by addition of 400 nM 4OHT to WI-38 fibroblasts expressing ER:RASv12 fusion gene and 500,000 cells were collected at the indicated time points.

value: WI38 fibroblasts

tag: treatment

value: RAS induced senescence

tag: sirna

value: siRNA RELA

tag: timepoint


title: Spt16dsRNA_b_H3K36me3_ip_Rep2

tag: antibody

value: H3K36me3 (Abcam, Cat# ab9050)


title: Spt16dsRNA_b_H3K36me3_ip_Rep1


title: SSRP1dsRNA_a_H3_input_Rep2

value: SSRP1 dsRNA

value: H3 (Abcam, Cat# ab1791)


title: WI38_RASOIS_144H_siRNA_RELA_2_REP1

tag: tissue


title: WI38_RASOIS_144H_siRNA_RELA_1_REP2


title: WI38_RASOIS_144H_siRNA_RELA_1_REP1


title: Hand2as+/+_E11.5_scRNA-seq

tag: strain

tag: genotype/variation

value: heart


title: Hand2asF/F_rep3 E16.5

source_name: E16.5 ventricle


title: WI38_RASOIS_144H_siRNA_JUN_2_REP1

source_name: WI38, RASOIS, 144H, siRNA JUN

value: siRNA JUN


title: AGO CLIP, individual 5

tag: age

value: M

value: replicate 5


title: AGO CLIP, individual 4

value: replicate 4


title: Hand2asF/F_rep2 E16.5

tag: developmental stage


title: AGO CLIP, individual 3

value: replicate 3

value: pool 1


title: Spt16dsRNA_a_H3K36me3_ip_Rep2

value: Spt16 dsRNA


title: Spt16dsRNA_a_H3K36me3_ip_Rep1


title: Hand2asF/F_rep1 E16.5

tag: genotype


title: SSRP1dsRNA_b_H3K36me3_ip_Rep2


title: WI38_RASOIS_144H_siRNA_JUN_2_REP2


title: Hand2asF/+_rep3 E16.5


title: SSRP1dsRNA_b_H3K36me3_ip_Rep1


title: AGO CLIP, individual 2

value: motor cortex (BA9)

value: rna complex:Pooled high molecular weight AGO:RNA complexes ~130-150kDa

value: replicate 2


title: WI38_RASOIS_144H_siRNA_JUN_1_REP2

value: WI38 fibroblasts


title: SSRP1dsRNA_a_H3K36me3_ip_Rep2


title: AGO CLIP, individual 1

value: replicate 1


title: Hand2asF/+_rep2 E16.5


title: WI38_RASOIS_144H_siRNA_JUN_1_REP1

value: RAS induced senescence


title: SSRP1dsRNA_a_H3K36me3_ip_Rep1

value: H3K36me3 (Abcam, Cat# ab9050)


title: HeLa RhoEα reintroduction

city: Houston

first: Jiang

last: Chang

state: TX

address: 2121 W. Holcombe Blvd.

department: Center for Translational Cancer Research

institute: Texas A&M University Institute of Biosciences and Technology

description: Sample 8

data_processing:
Illumina NovaSeq and HiSeq platform with paired-end 150 bp (PE 150) sequencing strategy was used.
Genome Htseq software was used to count the reads.
Genome_build: Hg38
Supplementary_files_format_and_content: Raw count

source_name: HeLa cells

growth_protocol: HEK 293 and HeLa cells were purchased from ATCC (Manassas, Virginia). Cells were cultured with DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent.
Libraries were prepared according to the Ultra Directional RNA Library Prep Kit for Illumina from NEB (Catalog: E7420S).

tag: cell line

value: HeLa

value: Rhoalpha reintroduction

tag: cell type

value: Cervical cancer derived human cells

tag: passages


title: Hand2asF/+_rep1 E16.5

value: heart


title: HeLa RhoE reintroduction

description: Sample 7

value: RhoE reintroduction


title: Hand2asF/F_rep3 E11.5


title: HeLa KO

description: Sample 6

value: KO


title: HeLa wild-type

description: Sample 5

value: wild-type


title: Hand2asF/F_rep2 E11.5


title: eGFPdsRNA_H3K36me3_ip_Rep2

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
RNA-seq reads were aligned to UCSC genome dm6 with STAR version 2.5.2b, with default settings, using Ensembl 84 gene models.
ChIPseq reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. Reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM).
For PROseq, adapter 5′-TGGAATTCTCGGGTGCCAAGG-3′ was removed. Reads were trimmed up to 36 bp. Reads with length less than 15 bp after trimming were removed. After reverse-complement, reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. The last basepair of the reads were used to generate bigWig files and downstream analysis.
Genome_build: dm6, Ensembl 84
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

value: eGFPdsRNA


title: Spt16dsRNA_b_H3K36me3_input_Rep2


title: Hand2asF/F_rep1 E11.5

data_processing:
Basecalls performed using CASAVA
All RNA-Seq data were mapped to the mouse reference genome (mm9) using TopHat (version 2.0.11). For samples E11.5 hearts and E16.5 ventricles of Hand2asF, reads were assigned to their transcribed strand (Tophat parameter “--library-type=fr-firststrand”).
FPKM was calculated by Cufflink version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for control (heterozygous or wildtype) and homozygous Hand2as KO mice heart tissues


title: eGFPdsRNA_H3K36me3_ip_Rep1


title: Spt16dsRNA_b_H3K36me3_input_Rep1


title: HEK 293 RhoEα reintroduction

description: Sample 4

source_name: HEK 293 cells

value: HEK 293

value: Human embryonic kidney 293 cells


title: WI38_RASOIS_144H_siRNA_ETS1_1_REP1

source_name: WI38, RASOIS, 144H, siRNA ETS1

value: siRNA EST1


title: Hand2asF/+_rep3 E11.5


title: WI38_RASOIS_144H_siRNA_ETS1_2_REP2


title: Spt16dsRNA_a_H3K36me3_input_Rep2

value: Spt16 dsRNA


title: Spt16dsRNA_a_H3K36me3_input_Rep1


title: WI38_RASOIS_144H_siRNA_ETS1_1_REP2


title: WI38_RASOIS_144H_siRNA_CTRL_REP5

source_name: WI38, RASOIS, 144H, siRNA Ctrl

value: siRNA Control


title: HEK 293 RhoE reintroduction

description: Sample 3


title: WI38_RASOIS_144H_siRNA_ETS1_2_REP1

value: WI38 fibroblasts


title: HEK 293 KO

description: Sample 2


title: Hand2asF/+_rep1 E11.5


title: WI38_RASOIS_144H_siRNA_CTRL_REP8


title: WI38_RASOIS_144H_siRNA_CTRL_REP3


title: HEK 293 wild-type

description: Sample 1


title: SSRP1dsRNA_b_H3K36me3_input_Rep2

value: SSRP1 dsRNA


title: WI38_RASOIS_144H_siRNA_CTRL_REP7

value: RAS induced senescence


title: eRpL22-like ribosome replicate 4

city: Bethlehem

first: Catherine

middle: M

last: Mageeney

state: PA

address: 111 Research Drive, B217

department: Biological Sciences

institute: Lehigh Univeristy

data_processing:
Low quality filter and removal of Illumina adaptors TrimGalore toolkit and Cutadapt (Martin, 2011).
Alignmnets were performed with STAR RNA-seq alignment tool to the r6v15 version of the Drosophila melanogaster genome and transcriptome.
The DESeq2 Bioconductor package with the R statistical programming environment was used for normalization and differential expression analysis and the false discovery rates.
Pathways enriched for differentially expressed genes  DAVID pathway analysis suite
Genome_build: D. melanogaster r6v15
Supplementary_files_format_and_content: tab-delimited file with log2 fold change, p-value, and normalization value

source_name: eRpL22-like pulldown from ribosome profile from testis extract

growth_protocol: WT day 2 - day 7 Drosphila grown on standard corn-meal media

extract_protocol:
Lysates were immunoprecipiatted using eRpL22 paralogue-specific antibodies then RNA was extracted using Trizol
A cDNA library was created using the Kapa Hyper prep kit. The cDNA quality was analyzed by the Agilent 2100 bioanalyzer (High Sensitivity DNA application) and the libraries were sequenced on an Illumina Hi-seq 4000 (50bp SR).

value: testis

value: WT


title: SSRP1dsRNA_b_H3K36me3_input_Rep1

source_name: S2 cells

extract_protocol:
For ChIP-seq, Briefly Drosophila S2 cells were crosslinked with 1% formaldehyde for 20 min at room temperature, after which crosslinking was quenched in 0.125 M glycine. Isolated nuclei were sonicated using  Misonix 3000 Sonicator, and the supernatant used for  immunoprecipitation with the indicated antibody. ChIP-seq libraries were then sequenced on the Illumina HiSeq 2500 platform. For RNA-seq,  total RNA was extracted using the QIAGEN RNeasy mini kit. Libraries were then prepared using the Illumina TruSeq Standard mRNA LT sample prep kit, and sequenced on the Illumina HiSeq 2500 platform. For PRO-seq, nuclei was first isolated from S2 Cells, followed by run on and biotin enrichment. biotinylated transcripts were then cloned using 5' and 3' RNA adaptors. Cloned transcripts were then reverse transcribed, PCR amplified, and sequenced on the Illumina Nextseq 500 platform. For ChIP nexus, briefly, Cells were cross-linked in 1.0% formaldehyde, lysed and sonicated using the Bioruptor Pico. Sheared chromatin was used in immunoprecipitation with the indicated antibodies. While the DNA is still bound to the antibodies, the DNA ends were repaired, dA-tailed, and ligated to adapters with single 3'-T overhangs and 5’ overhangs. Cloned fragments were blunted by Klenow 3’-5’ exo-polymerase followed by end-trimming using T4 DNA polymerase. The blunt end DNA was digested with λ-exonuclease followed by RecJf. Single stranded DNA products were then eluted, reverse cross-linked and purified. Purified DNA was then circularized using Circligase, and linearized using BamH1 after addition of an oligonucleotide complementary to the BamHI restriction site. Linearized single stranded DNA was then PCR-amplified using adaptor sequences. Libraries were then gel purified and sequenced on the Illumina NextSeq 500 platform.
ChIP-seq libararies were prepared using the KAPA HTP Library Prep Kit for Illumina and Bioo Scientific NEXTflex DNA barcodes. Libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies), a Caliper LabChip GX (Perkin Elmer) and a Qubit fluorometer (Life Technologies).  Post amplification size selection was performed on all libraries using the SPRIselect system (Beckman Coulter).  Libraries were re-quantified, normalized, pooled and sequenced on an Illumina HiSeq 2500 instrument as 50-bp single reads using HiSeq Control Software 2.2.58.
RNA-seq libraries were generated from 1ug of high quality total RNA, as assessed using the Bioanalyzer (Agilent). For samples in the RNAseq_1 series, libraries were made according to the manufacturer’s directions using the TruSeq Stranded mRNA LT Sample Prep Kit – set A (Illumina, Cat. No. RS-122-2101) kit. For samples in the RNAseq_2 series, libraries were made according to the manufacturer’s directions using the TruSeq Stranded mRNA LT Sample Prep Kit - set A and B (Illumina, Cat. No. RS-122-2101 and RS-122-2102) kit. The resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 50 bp single reads on the Illumina HiSeq 2500 instrument.
PRO-seq libraries were generated essentially as described in Mahat et al (2016), Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc. 11, 1455-76.   doi: 10.1038/nprot.2016.086.  Primers RPI4, RPI5, RPI6 and RPI7 were used to barcode cDNAs from eGFPdsRNA_rep1 (Non-targeting control, replicate 1), eGFPdsRNA_rep2(Non-targeting control, replicate 2), SSRP1kda1 (SSRP1 dsRNA mediated knockdown, replicate 1), and SSRP1kda2 (SSRP1 dsRNA mediated knockdown, replicate 2) respectively.
ChIP-nexus libraries: DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products.

value: H3K36me3 (Abcam, Cat# ab9050)


title: DU145_PTM3 (D2-5-3)

city: Shanghai

first: Lin

last: Liu

state: Shanghai

address: Shanghai

department: Renji‐Med X Clinical Stem Cell Research Center, Ren Ji Hospital

institute: Shanghai Jiao Tong University

description: DU145 cultured with 2.5 uM pentamidine in 6-well plates (1000000 cells/well) at 37°C for 48 hours

data_processing:
Illumina Novaseq 6000 PE150 used for sequencing
Paired-end clean reads were aligned to the reference genome using HISAT2 (v2.1.0).
Differential expression analysis of two groups was performed using the DESeq R package (1.18.1).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Genes with |log2(FoldChange)| > 1 and adjusted Pvalue <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: All.ReadsCount.txt and All.FPKM.exp.txt includes ReadsCount and FPKM values for each Sample; DU145_PTMVSDU145_CON.All.txt includes FPKM  values and statistical analysis data for pentamidine- and vehicle-treated DU145 cells; PC3_PTMVSPC3_CON.All.txt includes FPKM  values and statistical analysis data for pentamidine- and vehicle-treated PC3 cells.

source_name: prostate cancer cell line

growth_protocol: Cells were cultured with vehicle or 2.5 uM pentamidine in 6-well plates (1000000 cells/well) at 37°C for 48 hours

extract_protocol:
Total RNA was extracted from PC3 and DU145 cells treated with 2.5 uM pentamidine or vehicle using the TRIzol reagent (Invitrogen, 15596018) and mRNA was enriched by Oligo(dT) beads.
The enriched mRNA was fragmented into short fragments using the fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA fragments were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then these cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were then size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq 6000 PE150.

treatment_protocol: Cell culture medium containing 2.5 uM pentamidine or vehicle

value: wild type


title: Hand2asF/+_rep2 E11.5

extract_protocol:
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: heart


title: DU145_PTM2 (D2-5-2)


title: eRpL22-like ribosome replicate 3


title: eRpL22-like ribosome replicate 2


title: SSRP1dsRNA_a_H3K36me3_input_Rep1


title: eRpL22-like ribosome replicate 1


title: eGFPdsRNA_H3K36me3_input_Rep2


title: SSRP1dsRNA_a_H3K36me3_input_Rep2


title: eRpL22 ribosome replicate 4

source_name: eRpL22 pulldown from ribosome profile from testis extract


title: WI38_RASOIS_144H_siRNA_CTRL_REP2


title: WI38_RASOIS_144H_siRNA_CTRL_REP6


title: DU145_PTM1 (D2-5-1)


title: WI38_RASOIS_144H_siRNA_CTRL_REP4


title: DU145_CON3 (D0-3)

description: DU145 cultured with vehicle in 6-well plates (1000000 cells/well) at 37°C for 48 hours


title: WI38_RASOIS_72H_siRNA_RELA_2_REP1

source_name: WI38, RASOIS, 72H, siRNA RELA

value: siRNA RELA


title: DU145_CON2 (D0-2)


title: eRpL22 ribosome replicate 3


title: WI38_RASOIS_72H_siRNA_RELA_1_REP2


title: WI38_RASOIS_144H_siRNA_CTRL_REP1


title: WI38_RASOIS_72H_siRNA_JUN_1_REP2

source_name: WI38, RASOIS, 72H, siRNA JUN

value: siRNA JUN


title: WI38_RASOIS_72H_siRNA_RELA_1_REP1


title: WI38_RASOIS_72H_siRNA_RELA_2_REP2


title: Spt16dsRNA_b_H2Av_ip_Rep1

value: H2Av (Gift from R. Glaser)


title: WI38_RASOIS_72H_siRNA_JUN_1_REP1


title: eRpL22 ribosome replicate 1


title: eRpL22 ribosome replicate 2


title: PC3_PTM3 (P2-5-3)

description: PC3 cultured with 2.5 uM pentamidine in 6-well plates (1000000 cells/well) at 37°C for 48 hours


title: PC3_PTM2 (P2-5-2)


title: Spt16dsRNA_a_H2Av_ip_Rep1


title: eGFPdsRNA_H3K36me3_input_Rep1

value: eGFPdsRNA


title: PC3_PTM1 (P2-5-1)


title: Spt16dsRNA_b_H2Av_ip_Rep2


title: DU145_CON1 (D0-1)


title: PC3_CON3 (P0-3)

description: PC3 cultured with vehicle in 6-well plates (1000000 cells/well) at 37°C for 48 hours


title: SSRP1dsRNA_b_H2Av_ip_Rep2


title: SSRP1dsRNA_a_H2Av_ip_Rep2


title: PC3_CON1 (P0-1)


title: PC3_CON2 (P0-2)


title: SSRP1dsRNA_b_H2Av_ip_Rep1


title: Spt16dsRNA_a_H2Av_ip_Rep2


title: SSRP1dsRNA_a_H2Av_ip_Rep1


title: WI38_RASOIS_72H_siRNA_CTRL_REP2

source_name: WI38, RASOIS, 72H, siRNA Ctrl


title: WI38_RASOIS_T0_siRNA_RELA_2_REP2

source_name: WI38, RASOIS, T0, siRNA RELA


title: eGFPdsRNA_H2Av_ip_Rep2


title: Heart_8 week-old_rep1

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

description: Mouse heart, 8 week-old

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48°C on Affemetrix miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing:
Affymetrix GeneChip Command Console software (version 4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in P were chosen for further data analysis.
Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

label: Biotin

source_name: Mouse heart, 8 week-old

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: Heart tissues were collected and frozen immediately in liquid nitrogen.

extract_protocol: Trizol extraction of total RNA was performed using mirVanaTM RNA Isolation Kit according to the manufacturer's instructions.

value: Heart

tag: gender

value: male

value: 8 wk


title: eGFPdsRNA_H2Av_ip_Rep1


title: Heart_8 week-old_rep4

description: Mouse heart, 8 week-old


title: Heart_8 week-old_rep3

description: Mouse heart, 8 week-old


title: WI38_RASOIS_T0_siRNA_RELA_1_REP1


title: Heart_8 week-old_rep2

description: Mouse heart, 8 week-old


title: Heart_8 week-old_rep5

description: Mouse heart, 8 week-old


title: Spt16dsRNA_b_H2Av_input_Rep2

value: Spt16 dsRNA


title: WI38_RASOIS_T0_siRNA_RELA_2_REP1


title: WI38_RASOIS_72H_siRNA_CTRL_REP1

value: siRNA Control


title: Spt16dsRNA_b_H2Av_input_Rep1


title: WI38_RASOIS_T0_siRNA_RELA_1_REP2

value: WI38 fibroblasts


title: Heart_15 month-old_rep5

description: Mouse heart, 15 month-old

source_name: Mouse heart, 15 month-old


title: Heart_15 month-old_rep4

description: Mouse heart, 15 month-old


title: WI38_RASOIS_T0_siRNA_JUN_1_REP1

source_name: WI38, RASOIS, T0, siRNA JUN


title: Heart_15 month-old_rep2

description: Mouse heart, 15 month-old


title: Spt16dsRNA_a_H2Av_input_Rep1


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri30_Rep2

data_processing:
Library strategy: ChIP-nexus
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
RNA-seq reads were aligned to UCSC genome dm6 with STAR version 2.5.2b, with default settings, using Ensembl 84 gene models.
ChIPseq reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. Reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM).
For PROseq, adapter 5′-TGGAATTCTCGGGTGCCAAGG-3′ was removed. Reads were trimmed up to 36 bp. Reads with length less than 15 bp after trimming were removed. After reverse-complement, reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. The last basepair of the reads were used to generate bigWig files and downstream analysis.
Genome_build: dm6, Ensembl 84
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

value: SSRP1 dsRNA

value: Rpb3 (Gift from Zeitlinger Lab)


title: Heart_15 month-old_rep3

description: Mouse heart, 15 month-old


title: Heart_15 month-old_rep1

description: Mouse heart, 15 month-old


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri20_Rep2


title: SSRP1dsRNA_b_H2Av_input_Rep2


title: WI38_RASOIS_T0_siRNA_ETS1_2_REP1

source_name: WI38, RASOIS, T0, siRNA ETS1

value: RAS induced senescence

value: siRNA EST1


title: WI38_RASOIS_T0_siRNA_JUN_1_REP2


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri10_Rep2


title: WI38_RASOIS_T0_siRNA_ETS1_2_REP2


title: SSRP1dsRNA_a_H2Av_input_Rep2


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri5_Rep2


title: WI38_RASOIS_T0_siRNA_ETS1_1_REP2


title: SSRP1dsRNA_a_Rpb3_ChNex_DMSO_Rep2


title: SSRP1dsRNA_a_H2Av_input_Rep1


title: eGFPdsRNA_Rpb3_ChNex_Tri30_Rep2


title: WI38_RASOIS_T0_siRNA_ETS1_1_REP1


title: Spt16dsRNA_a_H2Av_input_Rep2


title: WI38_RASOIS_T0_siRNA_CTRL_REP3

source_name: WI38, RASOIS, T0, siRNA Ctrl


title: eGFPdsRNA_H2Av_input_Rep2


title: eGFPdsRNA_H2Av_input_Rep1


title: WI38_RASOIS_T0_siRNA_CTRL_REP4


title: WI38_RASOIS_T0_siRNA_CTRL_REP1


title: eGFPdsRNA_Rpb3_ChNex_Tri10_Rep2


title: WI38_RASOIS_T0_siRNA_CTRL_REP2


title: 17-043_SVZ

source_name: Extracted RNA from SVZ homogenate dissociated from the adult human brain, library 7


title: WI38_RASOIS_REP2_144H

hyb_protocol: Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on the Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

data_processing:
Raw Affymetrix HTA 2.0 array intensity data were analyzed using open-source Bioconductor packages on R. The quiescence and the RAS OIS time series data were normalized all together (2 conditions, 2 biological replicates per condition, 6 time points per replicates) using the robust multi-array average normalization approach implemented in the oligo package (Carvalho and Irizarry, 2010). Internal control probe sets were removed and average expression deciles over time-points were then defined independently for each treatment. Probes whose average expression was lower than the 4th expression decile in both conditions were removed for subsequent analyses.
To remove sources of unwanted variation and consider batch effects, data were finally corrected with the sva package. Principal component analysis and bi-clustering based on Pearson’s correlation and Ward’s aggregation criterion were used to check for consistency between biological replicates and experimental conditions at each step of the pre-processing.

source_name: WI38, RAS OIS, 144h

growth_protocol: WI-38 transduced expressing a 4OHT-inducible ER:RAS fusion protein were cultured in DMEM with 4.5g/L glucose and 10% FBS at 37˚C in the presence of 5% CO2 and 3% O2.

extract_protocol: RNA was extracted using the QIAGEN Rneasy Plus kit according to the manufacturer's instructions.

treatment_protocol: Oncogene-induced senescence was initiated by addition of 400 nM 4OHT to WI-38 fibroblast expressing ER:RASv12 fusion protein, and 500,000 cells were collected at the indicated time points. For the quiescence time-series, WI38 fibroblasts were incubated in DMEM 4.5g/l glucose and 0.2% FBS, and 500,000 cells were collected at the indicated time points.

tag: time point


title: SSRP1dsRNA_b_H2Av_input_Rep1


title: eGFPdsRNA_Rpb3_ChNex_Tri5_Rep2


title: 16-137_SVZ

source_name: Extracted RNA from SVZ homogenate dissociated from the adult human brain, library 6


title: WI38_RASOIS_REP2_96H

source_name: WI38, RAS OIS, 96h


title: eGFPdsRNA_Rpb3_ChNex_DMSO_Rep2


title: MSP_4HR_REP_2

city: Pullman

first: Brett

last: Vanderwerff

state: WA

address: PO Box 647620, Washington State University

institute: Washington State University

data_processing:
Reads were aligned to the human genome with STAR
The gene count matrix was generated from mapping reads with the featureCounts command of the Subread package
Genome_build: Ensembl human genome release 94
Supplementary_files_format_and_content: comma separated value file

growth_protocol: BxPC-3 cells were cultured in a “complete medium” preparation made from RPMI  supplemented with 10% fetal bovine serum (FBS), 100 U/ml Penicillin-Streptomycin, and 5 µg/ml Plasmocin. Cells were maintained in a 37°C 5% CO2 incubator

extract_protocol: Libraries were prepped with a KAPA mRNA HyperPrep Kit.

treatment_protocol: BxPC-3 cells were treated with vehicle control (PBS), HGF (80 ng/ml), or MSP (100 ng/ml) in triplicate. Total RNA was collected at 1 and 4 hours post-treatment.

value: BxPC-3 pancreatic cancer cells

value: MSP 4HR


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri20_Rep1


title: MSP_4HR_REP_1


title: MSP_4HR_REP_3


title: eGFPdsRNA_Rpb3_ChNex_Tri20_Rep2


title: HGF_4HR_REP_3

value: HGF 4HR


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri5_Rep1


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri10_Rep1


title: HGF_4HR_REP_2


title: HGF_4HR_REP_1


title: SSRP1dsRNA_a_Rpb3_ChNex_DMSO_Rep1


title: WI38_RASOIS_REP2_48H

source_name: WI38, RAS OIS, 48h


title: WI38_RASOIS_REP2_24H

source_name: WI38, RAS OIS, 24h


title: SSRP1dsRNA_a_Rpb3_ChNex_Tri30_Rep1

source_name: S2 cells


title: CONTROL_4HR_REP_3

value: CONTROL 4HR


title: eGFPdsRNA_Rpb3_ChNex_Tri20_Rep1


title: eGFPdsRNA_Rpb3_ChNex_Tri30_Rep1


title: CONTROL_4HR_REP_2


title: WI38_RASOIS_REP1_144H


title: WI38_RASOIS_REP1_96H


title: eGFPdsRNA_Rpb3_ChNex_Tri10_Rep1


title: CONTROL_4HR_REP_1


title: WI38_RASOIS_REP2_72H

source_name: WI38, RAS OIS, 72h


title: MSP_1HR_REP_3

value: MSP 1HR


title: eGFPdsRNA_Rpb3_ChNex_Tri5_Rep1


title: WI38_RASOIS_REP1_72H


title: eGFPdsRNA_Rpb3_ChNex_DMSO_Rep1


title: WI38_RASOIS_REP1_48H


title: SSRP1dsRNA_a_PROseq_Rep2

data_processing:
Library strategy: PRO-seq
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
RNA-seq reads were aligned to UCSC genome dm6 with STAR version 2.5.2b, with default settings, using Ensembl 84 gene models.
ChIPseq reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. Reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM).
For PROseq, adapter 5′-TGGAATTCTCGGGTGCCAAGG-3′ was removed. Reads were trimmed up to 36 bp. Reads with length less than 15 bp after trimming were removed. After reverse-complement, reads were aligned to UCSC genome dm6 with Bowtie2 version 2.2.9 with default settings. The last basepair of the reads were used to generate bigWig files and downstream analysis.
Genome_build: dm6, Ensembl 84
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

molecule: nuclear RNA


title: MSP_1HR_REP_1


title: MSP_1HR_REP_2


title: WI38_RASOIS_REP1_24H


title: WI38_QUIESCENCE_REP2_96H

source_name: WI38, quiescence, 96h

value: quiescence


title: WI38_RASOIS_REP1_T0

source_name: WI38, RAS OIS, T0


title: WI38_QUIESCENCE_REP2_72H

source_name: WI38, quiescence,72h


title: WI38_QUIESCENCE_REP2_24H

source_name: WI38, quiescence, 24h


title: HGF_1HR_REP_3

value: HGF 1HR


title: WI38_RASOIS_REP2_T0


title: HGF_1HR_REP_2


title: HGF_1HR_REP_1


title: eGFPdsRNA_PROseq_Rep1

value: eGFPdsRNA


title: CONTROL_1HR_REP_3

value: CONTROL 1HR


title: CONTROL_1HR_REP_2


title: CK-drought rep2 (CKM_D2)

first: Yan

last: Long

state: China

address: Zhongguancun South street No.12

institute: Chinese Academy of Agricultural Sciences

description: CKMD

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 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
After the raw data was generated and the data-processing steps were completed, the clean reads were mapped to the assembly transcriptome reference sequences (Long Y, Wang Y, Wu S, Wang J, Tian X, Pei X (2015) De Novo Assembly of Transcriptome Sequencing in Caragana korshinskii Kom. and Characterization of EST-SSR Markers. PLoS ONE 10(1): e0115805. doi:10.1371/journal.pone.0115805) using RSEM software
Gene expression levels were calculated based on the numbers of reads mapped to the reference sequence, using the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method
Genome_build: assembly transcriptome reference sequences described by Long et al., 2015
Supplementary_files_format_and_content: tab-delimited text file includes the average values from the two biological replicates

organism: Caragana korshinskii

source_name: seedling

growth_protocol: The seeds were first sown on damp filter paper and incubated at 4oC for four days before being placed at 23oC under long-day (16 h light/8 h dark) conditions. After the seedlings had reached the two-leaf stage, they were transferred to pots containing soil.

extract_protocol:
Total RNA from three different tissues, including leaves, stems, and roots, was extracted from the two biological replicates of the drought-treated and control plants with TRIzol Reagent (Invitrogen, 15596-026) according to the manufacturer’s instructions.
Each DGE library was constructed by pooling RNA from four plants. We used 3 μg of total RNA per sample as input material for RNA library preparation. The DGE sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kits for Illumina (NEB, USA). Following the instructions provided by Illumina, mRNA was purified from the pooled, total RNA using oligo dT magnetic beads (Novogene, China). Fragmentation buffer was added to reduce the mRNA molecules to short fragments. Reverse transcriptase and random primers were used to synthesize the first-strand cDNA from the mRNA fragments. Second-strand cDNA was synthesised using buffer, dNTPs, RNase H, and DNA polymerase I. The double-stranded cDNA was purified using QIAquick PCR extraction kits (QIAGEN, Hilden, Germany) and washed with EB buffer for end repair and addition of a terminal A (adenine) nucleotide. Illumina sequencing adapters were then ligated onto the cDNA fragments. The cDNA fragments containing terminal adapters were purified by AMPure XP beads and enriched by PCR to construct the library for RNA sequencing.

treatment_protocol: The seedlings were then grown in four pots (20 seedlings/pot) representing of the two treatments (drought and control). After the seedlings had grown for one month, one set of seedlings were subjected to drought stress, and the second set of seedlings was used as the control and were grown under normal water irrigation and light conditions. The treatment pots were not watered until the symptoms of wilting appeared. Wilting appeared after the plants had been without water for one week, so we choose this one week time point in which to find genes that respond to drought stress.

value: One month old

value: seedling

tag: stress

value: drought


title: CK-drought rep1 (CKM_D1)

description: CKMD


title: eGFPdsRNA_PROseq_Rep2

first: Joan

last: Conaway

institute: Stowers Institute for Medical Research


title: SSRP1dsRNA_a_PROseq_Rep1


title: CONTROL_1HR_REP_1


title: CK control rep2 (CKM_C2)

description: CKMC

value: control


title: WI38_QUIESCENCE_REP2_12H

source_name: WI38, quiescence, 12h


title: WI38_QUIESCENCE_REP2_T0

source_name: WI38, quiescence, T0


title: CK control rep1 (CKM_C1)

description: CKMC


title: KQ10-8d

status: Public on Jun 13 2019

city: Guangzhou

first: fanwei

last: dai

state: Guangdong

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mulberry transcriptome (NCBI accession no. SRP026705)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Mulberry transcriptome (NCBI accession no. SRP026705)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Morus alba var. atropurpurea

source_name: Root

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

treatment_protocol: Inoculation with  Ralstonia solanacearum

tag: resistance type

value: Resistance cultivar


title: WI38_QUIESCENCE_REP1_96H

tag: treatment


title: KQ10-3d

department: The Sericulture and Agri-Food Research Institute

institute: Guangdong Academy of Agricultural Sciences


title: WI38_QUIESCENCE_REP2_48H

source_name: WI38, quiescence, 48h


title: WI38_QUIESCENCE_REP1_48H


title: YSD10-8d

value: Susceptible cultivar


title: YSD10-3d


title: YS283-0d

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mulberry transcriptome (NCBI accession no. SRP026705)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Mulberry transcriptome (NCBI accession no. SRP026705)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

tag: cultivar


title: KQ10-1d


title: WI38_QUIESCENCE_REP1_12H


title: YSD10-1d


title: KQ10-0d


title: YSD10-0d


title: WI38_QUIESCENCE_REP1_24H


title: WI38_QUIESCENCE_REP1_72H


title: WI38_QUIESCENCE_REP1_T0


title: YS283-1d


title: IGR37_t12_R3 (3 phenotypically distinct states dataset)

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Two technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Raw fastq files were then trimmed of poly-A using  cutadapt {Martin, 2011 }
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC as well as mouse-Mitf
Counts per gene from STAR were used as input for differential gene expression analysis using EdgeR {Robinson, 2010 }.
Reads for each sample set were first filtered for genes whose expression is  count-per-million prior to glmQLFTest.
Genome_build: hg38
Supplementary_files_format_and_content: csv table of differential gene expression of treated vs control and the associated statistically analysis

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in DMEM (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

treatment_protocol: Cells were treated at 1% O2 level in hypoxia chamber for the indicated time

value: melanoma

value: 12h Hypoxia


title: IGR39_t12_R2 (3 phenotypically distinct states dataset)


title: IGR37_t24_R3 (3 phenotypically distinct states dataset)

value: 24h Hypoxia


title: IGR37_t12_R2 (3 phenotypically distinct states dataset)


title: IGR39_t24_R2 (3 phenotypically distinct states dataset)


title: IGR39_t12_R3 (3 phenotypically distinct states dataset)


title: IGR37_t24_R1 (3 phenotypically distinct states dataset)

description:
24h_Hypoxia
edgeR_IGR37_DMEM_1%O2_24h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv


title: IGR39_t24_R1 (3 phenotypically distinct states dataset)

description:
24h_Hypoxia
edgeR_IGR39_DMEM_1%O2_24h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv


title: IGR37_t24_R2 (3 phenotypically distinct states dataset)


title: IGR39_t0_R1 (3 phenotypically distinct states dataset)

description: Normoxia

value: Normoxia


title: IGR37_t48_R2 (3 phenotypically distinct states dataset)

value: 48h Hypoxia


title: IGR39_t48_R2 (3 phenotypically distinct states dataset)


title: IGR39_t24_R3 (3 phenotypically distinct states dataset)


title: IGR39_t48_R1 (3 phenotypically distinct states dataset)

description:
48h_Hypoxia
edgeR_IGR39_DMEM_1%O2_48h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv


title: IGR39_t48_R3 (3 phenotypically distinct states dataset)


title: IGR37_t48_R3 (3 phenotypically distinct states dataset)


title: IGR39_t0_R3 (3 phenotypically distinct states dataset)

description: Normoxia


title: IGR39_t12_R1 (3 phenotypically distinct states dataset)

description:
12h_Hypoxia
edgeR_IGR39_DMEM_1%O2_12h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv


title: IGR37_t12_R1 (3 phenotypically distinct states dataset)

description:
12h_Hypoxia
edgeR_IGR37_DMEM_1%O2_12h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv


title: 501_t48_R2 (3 phenotypically distinct states dataset)


title: IGR37_t0_R1 (3 phenotypically distinct states dataset)

description: Normoxia


title: 501_t24_R3 (3 phenotypically distinct states dataset)


title: IGR37_t0_R3 (3 phenotypically distinct states dataset)

description: Normoxia


title: 501_t48_R1 (3 phenotypically distinct states dataset)

description:
48h_Hypoxia
edgeR_501mel_DMEM_1%O2_48h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv


title: 501_t24_R2 (3 phenotypically distinct states dataset)


title: IGR39_t0_R2 (3 phenotypically distinct states dataset)

description: Normoxia


title: 501_t48_R3 (3 phenotypically distinct states dataset)


title: IGR37_t0_R2 (3 phenotypically distinct states dataset)

description: Normoxia


title: IGR37_t48_R1 (3 phenotypically distinct states dataset)

description:
48h_Hypoxia
edgeR_IGR37_DMEM_1%O2_48h_relative_to_0h_QLF-test_filtered_1cpm_3rep


title: 501_t12_R3 (3 phenotypically distinct states dataset)


title: 501_t12_R1 (3 phenotypically distinct states dataset)

description:
12h_Hypoxia
edgeR_501mel_DMEM_1%O2_12h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv


title: 501_t12_R2 (3 phenotypically distinct states dataset)


title: 501_t0_R3 (3 phenotypically distinct states dataset)

description: Normoxia


title: 501_t0_R1 (3 phenotypically distinct states dataset)

description: Normoxia


title: sample4_B1_i12F

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

institute: Leiden University Medical Center

data_processing:
For all samples Cell Ranger Single Cell Software Suite 2.1.1 was used to perform sample demultiplexing, barcode processing, read aligning and single cell 3’ gene counting using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: Compressed sparse column format for storing expression counts.

source_name: Adult Ovary Tissue

extract_protocol:
Tissue was cut in small pieces and treated overnight in 1mg/ml colII in 0.25% Trypsin/EDTA at 4C. Next day, it was incubated 1h at 37C in DMEM/F12 with DNAseI (27 IU/ml), filtered through a 100um strainer and single cells were cryopreserved. Before library preparation, cells were thawed, ressuspended in 1% BSA/DPBS and FACS-sorted for live cells (7AAD-negative cells).
Sequencing libraries were prepared according to the user guide of the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2, Product Code 120237.

tag: patient id

tag: batch

value: stroma


title: sample5_B2_i10E

tag: tissue


title: sample6a_B1_i12H


title: sampleC1_B1_i12E

value: Follicle 2-5mm


title: sample8b_B2_i10B


title: sample7_B2_i10C

value: Follicle 1-2mm


title: sample8a_B2_i10A


title: sample2_B1_i12B


title: sample13_B1_i12C


title: sample12_B2_i10G


title: sample11_B2_i10F


title: sample10_B2_i10D


title: sample1_B1_i12A


title: sample145_B1_i12D


title: TFIISmut_rep1 RNA-seq

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

description: mRNA-Seq

data_processing:
Sequenced reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 86 transcript annotations.
Reads were aligned against GRCh38 and Ensembl release 86 transcript annotations using STAR v2.5.2a via the transcript quantification software RSEM v1.2.31.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

source_name: HEK293 T-Rex TFIISmut plus Dox

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS (Gibco, 16000-044), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 15 μg/ml blasticidin.  Additionally, 80 ng/mL doxycycline was used to induce TFIISmut overexpression  where applicable.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, 74104) according to the manufacture’s instruction including the on-column DNase treatment. 2μg total RNA was used for oligo(dT) purification.
TruSeq HT kit (Illumina)

value: TFIIS mut over-expression

value: HEK293  T-Rex Flag-TFIISmut

value: plus 80ng/ml doxycycline


title: TFIISmut_rep2 RNA-seq

description: mRNA-Seq


title: Parental_rep2 RNA-seq

description: mRNA-Seq

source_name: HEK293 T-Rex  minus Dox

value: WT


title: Parental_rep1 RNA-seq

description: mRNA-Seq


title: TFIISmut_rep2 ChIP-seq

description: RNAPII (4H8) ChIP-Seq

data_processing:
Reads were Illumina adapter trimmed using cutadapt 2.7.12 (-e 0.1 –a AGATCGGAAGAGC –q 20,20) to a minimum length of 30bp.
Trimmed reads were aligned to the GRCh38 genome assembly using BWA-mem 0.12.7 (Li et al., 2009) with default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS (Gibco, 16000-044), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 15 μg/ml blasticidin.  Additionally, 80 ng/mL doxycycline was used to induce TFIISmut overexpression where applicable.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were harvested by trypsin treatment and fixed in suspension with formaldehyde, 1% final concentration for 10 min at RT

tag: crispr status

tag: antibody

value: RNAPII (4H8)


title: Parental_rep3 RNA-seq

description: mRNA-Seq

tag: genotype/variation


title: Parental_rep2 ChIP-seq

description: RNAPII (4H8) ChIP-Seq


title: 501_t0_R2 (3 phenotypically distinct states dataset)

description: Normoxia


title: TFIISmut_rep3 RNA-seq

description: mRNA-Seq


title: ZEB1+/- +LV_3

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

description:
ZEB1+/- +LV_3
ZEB1+-LV_03
processed data file: All_Processed_Data.txt

data_processing:
Raw reads in FASTQ files were aligned to the human hg38 genome build and transcript (Ensembl 92) quantities calculated using the kallisto (v0.44.0) per instructions.
Differential gene expression analysis was performed using the Sleuth (v0.30.0) R package. Differential expression was tested using a negative binomial test, and corrected for multiple testing using the Benjamini-Hochberg correction.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: All_Processed_Data.txt: The processed data file is a tab-delimited text file with Ensembl 92 gene symbol ID in the first column. Sample names are given on the first row with TPM values for each gene running down the column.

source_name: corneal endothelium

growth_protocol: Cells were cultured on laminin coated tissue culture treated plastic in F99 growth medium at 37C in a humidified chamber with 5% CO2.

extract_protocol:
TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit using an automated liquid handler (Janus G3 – PerkinElmer) according to manufacturer’s instruction at the UCLA Institute for Quantitative and Computational Biology.

tag: parental line

tag: transgene


title: ZEB1+/- +LV_2

description:
ZEB1+/- +LV_2
ZEB1+-LV_02
processed data file: All_Processed_Data.txt


title: ZEB1+/- +LV_1

description:
ZEB1+/- +LV_1
ZEB1+-LV_01
processed data file: All_Processed_Data.txt


title: ZEB1+/- -LV_3

description:
ZEB1+/- -LV_3
ZEB1+-_03
processed data file: All_Processed_Data.txt


title: ZEB1+/- -LV_2

description:
ZEB1+/- -LV_2
ZEB1+-_02
processed data file: All_Processed_Data.txt


title: sample3_B1_i12G


title: ZEB1+/- -LV_1

description:
ZEB1+/- -LV_1
ZEB1+-_01
processed data file: All_Processed_Data.txt


title: ZEB1+/+ -LV_3

description:
ZEB1+/+ -LV_3
ZEB1++_03
processed data file: All_Processed_Data.txt


title: ZEB1+/+ +LV_1

description:
ZEB1+/+ +LV_1
ZEB1++LV_01
processed data file: All_Processed_Data.txt


title: ZEB1+/+ -LV_2

description:
ZEB1+/+ -LV_2
ZEB1++_02
processed data file: All_Processed_Data.txt