title: ATACseq-Patski-Inv-Dxz4

description: ATAC-seq experiment in CRISPR/cas9-modified Patski cells.

data_processing:
ATAC-seq paired-end reads were mapped to the BL6 genome using the NCBI build v38/mm10 reference genome assembly obtained from the UCSC Genome Browser46 using BWA-MEM (v0.7.3) in paired-end mode using default parameters.
Primary mapped valid paired reads with MAPQ>=10 were de-duplicated and used for calling ATAC peaks based on biallelic reads using MACS2. ATAC peaks were called using all reads (unsegregated).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed, xls

extract_protocol: ATAC-seq was done on WT, Del-hinge, Inv-Dxz4 and 2-4-clone Patski cells using a published method.

value: Fibroblasts derived from hybrid embryonic kidney


title: RNAseq.patski.WT

status: Public on Nov 28 2017

type: SRA

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

country: USA

institute: University of Washington

description:
RNA-seq experiment in wild-type Patski cells.
RNAseq.patski.WT.H57VKBGXY.rep1.ACAGTG
Processed data file: RNAseq.geneCounts.tsv.gz

library_source: transcriptomic

data_processing:
RNA-seq single-end reads were mapped to the UCSC mm10 (NCBI build v38) refSeq transcriptome as downloaded and packaged in the iGenomes reference sequences and annotation files on July 17, 2015 (https://support.illumina.com/sequencing/sequencing_software/igenome.html). Tophat2 (v 2.0.12) (calling bowtie2 (v2.2.3)) was used to perform single-end mapping allowing 6 mismatches but otherwise default parameters.
To determine biallelic expression levels, mapped reads were assigned to refSeq genes using HT-seq and counts were converted into TPMs using custom R scripts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNAseq.geneCounts.tsv: Tab-delimited text file includes gene expression measured by read counts per gene.

molecule: total RNA

organism: Mus musculus x Mus spretus

source_name: Patski cells

extract_protocol:
RNA were extracted from Patski cells by the Qiagen RNeasy kit with on-column DNaseI digestion.
RNA-seq indexed libraries were prepared using Illumina TruSeq RNA sample preparation kit with standard Illumina protocols.

tag: cell line

value: Patski

tag: cell type

tag: strain/background

tag: genotype/variation

value: wild-type


title: RNAseq.patski.WT.0u5aza.rep1

description:
RNA-seq experiment in wild-type Patski cells with mock treatment.
RNAseq.patski.WT.0u5aza.rep1.HF5TFBGXY.ACAGTG
Processed data file: RNAseq.geneCounts.tsv.gz


title: ATACseq-Patski-2-4clone

description: ATAC-seq experiment in wild-type Patski clone.

library_source: genomic

molecule: genomic DNA


title: Input-DNA-Patski-WT

description: CTCF ChIP-seq experiment in wild-type Patski cells.

data_processing:
CTCF and input ChIP-seq paired-end reads were mapped to the BL6 genome using the NCBI build v38/mm10 reference genome assembly obtained from the UCSC Genome Browser46 using BWA-MEM (v0.7.3) in paired-end mode using default parameters.
Primary mapped valid paired reads with MAPQ>=10 were de-duplicated and used for calling CTCF peaks based on biallelic reads using MACS2. CTCF peaks were called using all reads (unsegregated) after normalization to their chromatin inputs.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed, xls

extract_protocol:
ChIP was performed using fixed chromatin from cell lines. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit.
Sequencing libraries were prepared from each CTCF ChIP sample from Patski cells using the Illumina seq sample prep kit. Size selection of the library was done by gel excision and purification of DNA in the 300-600bp range. Control sequencing library was prepared from genomic DNA.

value: Patski cells

tag: chip antibody


title: Input-DNA-Patski-Del-hinge

description: CTCF ChIP-seq experiment in CRISPR/cas9-modified Patski cells.

value: Del-hinge


title: ATACseq-Patski-Del-hinge


title: ATACseq-Patski-WT

description: ATAC-seq experiment in wild-type Patski cells.


title: Ribosome Profiling Ctrl Day 5

city: Portsmouth

first: Samuel

last: Robson

address: St Michael's Building

department: School of Pharmacy & Biomedical Science

country: United Kingdom

institute: University of Portsmouth

description: Total RNA (ribodepleted)

data_processing:
Library strategy: Riboprofiling
ChIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using bwa with parameters '-n 3 -k 2 -R 300 -t 4'. Multiple reads mapping to a single genomic locus were treated as PCR duplicates, and were removed using samtools rmdup. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag XT:A:U in the output bam file from bwa. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Peaks were called against input sample using MACS2 using default parameters. Peaks from all replicates were merged to give a master list of potential binding loci per condition, and read count (normalised by overall read depth of the library) for each replicate was calculated using the GenomicRanges package in R. Peaks were treated as potential binding loci if all replicates showed normalised score greater than 1 and did not overlap a peak called in the IgG.
m6A meRIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks2 and a single transcript database was generated using cuffmerge.
Riboprofiling: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks and a single transcript database was generated using cuffmerge.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files give coverage scores across the whole hg38 genome at each base position for the mapped reads. Normalized (read count normalized to total library read depth) and non-normalized coverage files are provided for each sample.

organism: Homo sapiens

source_name: Whole cell

growth_protocol: MOLM13 cells  were cultured in RPMI1640 (Invitrogen) supplemented with 10% FBS (PAA) and 1% penicillin/streptomycin/glutamine. 5*10^5 MOLM13 cells were infected using PLKO-TETon-Puro lentiviral vectors expressing shRNAs against the coding sequence of human METTL3 or a scramble control.

extract_protocol:
5*10^7 MOLM13 CTRL or METTL3 KD cells at day 5 or day 8 after doxycycline induction were treated with 0.1 mg/ml of cycloheximide for 1 minute and the ribosome protected fragment (RPF) fraction of mRNA or total input control mRNA was isolated using the RNeasy Mini Kit (Quiagen) following the manufacturer instruction. Ribosomal RNA was removed using the Illumina Ribozero Kit.
Single end 50 bp stranded libraries were prepared using the Illumina TRUseq Ribo Profile kit following manufacturer's recommendations. Reads were sequenced using HiSeq 1500 and multiplexed reads were split based on their barcodes using Illumina Basespace.

treatment_protocol: shRNA was induced by 200 ng/ml doxycycline treatment for the indicated times (5 days or 8 days).

value: leukemia cell line MOLM13

tag: truseq barcode

value: ATCACG

value: Scramble shRNA

tag: time

value: Day 5


title: CTCF-ChIPseq-Patski-2-4clone

description:
CTCF ChIP-seq experiment in wild-type Patski clone.
Input sample: Input-DNA-Patski-Del-hinge

value: Anti-CTCF Antibody (Rabbit Polyclonal Antibody; Millipore 07-729)


title: CTCF-ChIPseq-Patski-Del-hinge

description:
CTCF ChIP-seq experiment in CRISPR/cas9-modified Patski cells.
Input sample: Input-DNA-Patski-Del-hinge


title: CTCF-ChIPSeq-Patski-WT

description:
CTCF ChIP-seq experiment in wild-type Patski cells.
Input sample: Input-DNA-Patski-WT


title: insituDNaseHiC-WG-Patski-WT

description: in situ DNase Hi-C experiment in wild-type Patski cells.

data_processing:
Library strategy: DNase Hi-C
For each in situ DNase Hi-C library, we mapped each end of the paired-end reads separately to the BL6 genome using the NCBI build v38/mm10 reference genome assembly obtained from the UCSC Genome Browser and a pseudo-spretus genome using BWA-MEM (v0.7.3) in single-end mode using default parameters. A pseudo-spretus genome was assembled by substituting available SNPs (from Sanger Institute, SNP database 2014/10/27 v4) into the BL6 reference genome.
We retained only primary reads with MAPQ ≥30 for further analysis. Using heterozygous SNPs between the BL6 genome and the pseudo-spretus genome that were validated for our particular Patski cell line, we segregated all high-quality uniquely mapped reads (MAPQ ≥30).
In order to maximize the number of reads assigned to either the BL6 Xi or the spretus Xa, we required that only one end of the read be specifically mapped to one mouse species, while the other end was allowed to be ambiguously mapped. Each end of each read pair was assigned to one of three categories: (1) BL6-SNP reads containing only BL6-specific SNP(s); (2) spretus-SNP reads containing only spretus-specific SNP(s); (3) ambiguous reads that did not contain valid SNPs or that contained valid SNPs from both alleles. We refer to both BL6-SNP reads and spretus-SNP reads as “allele-specific reads”, and reads that do not contain valid SNPs as “allele-uncertain reads”. Reads were paired with their corresponding mates, and those read pairs with at least one end being allele-specific were retained for subsequent allele-specific analysis.
To eliminate the bias due to the PCR duplication step, we removed redundant paired-end reads defined as those pairs where both ends were mapped to identical locations in the same genome assembly. This resulted in a set of valid read pairs representing DNA-DNA interactions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: txt files, containing uniquely mapped and non-redundant read pairs. The files are tab-delimited. The columns are #1 read identifier, #2 strand of the 1st end, #3 mapped chr of the 1st end, #4 mapped coordinate of the 1st end, #5 allele of 1st read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #6 sequence of 1st end, #7 strand of the 2nd end, #8 mapped chr of the 2nd end, #9 mapped coordinate of the 2nd end, #10 allele of 2nd read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #11 sequence of 2nd end.

extract_protocol:
in situ DNase Hi-C: Cells are cross-linked with formaldehyde; chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor; and proximity ligation is carried out inside individual nuclei to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is created by shearing the DNA and selecting the biotin-containing fragments with streptavidin magnetic beads. After linear library amplification, a DNase Hi-C library is generated and can be sequenced to identify whole-genome chromatin contacts.
in situ DNase Hi-C.

tag: experiment

value: in situ DNase Hi-C

tag: library

value: whole-genome

tag: replicate


title: insituDNaseHiC-WG-Patski-Del-hinge

description: in situ DNase Hi-C experiment in CRISPR/cas9-modified Patski cells.


title: insituDNaseHiC-WG-Patski-Inv-Dxz4


title: insituDNaseHiC-WG-Patski-Del-Ds-TR

value: Del-Ds-TR


title: RNA_Hand2_Mutant

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: NTC.xlsx

data_processing:
The FASTQ files were aligned human genome (mm9) using TopHat v2.0.8 for RNAseq
Samtools v0.1.19 was used for File format conversions (bam to sam)
Reads at transcripts were counted using HTSeq (v0.5.4p1) for RNASeq
Normalization (for library size) was done using DESeq
Differential expression analysis was done using DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing normalized read counts

organism: Mus musculus

source_name: Neuron

extract_protocol:
RNA isolation was performed using RNA Mini Kit, Quiagen
RNA libraries were prepared using RNAeasy Mini Kit (Qiagen, Hilden, Germany)

tag: development stage

value: adult (P60)

tag: tissue

value: superior cervical ganglia and stellate ganglia

tag: pool (n)


title: insituDNaseHiC-WG-Patski-Del-Dxz4


title: insituDNaseHiC-WG-Patski-Inv-5'-Ds-TR


title: RT625PCR11_1004J1_p5_S6

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: We analyzed single-cells, which were sorted to 384-wells in total.

data_processing:
BCL files generated by Illumina NextSeq500 were converted to fastq files by bcl2fastq2 (v2.17.1.14) with demultiplexing pool barcodes.
Data for Quartz-Seq2 was processed by Quartz-Seq2 pipeline. Data for Drop-seq was processed by Drop-seq pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each gene for each cell

source_name: J1 ES cells (2i/LIF)

extract_protocol:
We performed two single-cell RNA-seq methods (Drop-seq and Quartz-Seq2). Drop-seq was performed as reported previously [Cell. 2015;161:1202–14]. Moreover, we established Quartz-Seq2 (a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads). We used two sets of RT primer for Quartz-Seq2. The set of v3.1 RT primers has 384 kinds of unique cell barcodes, with a length of 14 nucleotides (OPC purification, FASMAC). The set of v3.2 RT primers has 1,536 kinds of unique cell barcodes, with a length of 15 nucleotides (OPC purification, Sigma). The set of v3.1 RT primers corresponds to one set of the 384-well PCR plate with lysis buffer, the wells of which have unique barcodes. The set of v3.2 RT primers corresponds to four sets of the 384-well PCR plate with lysis buffer. Single cells were isolated in the 384-well PCR plate with 1 µL of lysis buffer (0.1111 µM respective RT primers, 0.12 mM dNTP mix, 0.3% NP-40, 1 unit/µL RNasin plus) containing ERCC spike mix I.
For Quartz-Seq2, cryopreserved 384-well plates with single-cell lysate were centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, we denatured total RNA in each 384 plate at 70ºC for 90 s and hybridized the RT primer to poly-adenylated RNA at 35ºC for 15 s using the C1000/S1000 thermal cycler. The resulting plates were again centrifuged at 10,000 g and 4ºC for 1 min. Next, the plates were placed on the 384 aluminum plate at 0ºC. We peeled away the seal and added 1 µL of RT premix (2x Thermopol buffer, 5 units/µL SuperScript III, 0.55 units/µL RNasin plus) to 1 µL of lysis buffer for each well using a Mantis microfluidic dispensing system (Formulatrix) or a 384 Transfer Plate system (1859-384S, Watson). The above RT solution was used for the RT25 condition. For the RT100 condition, we used the following RT solution: 2x Thermopol buffer, 20 units/µL SuperScript III, and 2.2 units/µL RNasin plus. We sealed the plates again and agitated them at 2,600 rpm and 4ºC for 1 min. The plates were then centrifuged at 10,000 g and 4ºC for 1 min. We then performed reverse transcription at 35ºC for 5 min and 50ºC for 50 min. The reverse transcription was stopped at 70ºC for 15 min. Then, the plates were placed on a prechilled aluminum block, after which we peeled off their seals. Subsequently, we turned the plates upside down on the assembled collector type A or type B (supplemental figure). We mainly used type A. We centrifuged the plates with an assemble collector at 3,010 g and 4ºC for 3 min with swing-bucket rotors. Subsequently, we collected the cDNA solution into a disposable reservoir. Typically, we obtained 650–700 µL of cDNA solution from one 384-well PCR plate. We purified and concentrated the cDNA solution using the DNA Clean & Concentrator™-5 kit (Zymo Research). We used three purification columns for one 384-well PCR plate in the case of the v3.1 RT primer system (384-cell barcode). Purified cDNA was extracted into 20 µL of nuclease-free water from one column purification and transferred into an eight-linked PCR tube (TaKaRa). The PCR tubes were placed on an aluminum PCR stand at 0ºC. We added 25 µL of TdT solution [1x Thermopol buffer, 2.4 mM dATP, 0.0384 units/µL RNase H (Invitrogen), 26.88 units/µL terminal transferase (Roche)] into 20 µL of extracted cDNA using a pipette at 0ºC. The resulting 45 µL of TdT solution was mixed with a pipette at 0ºC or ThermoMixer at 2,000 g and 0ºC for 1 min. Immediately thereafter, the PCR tubes were centrifuged at 10,000 g and 0ºC for 1 min. We used a C1000/S1000 thermal cycler equipped with the 96-Deep Well Reaction Module for the following steps. The PCR tubes were placed on the block of the thermal cycler, which had been prechilled to 0ºC. We then performed a poly-A tailing reaction at 37ºC for 75 s. The solution was inactivated at 65ºC for 10 min. The PCR tubes were placed on an aluminum PCR stand at 0ºC. We then dispensed approximately 11 µL of solution into four wells from 45 µL of TdT solution. We added 46.16 µL of PCR I premix (1.08492x MightyAmp Buffer version 2, 0.06932 µM Tagging primer, 0.05415 units/µL MightyAmp DNA polymerase) to 11 µL of TdT solution for the respective wells of the PCR tube. We performed gentle inversion mixing on the resulting solution in the PCR tube. The tubes were then centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, the solution was mixed with ThermoMixer at 2,000 rpm and 4ºC for 2 min. Then, we spun down the tube again. Next, we denatured the solution at 98ºC for 130 s and hybridized Tagging primer to poly-A-tailed cDNA at 40ºC for 1 min. After that, we performed the “Increment step” by heating to 68ºC at 0.2ºC every second and performed second-strand synthesis at 68ºC for 5 min. The tubes were placed on an aluminum PCR stand at 0ºC. We added 50.232 µL of PCR II premix (0.99697x MightyAmp Buffer version.2, 1.8952 µM gM primer) to 56.16 µL of PCR I solution. We performed gentle inversion mixing on the resulting solution in the PCR tube. The tubes were then centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, the solution was mixed with ThermoMixer at 2,000 rpm and 4ºC for 2 min, after which we spun down the tube again. We then placed it on the block of the thermal cycler at 68ºC. Subsequently, we amplified the cDNA for 11 cycles under the following conditions: 98ºC for 10 s, 65ºC for 15 s, and 68ºC 5 min. We then incubated the tube at 68ºC for an additional 5 min. Finally, we transferred all of the PCR solution, derived from one 384-well PCR plate, to a 50-mL Polypropylene Centrifuge Tube (Watson). Typically, we obtained approximately 1.2 mL of PCR solution per 384-well PCR plate. We added 32 µL of 3 M sodium acetate (pH 5.2) and 6420 µL PB-Buffer (Qiagen) to the PCR solution. The mixture was then purified using a MinElute Spin Column (Qiagen). Purified cDNA was extracted into 40 µL of nuclease-free water. We additionally purified the cDNA with 32 µL of Ampure XP beads. Finally, we obtained 32 µL of purified cDNA. We checked the length distribution of amplified cDNA with an Agilent High Sensitivity DNA Kit (Agilent). The typical average size of the amplified cDNA in Quartz-Seq2 was approximately 1,400 bp.   In the case of the usage of the v3.2 RT primer in Quartz-Seq2, we modified the above steps as follows. After reverse transcription, we collected cDNA solution into a disposable reservoir from four sets of 384-well plates, which corresponded to 1,536 wells. We purified and concentrated the cDNA solution using eight purification columns for four 384-well PCR plates in the case of the v3.2 RT primer system. In the PCR step, we amplified cDNA for nine cycles with the following conditions: 98ºC for 10 s, 65ºC for 15 s, and 68ºC for 5 min. Finally, we transferred all of the PCR solution derived from four 384-well plates to a 50-mL Polypropylene Centrifuge Tube (Watson). Typically, we obtained approximately 3.5 mL of PCR solution per four 384-well PCR plates. We added 88 µL of 3 M sodium acetate (pH 5.2) and 17.6 mL of PB-Buffer (Qiagen) to the PCR solution. The mixture was purified using the MinElute Spin Column (Qiagen). Subsequently, cDNA was again purified using Ampure XP magnetic beads.   For the Quartz-Seq1-like reaction, we performed the following procedure in accordance with our previous study. We added 1 µL of RT premix (2x PCR buffer, 5 units/µL SuperScript III, 0.55 units/µL RNasin plus) to 1 µL of lysis buffer. We then performed reverse transcription at 35ºC for 5 min and 45ºC for 20 min. This reverse transcription was stopped at 70ºC for 15 min. We added 5 µL of ExoIB solution (1.6x Exonuclease I buffer, 3.2x PCR buffer, 16 mM DTT) and 20 µL of TdT solution [1x PCR buffer, 3 mM dATP, 0.0384 units/µL RNase H (Invitrogen), 33.6 units/µL terminal transferase (Roche)] into 20 µL of extracted cDNA using a pipette at 0ºC. The PCR tubes were placed on the block of the thermal cycle

value: J1 ES single-cells

tag: strain

tag: Sex

value: male

tag: the number of single-cell/well contained in each data

tag: method name of single-cell rna-seq

value: Quartz-Seq2 (v3.1, RT6.25)

tag: type of sequence library preparation

value: Ligation

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: RT625PCR11_1004J1_p4_S5

tag: cell type

tag: cell line


title: RNA_Gata3_Mutant

description: NTC.xlsx

tag: genotype/variation


title: RNA_Gata3_Control

description: NTC.xlsx


title: RT625C3PCR10_1002J1_p3_S2


title: RT625C1PCR10_1002J1_p7_S4

value: Quartz-Seq2 (v3.1, RT6.25, column1)


title: HBS1_F2-driven metastatic tumor_dissected SJMMHB048053

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina base calling
BWA mapping
STAR mapping
HTSEQ counting
Genome_build: mm9
Supplementary_files_format_and_content: transcript level raw read count

source_name: peritoneum

growth_protocol: 3D stem cell culture

extract_protocol:
RNeasy Micro Kit (Qiagen).
total stranded RNA protocol

tag: sample type

value: Tissue

tag: condition

value: metastatic tumor


title: CTCF-ChIPSeq-Patski-Inv-Dxz4

value: Patski cells

value: Fibroblasts derived from hybrid embryonic kidney

tag: strain/background

tag: chip antibody


title: HBS1_F2-driven metastatic tumor_dissected SJMMHB048052


title: HBS1_F2-driven primary tumor_dissected SJMMHB048054

description: HBS1_F2-driven primary tumor_dissected

source_name: liver

value: primary tumor


title: Senp6-Mut primary rib chondrocytes rep2

city: Grand Rapids

first: Tao

last: Yang

state: MI

address: 333 Bostwick Ave NE

department: Cancer and Cell Biology

institute: Van Andel Research Institute

data_processing:
Raw Reads(Raw Data): By base calling, the original image data produced by the sequencer is transferred into sequences, which are defined as “raw reads” (or “raw data”) and saved as “.bam” files. As the raw reads may contain low quality reads and/or adaptor sequences, preprocessing is necessary before starting further analysis. Normally, data cleaning (or data filtering) is performed to obtain “clean reads” (or “clean data”) for further analysis.
Data Filtering(Data Cleaning): As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean data). The procedure include following steps: 1. Remove reads when length is less than threshold.2. Trim reads adapter;if length of trimmed reads is less than threshold, than remove it.3. Caculate the average quality of 20 bases from 3'end until the average quality is larger than 9, than trim the bases that have been counted.
Clean Reads(Clean Data): Clean reads are the high quality sequences after data cleaning, on which all following analyses are based. Clean reads are also saved as “.bam” files, which are provided as the original sequencing result. More detail please refer to "http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol".
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: Senp6-Mut primary rib chondrocytes

growth_protocol: Primary mouse rib chondrocyte cultures: Rib cages were dissected from E18.5 mouse embryos. The soft and bony tissues surrounded the cartilaginous parts of the rib were removed as much as possible. Rib cages were incubated in pronase (2 mg/ml in PBS) at 37 °C for 30 min, followed by incubation in collagenase D (3 mg/ml in DMEM without serum) at 37 °C for 30-60 min to further remove soft tissue. Then the cleaned rib cartilage pieces were transferred into 1.5-ml centrifuge tubes and incubated in collagenase D digestion solution (DMEM with 1.5 mg/ml collagenase D and 5% fetal bovine serum [FBS]) overnight at 37 °C. The dissociated chondrocytes were collected and plated in α-MEM medium with 10% FBS.

extract_protocol:
Total RNA was extracted form chondrocytes using TRIzol (Invitrogen), followed by use of a GenElute Mammalian Total RNA kit (Sigma) with on-column DNase digestion,
The mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primed reverse transcription. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads . End reparation is then performed. After the previous step, adaptors are ligated to the ends of these fragments. Next, ligation products were selected by size and purified on TAE-agarose gel. Finally, the fragments are enriched by PCR amplification, then purified by magnetic beads and dissolved in the appropriate amount of Epstein-Barr solution. During the QC step, Agilent 2100 Bioanaylzer are used to qualify and quantify of the sample library. The library products are ready for sequencing via Ion Proton paltform when necessary.RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Dermo1-Cre;Senp6f/f (Mut)

value: primary rib chondrocyte

tag: passages


title: Senp6-Mut primary rib chondrocytes rep1


title: HBS1_F2-driven metastatic tumor_dissected SJMMHB048056


title: HBS1-driven primary tumor_dissected SJMMHB048055

description: HBS1-driven primary tumor_dissected


title: WT primary rib chondrocytes rep1

source_name: WT primary rib chondrocytes

value: Senp6f/f (WT)


title: PNR primary tumor_dissected SJMMHB048048

description: PNR primary tumor_dissected


title: RT625_mES10pgV31_p26_S5

description: We analyzed 384 wells with 10 pg total RNA.

source_name: Purified total RNA from ES cells

value: 10pg total RNA from ES cells

tag: strain


title: HBS1_F2_cultured SJMMHB047560

value: organoids

value: Tumor organoids


title: HBS1_F2_cultured SJMMHB047559


title: RT25PCR9_1002J1_p6_S3

tag: Sex

value: Quartz-Seq2 (v3.1, RT25)


title: RT625C1PCR10_1002J1_p2_S1

value: J1 ES single-cells

tag: the number of single-cell/well contained in each data


title: RT25_mES10pgV31_p29_S8

value: male

tag: method name of single-cell rna-seq


title: RT25_mES10pgV31_p28_S7

tag: type of sequence library preparation


title: HBS1_F2_cultured SJMMHB047555


title: LCS5_cultured SJMMHB047548


title: HBS6_cultured SJMMHB047554


title: LCS5_cultured SJMMHB047547


title: HBS1_F2-driven primary tumor_dissected SJMMHB048051

description: HBS1_F2-driven primary tumor_dissected


title: HOb microRNA

city: Kaohsiung

first: Yi-Jen

last: Chen

address: 100, Shih-Chuan 1st Road

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
Sequencing data was processed with the Illumina software
Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 17 nucleotides
Only reads that mapped perfectly to the human genome five or less times were used for miRNA detection
Genome_build: Human genome from Genome Reference Consortium Human GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for samples 1 and 2; miRNA, raw read counts and normalized values for samples 3 and 4.

source_name: Osteoblasts

growth_protocol: Osteoblasts were grown in human osteoblast growth medium and maintained in 37 °C incubator containing 5% CO2 until confluence.

extract_protocol:
total RNAs from HOb and HObRA cells were extracted by Trizol Reagent according to the manufacturer’s instructions.
RNA library construction was carried out according to the manufacture’s protocol from Illumina, using Agilent's SureSelect Strand Specific RNA Library Preparation Kit for 75SE (Single-End or Paired-End) sequencing on Solexa platform.
Small RNA library construction and deep sequencing was carried out using Illumina sample preparation kit, according to the TruSeq Small RNA Sample Preparation Guide.

tag: tissue

value: Bone

tag: age

tag: gender

value: female

tag: disease

value: normal


title: LCS5_cultured SJMMHB047546


title: HObRA microRNA

value: rheumatoid arthritis


title: HBS1_F2_cultured SJMMHB045449


title: LCS5_cultured SJMMHB047545


title: RT25_mES10pgV31_p24_S3

tag: cell type

tag: cell line

value: Ligation

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: RT25_mES10pgV31_p25_S4


title: WT primary rib chondrocytes rep2

tag: genotype/variation


title: HObRA mRNA

data_processing:
The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit.
Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0
Trimmomatics was implemented to trim or remove the reads according to the quality score
Qualified reads were analyzed using TopHat/Cufflinks for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
CummeRbund was employed to perform statistical analyses of gene expression profiles.
Genome_build: Human genome from Genome Reference Consortium Human GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for samples 1 and 2; miRNA, raw read counts and normalized values for samples 3 and 4.


title: HBS5_cultured SJMMHB045447

tag: sample type

tag: condition


title: RT625_mES10pgV31_p23_S2

tag: strain

value: Quartz-Seq2 (v3.1, RT6.25)


title: HBS5_cultured SJMMHB045448


title: RT625_mES10pgV31_p22_S1

tag: Sex


title: HBS4_cultured SJMMHB045446


title: RT625_mES10pgV31_p27_S6

tag: the number of single-cell/well contained in each data


title: HOb mRNA


title: Strand-specific RNA-seq in siH2A.Z-treated proliferative WI38 hTERT RAF1-ER cells- Replicate #2

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in proliferative cells treated with H2A.Z siRNA was performed paired-end (HMKMGBGXY_siH2AZ_16s005988-1-1_Nicolas_lane116s005988_1_sequence.txt and HMKMGBGXY_siH2AZ_16s005988-1-1_Nicolas_lane116s005988_2_sequence.txt) by Illumina’s NextSeq 500 technology  at EMBL-GeneCore (stranded rRNA-minus RNA-seq) with ~100 millions paired reads per library. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR)  version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (HMKMGBGXY_siH2AZ_16s005988-1-1_Nicolas_lane116s005988_minus_normalized_hg38.bw and HMKMGBGXY_siH2AZ_16s005988-1-1_Nicolas_lane116s005988_plus_normalized_hg38.bw).

data_processing:
Paired-end reads of the strand-specific RNA-Seq (siCtrl or siH2A.Z) data were aligned using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified. For these alignments all parameters were kept as default.
After the alignment, we applied on all aligned datasets several steps using samtools software: we converted aligned file from Sequence Alignments/Map (sam) format into the Binary Alignment/Map (bam) format which stores the same data in a compressed, indexed, binary form and a cutoff was applied to keep only reads with MAPQ > 25. We sorted data by position on the genome, and created an index of each bam file (bai format). We then converted these cleaned files in wiggle files using R via the rtracklayer bioconductor package. On each dataset, we applied for each base position of the genome a normalization factor (100,000,000 / total numbers of aligned reads).
Note that, for the 1st replicates of siCtrl and siH2A.Z samples, although strand-specific RNA-seq  has been performed, we found that the data did not show strand-specificity. We thus only analyzed for this dataset intervals, which do not show evidence of transcription on the 2 strands of DNA, such as the intergenic regions of the convergent gene pairs to analyze START RNA expression.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

growth_protocol: Proliferative  WI38 hTERT RAF1-ER cells

extract_protocol:
Total RNA were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNAse (Epicentre). BGI or EMBL-GeneCore treated the RNA by Ribozero kit to remove ribosomal RNA.
Strand-specific RNA-seq, including the library construction, which is based on UTP incorporation in the second strand cDNA, was performed at BGI (HONG KONG) for the first replicates (lncRNA-seq) and at EMBL-GeneCore (Heidelberg, Germany) for the second replicates (stranded rRNA-minus RNA-seq).

treatment_protocol: Transfection with siRNA during three days.

value: WI38 hTERT RAF1-ER

tag: state

value: proliferative

tag: treatment

value: transfected with siRNA against H2A.Z for 3 days


title: Strand-specific RNA-seq in siCtrl-treated proliferative WI38 hTERT RAF1-ER cells- Replicate #2

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in proliferative cells treated with Control siRNA was performed paired-end (HMKMGBGXY_siCtrl_16s005987-1-1_Nicolas_lane116s005987_1_sequence.txt and HMKMGBGXY_siCtrl_16s005987-1-1_Nicolas_lane116s005987_2_sequence.txt) by Illumina’s NextSeq 500 technology  at EMBL-GeneCore (stranded rRNA-minus RNA-seq) with ~100 millions paired reads per library. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR)  version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (HMKMGBGXY_siCtrl_16s005987-1-1_Nicolas_lane116s005987_minus_normalized_hg38.bw and HMKMGBGXY_siCtrl_16s005987-1-1_Nicolas_lane116s005987_plus_normalized_hg38.bw).

value: transfected with control siRNA for 3 days


title: HBS3_cultured SJMMHB045443


title: RNA_Hand2_Control

description: NTC.xlsx

tag: development stage

value: adult (P60)

tag: tissue

value: superior cervical ganglia and stellate ganglia

tag: pool (n)


title: HBS2_cultured SJMMHB045442

value: organoids


title: PNR primary tumor_dissected SJMMHB045420

description: PNR primary tumor_dissected

value: Tissue

value: primary tumor


title: Strand-specific RNA-seq in senescent cells- Replicate #2

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in senescent cells was performed paired-end (HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_1_sequence.txt and HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_2_sequence.txt) by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq) with ~100 millions paired reads per library. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (minus (HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_minus_normalized_hg38.bw) and plus (HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_plus_normalized_hg38.bw)).

data_processing:
Paired-end reads of the strand-specific RNA-Seq (senescence or proliferation) data were aligned using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified. For these alignments all parameters were kept as default.
After the alignment, we applied on all aligned datasets several steps using samtools software: we converted aligned file from Sequence Alignments/Map (sam) format into the Binary Alignment/Map (bam) format which stores the same data in a compressed, indexed, binary form and a cutoff was applied to keep only reads with MAPQ > 25. We sorted data by position on the genome, and created an index of each bam file (bai format). We then converted these cleaned files in wiggle files using R via the rtracklayer bioconductor package. On each dataset, we applied for each base position of the genome a normalization factor (100,000,000 / total numbers of aligned reads).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

source_name: senescent WI38 hTERT RAF1-ER cells

growth_protocol: WI38 hTERT RAF1-ER cells were grown for three days in prescence (to induce senescence) or abscence (proliferative cells) of 4-hydroxytamoxifen.

value: senescent


title: LCS4_cultured SJMMHB045418

value: Tumor organoids


title: LCS3_cultured SJMMHB045414


title: LCS4_cultured SJMMHB045416


title: H2A.Z ChIP-seq in proliferative cells - Replicate #2

description: ChIP H2A.Z sequencing in proliferative cells was performed single-end (HL7KMBGXY_H2A_Z-PROLIF_16s006312-1-1_Nicolas_lane116s006312_sequence.txt) by Illumina’s NextSeq 500 technology at GeneCore with ~100 millions reads per library.  As Spike-in chromatin and Spike-in antibody (Active motif) were added in the ChIP experiments, alignment on human hg38 genome combined with drosophila dm6 genome was performed using Burrows-Wheeler transformation (bwa) version 0.7.5a-r405. The datasets were normalized by the aligned dm6 reads in proliferation and in senescence as recommended by the manufacturer (HL7KMBGXY_H2A_Z-PROLIF_16s006312-1-1_Nicolas_lane116s006312_normalizedDm6_hg38.nodups.bw).

data_processing:
Single-end reads of the ChIP-Seq H2A.Z or H3 (senescence or proliferation) data were aligned using Burrows-Wheeler transformation (bwa) version 0.7.5a-r405. For these alignments all parameters were kept as default.
After the alignment, we applied on all aligned datasets several steps using samtools software (v.1.3.1) : we converted aligned file from Sequence Alignments/Map (sam) format into the Binary Alignment/Map (bam) format which stores the same data in a compressed, indexed, binary form and a cutoff was applied to keep only reads with MAPQ > 25.
We sorted data by position on the genome, removed PCR duplicates (i.e. reads mapped at the exact same position on the genome) using the samtools command rmdup-s and created an index of each bam file (bai format).
We then converted these cleaned files in wiggle files using R via the rtracklayer bioconductor package. On these wiggle files, we then applied a normalization factor for each base position of the genome. This normalization factor depended whether Spike-in chromatin was added in the experiment, as described for each sample.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

source_name: Chromatin immunoprecipitation using H2A.Z antibodies in proliferative WI38 hTERT RAF1-ER cells

extract_protocol:
Nuclei were isolated and chromatin was sonicated and precleared. The H2A.Z or H3 histone-DNA complexes were isolated using antibody against H2A.Z (Abcam, ab4174) or using antibody against H3 (Abcam, ab1791) . The  immunoprecipitated DNA was then purified and 10 ng was sent to BGI (HONG KONG) or EMBL GeneCore (Heidelberg, Germany) to perform library construction and sequencing.
Library construction and sequencing was performed by BGI TECH SOLUTIONS (HONGKONG) for the first replicates of H2A.Z ChIP-Seq in proliferation and in senescence, and at EMBL GeneCore for the second replicates of H2A.Z ChIP-Seq in proliferation and in senescence as well as for the H3 ChIP-Seq in proliferation and in senescence.

treatment_protocol: Before harvesting the cells, they were subjected to formaldehyde crosslink.


title: LCS4_cultured SJMMHB045417


title: H2A.Z ChIP-seq in senescent cells - Replicate #2

description: ChIP H2A.Z sequencing in senescent cells was performed single-end (HL7KMBGXY_H2A_Z-SEN_16s006313-1-1_Nicolas_lane116s006313_sequence.txt) by Illumina’s NextSeq 500 technology at GeneCore with ~100 millions reads per library.  As Spike-in chromatin and Spike-in antibody (Active motif) were added in the ChIP experiments, alignment on human hg38 genome combined with drosophila dm6 genome was performed using Burrows-Wheeler transformation (bwa) version 0.7.5a-r405. The datasets were normalized by the aligned dm6 reads in proliferation and in senescence as recommended by the manufacturer (HL7KMBGXY_H2A_Z-SEN_16s006313-1-1_Nicolas_lane116s006313_normalizedDm6_hg38.nodups.bw).

source_name: Chromatin immunoprecipitation using H2A.Z antibodies in senescent WI38 hTERT RAF1-ER cells


title: H3 ChIP-seq in proliferative cells

description: ChIP H3 sequencing in proliferative cells was performed single-end (HL7KMBGXY_H3-PROLIF_16s006310-1-1_Nicolas_lane116s006310_sequence.txt) by Illumina’s NextSeq 500 technology at GeneCore with ~100 millions reads per library.  As Spike-in chromatin and Spike-in antibody (Active motif) were added in the ChIP experiments, alignment on human hg38 genome combined with drosophila dm6 genome was performed using Burrows-Wheeler transformation (bwa) version 0.7.5a-r405. The datasets were normalized by the aligned dm6 reads in proliferation and in senescence as recommended by the manufacturer (HL7KMBGXY_H3-PROLIF_16s006310-1-1_Nicolas_lane116s006310_normalizedDm6_hg38.nodups.bw).

source_name: Chromatin immunoprecipitation using H3 antibodies in proliferative WI38 hTERT RAF1-ER cells


title: BPK9_3

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
RNA-Seq reads were aligned to the hg19 genome using STAR. Gene-level counts were calculated using FeatureCounts. DESeq2 was used to generate FPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM.csv contains FPKM quantification for all RNA-Seq samples.

molecule: polyA RNA

source_name: H460 cells

growth_protocol: H460 cells were grown in RPMI (10% FBS).

extract_protocol:
RNA was extracted using qiagen RNAeasy kit.
mRNA-seq libraries were prepared using the TruSeq RNA library preparation kit (version 2) according to the manufacturer's instructions.

treatment_protocol: Cells were plated the night before in 6-well plates (0.25e6/well) and treated with DMSO or 30uM of compound for 12hrs.

tag: cancer type

value: NSCLC


title: HBS1-driven primary tumor_dissected SJMMHB044775

description: HBS1-driven primary tumor_dissected


title: BPK9_2


title: HBS1_cultured SJMMHB043042


title: BPK9_1


title: HBS1_cultured SJMMHB043041


title: RPE_ChIPSeq_DMSO_RNA_pol_II

status: Public on Nov 29 2017

city: Boulder

first: Xuedong

last: Liu

state: CO

address: 3415 Colorado Avenue C318

department: Chemistry and Biochemistry

institute: University of Colorado Boulder

data_processing:
Reads were filtered by Illumina CASAVA 1.8.2 software
ChIP-seq datasets were aligned using Bowtie mapping software version 0.12.7. To maintain the same read length across all experiments, 1X150 bp ChIP-seq raw datasets (fastq files) were trimmed to 50bp using FASTX-toolkit version 0.0.13.2 or Trimmomatic version 0.36. All reads were mapped to the hg18 reference human genome with a number of base pairs mismatch not greater than 2 (96% sequence match). We used SAMtools version 0.1.19 to generate a sorted pileup format of the aligned reads. Reads were then extended from the 3’–end to a final length of 150bp. For each experiment, genome coverage bed graph files were generated using BEDTools2 version 2.25.0 and then normalized by multiplying the read density times 100 and dividing by the total number of mapped reads.
Genome_build: hg18
Supplementary_files_format_and_content: bigwig

source_name: RPE

growth_protocol: Cells were cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (Sigma), 1% penicillin streptomycin, and 1% GlutaMAX (Invitrogen) and maintained at 37°C and 5% CO2. Prior to treatment, HCT116 and RPE cells were grown in complete media and passaged for 3 consecutive days.

extract_protocol:
RPE cells were treated with largazole or vehicle for 16 hours and cross-linked with 1% formaldehyde for 15 minutes at room temperature (25°C). Cells were washed two times with PBS and membranes ruptured in hypotonic buffer (50 mM NaCl, 1% NP-40 alternative, 2 mM EDTA, 10 mM Tris, 1 mM DTT, 2 mM EDTA, 1X protease inhibitor cocktail (Roche # 04693124001).  The cell nuclei were recovered by centrifugation and resuspended in lysate buffer (150 mM NaCl, 0.5% Triton X-100, 2 mM EDTA, 0.1% SDS, 20 mM Tris, 1 mM DTT, 1X protease inhibitor cocktail). Resuspended samples were sonicated for 25 cycles (30s ‘on’ at high level and 30s ‘off’ per cycle) using a Bioruptor (Diagenode; Denville, NJ, USA) and spun for 10 minutes at 16,000x g in a microcentrifuge. Samples were incubated for 5 hours at 4°C with 5 to 20 μg of antibodies and 20 μl of 50% slurry with protein A beads (Millipore; Billerica, MA, USA). The immunoprecipitated chromatin was then recovered and DNA purified using phenol chloroform extraction.
ChIP sequencing libraries were prepared using an Illumina ChIP-Seq DNA Sample Prep Kit (cat. # IP-102-1001), with a starting sample varying from 2 to 20 ng of DNA isolated from the immunoprecipitation step.
Libraries were prepared according to Illumina's protocol. Barcodes were assigned as follows: RPE_Input.fastq.gz;CCAACACT, RPE_ChIPSeq_DMSO_H3K27ac.fastq.gz;TCTTCGAC,RPE_ChIPSeq_largazole_37.5nM_H3K27ac.fastq.gz;CTTCCTTC,RPE_ChIPSeq_largazole_75nM_H3K27ac.fastq.gz;AACTTGCC,RPE_ChIPSeq_largazole_300nM_H3K27ac.fastq.gz;CGACCTAA, RPE_ChIPSeq_DMSO_H3K4me1.fastq.gz;GACTACGA,RPE_ChIPSeq_largazole_37.5nM_H3K4me1.fastq.gz;ACCATCCT, RPE_ChIPSeq_largazole_75nM_H3K4me1.fastq.gz;GTACACCT,RPE_ChIPSeq_largazole_300nM_H3K4me1.fastq.gz;TACATCGG, RPE_ChIPSeq_DMSO_RNAPII.fastq.gz;ACTCCTAC,RPE_ChIPSeq_largazole_75nM_RNAPII.fastq.gz;ACGAGAAC, RPE_ChIPSeq_largazole_300nM_RNAPII.fastq.gz;ATCGTCTC.

treatment_protocol: Cells were treated with the indicated largazole concentration or equivalent amount of vehicle (DMSO) at 70% confluency and harvested after 16 hours for all ChIP-seq or RNA-seq experiments.

tag: tisue

value: retina

tag: disease

tag: chip antibody

value: RNAPII (Santa Cruz, sc-899, lot K0111)

tag: agent

value: DMSO


title: BPK29_3

tag: cell line


title: BPK29_2


title: HBS5_cultured SJMMHB043037


title: BPK29_1


title: HBS1_cultured SJMMHB043040


title: PNR primary tumor_dissected SJMMHB042783

description: PNR primary tumor_dissected


title: DMSO_3


title: HBS1_cultured SJMMHB043038


title: Strand-specific RNA-seq in proliferative cells- Replicate #2

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in proliferative cells was performed paired-end (HMKMGBGXY_Prolif_16s005985-1-1_Nicolas_lane116s005985_1_sequence.txt and HMKMGBGXY_Prolif_16s005985-1-1_Nicolas_lane116s005985_2_sequence.txt) by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq) with ~100 millions paired reads per library. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (minus (HMKMGBGXY_Prolif_16s005985-1-1_Nicolas_lane116s005985_minus_normalized_hg38.bw) and plus (HMKMGBGXY_Prolif_16s005985-1-1_Nicolas_lane116s005985_plus_normalized_hg38.bw)).

source_name: proliferative WI38 hTERT RAF1-ER cells


title: PNR primary tumor_dissected SJMMHB042782

description: PNR primary tumor_dissected


title: DMSO_1


title: DMSO_2


title: H3 ChIP-seq in senescent cells

description: ChIP H3 sequencing in senescent cells was performed single-end (HL7KMBGXY_H3-SEN_16s006311-1-1_Nicolas_lane116s006311_sequence.txt) by Illumina’s NextSeq 500 technology at GeneCore with ~100 millions reads per library.  As Spike-in chromatin and Spike-in antibody (Active motif) were added in the ChIP experiments, alignment on human hg38 genome combined with drosophila dm6 genome was performed using Burrows-Wheeler transformation (bwa) version 0.7.5a-r405. The datasets were normalized by the aligned dm6 reads in proliferation and in senescence as recommended by the manufacturer (HL7KMBGXY_H3-SEN_16s006311-1-1_Nicolas_lane116s006311_normalizedDm6_hg38.nodups.bw).

source_name: Chromatin immunoprecipitation using H3 antibodies in senescent WI38 hTERT RAF1-ER cells


title: PNR primary tumor_dissected SJMMHB042780

description: PNR primary tumor_dissected


title: PNR primary tumor_dissected SJMMHB042778

description: PNR primary tumor_dissected


title: H460_shSNW1_2

data_processing:
RNA-Seq reads were aligned to the hg19 genome using STAR. Gene-level counts were calculated using FeatureCounts. DESeq2 was used to generate FPKM values.
ChIP-Seq reads were aligned to the hg19 genome using bowtie2. Peaks were called using HOMER
Genome_build: hg19
Supplementary_files_format_and_content: NR0B1_FPKM.csv contains FPKM quantification for all RNA-Seq samples. NR0B1_peaks.bed contains NR0B1 peaks called from the ChIP-Seq data.

extract_protocol:
RNA was isolated by RNeasy Kit (Qiagen) and digested with DNase (Qiagen).
mRNA-seq libraries were prepared using the TruSeq RNA library preparation kit (version 2) according to the manufacturer's instructions.

value: H460 cells

tag: length of knockdown

tag: knockdown target


title: H460_shNR0B1_3


title: PNR primary tumor_dissected SJMMHB042777

description: PNR primary tumor_dissected

tag: sample type

tag: condition


title: normal liver organoids_cultured SJMMNORM040740

description: normal liver organoids_cultured

source_name: organoids

extract_protocol:
RNeasy Micro Kit (Qiagen).
total stranded RNA protocol
RNA SEQ gene level

value: normal organoids


title: H460_shNRF2_3


title: normal liver organoids_cultured SJMMNORM040745

description: normal liver organoids_cultured


title: H460_shNRF2_2


title: H460_shNR0B1_1


title: normal liver organoids_cultured SJMMNORM040737

description: normal liver organoids_cultured


title: H460_shGFP_3

value: GFP


title: H460_shNRF2_1


title: normal liver organoids_cultured SJMMHB045445

description: normal liver organoids_cultured


title: H460_shGFP_2


title: normal liver organoids_cultured SJMMHB045444

description: normal liver organoids_cultured


title: normal liver_dissected SJMMNORM016167

description: normal liver_dissected

source_name: Tissue

value: normal tissue


title: H460_shGFP_1


title: PNR primary tumor_dissected SJMMHB042781

description: PNR primary tumor_dissected


title: H2122_shNRF2_3

source_name: H2122 cells

value: H2122 cells


title: H2122_shNRF2_2


title: PNR primary tumor_dissected SJMMHB042779

description: PNR primary tumor_dissected


title: H460_shSNW1_1


title: Liver cancer organoids_cultured_LCS3 SJMMHB045435

description: Liver cancer organoids_cultured_LCS3

value: cancer organoids


title: H460_shSNW1_3


title: Liver cancer organoids_cultured_LCS3 SJMMHB045434

description: Liver cancer organoids_cultured_LCS3


title: H2122_shNRF2_1


title: H2122_shGFP_3


title: PPTR tumor intrahepatic metastasis_dissected SJMMHB044785

value: metastatic tumor


title: H460_shNR0B1_2


title: LCS-driven primary tumor_dissected SJMMHB044784

description: LCS-driven primary tumor_dissected


title: H2122_shGFP_2


title: PPTR tumor peritoneal metastasis_dissected SJMMHB044783


title: H2122_shGFP_1


title: PPTR primary tumor_dissected SJMMHB044782

description: PPTR primary tumor_dissected


title: normal liver organoids_cultured SJMMNORM016154

description: normal liver organoids_cultured


title: LCS-driven lung metastasis_dissected SJMMHB044780

description: LCS-driven lung metastasis_dissected


title: PPTR primary tumor_dissected SJMMHB044779

description: PPTR primary tumor_dissected


title: LCS-driven primary tumor_dissected SJMMHB044773

description: LCS-driven primary tumor_dissected


title: PPTR tumor intestine metastasis_dissected SJMMHB044777


title: LCS-driven lung metastasis_dissected SJMMHB044774

description: LCS-driven lung metastasis_dissected


title: Liver cancer organoids_cultured_LCS3 SJMMHB045436

description: Liver cancer organoids_cultured_LCS3


title: LCS-driven peritoneal metastasis_dissected SJMMHB044766


title: LCS-driven lung metastasis_dissected SJMMHB044771

description: LCS-driven lung metastasis_dissected


title: LCS-driven peritoneal metastasis_dissected SJMMHB044770


title: nRNA_24_NO

city: Vari

first: Maria

last: Fousteri

address: 34 Fleming Street

department: Institute for Fundamental Biomolecular Research

country: Greece

institute: Biomedical Sciences Research Center "Alexander Fleming"

description: nascent RNA NO UV (Recovery time=24h) , bigWig normalised with nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons

data_processing:
Base calling and Quality filtering were done with default parameters within Illumina pipeline.
All reads were aligned to hg19 genome assembly using bwa-mem (ChIP-seq, CPDIP-seq), bowtie (nascent-RNA-seq) and Tophat (mRNA-seq).
Reads were filtered by using FAStQC and
Genome_build: hg19
Supplementary_files_format_and_content: Normalised BigWig files were generated using in-house developed shell, perl, and R scripts, compiling functions of software commonly used by most laboratories.

source_name: Cell line

growth_protocol: VH10 cells were maintained in DMEM containing 10% FBS at 37 C and 5% CO2.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei and chromatin was isolated and precipitated with antibodies as follows: anti-RNAPII CTD (ser2P) (ab5095, lot GR231750-2) from abcam; anti-RNAPII CTD (ser5P) (3E8; 04-1572-I, lot: 2395817) and anti RNAPII CTD (hypo) (8WG16; 05-952, lot: 2262610) from Millipore. totalRNA was harvested using Trizol reagent. Nacent RNA (nRNA) was obtained according to manufacturer's protocol (Nascent RNA purification kit, Invitrogen) using 5 to 10 minutes for incubation with 100uM EU, mRNA was isolated with polydT dynabeads. Genome-wide capture of damaged DNA (CPD lesion) was achieved by adatation of a MeDIP-seq protocol: single stranded DNA was obtained from reverse crosslinked and purified genomic DNA isolated immediately after UV-C irradiation, then anti-CPD antibody (Anti Cyclobutane Pyrimidine Dimers, clone TDM-2, cat: NMDND001, lot TMC-05) was used to pull down damage DNA before purification and library preparation
Libraries were prepared according to Illumina's instructions. ChIP-Seq, nascent RNA-seq ( nRNA-seq) and mRNA-seq ) were prepared by generating fragmented double-stranded cDNA intermediates. In all cases, DNA libraries were generated by ligation adapters and amplification by LM-PCR (Truseq) or (NEBNext). Briefly, double stranded DNA in the range of 100-400 bp was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment  and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. ALternatively, we used NEBnext and Truseq approaches to multiplex samples for sequencing different samples in a single lane of the flowcell. qPCR with Illumina primers was used to control for overamplification. The purified DNA library was size selected by AMpure beads purification as previously described and was tyoically in the range of 200 to 500 bp. Libraries were sequenced on Hiseq2000 or 2500 in Genecore, EMBL following manufacturer's protocols.

treatment_protocol: VH10 cells were irradiated with  UV-C (8 or 20 J/m2) as previously described (Fousteri et al., Molecular Cell, 2006) and transcriptional changes (RNA and RNA polymerases) and DNA integrity (CPDIP-seq) were monitored during reccovery from DNA damage. Inhibitor of transcription DRB was used prior to UV to synchronize transcription and during UV irradiation and recovery to inhibit release of RNA polymerases from Promoter-proximal regions.

tag: cell type

value: Fibroblast cells immortalized with hTERT


title: nRNA_24_15J

description: nascent RNA +UV (Recovery time=24h, 15J/m2) , bigWig normalised with nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons


title: Strand-specific RNA-seq in siCtrl-treated proliferative WI38 hTERT RAF1-ER cells- Replicate #1

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in proliferative cells treated with Control siRNA was performed paired-end (READS1( siCONT3_L1_1.fq) and READS 2 (siCONT3_L1_2.fq) by Illumina’s HiSeq technology at BGI (lncRNA-seq) with at least 50 millions clean reads (after removing adaptor pollution and low quality sequence). After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR)  version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (siCONT3_L1_minus_normalized_hg38.bw and siCONT3_L1_plus_normalized_hg38.bw).

value: WI38 hTERT RAF1-ER

value: proliferative

value: transfected with control siRNA for 3 days


title: LCS-driven primary tumor_dissected SJMMHB044768

description: LCS-driven primary tumor_dissected

value: Tissue

value: primary tumor


title: LCS-driven peritoneal metastasis_dissected SJMMHB044765


title: strand-specific RNA-seq in siH2A.Z-treated  proliferative WI38 hTERT RAF1-ER cells- Replicate #1

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in proliferative cells treated with H2A.Z siRNA was performed paired-end (READS1 (siH2A_Z26_2_L1_1.fq) and READS 2 (siH2A_Z26_2_L1_2.fq)) by Illumina’s HiSeq technology at BGI (lncRNA-seq) with at least 50 millions clean reads (after removing adaptor pollution and low quality sequence). After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (siH2A_Z26_2_L1_minus_normalized_hg38.bw and siH2A_Z26_2_L1_plus_normalized_hg38.bw).

value: transfected with siRNA against H2A.Z for 3 days


title: Strand-specific RNA-seq in proliferative cells- Replicate #1

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in proliferative cells was performed paired-end (READS1( CONT_L1_1.fq) and READS 2 (CONT_L1_2.fq) by Illumina’s HiSeq technology at BGI (lncRNA-seq) with at least 50 millions clean reads (after removing adaptor pollution and low quality sequence). After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (minus (CONT_L1_minus_normalized_hg38.bw) and plus (CONT_L1_plus_normalized_hg38.bw)).


title: LCS-driven lung metastasis_dissected SJMMHB018124

description: LCS-driven lung metastasis_dissected


title: LCS-driven lung metastasis_dissected SJMMHB018122

description: LCS-driven lung metastasis_dissected


title: H2A.Z ChIP-seq in proliferative cells- Replicate #1

description: ChIP H2A.Z sequencing in proliferative cells was performed single-end (H2AZ_CONT.fq) by Illumina’s HiSeq technology at BGI with at least 40 millions clean reads (after removing adaptor pollution and low quality sequence). Alignment on human genome hg38 was performed using Burrows-Wheeler transformation (bwa) version 0.7.5a-r405. Normalization by the total number of aligned reads (10,000,000 / total numbers of aligned reads) was performed. In addition, a standardization factor was calculated that is the difference between the variation in senescence versus proliferation obtained by ChIP-seq data and the variation in senescence versus proliferation obtained by conventional ChIP-qPCR experiments. This factor (2.27) was multiplied to the number of reads per base in proliferation to obtain standardized data used throughout the paper (H2AZ_CONT_normalized_standardized_hg38_nodups.bw).


title: PPTR primary tumor_dissected SJMMHB044781

description: PPTR primary tumor_dissected


title: Liver cancer organoids_cultured_LCS1 SJMMHB016959

description: Liver cancer organoids_cultured_LCS1

value: organoids


title: Liver cancer organoids_cultured_LCS2 SJMMHB016972

description: Liver cancer organoids_cultured_LCS2


title: Liver cancer organoids_cultured_LCS2 SJMMHB016971

description: Liver cancer organoids_cultured_LCS2


title: Liver cancer organoids_cultured_LCS1 SJMMHB016958

description: Liver cancer organoids_cultured_LCS1


title: Liver cancer organoids_cultured_LCS1 SJMMHB016960

description: Liver cancer organoids_cultured_LCS1


title: Liver cancer organoids_cultured_LCS2 SJMMHB016970

description: Liver cancer organoids_cultured_LCS2


title: normal liver_dissected SJMMHB016151

description: normal liver_dissected


title: LCS-driven primary tumor_dissected SJMMHB016153

description: LCS-driven primary tumor_dissected


title: H2A.Z ChIP-seq in senescent cells - Replicate #1

description: ChIP H2A.Z sequencing in senescent cells was performed single-end (H2AZ_SEN.fq) by Illumina’s HiSeq technology with at least 40 millions clean reads (after removing adaptor pollution and low quality sequence). Alignment on human genome hg38 was performed using Burrows-Wheeler transformation (bwa) version 0.7.5a-r405. Normalization by the total number of aligned reads (10,000,000 / total numbers of aligned reads) was performed (H2AZ_SEN_normalized_hg38_nodups.bw).

value: senescent


title: Liver cancer organoids_cultured_LCS2 SJMMHB016156

description: Liver cancer organoids_cultured_LCS2


title: mRNA-seq_0_NO_2

description:
mRNA-seq NO UV replicate 2 (Recovery time=0h); bigWigcomputed on catenated samples rep1 and rep2 raw files
processed data file: VH10_NO_UV_rep_cat_ok.bigWig

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei and chromatin was isolated and precipitated with antibodies as follows: anti-RNAPII CTD (ser2P) (ab5095, lot GR231750-2) from abcam; anti-RNAPII CTD (ser5P) (3E8; 04-1572-I, lot: 2395817) and anti RNAPII CTD (hypo) (8WG16; 05-952, lot: 2262610) from Millipore. totalRNA was harvested using Trizol reagent. Nacent RNA (nRNA) was obtained according to manufacturer's protocol (Nascent RNA purification kit, Invitrogen) using 5 to 10 minutes for incubation with 100uM EU, mRNA was isolated with polydT dynabeads. Genome-wide capture of damaged DNA (CPD lesion) was achieved by adatation of a MeDIP-seq protocol: single stranded DNA was obtained from reverse crosslinked and purified genomic DNA isolated immediately after UV-C irradiation, then anti-CPD antibody (Anti Cyclobutane Pyrimidine Dimers, clone TDM-2, cat: NMDND001, lot TMC-05) was used to pull down damage DNA before purification and library preparation
Libraries were prepared according to Illumina's instructions. ChIP-Seq, nascent RNA-seq ( nRNA-seq) and mRNA-seq ) were prepared by generating fragmented double-stranded cDNA intermediates. In all cases, DNA libraries were generated by ligation adapters and amplification by LM-PCR (Truseq) or (NEBNext). Briefly, double stranded DNA in the range of 100-400 bp was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment  and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. ALternatively, we used NEBnext and Truseq approaches to multiplex samples for sequencing different samples in a single lane of the flowcell. qPCR with Illumina primers was used to control for overamplification. The purified DNA library was size selected by AMpure beads purification as previously described and was tyoically in the range of 200 to 500 bp. Libraries were sequenced on Hiseq2000 or 2500 in Genecore, EMBL following manufacturer's protocols.
double-stranded DNA-seq was performed for ChIP-seq, Input-seq, nRNA-seq, mRNA-seq and CPDIP-seq.

tag: treated with

value: NO UV (Recovery time=0h)


title: Strand-specific RNA-seq in senescent cells- Replicate #1

description:
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in senescent cells was performed paired-end (READS1 (SEN_L1_1.fq) and READS 2 (SEN_L1_2.fq)) by Illumina’s HiSeq technology at BGI (lncRNA-seq) with at least 50 millions clean reads (after removing adaptor pollution and low quality sequence). After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (minus (SEN_L1_minus_normalized_hg38.bw) and plus (SEN_L1_plus_normalized_hg38.bw)).

tag: state


title: LCS-driven primary tumor_dissected SJMMHB016150

description: LCS-driven primary tumor_dissected


title: mRNA-seq_0_NO_1

description:
mRNA-seq NO UV replicate 1 (Recovery time=0h); bigWigcomputed on catenated samples rep1 and rep2 raw files
processed data file: VH10_NO_UV_rep_cat_ok.bigWig


title: LCS-driven primary tumor_dissected SJMMHB016146

description: LCS-driven primary tumor_dissected


title: LCS-driven primary tumor_dissected SJMMHB016149

description: LCS-driven primary tumor_dissected


title: preDRB_nRNA_120min_20J

description: nascent RNA +UV (Recovery time=120min, 20J/m2); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated

value: +UV (Recovery time=120min)


title: LCS-driven primary tumor_dissected SJMMHB016148

description: LCS-driven primary tumor_dissected


title: LCS-driven primary tumor_dissected SJMMHB016147

description: LCS-driven primary tumor_dissected


title: PPTR primary tumor_dissected SJMMHB016145

description: PPTR primary tumor_dissected


title: normal liver_dissected SJMMHB016139

description: normal liver_dissected


title: preDRB_nRNA_10min_20J

description: nascent RNA +UV (Recovery time=10min, 20J/m2); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated

value: +UV (Recovery time=10min)


title: LCS-driven primary tumor_dissected SJMMHB016152

description: LCS-driven primary tumor_dissected


title: preDRB_nRNA_0_20J

description: nascent RNA +UV (Recovery time=0h, 20J/m2); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated

value: +UV (Recovery time=0h)


title: preDRB_nRNA_60min_NO

description: nascent RNA NO UV (Recovery time=60min); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated

value: NO UV (Recovery time=60min)


title: preDRB_nRNA_10min_NO

description: nascent RNA NO UV (Recovery time=10min); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated

value: NO UV (Recovery time=10min)


title: preDRB_nRNA_60min_20J

description: nascent RNA +UV (Recovery time=60min, 20J/m2); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated

value: +UV (Recovery time=60min)


title: PPTR primary tumor_dissected SJMMHB016138

description: PPTR primary tumor_dissected


title: PPTR primary tumor_dissected SJMMHB016136

description: PPTR primary tumor_dissected


title: preDRB_nRNA_0_NO

description: nascent RNA NO UV (Recovery time=0h); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated


title: PPTR primary tumor_dissected SJMMHB016137

description: PPTR primary tumor_dissected


title: nRNA_2_15J

description: nascent RNA +UV (Recovery time=2h, 15J/m2); bigWig normalised with nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons

value: +UV (Recovery time=2h)


title: CPDIP_0_8J

description: CPDIP-seq on CPD-IP enriched genomic DNA (Recovery time=0h, 8J/m2)

value: Fibroblast cells immortalized with hTERT

value: (Recovery time=0h, 8J/m2)

value: anti-CPD antibody


title: normal liver_dissected SJMMHB016142

description: normal liver_dissected

value: normal tissue


title: preDRB_nRNA_20min_NO

description: nascent RNA NO UV (Recovery time=20min); bigWig normalised with preDRB_nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons, non-duplicated

value: NO UV (Recovery time=20min)


title: normal liver_dissected SJMMHB016135

description: normal liver_dissected

value: Tissue


title: PPTR tumor lung metastasis_dissected SJMMHB016134

description: PPTR tumor lung metastasis_dissected

value: metastatic tumor


title: nRNA_0.5_15J

description: nascent RNA +UV (Recovery time=0.5h, 15J/m2); bigWig normalised with nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons

value: +UV (Recovery time=0.5h)


title: nRNA_0_NO

description: nascent RNA NO UV (Recovery time=0h); bigWig normalised with nRNA samples, excluding ribosomal RNA reads, excluding reads overlaping exons


title: PPTR primary tumor_dissected SJMMHB016133

description: PPTR primary tumor_dissected

value: primary tumor


title: NODRB_ser2P_0_NO

description: anti-RNAPII-ser2P ChIP-seq NO UV NO DRB (Recovery time=0h); bigWig normalised with DRB_ser2P ChIP-seq samples

value: NO UV NO DRB (Recovery time=0h)


title: PPTR tumor intestine metastasis_dissected SJMMHB016132


title: DRB_ser2P_10min_20J

description: anti-RNAPII-ser2P ChIP-seq +UV in DRB (Recovery time=10min, 20J/m2); bigWig normalised with  DRB_ser2P ChIP-seq samples

value: +UV in DRB (Recovery time=10min)


title: DRB_ser2P_30min_20J

description: anti-RNAPII-ser2P ChIP-seq +UV in DRB (Recovery time=30min, 20J/m2); bigWig normalised with  DRB_ser2P ChIP-seq samples

value: +UV in DRB (Recovery time=30min)


title: PPTR primary tumor_dissected SJMMHB016130

description: PPTR primary tumor_dissected


title: normal liver_dissected SJMMHB016131

description: normal liver_dissected


title: DRB_ser2P_30min_NO

description: anti-RNAPII-ser2P ChIP-seq NO UV in DRB (Recovery time=30min); bigWig normalised with  DRB_ser2P ChIP-seq samples

value: NO UV in DRB (Recovery time=30min)


title: DRB_ser2P_10min_NO

description: anti-RNAPII-ser2P ChIP-seq NO UV in DRB (Recovery time=10min); bigWig normalised with  DRB_ser2P ChIP-seq samples

value: NO UV in DRB (Recovery time=10min)


title: PPTR primary tumor_dissected SJMMHB016128

description: PPTR primary tumor_dissected


title: DRB_ser2P_0_NO

description: anti-RNAPII-ser2P ChIP-seq NO UV in DRB (Recovery time=0h); bigWig normalised with DRB_ser2P ChIP-seq samples

value: NO UV in DRB (Recovery time=0h)


title: Liver cancer organoids_cultured_LCS1 SJMMHB016127

description: Liver cancer organoids_cultured_LCS1

value: organoids

value: cancer organoids


title: preDMSO_ser2P_1h_20J

description: anti-RNAPII-ser2P ChIP-seq +UV preDMSO (Recovery time=1h, 20J/m2); bigWig normalised with preDRB or preDMSO ChIP-seq samples

value: Fibroblast cells immortalized with hTERT

value: +UV preDMSO (Recovery time=1h


title: preDRB_ser2P_1h_20J

description: anti-RNAPII-ser2P ChIP-seq +UV preDRB (Recovery time=1h, 20J/m2); bigWig normalised with preDRB or preDMSO ChIP-seq samples

value: +UV preDRB (Recovery time=1h


title: preDRB_ser2P_1_NO

description: anti-RNAPII-ser2P ChIP-seq NO UV preDRB (Recovery time=1h); bigWig normalised with preDRB or preDMSO ChIP-seq samples

value: NO UV preDRB (Recovery time=1h)


title: NOF6

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

institute: Newcastle University

data_processing:
Illumina CASAVA (1.7.0) was used for the base calling and quality score calculations
FastQC was used to first check quality of the reads. Trim-galore (Krueger) was then used to trim off low quality bases from both ends of reads and remove sequencing adaptors when they were found at 3’ end. After quality control, Tophat2 was used to map reads to the human reference genome hg38
Mapped reads were then assembled into complete transcripts using the splice junction mapping tool Cufflinks, with option –G which utilises the Ensembl reference gene track to improve mapping. Cuffmerge was used to merge the assembled transcripts into a consensus gene track from the all of the mapped samples. Ensembl transcript biotypes were applied to identify lncRNAs and other non-coding RNA species.
Genome_build: hg38
Supplementary_files_format_and_content: Excel spreadsheet abundance measurements

source_name: neck of femure fracture hip cartilage

extract_protocol:
Cartilage samples were ground into powder and homogenized using Invitrogen TRIzol Reagent after which RNA was isolated by RNeasy Kit
cDNA libraries were prepared for sequencing from 5µg of total RNA using Illumina TrueSeq mRNA kits with the manufacturers’ protocols

value: neck of femure fracture hip cartilage

tag: Sex

value: Female

tag: age

value: Chondrocyte


title: hypo_48_8J

description: anti-RNAPII-hypo ChIP-seq +UV (Recovery time=48h, 8J/m2); bigWig normalised with hypo samples

value: +UV (Recovery time=48h)

value: anti-RNAPII-hypo


title: hypo_1.5_8J

description: anti-RNAPII-hypo ChIP-seq +UV (Recovery time=1.5h, 8J/m2); bigWig normalised with hypo samples

value: +UV (Recovery time=1.5h)


title: preDMSO_ser2P_1_NO

description: anti-RNAPII-ser2P ChIP-seq preDMSO NO UV (Recovery time=1h); bigWig normalised with preDRB or preDMSO ChIP-seq samples

value: preDMSO NO UV (Recovery time=1h)


title: NOF5

tag: tissue


title: NOF4


title: NOF3


title: NOF2


title: hypo_0_NO

description: anti-RNAPII-hypo ChIP-seq NO UV (Recovery time=0h); bigWig normalised with hypo samples

value: NO UV (Recovery time=0h)


title: NOF1


title: H460_NR0B1_ChIP

extract_protocol:
H460 cells were fixed in 1% formaldehyde (Sigma-Aldrich) for 15 minutes at 25°C. After lysis, samples were sonicated using a biorupter sonicator (Diagenode) for 60 cycles (30 seconds per cycle/30 seconds cooling) at a high power level. Chromatin sheering was optimized to a size range of 200 to 600 bp. Chromatin (100 μg) was immunoprecipitated with the NR0B1 antibody (Cell Signaling Technology).
ChIP-Seq libraries were prepared according to Illumina's protocols.

value: H460 cells


title: H460_input


title: PPTR primary tumor_dissected SJMMHB016129

description: PPTR primary tumor_dissected

value: Tissue

value: primary tumor


title: ser5P_0_NO

description: anti-RNAPII-ser5P ChIP-seq NO UV (Recovery time=0h); bigWig normalised with ser5P samples


title: ser5P_0.5_8J

description: anti-RNAPII-ser5P ChIP-seq +UV (Recovery time=0.5h, 8J/m2); bigWig normalised with ser5P samples

value: +UV (Recovery time=0.5h)


title: ser2P_48_20J

description: anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=48h, 20J/m2); bigWig normalised with ser2P samples


title: his-3 RNAi rep3

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped using STAR aligner version 2.5.3a to the Ensembl release 89 Caenorhabditis_elegans genome [Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa genome sequence and the Caenorhabditis_elegans.WBcel235.89.gtf annotation].  The --sjdbOverhang setting of the genomeGenerate step was set to 99.
Read counts per gene were obtained using HTseq-count with the following settings: htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id
Genome_build: Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa
Supplementary_files_format_and_content: The count table is a tab-separated text file with counts per gene.

organism: Caenorhabditis elegans

source_name: his-3 RNAi

growth_protocol: C. elegans were synchronized by hypochlorite bleaching and plated to RNAi plates as L1 larvae. Nematodes were collected for RNA extraction at L4 larvae.

extract_protocol:
Total RNA was extracted with TriPure Isolation Reagent (Roche)
Illumina Truseq stranded mRNA library

treatment_protocol: Standard C. elegans RNAi on NGM plates

tag: strain

tag: genotype/variation

value: his-3 knockdown

tag: developmental stage

value: L4 larvae


title: his-3 RNAi rep2


title: ser2P_1_20J

description: anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=1h, 20J/m2); bigWig normalised with ser2P samples

value: Fibroblast cells immortalized with hTERT

value: +UV (Recovery time=1h)


title: ser2P_48_8J_2

description:
anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=48h, 8J/m2); bigWig normalised with ser2P samples_fastq_rep2was catenated to ser2P_48_8J_1 before mapping
processed data file: VH1048h8J_merged_fixed.bigWig


title: ser2P_48_8J_1

description:
anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=48h, 8J/m2); bigWig normalised with ser2P samples fastq_rep1 was catenated to ser2P_48_8J_2 before mapping
processed data file: VH1048h8J_merged_fixed.bigWig


title: his-3 RNAi rep1


title: cco-1 RNAi rep3

source_name: cco-1 RNAi

value: cco-1 knockdown


title: ser2P_6_8J

description: anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=6h, 8J/m2); bigWig normalised with ser2P samples

value: +UV (Recovery time=6h)


title: ser2P_2_20J

description: anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=2h, 20J/m2); bigWig normalised with ser2P samples

value: +UV (Recovery time=2h)


title: cco-1 RNAi rep1


title: cco-1 RNAi rep2


title: ser5P_48_8J

description: anti-RNAPII-ser5P ChIP-seq +UV (Recovery time=48h, 8J/m2); bigWig normalised with ser5P samples


title: ser2P_2_8J

description: anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=2h, 8J/m2); bigWig normalised with ser2P samples


title: EV (empty vector) rep3

source_name: empty vector

value: wild-type


title: ser2P_0.5_8J

description: anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=0.5h, 8J/m2); bigWig normalised with ser2P samples

value: +UV (Recovery time=0.5h


title: EV (empty vector) rep2


title: hMeDIP-seq

city: London

first: Alison

last: Brewer

address: JBC, 125 Coldharbour Lane

department: Cardiology

institute: King's College London

data_processing:
Illumina's BaseSpace was used to convert *.bcl files into FASTQ files, which contain base call and quality information for all reads passing filtering.
FASTQ Groomer in Galaxy (version 2.1) was used for adaptor trimming.
Output files were mapped to mm9 using Bowtie for illumina in Galaxy (version 2.1) to generate SAM files.
SAM files were converted to BAM files using SAM tools in Galaxy (version 2.1).
The peak calling was made using MACS (version 1.0.1) in Galaxy .
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS (BAM to BED to WIG files); Scores represent P = 1e-05 for peak detection.

source_name: mESCs, day 3 differentiated, 5-hmC enriched

growth_protocol: R1 mouse embryonic stem cells (ATCC) were maintained under "2i" conditions on gelatin coated flasks (in DMEM/F12)

extract_protocol:
Genomic DNA was prepared by 350mg/ml proteinase K (Sigma) digestion in 15 mM NaCl, 1%SDS, 100mM EDTA, 50mM Tris-HCl pH 8 at 55°C for 4 hours. Samples were sonicated (Branson 150 sonfier) to obtain 200-1000bp fragments and RNaseA (140µg/ml) (Qiagen), digested at 55°C for 30 minutes. DNA was phenol/chloroform extracted and ethanol precipitated. hMeDIP (Active Motif) was performed on 1µg of fragmented genomic DNA, pooled from triplicate samples, according to manufacturer’s instructions.
Libraries were prepared from the test sample (day 3-differentiated mESCs grown under atmospheric O2; 2.5ng), and equivalent amount of control, total genomic DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs; E7645), following the manufacturer’s protocol. DNA fragments were end-repaired and ligated to adaptors. Fragments with 200bp inserts were size selected using Agencourt Ampure XP Beads (Beckman Coulter), eluted in 10mM Tris, and indexed and amplified by PCR for 12 cycles. The libraries were quantified by qPCR using NEBNext Library Quant Kit for Illumina (New England Biolabs; E7630), and pooled at 4nM concentration. The library pool was sequenced on the MiSeq single read for 50 cycles. Data was analysed using BaseSpace (Illumina) and Galaxy (https://usegalaxy.org/).

treatment_protocol: mouse ESCs were induced to differentiate into embryoid bodies by culture onto non-adherant petri dishes (using KnockOut DMEM with 15% KnockOut serum)

value: R1 mESCs day 3 unbiased differentiation

tag: passages

tag: antibody

value: pAb 5hmC from ActiveMotif (55010)


title: ser2P_1_8J

description: anti-RNAPII-ser2P ChIP-seq +UV (Recovery time=1h, 8J/m2); bigWig normalised with ser2P samples

tag: chip antibody


title: IP KD2 Day8 Rep2

description: m6A meRIP seq

data_processing:
ChIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using bwa with parameters '-n 3 -k 2 -R 300 -t 4'. Multiple reads mapping to a single genomic locus were treated as PCR duplicates, and were removed using samtools rmdup. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag XT:A:U in the output bam file from bwa. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Peaks were called against input sample using MACS2 using default parameters. Peaks from all replicates were merged to give a master list of potential binding loci per condition, and read count (normalised by overall read depth of the library) for each replicate was calculated using the GenomicRanges package in R. Peaks were treated as potential binding loci if all replicates showed normalised score greater than 1 and did not overlap a peak called in the IgG.
m6A meRIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks2 and a single transcript database was generated using cuffmerge.
Riboprofiling: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks and a single transcript database was generated using cuffmerge.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files give coverage scores across the whole hg38 genome at each base position for the mapped reads. Normalized (read count normalized to total library read depth) and non-normalized coverage files are provided for each sample.

source_name: Whole cell

extract_protocol:
Total RNA was isolated from MOLM13 Ctrl cells or METTL3 KD cells 8 days after doxycycline administration using the RNeasy midi Kit (Quiagen). Successively polyA+ RNA was purified from 300 ug of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). 500 ng of polyA+ purified RNA were used for each immunoprecipitation reaction. The m6A RNA immunoprecipitation was performed using the Magna MeRIP m6A kit (Millipore) according with the manufacturer instructions.
Single end 50 bp stranded libraries were prepared using the Bioo Scientific NEXTflex Rapid Directional RNA kit following manufacturer's recommendations. Reads were sequenced using HiSeq 4000 and multiplexed reads were split based on their barcodes using Illumina Basespace.

tag: cell line

value: leukemia cell line MOLM13

tag: truseq barcode

value: GTCCGC

value: METTL3 KD2 shRNA

tag: time

tag: ip antibody

value: Magna MeRIP m6A kit

tag: antibody vendor

value: Millipore

tag: antibody catalog num

tag: antibody lot num


title: IP KD2 Day8 Rep1

description: m6A meRIP seq

value: GATCAG


title: IP KD1 Day8 Rep2

description: m6A meRIP seq

value: CCGTCC

value: METTL3 KD1 shRNA


title: DNA input sequence

source_name: mESCs, day 3 differentiated, input

tag: cell type


title: IP Ctrl Rep1

description: m6A meRIP seq

value: AGTCAA

value: Scramble shRNA


title: IP KD1 Day8 Rep1

description: m6A meRIP seq

value: ATGTCA


title: IP Ctrl Rep2

description: m6A meRIP seq

value: AGTTCC


title: Sample WT (internal ID 9495)

city: Vienna

first: Ilka

last: Reichardt-Gomez

address: Dr. Bohr Gasse 3

country: Austria

institute: Gregor-Mendel-Institute

data_processing:
Basecalls performed using RTA 1.8.70.0
The strand specific paired-end reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). Non matching reads were considerd downstream.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches.  Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44).
The aligned reads were counted with HTSeq. SnRNA, rRNA, tRNA, snoRNA and pseudogenes are masked.
The polyA containing transcripts were subjected to differential expression analysis with DESeq (v1.8.3). DESeq parameters were chosen to match the DESeq publication (Anders S, Huber W., 2010). Additionally, DESeq was instructed to ignore the condition labels and estimate the variance by treating all the samples as if they were replicates of the same condition (method=“blind”).
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample (Standard output Htseq count); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq).

organism: Drosophila melanogaster

source_name: control larval type II neuroblast and 24h progeny

growth_protocol: Flies expressing UAS-dicer2; wor-Gal4, asense-Gal4; UAS-CD8::GFP were crossed to flies expressing ;;tub-Gal80ts with or without brat RNAi (VDRC TID:105054). The progeny was raised at 18C and shifted to 29C by 3rd instar stage. Larval brains were dissected 24h after temperature shift and prepared for FACS-sorting.

extract_protocol: Type II neuroblasts and 24h progeny were FACS sorted from control or brat RNAi, and RNA was isolated using Trizol LS reagent. Total RNA was enriched for polyA mRNA, fragmented and first strand and second strand  was generated. Library preparation was done using the Illumina NEB ultra Kit.

value: Neuroblasts

tag: Stage

value: late third instar larva

tag: marker

value: cells express membrane-bound GFP marker (UAS-CD8::GFP)

value: larval brain


title: Input KD2 Day8 Rep2

description: m6A meRIP seq

value: TAGCTT


title: Input KD1 Day8 Rep2

description: m6A meRIP seq

value: leukemia cell line MOLM13

value: CGTACG


title: Input KD2 Day8 Rep1

description: m6A meRIP seq

value: GAGTGG

value: METTL3 KD2 shRNA


title: Sample brat (internal ID 9496)

source_name: brat RNAi larval type II neuroblasts and 24h progeny

tag: tissue


title: Input Ctrl Rep2

description: m6A meRIP seq

value: GTGGCC


title: Input Ctrl Rep1

description: m6A meRIP seq

value: GTGAAA


title: ser2P_0_NO

description: anti-RNAPII-ser2P ChIP-seq NO UV (Recovery time=0h); bigWig normalised with ser2P samples

value: Fibroblast cells immortalized with hTERT

tag: treated with

value: NO UV (Recovery time=0h)


title: EV (empty vector) rep1

tag: strain

tag: genotype/variation

value: wild-type

value: L4 larvae


title: Input KD1 Day8 Rep1

description: m6A meRIP seq

value: GTTTCG

value: METTL3 KD1 shRNA


title: female_PSNL_neurons_2

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

description:
SNL_female_258120
Supplementary Table 2 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)

data_processing:
alignment using STAR to mm10 (standard parameters, except with --outFilterMultimapNmax 1)
merging of bam files across lanes using samtools
cufflinks for expression level determination (including fragment bias, length and multi-read corrections)
cufflinks expression cut-off deemed mathematically and biologically appropriate: FPKM >= 1
Deseq2 for differential expression level analysis (standard parameters)
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary Table 1: cufflinks-derived FPKM values for FACSed naïve DRG neurons with & without expression cut-off
Supplementary_files_format_and_content: Supplementary Table 2: cufflinks-derived FPKM values for MACSed DRG neurons after PSNL with and without expression cut-off
Supplementary_files_format_and_content: Supplementary Table 3: DESeq2 comparing male vs. female DRG neurons
Supplementary_files_format_and_content: Supplementary Table 6: RNA RIN values and alignment stats

source_name: MACSed DRG neurons

extract_protocol:
RNA extractions were performed in a single, gender-matched batch using a Qiagen RNeasy micokit, following manufacturer’s protocols with some minor modifications. RNA quality was assessed using an Agilent Bioanalyser PicoChiP (for RIN values of sequencing samples see Supplementary Table 6).
RNA was sent for batch-controlled library preparation (SMARTer Ultra Low Input HV kit, 634820, Clontech) and sequencing at the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics at Oxford University. After amplification, samples were multiplexed in replicate flow cells on an Illumina HiSeq4500 platform to yield 75 bp reads of at least 25 M read depth.

value: DRG neurons

tag: Sex

value: female

tag: injury condition

value: day 8 after PSNL

tag: estrus identification

value: yes

tag: contaminant

value: erythrocytes


title: female_PSNL_neurons_3

description:
SNL_female_260144
Supplementary Table 2 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)


title: female_PSNL_neurons_1

description:
SNL_female_253155
Supplementary Table 2 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)


title: male_PSNL_neurons_2

description:
SNL_male_252143
Supplementary Table 2 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)

value: male


title: female_naive_neurons_10

description:
S229_female
Supplementary Table 1 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)

source_name: FACSed DRG neurons

value: naïve

value: no

value: satellite glial cells


title: male_PSNL_neurons_1

description:
SNL_male_249107
Supplementary Table 2 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)


title: male_PSNL_neurons_3

description:
SNL_male_256191
Supplementary Table 2 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)


title: INPUT_0_NO

description: Input-seq normalised with ser2P samples

tag: cell line


title: female_naive_neurons_9

description:
S228_female
Supplementary Table 1 (cufflinks), Supplementary Table 3 (deseq2), Supplementary Table 6 (QC)


title: 24#-12 RNA-seq

city: Shanghai

first: Hailiang

address: NO 1239, siping road

country: China

institute: Tongji university

description: 24#-12 RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC v0.10.1 used for quality control （default parameter）
Sequenced reads were trimmed  by Trimmomatic v0.32 (parameter: PE -threads 16 -phred33  HEADCROP:9 MINLEN:19)
Reads were mapped to JGI 221 G.raimondii D genome using TopHat v2.0.13(bowtie2 v2.2.4) (default parameter)
Alignment results converted from bam file to sam file and sorted by samtools(0.1.19)
Counting reads in genes using HTSeq( 0.6.0)(parameter: -t CDS -s no)
Calculating the adjusted p-value of genes(padj) of different samples by R package DESeq(1.18.0)
Genome_build: Gossypium raimondii (D5) genome JGI assembly v2.0 (annot v2.1)
Supplementary_files_format_and_content: Excel file contains DESeq output where all cotton color genotypes have been combined for a comparison between day 0 and day 12.

organism: Gossypium hirsutum

source_name: Transgenic White cotton fiber 12 day

extract_protocol:
Total RNA was extracted according to a guanidine thiocyanate method
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products are then purified and enriched with PCR to create the final cDNA library.  The cDNA library of each sample was constructed according to the instructions given in “Preparing Samples for Sequencing of mRNA Test Kits” (Illumina). Products were checked to verify the cDNA library quality and fragment length using an Agilent 2100 DNA 1000 Kit. Sequencing of the resulting cDNA library was carried out on an Illumina HiSeq 2000 paired-end 100-bp (PE 100) system.

tag: day post-anthesis

value: fiber development 12 day

value: cotton fiber


title: 6#-12 RNA-seq

description: 6#-12 RNA-seq

source_name: Transgenic Green cotton fiber 12 day