title: R1_4sU_Seq_HighMyc_Plus_Strand

description: nascent RNA

tag: cell line

value: siCTR+Dox


title: tumor_bearing_mouse_1 [mouse_t_1_1]

status: Public on Apr 09 2019

type: SRA

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description: Analyses in the publication (Zilionis et al. 2019) used t_1_1 library counts (GSM3635309_mouse_t_1_1_raw_counts.tsv.gz) generated from one sequencing run (SRR8646222). Additional reads were obtained for the library t_1_1 [SRR10097589] and are made available on SRA for completeness.

library_source: transcriptomic

data_processing:
All  processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops). The following steps are provided as an overview on the internal workings of inDrops.py. FASTQ files and processing steps are provided for mouse only.
inDrops.py first filters reads  for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 12 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > 600; ii) mitochondrial gene content <15.  Counts were total counts normalized as described in methods, and combined into a single genes x cells normalized filtered matrix per species. Putative cell doublets were identified using Scrublet (Wolock et al., 2018) and removed from further analysis. The resulting count matrixes are provided as mouse_counts_normalized_15939x28205.mtx and human_counts_normalized_54773x41861.mtx
Genome_build: GRCm38/91 (mouse) and GRCh38/81 (human)
Supplementary_files_format_and_content: human_counts_normalized_54773x41861.mtx contains filtered normalized counts from human samples.  human_cell_metadata_54773x25.tsv contains per-cell meta data for human samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_human_41861.tsv contains the list of human gene names.  mouse_counts_normalized_15939x28205.mtx contains filtered normalized counts from mouse samples.  mouse_cell_metadata_15939x12.tsv contains per-cell meta data for mouse samples, such as cell subset labels, xy coordinates for scatterplot shown in the publication, percentage of mitochondrial counts, total counts.  gene_names_mouse_28205.tsv contains the list of mouse gene names.  human_*_raw_counts.tsv.gz contain unfiltered raw counts from human samples prior to normalization; one file per sequencing library.  mouse_*_raw_counts.tsv.gz contain unfiltered raw counts from mouse samples prior to normalization; one file per sequencing library.

molecule: polyA RNA

organism: Mus musculus

source_name: lung tumor

extract_protocol:
Single cell suspensions were obtained from lung tissue of C57BL/6 male mice which were perfused with PBS. Small tissue pieces were generated from perfused lungs using scissors and digested (RPMI containing 0.2 mg/ml collagenase type I, Worthington Biochemical Corporation) for 15min at 37°C while shaking (700rpm). Digested lung tissue was gently meshed through 70µM cell strainers using a plunger. Single cell suspensions were then stained with a fluorescent conjugated antibody specific to CD45 (clone 30-F11, Biolegend) for 45min at 4°C. The cells were washed with staining buffer (PBS containing 0.5% BSA and 2 mM EDTA) and CD45+ live cells were sorted on a FACS Aria cell sorter (BD) into FBS containing tubes which were kept on ice until the cells were further processed for scRNASeq. 7-aminoactinomycin (7AAD, Sigma) positivity was used to exclude dead cells.
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols.

treatment_protocol: Murine KP1.9 lung adenocarcinoma tumor cells were injected into C57BL/6 male mice intravenously (2.5x105 cells in 100µl PBS) to develop orthotopic tumors in the lung. The tumor cell line was derived from lung tumor nodules of a C57BL/6 KrasLSL-G12D/WT;p53Flox/Flox (KP) mouse and was kindly provided by Dr. Zippelius (University Hospital Basel, Switzerland). Mice were analyzed for tumor phenotypes 4 weeks post-tumor initiation.

tag: strain

tag: gender

value: M

tag: treatment received prior to surgery (1= treated; 0=untreated)

tag: tumor cell line injected

value: KP1.9 lung adenocarcinoma tumor cells from lung tumor nodules of a C57BL/6 KrasLSL-G12D/WT;p53Flox/Flox male mouse

tag: age at injection of tumor cell line (weeks)

tag: purification

value: RBC-depletion; CD45+ cells

tag: age at sacrifice (weeks)


title: input_vp16srf

status: Public on Mar 14 2019

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

library_source: genomic

data_processing:
Sequencer: Illumina HiSeq 2500 (SND00104). Basecalling pipeline: HiSeq Control Software 2.2.58; Gerald version 1.8
Run:
RNAseq: Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequenced reads were mapped to the mouse genome (build GRCm38/mm10) using STAR (v2.5.0c). SAM/BAM files were further processed using SAMTOOLS v1.3. Read count quantifications were obtained using HTSeq (v0.6.1). Further data process was performed with custom scripts in the R programming language (https://cran.r-project.org/). Normalization of read counts and differential expression analysis between genotypes was carried out using DESeq2 R package from Bioconductor v3.2 (BiocInstaller 1.20.3). GO analysis was performed with Panther (Huaiyu Mi et al., 2013)
ChIPseq: Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Libraries were trimmed from adapters and low quality bases using Trimmomatic v0.36 (Bolger et al., 2014), and mapped to reference genome (Ensembl GRCm38) using Bowtie2 v2.3.2 (Langmead et al., 2009). Data was further processed using samtools (v1.5) (Li et al., 2009) and bedtools (v2.26.0) (Quinlan and Hall, 2010). Peak calling was performed using MACS2 (v2.1.1) (Zhang et al., 2008). SeqMINER (Ye et al 2011) was used to generate the k-means clustering data and the merged ChIP-seq profiles. Further analyses were performed with custom scripts in the R programming language (https://cran.r-project.org/). GO analysis was performed with the R bioconductor package ChIPpeakAnno v3.8.9. Data from Kim et al 2010 were lifted over from mm9 to mm10 using the R package rtracklayer.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl gene identifiers (ENSMUSG) and raw counts; bigwig files

molecule: genomic DNA

extract_protocol:
RNA-seq: Total RNA from cortical cultures was extracted with TRI reagent (Sigma-Aldrich) and digested with DNase I (QIAGEN®). RNA samples were extracted and re-precipitated using acid phenol-chloroform and ethanol.   .
ChIP-seq: Primary hippocampal neurons were obtained from E17 embryos. Cultured neurons were infected with syn-VP16-SRF/Syn-GFP viral vector at DIV3. After 7 days post-infection neurons were collected and genomic DNA from 5 × 10^6 hippocampal neurons was fragmented by sonication and immunoprecipitated with anti-VP16 antibody (Santa Cruz, sc-7545) as previously described (Scandaglia et al., 2015). Immunoprecipitated DNA was resuspended in 40 μL of water
Single-End stranded Chip and RNA libraries were prepared for sequencing using standard Illumina protocols (HiSeq Sequencing v4 Chemistry), with read length 50 and application Truseq Stranded mRNA.  Service provided by CRG.

tag: strain/background

value: ICR

tag: tissue

value: Primary neurons

tag: chip antibody

value: none; WCE

tag: flowcell

tag: index

value: GTGAAACG


title: Pool8

status: Public on May 03 2019

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Standard Illumina base calling pipeline, generating FASTQ files
Data analysis using Close Call v0.1.0 with HISAT2 v2.1.0 used as the mapper
Genome_build: Human GRCh38 / HISAT2 used RNA splice sites as listed in GRCh38.78
Supplementary_files_format_and_content: Monte Carlo simulation results: listing observed, simulated interactions frequencie and adjusted P-values
Supplementary_files_format_and_content:local_RNA_connectivity.xlsx description:
Supplementary_files_format_and_content:To derive local RNA density and/or connectivity for individual transcripts, we introduced a measure describing how often a transcript was detected singly or cobarcoded with one or multiple other RNA molecules. This so-called ?valency? of a given transcript was inferred from relative enrichments or depletions (z-score) in the number of reads mapping to the transcript in barcode groups encompassing one, two and three transcripts, respectively, compared with the nuclear transcriptome average.
Supplementary_files_format_and_content:
Supplementary_files_format_and_content:Pools_2_5_8_simulation_format_combined_file.txt.gz description:
Supplementary_files_format_and_content:The file lists all the identified transcripts allocated to each complex via a unique barcode.  This is the data file taken as input by the Monte Carlo simulation.

molecule: total RNA

organism: Homo sapiens

source_name: SHY neuroblasts

growth_protocol: Proximity RNA-Seq & Hi-C  Human neuroblastoma cells, SH-SY5Y, were cultured in high-glucose DMEM medium (Thermo Fisher Scientific) containing 10% fetal bovine serum (Hyclone) and Streptomycin, Penicillin (Thermo Fisher Scientific).

extract_protocol: Proximity RNA-Seq    Frozen cell pellets from single 150 mm dishes were thawed on ice in 1 ml 20 mM Tris pH 7.2, spun and resuspended in 1.5 ml hypotonic Igepal C-630 lysis buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.2% Igepal C-630, 2 mM EDTA, 1 mM EGTA) supplemented with 1x Complete, EDTA-free protease inhibitor cocktail (Roche Applied Science) and 0.5 units/µl SUPERase IN RNase inhibitor (Thermo Fisher Scientific). Cells were kept on ice for 30 min with occasional mixing. Nuclei were spun at 2 krpm for 5 min in a benchtop centrifuge at room temperature, and the buffer exchanged with SDS washing buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.3% SDS, 2 mM EDTA, 1 mM EGTA) supplemented with inhibitors as listed for the hypotonic Igepal C-630 lysis buffer. Samples were incubated for 20 min at room temperature in a thermoblock with constant mixing at 750 rpm. After 10 min of the incubation, Triton X-100 was added for a final concentration of 1.7%. Nuclei were then washed once in 10 mM Tris pH 7.2, 5 mM NaCl, 0.5 mM EDTA, 1% Triton X-100, supplemented with inhibitors as specified above, and once in the same buffer with only 0.05% Triton X-100. Nuclei were resuspend in 0.2 ml wash buffer with 0.05% Triton X-100 and sonicated in 15 ml falcon tubes using a bioruptor UCD-200 sonicator (Diagenode) with power set to medium for 3-5 cycles of 10 seconds on followed by 10 seconds off at 8C. After 3 cycles of sonication, the disruption of nuclei was inspected using trypan blue staining and light microscopy. Sonicated nuclear homogenates were flash frozen in liquid nitrogen and stored at -80C until use.  Proximity RNA-Seq - further details discussed in doi: https://doi.org/10.1101/196147

treatment_protocol: Proximity RNA-Seq Crosslinking    At 70-80 % confluency in 150 mm dishes, cells were crosslinked. Culture medium was replaced by 19.8 ml pre-warmed 1x PBS, and 0.2 ml freshly prepared 10 mM EGS (Thermo Fisher Scientific) in DMSO was added drop-wise for 1 mM final concentration. Cells were incubated for 10 min at 37C. 1.4 ml 16% formaldehyde (Agar Scientific) were subsequently added to dishes for a final concentration of 1% and the incubation was extended for another 10 min at room temperature. To quench crosslinking reactions, 3.5 ml 1M glycine was added and cells were scraped immediately and pelleted in a 50 ml falcon tube at 210 x g for 5 min at 4C. The supernatant was removed and cell pellets washed with 1x PBS supplemented with 125 mM glycine. A second wash with 1x PBS was carried out subsequently. Cell pellets were flash frozen in liquid nitrogen and stored at -80C until use.

value: SHY neuroblasts


title: R1_4sU_Seq_HighMyc_Minus_Strand

status: Public on Mar 27 2019

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

description: nascent RNA

data_processing:
Library strategy: 4sU Seq
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
genome build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: U2OS cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using miRNeasy columns and biotinylated. This was followed by pulldown using streptavidin-MyOne beads and elution
NEB Ultra/Ultra Directional RNA Seq

treatment_protocol: Dox - 12-16 hours (when dox is added)/48 hours

tag: treatment

tag: sirna

tag: antibody


title: Nestin-cKO_Bic_replica3

tag: genotype/variation

value: Nestin-cKO

value: Stimulated with bicuculline

value: Hippocampal cultures of CBP-deficient neurons

value: AGTTCC


title: Hi-C_Rep1

data_processing:
Standard Illumina base calling pipeline, generating FASTQ files
Data analysis using HiCUP and Bowtie2
Genome_build: Human GRCh38

extract_protocol:
Hi-C    Nuclei were prepared by lysing cells (2-10 million cells) in 10 mM Tris pH 8, 0.2 % Igepal CA-420, 10 mM NaCl supplemented with protease inhibitor cocktail tablet (Roche complete, EDTA-free) for 30 min on ice. Nuclei were pelleted at 300 x g for 5 minutes at 4C, then nuclei were washed in 1 ml ice-cold 1.25x NEbuffer 2 and resuspended in 360 µl of the same buffer. 11 µl 10% SDS per tube (0.3% final) were added, mixed carefully by pipetting, and incubated at 37°C for 45 min, shaking at 950 rpm. To disrupt remaining clumps, nuclei were pipetted up and down several times during incubation. 75 µl 10% Triton X-100 per tube (1.6% final) was added, and the mixture was incubated at 37°C for 45 min, shaking at 950 rpm
To digest the chromatin 1500 units of HindIII (15 µl at 100U/µl NEB) were added and the reaction mix was incubated at 37°C overnight while rotating at 950 rpm. The reaction was then placed on ice. To fill in the restriction fragment overhangs and mark the DNA ends with biotin, 1.5 µl 10 mM dCTP, 1.5 µl 10 mM dGTP, 1.5 µl 10 mM dTTP, 37.5 µl 0.4 mM biotin-14-dATP (Invitrogen) and 10 μl 5 U/μl Klenow (DNA polymerase I large fragment, NEB) were added and mixed before incubation for 75 minutes at 37°C while shaking at 700 rpm every 30 seconds for a duration of 10 seconds. Repaired ends were then re-ligated. A 2x ligation mix of following composition was added: 100 µl 10x ligation buffer (NEB), 10 μl 10mg/ml BSA, 15 µl 1U/μl T4 DNA ligase (Invitrogen) and 425 µl water. The reaction was mixed by pipetting and incubated overnight at 16ºC. After pelleting at 300 x g for 2 min, nuclei were resuspended in 400 µl TLE and 50 µl 10 mg/ml Proteinase K (Roche) and incubated at 37ºC for two hours. Formaldehyde crosslinks were reversed by increasing the temperature to 65ºC for the duration of around 16 hours. Then 20 µl of 10 mg/ml RNase A were added and the mixture incubated at 37ºC for 1 hour. DNA was purified by Phenol/chloroform extraction and ethanol/Na acetate precipitation. Purified DNA was quantitated using the Quant-iT PicoGreen kit (Invitrogen) according to manufacturer’s instructions. DNA was then sonicated using a Covaris LE220 sonicator. The sample (from 5 to 10 µg) was diluted in 130 µl water per tube and sonicated to 300-500 bp fragments using the following settings: fill level 10, duty cycle 15, peak incident power (w) 500, cycles per burst 200, time (seconds) 58.   Ends were repaired and accessible biotin removed by the addition of 16 µl ligation buffer (10X), 2 µl 10 mM dATP, 5 µl T4 DNA Polymerase (15 U per 5 µg HiC library, NEB), 7 µl water for a total of 160 µl. The mix was incubated at 20ºC for 30 min. Then 5 µl of 10 mM dNTPs, 4 µl 10x Ligation buffer, 5 µl T4 PNK (10 U/µl, NEB), 1 µl Klenow and 25 µl water for a total of 200 µl was added, and the mixture was incubated at 20ºC for 30 min. The reaction was terminated by purification and size selection of DNA fragments aiming at a length of around 250-550 bp using Ampure XP beads (Beckman Coulter) according to manufacturer’s instructions. A first round of selection was performed with a volume of Ampure XP beads 0.6 x the DNA sample volume followed by a second round with 0.9 x the volume. DNA was finally eluted in 300 µl TLE. Ligation products with internal biotin were selected using 150 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen). Beads were washed in 400 µl 5 mM Tris pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween (TB) and then resuspended in 300 µl Tris-HCl pH8.0, 1mM EDTA, 2M NaCl (NTB). Beads were then mixed with Hi-C DNA and incubated for 20 min. Subsequently, beads were capture on a magnetic rack and washed twice with 5 mM Tris pH 8.0, 0.5 mM EDTA, 1M NaCl and once in 0.5 x TB for 3 min at 55ºC rotating at 750 rpm. Beads were then washed once in 1x NEB2 buffer (NEB) and resuspended in 10 µl 10 x NEB 2, 5 µl 10mM dATP, 5 µl Klenow exo- (NEB) and 80 µl water to A-tail DNA ends. The mixture was incubated for 37ºC for 30 min. Two washes followed with 400 µl 0.5x TB incubating at 55ºC for 3 min rotating at 750 rpm. After an additional wash in 1x T4 DNA ligation buffer (NEB), beads were resuspended in 50 µl 1x ligation buffer and transferred to a new tube. 4 µl of Hi-C adapter (15 µM stock) and 2 µl NEB T4 Ligase (400 U/µl, NEB) were added, and the reaction was incubated at room temperature for 2 hours. Beads were captured on the magnetic rack and then washed twice in TB, once in NTB and finally in 1x NEB2 buffer before resuspension in 40 µl 1x NEB2. Hi-C libraries were amplified by PCR off the beads using 5 µl beads in a 50 µl reaction using PCR kit (Phusion, NEB) according to manufacturer’s instructions. PCR products were purified with 0.85 x volume Ampure XP beads according to manufacturer’s instructions and eluted with 30 µl TLE. The concentration and fragment size distribution of libraries were determined by Bioanalyzer profiles (Agilent Technologies) and Kapa Illumina SYBR green qPCR (Kapa Biosystems) according to manufacturer’s instructions.

treatment_protocol: Hi-C Crosslinking    SH-SY5Y cells were cross-linked with 2% formaldehyde in DMEM medium, supplemented with 10% FBS, in tissue culture dishes for 10 minutes at room temperature. Then glycine was added to a final concentration of 100 mM. Cells were scraped on ice and pelleted at 210 x g for 5 min at 4C. Subsequently, cells were washed once in 1x PBS with 100 mM glycine and once in 1x PBS at 4C. After removing PBS, cell pellets were flash-frozen and stored at -80C.


title: Hi_C_Rep2


title: Nestin-cKO_NS_replica3

value: Non stimulated

value: CTTGTA


title: Pool7

extract_protocol: Proximity RNA-Seq    Frozen cell pellets from single 150 mm dishes were thawed on ice in 1 ml 20 mM Tris pH 7.2, spun and resuspended in 1.5 ml hypotonic Igepal C-630 lysis buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.2% Igepal C-630, 2 mM EDTA, 1 mM EGTA) supplemented with 1x Complete, EDTA-free protease inhibitor cocktail (Roche Applied Science) and 0.5 units/µl SUPERase IN RNase inhibitor (Thermo Fisher Scientific). Cells were kept on ice for 30 min with occasional mixing. Nuclei were spun at 2 krpm for 5 min in a benchtop centrifuge at room temperature, and the buffer exchanged with SDS washing buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.3% SDS, 2 mM EDTA, 1 mM EGTA) supplemented with inhibitors as listed for the hypotonic Igepal C-630 lysis buffer. Samples were incubated for 20 min at room temperature in a thermoblock with constant mixing at 750 rpm. After 10 min of the incubation, Triton X-100 was added for a final concentration of 1.7%. Nuclei were then washed once in 10 mM Tris pH 7.2, 5 mM NaCl, 0.5 mM EDTA, 1% Triton X-100, supplemented with inhibitors as specified above, and once in the same buffer with only 0.05% Triton X-100. Nuclei were resuspend in 0.2 ml wash buffer with 0.05% Triton X-100 and sonicated in 15 ml falcon tubes using a bioruptor UCD-200 sonicator (Diagenode) with power set to medium for 3-5 cycles of 10 seconds on followed by 10 seconds off at 8C. After 3 cycles of sonication, the disruption of nuclei was inspected using trypan blue staining and light microscopy. Sonicated nuclear homogenates were flash frozen in liquid nitrogen and stored at -80C until use.   Proximity RNA-Seq - further details discussed in doi: https://doi.org/10.1101/196147


title: Nestin-cKO_Bic_replica2

value: CCGTCC


title: Pool5

extract_protocol:
Proximity RNA-Seq Frozen cell pellets from single 150 mm dishes were thawed on ice in 1 ml 20 mM Tris pH 7.2, spun and resuspended in 1.5 ml hypotonic Igepal C-630 lysis buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.2% Igepal C-630, 2 mM EDTA, 1 mM EGTA) supplemented with 1x Complete, EDTA-free protease inhibitor cocktail (Roche Applied Science) and 0.5 units/µl SUPERase IN RNase inhibitor (Thermo Fisher Scientific). Cells were kept on ice for 30 min with occasional mixing. Nuclei were spun at 2 krpm for 5 min in a benchtop centrifuge at room temperature, and the buffer exchanged with SDS washing buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.3% SDS, 2 mM EDTA, 1 mM EGTA) supplemented with inhibitors as listed for the hypotonic Igepal C-630 lysis buffer. Samples were incubated for 20 min at room temperature in a thermoblock with constant mixing at 750 rpm. After 10 min of the incubation, Triton X-100 was added for a final concentration of 1.7%. Nuclei were then washed once in 10 mM Tris pH 7.2, 5 mM NaCl, 0.5 mM EDTA, 1% Triton X-100, supplemented with inhibitors as specified above, and once in the same buffer with only 0.05% Triton X-100. Nuclei were resuspend in 0.2 ml wash buffer with 0.05% Triton X-100 and sonicated in 15 ml falcon tubes using a bioruptor UCD-200 sonicator (Diagenode) with power set to medium for 3-5 cycles of 10 seconds on followed by 10 seconds off at 8C. After 3 cycles of sonication, the disruption of nuclei was inspected using trypan blue staining and light microscopy. Sonicated nuclear homogenates were flash frozen in liquid nitrogen and stored at -80C until use.
Proximity RNA-Seq - further details discussed in doi: https://doi.org/10.1101/196147


title: Nestin-cKO_Bic_replica1

value: TGACCA


title: Nestin-cKO_NS_replica1

value: CGATGT


title: NET-CAGE_GM12878_6M_biologicalRep2

status: Public on Jun 10 2019

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

country: Japan

institute: RIKEN, Yokohama

description: CNhi11026_171220_SN554_0340_ACBAYYACXX_NoIndex_L003_R1_001_TAC

data_processing:
Library strategy: RNA-seq (CAGE)
For all our datasets we performed the following steps, (i) split reads by barcode, (ii) trimmed reads to remove barcode sequences and (iii) removed reads aligned to rRNA sequences (Human: GenBank U13369.1; Mouse: GenBank BK000964.3). These steps were performed using MOIRAI (Hasegawa et al., 2014) for human cell line data and using Trimmomatic v 0.36 (Bolger et al., 2014) and MOIRAI (Hasegawa et al., 2014) for mouse tissue data. For all CAGE based data and mouse RNA-seq data, sequences with base ‘N’ were also removed.
Non rRNA reads were mapped hg19 genome and human reference gene model Gencode v27lift37 comprehensive using  STAR v 2.5.0a with the following parameters for indexing: --runThreadN 12 --runMode genomeGenerate --genomeDir genome.fa --sjdbGTFfile Gencodeannotation.gtf and the following parameters for mapping: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --out FilterMultimapNmax 1 --readFilesCommand zcat.
Transcription start sites for CAGE based data were identified using bedtools v 2.2.25 (Quinlan and Hall, 2010) as described here: http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment
Genome_build: Human: hg19 and Mouse:mm9
Supplementary_files_format_and_content: Bed 6 file for trasncription start sites. Scores represent aggregated tags with same starting position.

source_name: Blood

growth_protocol: MCF-7, HeLa-S3 and HepG2 cells were cultured at 37 ˚C under 5% CO2 in DMEM with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS. GM12878 and K562 cells were cultured at 37 ˚C under 5% CO2 in RPMI 1640 with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS.

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Approximately 1.0 × 107 cells were used for total and nascent RNA fractionation. Culture medium was transferred to a conical centrifuge tube and centrifuged at 800 G for 5 minutes at 4 ˚C. The supernatant was removed and the cell pellets were washed with 5 mL of ice-cold D-PBS. To lyse cells, 1,000 μL of Buffer A (Nuclei ez lysis buffer (Sigma-Aldrich), 25 μM alpha-amanitin (FUJIFILM Wako Pure Chemical), 1× cOmplete Protease Inhibitor solution (Sigma-Aldrich) and 20 units of SUPERase IN RNase Inhibitor (Thermo Fisher Scientific)) was added to the cell pellets and resuspended by gentle vortex. 100 μL of the cell lysate was sampled and mixed with 700 μL of QIAzol for total RNA extraction. The remaining lysate was set on ice for 10 minutes. Then the lysate was centrifuged at 800 G for 5 minutes at 4 ˚C. The pellets were washed once with 600 μL of Buffer A.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

treatment_protocol: For the time course experiment, MCF-7 cells were serum-starved for 16 hours, and heregulin beta-1 was added to the medium at a final concentration of 10 nM. Cells were harvested at 0 (no treatment), 15, 30, 45, 60, 120, 180 and 360 minutes in triplicates.

value: GM12878 cell line

tag: urea treatment

value: 6 M

tag: molecule subtype

value: Nascent RNA


title: cWT_Bic_replica1

value: Wild type

value: Hippocampal cultures of neurons

value: GTGAAA


title: cWT_NS_replica2

value: ACAGTG


title: 4-OH Tamoxifen 3

status: Public on May 26 2019

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

country: USA

institute: University of Illinois at Urbana-Illinois

data_processing:
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.36). Next, the reads were mapped to the Homo sapiens reference genome from Ensembl database and aligned using the STAR alignment tool (Version 2.5.3). After this, the read counts were generated from SUBREAD (Version 1.5.2) and featured counts were outputted for statistical analysis in R. Quality control and normalization was conducted in R using edgeR (Version 3.20.9).
Statistical Analysis and DEGs: Statistical analysis was conducted in R using limma (Version 3.34.9). Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >1.5 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: count files

source_name: mammary cells

growth_protocol: BT474 were cultured in ATCC recommended Hybri-care medium with 10% inactivated FBS, sodium bicarbonate and antibiotics. MDA-MB-134 cells were cultured in Leibovitz’s medium with 20% FBS (HyClone), and 100 g/ml penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies) according to manufacturer protocol and cleaned using QIAGEN clean-up kit. RNA quality was assessed using bioanalyzer.
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

treatment_protocol: BT474 cells were treated with Veh (0.5% EtOH), 10-7 M 4-OH Tamoxifen (Sigma, St. Louis, MO), 10-7 M Selinexor (SXR) (Selleckchem, Houston, TX) or 4-OH Tamoxifen and SXR combination for 24 hours.

tag: cell type


title: cWT_NS_replica1


title: Pool2

extract_protocol:
Proximity RNA-Seq    Frozen cell pellets from single 150 mm dishes were thawed on ice in 1 ml 20 mM Tris pH 7.2, spun and resuspended in 1.5 ml hypotonic Igepal C-630 lysis buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.2% Igepal C-630, 2 mM EDTA, 1 mM EGTA) supplemented with 1x Complete, EDTA-free protease inhibitor cocktail (Roche Applied Science) and 0.5 units/µl SUPERase IN RNase inhibitor (Thermo Fisher Scientific). Cells were kept on ice for 30 min with occasional mixing. Nuclei were spun at 2 krpm for 5 min in a benchtop centrifuge at room temperature, and the buffer exchanged with SDS washing buffer (20 mM Tris, pH 7.2, 5 mM NaCl, 0.3% SDS, 2 mM EDTA, 1 mM EGTA) supplemented with inhibitors as listed for the hypotonic Igepal C-630 lysis buffer. Samples were incubated for 20 min at room temperature in a thermoblock with constant mixing at 750 rpm. After 10 min of the incubation, Triton X-100 was added for a final concentration of 1.7%. Nuclei were then washed once in 10 mM Tris pH 7.2, 5 mM NaCl, 0.5 mM EDTA, 1% Triton X-100, supplemented with inhibitors as specified above, and once in the same buffer with only 0.05% Triton X-100. Nuclei were resuspend in 0.2 ml wash buffer with 0.05% Triton X-100 and sonicated in 15 ml falcon tubes using a bioruptor UCD-200 sonicator (Diagenode) with power set to medium for 3-5 cycles of 10 seconds on followed by 10 seconds off at 8C. After 3 cycles of sonication, the disruption of nuclei was inspected using trypan blue staining and light microscopy. Sonicated nuclear homogenates were flash frozen in liquid nitrogen and stored at -80C until use.
Proximity RNA-Seq - further details discussed in doi: https://doi.org/10.1101/196147

value: SHY neuroblasts


title: R1_4sU_Seq_MYC_OFF_Plus_Strand

description: nascent RNA

tag: cell line

value: siMYC+EtOH


title: 1065

status: Public on Mar 04 2019

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

institute: Institute of Cancer Research (ICR), London

data_processing:
Base-calling was performed using Illumina Casava.
Quality of fastq files was checked using fastqc (v0.11.4) for read counts and quality.
Mapping to the reference transcriptome (hg19) and assessment of mapping quality was performed using RSEM (v1.2.29) and samtools flastat (v.1.3)
Percentage of reads aligned to ribosomal, coding, UTR, intronic and intergenic regions was assessed using CollectRnaSeqMetrics from picard (v2.1.0) on mapping to the reference genome (hg19).
Transcripts per million (TPM) values were collected from RSEM, and genes with <20% missing values were retained and log2(TPM+1) transformed.
Genome_build: hg19
Supplementary_files_format_and_content: .genes.results files provide raw counts, TPM and FPKM values for each sample as output from RSEM.

source_name: RNA; Rectum: upper rectum

extract_protocol:
15 mg of tissues were homogenized using 1mL of Invitrogen™ TRIzol™ with gentleMACS™ M tube using Miltenyi Biotec gentleMACS™ Octo Dissociator as per the manufacturers’s instructions. The total RNA from homogenized tissues was extracted using QIAGEN RNeasy Mini Kit, following the manufacturer’s protocol. The samples were checked for their quality and quantity using Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA)  and NanoDrop 2000 Spectrophotometer respectively.
RNAseq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Singapore). Libraries were quality controlled using KAPA qPCR (Roche, Singapore) and Agilent Bioanalyzer, before pooling and sequencing on the Illumina HiSeq.

tag: cohort

value: Singapore

value: Primary CRC total RNA

tag: site

tag: age

tag: gender

value: Male

tag: grade

value: AJCC G2:Moderately differentiated

tag: Stage

value: IIA

tag: t

tag: n

tag: m


title: 1190

tag: tissue

value: Female

value: IIIC


title: 1073

source_name: RNA; Colon: sigmoid colon

value: Colon

value: IV


title: cWT_Bic_replica2

tag: strain/background

tag: treatment

value: Stimulated with bicuculline

tag: flowcell

tag: index

value: GCCAAT


title: 1165

source_name: RNA; Colon: splenic flexure

value: Colon:splenic flexure

value: AJCC G3:Poorly differentiated

value: IIB


title: 1054

value: IIIB


title: 1144


title: 1146

source_name: RNA; Colon: rectosigmoid colon


title: 1201

source_name: RNA; Colon: hepatic flexure

value: Colon:hepatic flexure


title: 1066

source_name: RNA; Colon: ascending colon


title: 1227


title: Nestin-cKO_NS_replica2

tag: genotype/variation

value: Nestin-cKO

value: Non stimulated

value: Hippocampal cultures of CBP-deficient neurons

value: CAGATC


title: 1158

value: Singapore

value: Primary CRC total RNA

value: AJCC G2:Moderately differentiated


title: 1099

source_name: RNA; Rectum: rectum

value: Rectum

value: Female

value: IIA


title: 1079

value: IV


title: 1017

source_name: RNA; Colon: descending colon

value: Colon

value: Male

value: Mucinous

value: IIIC

value: MX


title: 980

value: IIB


title: 1053

source_name: RNA; Colon: ascending large bowel


title: 1311

value: Colon:splenic flexure


title: 6008

type: RNA

hyb_protocol: The hybridization reactions were prepared according to the manufacturers’ instructions for 18 h at 65 °C using standard chemistry reagents.

scan_protocol: Scanning was performed using the NanoString nCounter Digital Analyzer.

data_processing: Following the manufacturer's guidelines and using the NanoString nSolver analysis software (version 3), counts were firstly corrected to background noise using the geometric mean of 8 negative and 6 positive control spike-ins in each lane. Housekeeping genes with raw count >50 and selected by the geNorm algorithm were retained for normalisation.

label: biotin

source_name: RNA; Colon: right; Adenocarcinoma of colon

label_protocol: For standard chemistry, custom CodeSets (capture probes tagged to biotin labels and reporter probes tagged to fluorescently color coded molecular barcodes) for selected genes were designed and built by NanoString Technologies.

extract_protocol: Total RNA for OriGene samples was purchased directly from OriGene (Rockville, MD, USA). Total RNA for Montpellier samples was extracted as detailed in Del Rio et. al., Journal of Clinical Oncology (2007) DOI:10.1200/JCO.2006.07.4199. Total RNA for RETRO-C FFPE samples was extracted using the Ambion RecoverAll™ protocol as per manufacturer’s instructions (Life Technologies, CA, USA). The samples were checked for their quality and quantity using Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA)  and NanoDrop 2000 Spectrophotometer respectively.

value: RETRO-C

value: III


title: 6005

source_name: RNA; Rectum; Adenocarcinoma of rectum

value: II


title: 5001

source_name: RNA; Colon: left; Adenocarcinoma of colon


title: 6006


title: 4047


title: 4042


title: 4033


title: 4045


title: CR561163

hyb_protocol: Following the Affymetrix standard protocol, single-stranded cDNA was fragmented and biotin labelled, then hybridized at 45C for 16 hours to the GeneChip HTA Array 2.0.

scan_protocol: GeneChips were washed and stained using an Affymetrix Fluidics Station 450 and SAPE. The arrays were then scanned using an Affymetrix GeneChip Scanner.

data_processing: CEL files were directly exported from the GeneChip scanner and subsequently processed in R v3.3.2 using packages oligo v1.38.0 and affy v1.52.0 and RMA normalisation.

source_name: RNA (5 µg); Colon: right; Adenocarcinoma of colon, mucinous

label_protocol: Biotin labelled cRNA was prepared following the Affymetrix standard protocol using 100 ng RNA.

extract_protocol: Total RNA was purchased directly from OriGene (Rockville, MD, USA).

value: Not Reported


title: CR560523

source_name: RNA (5 µg); Colon: right; Adenocarcinoma of colon

value: Primary CRC total RNA

value: AJCC G1:Well differentiated


title: 4019


title: CR560527

source_name: RNA (5 µg); Colon: left; Adenocarcinoma of colon


title: CR560590

source_name: RNA (5 µg); Cecum; Adenocarcinoma of colon

value: Cecum


title: CR560798

source_name: RNA (5 µg); Colon; Adenocarcinoma of colon, metastatic

value: Liver metastasis CRC total RNA

value: Liver

value: AJCC G2:Moderately differentiated

value: TX

value: NX


title: CR560080

value: Male

value: I


title: CR560403

source_name: RNA (5 µg); Colon: sigmoid; Adenocarcinoma of colon

value: MX


title: CR560126

source_name: RNA (5 µg); Colon: rectosigmoid; Adenocarcinoma of colon

value: IIIC


title: CR560603

source_name: RNA (5 µg); Colon: transverse; Adenocarcinoma of colon

value: Female

value: IIA


title: CR561060

source_name: RNA (5 µg): NA

value: Total RNA


title: CR560671


title: CR560973

value: IIIB


title: 4002

value: RETRO-C

value: Rectum

value: III


title: CR560367

value: Primary CRC total RNA

value: Cecum

value: AJCC G3:Poorly differentiated


title: CR560476

value: AJCC G2:Moderately differentiated


title: 6008REC_1

hyb_protocol: The hybridization reactions were prepared according to the manufacturers’ instructions for 20 h at 67 °C using elements chemistry reagents.

source_name: RNA; Colon: right; Adenocarcinoma of colon; Local recurrence

label_protocol: For elements chemistry, nCounter Elements™ TagSets reagents containing nCounter Elements TagSet (NanoString Technologies) and custom-designed target-specific oligonucleotide probe pairs (reporter - Probe A and capture - Probe B probes; from Integrated DNA Technologies, Inc.; IDT, Leuven, Belgium) were obtained. The TagSets consists of fluorescently-labeled specific Reporter Tags (to resolve and count individual nucleic acid targets during data collection; Probe A) and a biotinylated universal Capture Tags (to capture the hybridized target nucleic acid to the streptavidin-coated imaging surface; Probe B). In order to assemble the nCounter Elements™ TagSets and probe pairs to be ready for hybridization, master stocks and working stocks of Probe A (at final hybridizing concentration of 20 pM) and Probe B (at final hybridizing concentration of 100 pM) concentrations were prepared. The Probe A and TagSets were first mixed to create a partial master mix followed by Probe B to create a complete master mix, all at the room temperature.

extract_protocol: Total RNA for OriGene samples was purchased directly from OriGene (Rockville, MD, USA). Total RNA for Del Rio samples was extracted as detailed in Del Rio et. al., Journal of Clinical Oncology (2007) DOI:10.1200/JCO.2006.07.4187. Total RNA from homogenized tissues for the Singapore cohort was extracted using QIAGEN RNeasy Mini Kit, following the manufacturer’s protocol.  Total RNA for RETRO-C FFPE samples was extracted using the Ambion RecoverAll™ protocol as per manufacturer’s instructions (Life Technologies, CA, USA). The samples were checked for their quality and quantity using Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA)  and NanoDrop 2000 Spectrophotometer respectively.

tag: replicate

value: TRUE

value: Local recurrence CRC total RNA


title: 4001


title: CR559521

source_name: RNA (5 µg); Rectum; Adenocarcinoma of rectum

value: Male


title: CR559251

value: IV


title: CR560026

value: AJCC G1:Well differentiated


title: 4023


title: 1075_1


title: 6008REC

value: FALSE


title: 6006REC

source_name: RNA; Rectum; Adenocarcinoma of rectum; Local recurrence

value: II


title: 4042REC_1

value: Female


title: 6006REC_1


title: 4047REC_1

source_name: RNA; Rectum; Adenocarcinoma of rectum; Liver metastasis

value: Liver metastasis CRC total RNA


title: 4047REC


title: 4042REC


title: 2009REC

source_name: RNA; Colon: rectum-sigmoid junction; Adenocarcinoma of colon; Liver metastasis

value: Colon:rectum-sigmoid junction


title: 6006

value: RETRO-C


title: 6008

source_name: RNA; Colon: right; Adenocarcinoma of colon


title: 6005

source_name: RNA; Rectum; Adenocarcinoma of rectum

value: Rectum


title: 4047


title: 5001

source_name: RNA; Colon: left; Adenocarcinoma of colon

value: III


title: 4045

value: Primary CRC total RNA


title: 4023


title: 4033


title: 4019


title: 4002


title: 4042


title: 1120


title: 1141


title: 1071


title: 1075


title: 1093


title: 1147


title: 1013


title: CR560671_1

extract_protocol: Total RNA for OriGene samples was purchased directly from OriGene (Rockville, MD, USA). Total RNA for Montpellier samples was extracted as detailed in Del Rio et. al., Journal of Clinical Oncology (2007) DOI:10.1200/JCO.2006.07.4187. Total RNA from homogenized tissues for the Singapore cohort was extracted using QIAGEN RNeasy Mini Kit, following the manufacturer's protocol. The samples were checked for their quality and quantity using Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA) and NanoDrop 2000 Spectrophotometer respectively.

value: OriGene

value: I

value: MX


title: CR560367_1

source_name: RNA; Cecum; Adenocarcinoma of colon

value: TRUE

value: Cecum

value: AJCC G3:Poorly differentiated

value: IIIB


title: CR560026_1

value: Male

value: AJCC G1:Well differentiated

value: IV


title: CR559521_1

value: AJCC G2:Moderately differentiated

value: IIA


title: CR560798

source_name: RNA; Colon: liver metastasis; Adenocarcinoma of colon

value: FALSE

value: Metastatic CRC total RNA

value: Liver

value: TX

value: NX


title: CR559251_1

value: OriGene

value: Primary CRC total RNA


title: CR560527

value: IIIC

value: MX


title: 4001

value: RETRO-C

value: Female

value: III


title: CR560403

source_name: RNA; Colon: sigmoid; Adenocarcinoma of colon

value: Male

value: IIB


title: CR560973_E

value: Cecum

value: AJCC G1:Well differentiated

value: IIIB


title: CR561163_E

source_name: RNA; Colon: right; Adenocarcinoma of colon, mucinous

value: FALSE

value: IIA


title: CR560026

value: IV


title: CR560603_E

source_name: RNA; Colon: transverse; Adenocarcinoma of colon

value: AJCC G2:Moderately differentiated


title: CR561060_E

source_name: RNA: NA

value: Total RNA


title: CR560671_E

value: OriGene

value: I


title: CR560476_E

value: Primary CRC total RNA


title: CR559521_E

value: Rectum

value: MX


title: CR560367_E

value: Female

value: AJCC G3:Poorly differentiated


title: CR560080_E

value: Male


title: 1311

source_name: RNA; Colon: splenic flexure

value: Singapore

value: Colon:splenic flexure


title: CR559251_E


title: CR560590

source_name: RNA; Colon: cecum; Adenocarcinoma of colon

value: Cecum

value: AJCC G1:Well differentiated

value: IIIC


title: 1201

source_name: RNA; Colon: hepatic flexure

value: FALSE

value: Colon:hepatic flexure


title: 1218

source_name: RNA; Rectum: rectum


title: CR560523


title: 1158

source_name: RNA; Colon: rectosigmoid colon

value: AJCC G2:Moderately differentiated

value: IV


title: 1190

source_name: RNA; Rectum: upper rectum


title: 1165

value: IIB


title: 1146

value: IIA


title: 1145

value: Primary CRC total RNA

value: IIIB


title: 1127

source_name: RNA; Rectum: lower rectum

value: I


title: 973

source_name: RNA; Colon: sigmoid colon


title: 980

source_name: RNA; Colon: ascending colon

value: Colon


title: CR560126

source_name: RNA; Colon: rectosigmoid; Adenocarcinoma of colon

value: OriGene

value: MX


title: 1079

value: Singapore

value: Female


title: 1073

value: Male


title: 1227

value: Colon:splenic flexure


title: 1099

value: Rectum


title: 1066

value: FALSE


title: 1053

source_name: RNA; Colon: ascending large bowel


title: 1054


title: 1235

source_name: RNA; Colon: sigmoid


title: 1017

source_name: RNA; Colon: descending colon

value: Mucinous

value: IIIC


title: FP

value: Montpellier

value: IV


title: 1144

value: AJCC G2:Moderately differentiated

value: IIA


title: 1011

source_name: RNA; Colon: rectum

value: Primary CRC total RNA

value: IIIB


title: SS

source_name: RNA; Colon: left; Adenocarcinoma of colon


title: GB


title: JR_E


title: TD_E


title: PEC


title: JGI_E


title: RG


title: PM_E


title: CB_E

source_name: RNA; Colon: right; Adenocarcinoma of colon


title: NC_E

source_name: RNA; Colon: transverse; Adenocarcinoma of colon


title: AM_E

source_name: RNA; Colon: rectum-sigmoid junction; Adenocarcinoma of colon

value: Colon:rectum-sigmoid junction


title: PD_E


title: 1065


title: JC_E


title: MB_E


title: MV_E


title: TD

label_protocol: For standard chemistry, custom CodeSets (capture probes tagged to biotin labels and reporter probes tagged to fluorescently color coded molecular barcodes) for selected genes were designed and built by NanoString Technologies

extract_protocol: Total RNA for OriGene samples was purchased directly from OriGene (Rockville, MD, USA). Total RNA for Montpellier samples was extracted as detailed in Del Rio et. al., Journal of Clinical Oncology (2007) DOI:10.1200/JCO.2006.07.4199


title: JR


title: JGI


title: AM


title: PM


title: CB


title: NC


title: MT


title: PD


title: JC


title: MB


title: CR560973

source_name: RNA; Cecum; Adenocarcinoma of colon

value: OriGene

value: Cecum

value: AJCC G1:Well differentiated


title: CR560671

value: Female

value: I

value: MX


title: MV


title: CR561060

source_name: RNA: NA

value: Total RNA


title: CR560476


title: CR560603


title: MT_E

value: FALSE

value: Male


title: CR560080


title: FW5559_Spt16-AID degron induction 2 hours total RNA-Seq biological replicate 2

status: Public on Dec 20 2018

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to all S. cerevisiae genes downloaded from the Ensembl genome browser (assembly R64-1-1, release 90; Kersey et al., 2016). The parameters used were “--star-output-genome-bam --forward-prob 0”, and all other parameters were kept as default.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Prior to generation of genome-wide bigWig files STAR genome BAM files were filtered using the BamTools filter command with parameters "-mapQuality 255 -isMapped true -isMateMapped true -isPaired true -isProperPair true -isPrimaryAlignment true" (Barnett et al., 2011).
Strand-specific bedGraph files were generated from filtered STAR genome BAM files using the genomeCoverageBed command from BEDTools (Quinlan & Hall, 2010) with parameters "-bg -split -scale <NORM_FACTOR> -strand <STRAND> -du". Normalisation factors generated by DESeq2 with respect to the transcriptome were used to scale the tracks. Strand was set to "-" and "+" for sense and antisense coverage, respectively. For antisense bedGraph files, negative coverage values were obtained with the command sed 's/[^\t]*/-&/4'. bedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).
Genome_build: Ensembl R64-1-1 release 90
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

organism: Saccharomyces cerevisiae

source_name: FW5559 (MATa leu2Δ0 met15Δ0 ura3Δ0 spt16::SPT16-3V5-IAA7::KANMX6 his3::pGPD1-osTIR::HIS3) BY4741 derivative

growth_protocol: Cells were grown in yeast extract-peptone-dextrose (YPD) medium in conical flasks at 30 °C, shaking at 300 RPM in incubators.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water.
Total RNA from yeast was incubated with rDNase (Machery-Nagel rDNase Set) and column purified (Machery-Nagel NucleoSpin RNA) prior to sequencing library preparation. For total RNA-Seq libraries, intact yeast total RNA was depleted of rRNA with the Illumina RiboZero Gold rRNA removal kit (yeast) (Illumina MRZY1324). 1 μg of yeast total RNA was used to generate strand-specific libraries for total RNA sequencing using the TruSeq Stranded mRNA Kit (Illumina 20020594) according to the manufacturer’s instructions. Library quality control was performed using the Agilent 2200 TapeStation with D1000 screentape (Agilent Technologies). Each library was sequenced on the HiSeq 2500 platform using V4 chemistry (Illumina) and typically generated ~37 million 101 bp strand-specific paired-end reads per sample.

treatment_protocol: Cells were either left untreated (wild-type or gene deletion strains), or treated during exponential growth (OD600 ~0.8) by adding 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO, or an equivalent volume of DMSO (vehicle).

tag: strain

value: yeast strains in small batch culture

value: 500 μM auxin 3-IAA (2h)


title: FW5559_Spt16-AID degron induction 2 hours total RNA-Seq biological replicate 1


title: CR559251

tag: cohort

value: IV


title: CR560367

tag: site

value: AJCC G3:Poorly differentiated


title: CR559521

source_name: RNA; Rectum; Adenocarcinoma of rectum

value: Rectum

tag: age

value: AJCC G2:Moderately differentiated

value: IIA


title: FW5555_Spt6-AID degron induction 2 hours total RNA-Seq biological replicate 1

source_name: FW5555 (MATa leu2Δ0 met15Δ0 ura3Δ0 spt6::SPT6-3V5-IAA7::KANMX6 his3::pGPD1-osTIR::HIS3) BY4741 derivative


title: FW5555_Spt6-AID degron induction 2 hours total RNA-Seq biological replicate 2


title: FW5559_Spt16-AID degron no induction total RNA-Seq biological replicate 1

value: DMSO (2h)


title: FW5559_Spt16-AID degron no induction total RNA-Seq biological replicate 2


title: FW5555_Spt6-AID degron no induction total RNA-Seq biological replicate 2


title: FW5555_Spt6-AID degron no induction total RNA-Seq biological replicate 1


title: FW5609_Rlf2 deletion total RNA-seq biological replicate 2

source_name: FW5609 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rlf2::NATMX4) BY4741 derivative

value: no treatment


title: CR561163

source_name: RNA; Colon: right; Adenocarcinoma of colon, mucinous

value: OriGene

value: Primary CRC total RNA

tag: gender


title: FW5609_Rlf2 deletion total RNA-seq biological replicate 1


title: FW5543_Spt10 deletion total RNA-seq biological replicate 2

source_name: FW5543 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 spt10::NATMX4) BY4741 derivative


title: FW5547_Spt21 deletion total RNA-seq biological replicate 1

source_name: FW5547 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 spt21::NATMX4) BY4741 derivative


title: FW5138_Rap1-AID degron induction 2 hours rescue Rap1 (1-600, CTD_del) total RNA-seq biological replicate 1

source_name: FW5138 (MATa his3Δ1 met15Δ0 ura3Δ0 rap1::RAP1-3V5-IAA7::KANMX6 leu2::pGPD1-osTIR::LEU2 his3::UASRap1-Myc5-NLS-Rap1(1-600)::HIS3) BY4741 derivative


title: LNCAP_H3K27ac_DSG

status: Public on Dec 27 2018

city: Amsterdam

first: Abhishek

last: Singh

address: Plesmanlaan

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (Ensembl release 55: Homosapiens GRCh 37.55) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Genome_build: GRCh 37.55

source_name: LNCAP cell line

growth_protocol: fresh frozen material

extract_protocol:
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

treatment_protocol: Surgical resections from Prostate, breast and endometrium tumors.

tag: chip antibody

value: H3K27ac (Active Motif; 39133)

tag: patient id

tag: case/control

value: DSG


title: FW3877_Rap1-AID degron no induction total RNA-Seq biological replicate 2

source_name: FW3877 (MATa leu2Δ0 met15Δ0 ura3Δ0 rap1::RAP1-3V5-IAA7::KANMX6 his3::pGPD1-osTIR::HIS3) BY4741 derivative


title: FW3877_Rap1-AID degron no induction total RNA-Seq biological replicate 1


title: Rap1-AID degron no induction polyA RNA-Seq biological replicate 1

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_POLYA_UNINDUCED_30M_R1

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters "--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC".
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to all S. cerevisiae genes downloaded from the Ensembl genome browser (assembly R64-1-1, release 90; Kersey et al., 2016). The parameters used were "--star-output-genome-bam --forward-prob 0", and all other parameters were kept as default.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Prior to generation of genome-wide bigWig files STAR genome BAM files were filtered using the BamTools filter command with parameters "-mapQuality 255 -isMapped true -isMateMapped true -isPaired true -isProperPair true -isPrimaryAlignment true" (Barnett et al., 2011).
Strand-specific bedGraph files were generated from filtered STAR genome BAM files using the genomeCoverageBed command from BEDTools (Quinlan & Hall, 2010) with parameters "-bg -split -scale <NORM_FACTOR> -strand <STRAND> -du". Normalisation factors generated by DESeq2 with respect to the transcriptome were used to scale the tracks. Strand was set to "-" and "+" for sense and antisense coverage, respectively. For antisense bedGraph files, negative coverage values were obtained with the command sed 's/[^\t]*/-&/4'. bedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).
Genome_build: Ensembl R64-1-1 release 90
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.
Genome-wide bigWig files for both sense and antisense coverage.

source_name: yeast strains in small batch culture

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water.
Total RNA from yeast was incubated with rDNase (Machery-Nagel rDNase Set) and column purified (Machery-Nagel NucleoSpin RNA) prior to sequencing library preparation. For total RNA-Seq libraries, intact yeast total RNA was depleted of rRNA with the Illumina RiboZero Gold rRNA removal kit (yeast) (Illumina MRZY1324). 1 μg of yeast total RNA was used to generate strand-specific libraries for total RNA sequencing using the TruSeq Stranded Total RNA Library Prep Kit (Illumina RS-122-2202) according to the manufacturer’s instructions. For polyA RNA-Seq libraries, 500 ng of intact yeast total RNA was used to generate strand-specific libraries for polyadenylated RNA sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina RS-122-2101) according to the manufacturer’s instructions. Library quality control was performed using the Agilent 2200 TapeStation with D1000 screentape (Agilent Technologies). Each library was sequenced on the HiSeq 2500 platform using V4 chemistry (Illumina) and typically generated ~55 million 101 bp strand-specific paired-end reads per sample.

treatment_protocol: Cells were either left untreated (wild-type samples), or treated during exponential growth (OD600 ~0.8) by adding 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO, or an equivalent volume of DMSO (vehicle).

value: FW3877 (MATa leu2Δ0 met15Δ0 ura3Δ0 rap1::RAP1-3V5-IAA7::KANMX6 his3::pGPD1-osTIR::HIS3) BY4741 derivative

value: DMSO (30min)


title: Rap1-AID degron no induction polyA RNA-Seq biological replicate 2

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_POLYA_UNINDUCED_30M_R2


title: FW5141_Rap1-AID degron induction 2 hours rescue Rap1 (339-600, DBD) total RNA-seq biological replicate 2

source_name: FW5141 (MATa his3Δ1 met15Δ0 ura3Δ0 rap1::RAP1-3V5-IAA7::KANMX6 leu2::pGPD1-osTIR::LEU2 his3::UASRap1-Myc5-NLS-Rap1(339-598)::HIS3) BY4741 derivative


title: FW5141_Rap1-AID degron induction 2 hours rescue Rap1 (339-600, DBD) total RNA-seq biological replicate 1


title: Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 3

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_IAA_2H_R3


title: Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 2

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_IAA_2H_R2


title: Rap1-AID degron induction 2 hours polyA RNA-Seq biological replicate 3

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_POLYA_IAA_2H_R3


title: FW5138_Rap1-AID degron induction 2 hours rescue Rap1 (1-600, CTD_del) total RNA-seq biological replicate 2


title: Rap1-AID degron induction 2 hours polyA RNA-Seq biological replicate 2

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_POLYA_IAA_2H_R2


title: Rap1-AID degron induction 30 minutes total RNA-Seq biological replicate 1

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_IAA_30M_R1

value: 500 μM auxin 3-IAA (30min)


title: Rap1-AID degron no induction polyA RNA-Seq biological replicate 3

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_POLYA_UNINDUCED_30M_R3


title: Rap1-AID degron induction 2 hours polyA RNA-Seq biological replicate 1

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_POLYA_IAA_2H_R1


title: Rap1-AID degron no induction total RNA-Seq biological replicate 1

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_UNINDUCED_R1


title: Wild-type total RNA-Seq biological replicate 2

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
WT_TOTAL_R2

value: FW629 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) BY4741 derivative


title: Rap1-AID degron induction 30 minutes total RNA-Seq biological replicate 3

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_IAA_30M_R3


title: Rap1-AID degron induction 30 minutes total RNA-Seq biological replicate 2

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_IAA_30M_R2


title: Rap1-AID degron no induction total RNA-Seq biological replicate 2

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_UNINDUCED_R2


title: Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 1

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_IAA_2H_R1


title: Wild-type 5' seq replicate 2

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=20 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The primer sequence specific to the protocol was removed by rerunning cutadapt with the parameters “--minimum-length=20 --quality-cutoff=20 -g GCACTCTGAGCAATACC”, and only the reads containing the primer sequence were used for further analysis.
BWA (version 0.5.9-r16) (Li and Durbin, 2009) using default parameters was used to perform the read mapping to the S. cerevisiae genome (assembly R64-1-1, release 90; Kersey et al., 2016).
Uniquely mapped alignments corresponding to the sense and antisense strands were obtained using SAMtools view (version 1.3.1) (Li et al., 2009) with the flags “-q 1 -F 20” and “-q 1 -f 16”, respectively.
BedGraph coverage tracks representing the 5-prime signal per million mapped reads were generated using BEDTools genomeCoverageBed (version 2.26.0) (Quinlan and Hall, 2010) with the parameters “-bg -5 -scale <SCALE_FACTOR>”. For antisense bedGraph files, negative coverage values were obtained with the command sed 's/[^\t]*/-&/4'.
BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).
Genome_build: Ensembl R64-1-1 release 90
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

source_name: FW629 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) BY4741 derivative

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water.
To obtain libraries representing the 5’ ends of polyadenylated and capped transcripts, approximately 5 µg of poly(A)+-RNA together with in-vitro spike ins were first subjected to zinc-mediated fragmentation (Ambion) at 70 °C. The reaction was cleaned up using Qiagen min-elute columns to isolate RNA fragments with mode length of ~200 nt. These fragments were then incubated with shrimp alkaline phosphatase at 37 °C to remove the 5’ phosphate groups of non-capped fragments followed by acid-phenol/chloroform extraction and ethanol precipitation. With the exception of a non-decapping control sample, dephosphorylated fragments were next treated with Cap-Clip™ acid pyrophosphatase (CellScript) to remove the 5’-terminal caps from fragments representing the bona fide 5’ ends of transcripts. After another round of acid-phenol/chloroform extraction and ethanol precipitation, all samples were treated with T4 RNA ligase 1, high concentration (NEB) to introduce a custom adapter sequence to the 5’ un-capped ends of fragments. Excess adapters were removed via a column clean up step. First strand cDNA synthesis was performed using Superscript IV (ThermoFisher) and second strand synthesis was performed using a KAPA HiFi HotStart ReadyMix (KAPA Biosystems). Double-stranded cDNA was quantified by Qubit (Life Technologies) and used as input for library preparation using a KAPA Hyper Prep kit (KAPA Biosystems) and KAPA Single-indexed adapters (KAPA Biosystems). Libraries quantified by Qubit and were sequenced on the Illumina HiSeq 4000 platform with 75-base single-end reads.

treatment_protocol: Cells were either left untreated (wild-type samples), or treated during exponential growth (OD600 ~0.8) by adding 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO.

value: yeast strains in small batch culture


title: Wild-type total RNA-Seq biological replicate 1

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
WT_TOTAL_R1


title: Wild-type total RNA-Seq biological replicate 3

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
WT_TOTAL_R3


title: Rap1-AID degron no induction total RNA-Seq biological replicate 3

description:
allSamples_EXP1_RNASeq_RSEM_TPM.tsv.gz
RAP1_TOTAL_UNINDUCED_R3


title: Wild-type 5' seq replicate 3


title: FW3877_Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 1

value: 500 μM auxin 3-IAA (2h)


title: Wild-type 5' seq no decapping control


title: FW629_Wild-type total RNA-Seq biological replicate 2


title: FW5547_Spt21 deletion total RNA-seq biological replicate 2


title: Wild-type 5' seq replicate 1


title: FW3877_Rap1-AID degron induction 2 hours total RNA-Seq biological replicate 2


title: FW5543_Spt10 deletion total RNA-seq biological replicate 1


title: Rap1-AID degron induction 2 hours 5' seq replicate 3


title: FW629_Wild-type total RNA-Seq biological replicate 1


title: Methylation_LM3

status: Public on Dec 17 2018

city: Shanghai

first: Jin

last: Li

state: Shanghai

address: 130 Dong-An Road

department: Institutes of Biomedical Sciences (IBS)

country: China

institute: Fudan University

data_processing:
ChIP-seq: We firstly filtered out low quality reads. The remaining reads were aligned to human reference genome (hg19) with Bowtie (version 1.0.0). The alignment was unique mapping and allowed up to 2 mismatches. Peaks were identified with the MACS (version14) with default parameters and --nomodel
RNA-seq: We firstly filtered out low quality reads. Then mRNA-seq reads were aligned to hg19 with TopHat2 (v2.0.12) with default parameters. The mapped reads were further analyzed by Cufflinks (v2.2.1) with default parameters to call FPKM of genes.
Methylation sequencing: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters except '-k 20'. We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2.
Repetitive elements methylation by GPS: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters to find the best aligned locus. Mapped reads with MAPQ less than 20 were removed. We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation level/ChIP peak loci/ gene FPKM values for each Sample
tab-delimited CpG.repeat file includes methylation level values only on repeat elements

source_name: hepatoma cell line

growth_protocol: Cell lines were cultured at 37˚C in 5% CO2 in high-glucose DMEM (Hyclone, USA) supplemented with 10% fetal bovine serum (Hyclone, USA), and collected under standard culture protocols.

extract_protocol:
Methylation: Genomic DNA from tissues and cell lines was extracted using QIAamp DNA Mini Kit (Qiagen, 51306, Valencia, CA). 3μg genomic DNA was fragmented into 300-500bp by sonication. ChIP:Approximate 300 ug fixed chromatin and 5 ug antibody were used for each ChIP pull-down. RNA-seq: We extracted approximate 6 micrograms of total RNA, removed ribosomal RNA (rRNA) according to the manufacturer’s instructions with minor modifications.
Libraries were prepared for sequencing using standard Illumina protocols
DNA Methylation sequencing, ChIP-seq and RNA-seq

tag: cell line

value: liver


title: Methylation_GPS_primary_liver_cancer

data_processing:
ChIP-seq: We firstly filtered out low quality reads. The remaining reads were aligned to human reference genome (hg19) with Bowtie (version 1.0.0). The alignment was unique mapping and allowed up to 2 mismatches. Peaks were identified with the MACS (version14) with default parameters and --nomodel
RNA-seq: We firstly filtered out low quality reads. Then mRNA-seq reads were aligned to hg19 with TopHat2 (v2.0.12) with default parameters. The mapped reads were further analyzed by Cufflinks (v2.2.1) with default parameters to call FPKM of genes.
Methylation by GPS: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters except "-k 20". We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Methylation by WGBS: We firstly filtered out low quality reads. Read1 and Read2 were aligned onto reference genome (hg19) using BSMAP with default parameters except -v 3 -g 1. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Repetitive elements methylation by GPS: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters to find the best aligned locus. Mapped reads with MAPQ less than 20 were removed. We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation level/ChIP peak loci/ gene FPKM values for each Sample
tab-delimited CpG.repeat file includes methylation level values only on repeat elements

source_name: liver cells

extract_protocol:
Methylation: Genomic DNA from tissues and cell lines was extracted using QIAamp DNA Mini Kit (Qiagen, 51306, Valencia, CA). 3μg genomic DNA was fragmented into 300-500bp by sonication. ChIP:Approximate 300 ug fixed chromatin and 5 ug antibody were used for each ChIP pull-down. RNA-seq: We extracted approximate 6 micrograms of total RNA, removed ribosomal RNA (rRNA) according to the manufacturer’s instructions with minor modifications.
Libraries were prepared for sequencing using standard Illumina protocols

value: primary liver cancer cells


title: Rap1-AID degron induction 2 hours 5' seq replicate 2


title: Methylation_97L


title: Rap1-AID degron induction 2 hours 5' seq replicate 1


title: Transition phase between exponential and stationary phase_2

status: Public on Oct 01 2018

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

hyb_protocol: 300 ng of Cy3-labeled RNA and 300 ng of Cy5-labeled RNA were mixed and fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA) using the software Agilent Scan Controll 8.4.1

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Clostridioides difficile 630

source_name: Clostridioides difficile 630∆erm at transition growth phase (between exponential and stationary phase)

label_protocol: RNA samples were labelled with Cy3 (later growth phases) and Cy5 (exponential growth phase) using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: The C. difficile 630∆erm strain (DSM28645) (Hussain, HA, 2005) obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany) was grown anaerobically at 37 °C in a defined medium containing 10 g/L casamino acids and 2 g/L glucose (Cartman and Minton, 2010; Neumann-Schaal et al. 2015).

extract_protocol: Bacterial RNA was extracted using the Qiagen RNeasy Kit Mini (Qiagen, Hilden, Germany) according to manufacturer’s instructions with minor modifications. Briefly, pellets from a 45 mL culture were resolved in 200 µl TE buffer and 15 mg/ml lysozyme, incubated for 30 min at room temperature and vigorously mixed every 2 min for 10 sec for enzymatically disruption of cells. Approximately 700 µL of RLT buffer and one spatula of glass beads were added and mixed vigorously for 3 min for mechanical disruption of cells. Samples were centrifuged (3 min, 10.000 rpm) and supernatant was mixed with 470 µL of 100% ethanol. Afterwards, RNA purification was carried out using the Qiagen RNeasy Kit protocol. DNA contaminating the RNA samples was removed using RNase-free DNase I twice (Qiagen, Hilden, Germany). The RNA was further assessed by analysis on the Bionanalyzer 2100 (Agilent, Santa Clara, CA) and RNA 6000 Nano Reagents (Agilent, Santa Clara, CA). According to the amount of RNA extracted and its quality (RINs>8), the best samples per time point were used for transcriptomic analysis.

treatment_protocol: Samples were taken at different time points along the growth curve: exponential growth (exp), transient phase (trans), ODmax (stat1), ODmax + 5 h (stat2) and + ODmax 10 h (stat3).

tag: growth phase

source_name: Clostridioides difficile 630∆erm at exponantial growth phase

value: exponantial growth phase


title: Transition phase between exponential and stationary phase_4


title: Transition phase between exponential and stationary phase_3


title: Methylation_Liver

source_name: liver

value: normal liver cells

tag: tissue


title: Stationary phase III (max. OD + 10h)_1

source_name: Clostridioides difficile 630∆erm at stationary growth phase III (10 hours after max. OD)

value: Stationary phase III (maximal OD + 10 h)


title: Stationary phase II (max. OD + 5h)_2

source_name: Clostridioides difficile 630∆erm at stationary growth phase II (5 hours after max. OD)

value: Stationary phase II (maximal OD + 5 h)


title: Stationary phase II (max. OD + 5h)_1


title: Stationary phase I (max. OD)_4

source_name: Clostridioides difficile 630∆erm at stationary growth phase I (max. OD)

value: Stationary phase I (maximal OD)


title: DRIP-S9.6-Bcell

status: Public on Aug 03 2018

city: Ann Arbor

first: Zhengwei

last: Zhu

address: 210 Washtenaw Ave

institute: University of Michigan

data_processing:
Illumina high-seq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
PAR-clip reads were aligned to the human genome hg19 using PARalyzer. DRIP-seq reads were analyzed using MACS2.0 program. RNA-IP reads were analyzed using Antanaviciute's M6A program.
normalized reads and clusters were combined in a csv file
Genome_build: hg19
Supplementary_files_format_and_content: Output from PARalyzer, MACS2.0, M6A viewer. Files are in excel format.

source_name: Human cultured B-cells

growth_protocol: Immortalized B cells (Coriell) were cultured to a density of 5X105 cells/mL in RPMI 1640 supplemented with 15% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin.

extract_protocol:
DNA was eluted from protein G beads using elution buffer (0.1M NaHCO3, 1% SDS).  DNA was precipitated in 0.3M NaAc, pH 5.5 and 100% EtOH.
DRIP-seq libraries were prepared from DRIP DNA and corresponding input DNA using Ovation Ultralow System (NuGen).

treatment_protocol: 5X106 cultured B-cells were lysed in 400 μL cell lysis buffer (50 mM PIPES, pH 8.0, 100 mM KCl, 0.5% NP-40) and nuclei were collected by centrifugation.  Nuclei pellet was resuspended in 200 μL nuclear lysis buffer (25 mM Tris-HCl, pH 8.0, 1% SDS, 5 mM EDTA).  Genomic DNA containing R-loops was then extracted by phenol:chloroform and precipitated by ethanol.  Purified material was resuspended in 200 μL IP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.01% SDS, 1% Triton X-100, 167 mM NaCl) and sonicated at 4°C in Bioruptor (Diagenode) at Hi setting (30sec on/30sec off) for 5 minutes, three times to fragments with average size of 500 bp.  3 μg of S9.6 monoclonal antibody (a gift from Dr. Stephen H. Leppla at NIH) or non-specific mouse IgG (Santa Cruz) was used for each immunoprecipitation.

tag: passages

tag: ip-antibody

value: S9.6 antibody (gift from Dr.Stephen H. Leppla)


title: H3_total_rep2

status: Public on Jul 26 2018

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

institute: RIKEN

data_processing:
ChIP-seq and input reads were aligned to the mm10 genome assembly using CLC Genomics Workbench (version 11.0) with default setting, and non-specific reads were ignored.
BAM files were converted to BED files by BED tool, BAMtoBED (v2.27.0).
BED files were converted to BedGraph files by BED tool, genomecov (v2.27.0).
BedGraph files were converted to BW files by Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: BW files show read coverage after scaling by read number mapped to 3kb around TSS.

source_name: Spermatozoa

growth_protocol: Caudal epididymis and vas deferens were incubated in M2 medium for 1 hour at 37C to prepare total sperm fraction.

extract_protocol:
After treatment of sperm decondensation buffer, lysates were prepared from sonicated sperm cells, and then H3-DNA complexes were isolated by H3 antibody.
ChIP-seq libraries were prepared by the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), and sequenced on Illumina Nextseq (151-bp paired end).

treatment_protocol: After mild sonication to separate sperm head from the tail, HRCS (Histone Replacement- Complete Sperm) was isolated from total sperm fraction by 82% Percoll precipitation. Each type of sperm cells were fixed by 1% FA for 10min at room temparature.

tag: sperm fraction

value: Total sperm


title: SRSF1_PARClip-Bcell

source_name: HEK293 cells

growth_protocol: FLAG-HA-SRSF1 HEK293 were grown in DMEM containing 10% fetal bovine serum (Gibco), 100 U/ml penicillin, 100 µg/ml streptomycin, 10 µg/ml blasticidin and 100 µg/ml hygromycin B

extract_protocol:
FH-SRSF1 expressing cells were lysed using NP40 lysis buffer and lysate was ceared by centrifugation. First RNase T1 was followed by immunoprecipitation with FLAG-M2 antibody. After washing, second RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was radioactively 5´end-labeled using l T4 PNK and 32P-γ-ATP. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, small RNA cDNA library preparation was performed.
Preadenylated,  3´adapter oligonucleotide TCACTTCGTATGCCGTCTTCTGCTTG was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 15 h before cell harvesting, transgene expression was induced with 2.5 ug/ml doxycycline in ESC. Cells were crosslinked with 312 nm UV-light for 5 min

tag: transgene

value: doxycycline-inducible expressing FLAG-HA tagged SRSF1 transgene

value: Monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich, catalog# M8823)


title: input_HRCS

value: HRCS


title: RIP-antiSRSF1-Bcell

extract_protocol:
Beads-bound immunoprecipitates were then washed six times using cold Wash Buffer with RNase inhibitor, and incubated with protease K in presence of 1% SDS at 55°C for 30 minutes.  RNA and DNA were then extracted from supernatants using phenol:chloroform:isoamyl alcohol and precipitated using ethanol.  Precipitated RNA was digested by DNase I (DNA-free kit, Ambion).  cDNA was synthesized using random hexamer primer by Taqman Reverse Transcription Reagent kit (Applied Biosystems).
RNA from anti-SRSF1 immunoprecipitate and input RNA were prepared into RNA-seq libraries using Illumina TruSeq Stranded Total RNA Library Prep kit (Illumina, #20020596).

treatment_protocol: 2X107 cultured human B-cells or primary skin fibroblasts were harvested and lysed in 100 µl of Lysis Buffer with protease and RNase inhibitors.  5 µg of anti-SRSF1 antibody (ABCAM, #ab38107) ornegative control IgG (Millipore) were conjugated to Magnetic Protein A/G beads.  100 µl of cell lysate was added into 900 µl Immunoprecipitation Buffer with RNase inhibitor and incubated with 50 µl beads-antibody complex at 4°C overnight.

value: anti-SRSF1 antibody (ABCAM, #ab38107)


title: Stationary phase III (max. OD + 10h)_3


title: H3_total_rep1


title: H3_HRCS_rep2


title: input_total


title: H3_HRCS_rep1


title: Transition phase between exponential and stationary phase_1


title: Stationary phase II (max. OD + 5h)_4


title: Stationary phase III (max. OD + 10h)_4


title: Stationary phase III (max. OD + 10h)_2


title: Stationary phase II (max. OD + 5h)_3


title: InVitro_OCI-My5_FAM46C_knockout_2

status: Public on Sep 05 2018

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression in OCI-My5/FAM46C-KO_clone#2

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression v3 8x60K Microarray  (G4851C-  072363) for 17 hours at 65 ℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: OCI-My5_FAM46C-KO_2, normal culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The MM cell lines were incubated in a RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cells were then incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: myeloma cell line

tag: genotype

value: FAM46C KO

value: female

value: unknown

tag: representative genomic abnormality


title: InVitro_OCI-My5_FAM46C_knockout_1

description: Gene expression in OCI-My5/FAM46C-KO_clone#1

source_name: OCI-My5_FAM46C-KO_1, normal culture


title: InVitro_OCI-My5_FAM46C_wildtype_1

description: Gene expression in OCI-My5/FAM46C-WT clone#1

source_name: OCI-My5_FAM46C-wildtype (WT)_1, normal culture

value: WT


title: InVitro_OCI-My5_FAM46C_wildtype_2

description: Gene expression in OCI-My5/FAM46C-WT clone#2

source_name: OCI-My5_FAM46C-WT_2, normal culture


title: Stationary phase I (max. OD)_1


title: Stationary phase I (max. OD)_2


title: GABAergic neuron_SCZ1-2

status: Public on Jul 10 2018

city: shinjuku-ku, Tokyo

first: Takaya

last: Ishii

department: School of medicine

institute: Keio university

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, human. GeneChips were washed and stained in the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 3000 7G (Thermo Fisher Scientific)

data_processing: Data were processed using the Transcriptome Analysis Console (TAC) 4.0 Software (Thermo Fisher Scientific).

source_name: GABAergic neuron induced from iPSC

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip™ WT PLUS Reagent Kit)

growth_protocol: neurons were induced from iPSCs and cultured in neuron culture medium

extract_protocol: Total RNA was extracted from induced neuron by Rneasy kit (QIAGEN)

value: GABAergic neuron

tag: iPSc clone

tag: diagnosis

value: Schizophrenia


title: GABAergic neuron_BP1-2

value: Bipolar disorder


title: DGM-11964_sm

status: Public on Apr 04 2018

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include the UniqueID (GeneID_location), GeneID and the FPKM values for all samples

source_name: small airway epithelial cells

growth_protocol: Pure populations of nonsmoker large and small airway samples and nonsmoker derived large and small airway basal cells (BC) were obtained and characterized using detailed protocols as previously described (PMID:1572528). Primary BC were maintained in Bronchial Epithelial Growth Media (BEGM, Lonza, Walkersville, MD) and passaged by seeding at a cell density of 3000 cells/cm2 in BEGM with fresh media changed every 2 days (PMID:24298994). RNA sequencing of primary (Passage 0) BC was performed on cells once they had reached 70-80% confluence as well as large and small airway samples.

extract_protocol:
Total RNA from nonsmoker epithelium and  harvested nonsmoker basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500.  HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

tag: smoking status

value: nonsmoker

value: small airway epithelial cells


title: DGM-11374_lg

source_name: large airway epithelial cells

value: large airway epithelial cells


title: DGM-11852_lg


title: DGM-11525_M0_sm


title: DGM-10565_M6_lg


title: GABAergic neuron_SCZ1-1


title: GABAergic neuron_BP1-1


title: DGM-10503_M6_lg


title: DGM-10500_M0_lg


title: Glutamatergic neuron_SCZ1-2

source_name: Glutamatergic neuron induced from iPSC

value: Glutamatergic neuron


title: GABAergic neuron_201B7

value: healthy


title: DGM-10284_M6_lg


title: GABAergic neuron_1210B2


title: Stationary phase I (max. OD)_3

value: Stationary phase I (maximal OD)

value: exponantial growth phase


title: Glutamatergic neuron_SCZ1-1


title: Glutamatergic neuron_201B7


title: Glutamatergic neuron_BP1-2


title: DGM-10194_M3_lg


title: Glutamatergic neuron_BP1-1


title: DGM-10123_M0_lg


title: DGM-01774_090416_lg


title: DGM-01620_lg


title: gr-ed20-2

status: Public on Sep 24 2017

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
Chromatin immunoprecipitation (ChIP) sequencing reads were mapped to the hg19 genome assembly using Bowtie2 (Langmead and Salzberg, 2012)
Genome_build: hg19
Supplementary_files_format_and_content: Tag read densities were generated by the makeTagDirectory from the Homer suite

source_name: MCF10A_EGF + DEX_20 min

growth_protocol: MCF10A cells were cultured as described (Tarcic et al., 2012) in DME:F12 medium (Gibco BRL, Grand Island, NY) supplemented with 10 µg ml-1 insulin, 0.1 µg ml-1 cholera toxin, 0.5 µg ml-1 hydrocortison, 5% heat-inactivated horse serum (Biological Industries, Beit-Haemek, Israel) and 10 ng ml-1 EGF.

extract_protocol:
Cell fixation and chromatin immunoprecipitation were performed as described (Blecher-Gonen et al., 2013)
Library construction and sequencing were performed as described (Blecher-Gonen et al., 2013)

treatment_protocol: Cells were starved overnight in medium without additives and then stimulated with DEX (d) or the combination of epidermal growth factor (EGF) + DEX (ed) for the indicated time intervals (minutes) before sequencing

tag: treated with

value: EGF + DEX

tag: treatment time

value: 20 min

value: rabbit anti-GR polyclonal antibody (Thermo Fisher Scientific, PA1-511A)


title: gr-ed20-1

tag: chip antibody


title: gr-ed60-1

source_name: MCF10A_EGF + DEX_60 min

value: 60 min


title: gr-d60-2

source_name: MCF10A_dexamethasone (DEX)_60 min

value: dexamethasone (DEX)


title: gr-d60-1


title: gr-d20-2

source_name: MCF10A_dexamethasone (DEX)_20 min


title: gr-con-1

source_name: MCF10A_none (untreated control)_1 hour

value: none (untreated control)

value: 1 hour


title: gr-con-2


title: gr-d20-1


title: FOXA1_r1881_repl1

status: Public on Sep 05 2017

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

institute: Radboud University

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-5. DFilter was run with bs=50, ks=30, refine, nonzero.
Genome_build: hg19

source_name: prostate

growth_protocol: LNCaP cells were cultured in RPMI-1640 supplemented with 10% FBS. Cells were hormone deprived three days before R1881 stimulation.

extract_protocol:
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Embo Mol Med 2015) For each ChIP, 5-10μg of antibody prebound to protein A or protein G beads was used.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Kapa Biosystems kit,KK8234).

treatment_protocol: Cells were treated with 10nM R1881 or vehicle for 4 hours.

value: Prostate cancer cell line LNCaP

tag: procedure

value: Chromatin IP against FOXA1

value: FOXA1 (sc-6554; Santa Cruz)


title: AR_r1881_repl1

value: Chromatin IP against AR

value: AR (sc-816; Santa Cruz)


title: AR_veh_repl1


title: gr-ed60-2

tag: cell line


title: H3K4me1_wt

status: Public on Aug 18 2017

city: Sant Joan d'Alacant

first: Angel

last: Barco

institute: Instituto de Neurociencias (UMH-CSIC)

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software 2.2.58.
Run: Mode HiSeq High-Output (HO) Version 4. Number of cycles: 1x50; Number of lanes: 1; Flow cell version: HiSeq Flow Cell v4; Kit version: TruSeq SBS Kit v4.Q30: >95%.
Sequenced reads were mapped to the mouse genome (Mus_musculus.GRCm.38.83) using bowtie 2 v2.2.9 (Langmead and Salzberg, 2012) . SAM/BAM files were further processed using SAMTOOLS v1.3.1 (Li et al., 2009).
Peak calling was performed using MACS2 (v2.1.0) (Zhang et al., 2008) with default parameters. Read counts on aligned bam files were performed using Rsubread (v1.22.3) (Liao et al., 2014). Differential peak methylation analysis was performed using DESeq2 (v1.10.0) (Love et al., 2014) of the bioconductor suite (Huber et al., 2015) in the R (v3.3) statistical computing platform. For consideration of differentially methylated regions between conditions, we used adjusted p-value < 0.05 as indicated in the manuscript.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: For H3K4me3: Tab-delimited text files include genomic positions of detected H3K4me3 peaks using MACS2 (2.1.0) in all samples in this study (36005) and raw counts at these regions using Rsubread (1.22.3). Peak calling was done in each sample. Subsequently, peak regions were merged using ChIPpeakAnno R package (Zhu et al., 2010) and non-overlapping peaks were included to have a full set of detetected peaks (36005). For Kdm5C and H3K4me1: Tab-delimited text files contain raw counts of reads at Kdm5C-bound genomic locations in wild-type mice. Peak calling for Kdm5c ChIP-seq in wild-type mice was run using MACS2 (v2.1.0) with the following parameters: -q 0.01 --nomodel --extsize 131 --broad --broad-cutoff 0.1. Read counts on aligned bam files were performed using featureCounts (Rsubread v1.22.3) (Liao et al., 2014).

source_name: hipocampal tissue from adult mice

growth_protocol: Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against H3K4me3 (Millipore, #07-473), H3K4me1 (Abcam, #ab8895), or Kdm5C (Iwase et al., 2016).
Single-end DNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq V4 Sample Prep Kit). Service provided by CRG (Barcelona. Spain)

treatment_protocol: Exposure to novelty consisted of placing an individual animal in a white Plexiglas square box containing plastic tubing and small toys for 1h. ChIP assays were carried out in adult male mice and in all cases the mice used as control were littermates. The brains were removed and hippocampi rapidly dissected, minced in small pieces and crosslinked by addition of 1/10 volume of fresh 11% formaldehyde solution.

value: Wild-type

tag: Sex

value: male

tag: age

value: Adult mice (2-4-month-old)

tag: strain

value: pure C57BL/6J background

tag: antibody

value: H3K4me1 (Abcam, #ab8895)