title: Input_PAX7+ prolif_myog_prog

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
RNA-seq: Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 ".
ChIP-seq: reads were then aligned to the human genome (hg38) using Bowtie2 followed by removal of PCR duplicates using the SAM tool rmdup 1.0.1 . Peak calling was performed using MACS 1.0.1 (parameters: -s 51 -bw 300, -p 1e-05 -m 16). Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS using the tool wigtoBigWig.
Genome_build: RNA-seq: hg19. ChIP-seq: hg38
Supplementary_files_format_and_content: RNA-seq: Excel .xlsx file containing TPM expression estimates calculated by RSEM.
Supplementary_files_format_and_content: ChIP-seq: BigWig files of Input and ChIP samples and list of PAX7-bound peaks in .bed format after removal of overlapping peaks detected in the Input and the human blacklist dataset

organism: Homo sapiens

source_name: GFP+ sorted cells collected at day 23

growth_protocol: Inducible PAX7 H9 ES cells were plated in 6cm non-adherent Petri dishes and incubated at 37°C, 5% CO2 on a shaker at 60 RPM. After 2 days, mTeSR was replaced with EB Myogenic (EBM) Media supplemented with 10µM Y-27632 and 5µM GSK3 inhibitor (CHIR990217). 2 days later, media was replaced to remove GSK3 inhibitor and the formed EBs were cultured in suspension on the shaker up to day 7. After plating EBs on gelatin-coated flasks using EBM + 10ng/ml human basic FGF (bFGF), EBs were let to adhere on the flasks for 3 days and then supplemented with 1µg/ml doxycycline (dox) for PAX7 induction. At day 14, cells were harvested using Trypsin+EDTA solution and FACS sorted based on GFP expression. GFP+ cells were then plated at 1.5*10^6 cells per T25 on gelatin-coated flasks using EBM supplemented with 5ng/ml bFGF, 1µg/ml dox and 5µM ROCK inhibitor (ROCK inhibitor was removed the day after) and cultured as monolayer. At ~90% cell density, cells were passaged using Trypsin+EDTA and replated on new gelatin-coated flasks. Terminal differentiation was induced by switching 100% confluent cultures to KOSR differentiation media (KnockOut™ DMEM + 20% KnockOut™ Serum Replacement + 1% Penicillin/Streptomycin + 2mM GlutaMAX™ - all products from Gibco).

extract_protocol:
ChIP-seq: Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF. Each sample was subjected to 5-6 cycles of sonication to reach an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. For each ChIP, 20µg of chromatin (diluted to 400µl) were precleared for 4h at 4°C with 15µl of BSA-blocked Protein G-conjugated sepharose beads (GE healthcare) and then supplemented with 1/10 volume of 10% Triton X-100. Immunoprecipitation was performed by overnight incubation with normal mouse IgG (8µg – Santa Cruz Biotechnology) or anti-Pax7 antibody (1:50 – Developmental Studies Hybridoma Bank). Immune complexes were recovered by incubation with 15µl of BSA-blocked Protein G-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
ChIP-seq: Libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program.

value: H9 cells

tag: doxycycline-treatment

value: dox-treated from (day 10 to 23)

tag: collection time

value: day 23 of differentiation

tag: chip antibody

value: none (input)


title: Young_Needles_Vascular

status: Public on Jun 30 2017

type: SRA

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description:
Gene expression in Young Needles Vascular
YNV

library_source: transcriptomic

data_processing:
We assembled the transcriptome for P. pinaster from the 454 sequencing reads by using Newbler (v2.8.1). Before feeding reads to Newbler, we removed reads with adapter sequences and reads shorter than 75bp through seqclean. Newbler then assembled the remaining rest reads in six rounds for P. pinaster, until all of the over-represented sequences were removed. CD-HIT-EST (Weizhong Li & Godzik 2006) then clustered the Newbler assemblies in each isogroup, which stands for unique transcriptional locus in Newbler assembly result, and selected the longest transcript, which had to be ≥ 150 bp, to represent each isogroup.
For the read mapping the raw data was first checked for quality using the fastqc software.
Based on examination of the output quality plots it was decided to clip off the first 35bp of each read. To that end, we used the FastX toolkit (fastx_trimmer).
Next the reads where filtered for overall quality using fastq_quality_filter with a minimum Q-score of 30 and minimum remaining length of 60%.
The remaining reads where subsequently used for read mapping with the BWA software (default parameter settings) against the reference transcriptome composed by  206,574 contigs.
Contigs with at least 25 reads in a sample were conserved, the rest of contigs were filterd. Filtering and normalization were done using edgeR package for R.
Gene co-expression analyses were made using the WGCNA package for R.
Genome_build: Reference transcriptome composed by 206,574 contigs from PROCOGEN and SUSTAINPINE pojects and Genbank (http://www.bmbq.uma.es/fmp/Datos/ALL_Procogen.fasta)
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each sample (AM, EN, YNM, YNV, CM, CV, HC, HV, HP, RC, RV, DRC, DRV and RM).The column ID_REF is the sequence identifier.

molecule: total RNA

organism: Pinus pinaster

source_name: Young Needles Vascular

growth_protocol: Maritime pine seeds (Pinus pinaster Ait.) from the Oria provenance were provided by Centro de Recursos Genéticos Forestales “El Serranillo” (Ministerio de Medio Ambiente y Medio Rural y Marino, Spain). Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were cultivated in a growth room at 25˚C and 50/70% relative humidity with a 16/8-h photoperiod and watered twice a week with distilled water. Fourteen days after imbibitions, seedlings were individually transferred to a 0.2-L pot with soil and watered twice a week with distilled water. The seedlings were harvested 1 month after the emergence of the shoots over the vermiculite.

extract_protocol:
The Laser Capture Microdissection (LCM) procedure was carried out as previously described in Cañas et al. (Tree Physiol. 34:1278-1288). The microdissection samples were placed into the caps of 0.5 mL tubes containing 10 L lysis buffer from the RNAqueous-Micro RNA Isolation Kit (Ambion, USA). Before RNA extraction all the samples were placed at -80ºC. All the RNA extractions from the microdissection of the samples were made using the standard-volume protocol (non-LCM) for the RNAqueous-Micro RNA Isolation Kit (Ambion, USA). RNA quality and first quantification was assessed using the RNA Pico Assay for the 2100 Bioanalyzer (Agilent, USA). The RNA samples with a RNA integrity number (RIN) higher than 7 were used for the subsequent mRNA amplification and 454 pyrosequencing.
As the amounts of RNA isolated form LCM samples were not enough for 454 pyrosequencing, a previous cDNA synthesis and amplification was made using the Conifer RNA Amplification (CRA+) protocol described in  Cañas et al. (Tree Physiol. 34:1278-1288). Transcriptome sequencing was performed at the Universidad de Málaga ultrasequencing facility using the GS-FLX+ platform with a GS FLX Titanium kit, Roche Applied Sciences (Indianapolis, IN, USA). Each sample was run in one half of a 454 PicoTiterPlate following the manufacturer’s sequencing protocol. The quantity of the cDNA libraries was determined using the Quant-iT™ PicoGreen® dsDNA Kit (Invitrogen, Paisley, UK). The quality of the cDNA libraries was determined using the Agilent High Sensitivity DNA Kit in the 2100 Bioanalyzer (Agilent, CA, USA). The runs were analysed using the Roche GS-FLX+ software.

treatment_protocol: The seedlings were cut and tissue sections of 5 mm were mounted in a specimen holder with optimal cutting temperature (OCT) embedding medium (Tissue-Tek, USA) and snap-frozen in liquid nitrogen for cryostat sectioning. The frozen samples were stored at -80ºC until use.

tag: tissue

value: Young Needles Vascular

tag: provenance

value: Oria

tag: developmental stage

value: 1 month-old seedling

tag: culture

value: In soil

tag: culture place

value: Culture chamber at Universidad de Malaga (Malaga, Spain)


title: Cotyledon_Mesophyll

description:
Gene expression in Cotyledon Mesophyll
CM

source_name: Cotyledon Mesophyll

value: Cotyledon Mesophyll


title: Hypocotyl_Pith

description:
Gene expression in Hypocotyl Pith
HP

source_name: Hypocotyl Pith

value: Hypocotyl Pith


title: diff_myo_rep4

country: USA

source_name: GFP+ cells collected 7 days post dox-withdrawal

extract_protocol:
RNA-seq: Cells were resuspended in Trizol (Invitrogen) and RNAs were purified using the Purelink RNA mini kit (Life Technologies) following the manufacturer’s instructions. DNase treatment was performed on column during the RNA isolation procedure. ChIP-seq: Day 23 Proliferating Myogenic progenitors (+dox) were collected using trypsin and reaction was inhibited by adding 10%FBS/PBS. Single cells were washed once with PBS, resuspended in 10%FBS/PBS and supplemented with formaldehyde (final concentration 1%) for crosslinking of protein-DNA complexes (10 minutes at RT) followed by quenching with glycine. Cells were snap-frozen in liquid nitrogen and stored at -80°C if not processed immediately.
RNA-seq: Sequencing libraries were generated from 100 ng of total RNA using the Ligation Mediated Sequencing (LM-Seq) protocol (Hou et al., 2015) quantitated using the Qubit fluorometer (Life Technologies) following the author’s instructions. ChIP-seq: Libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program.

tag: cell type

value: day 30 of differentiation


title: Hypocotyl_Cortex

description:
Gene expression in Hypocotyl Cortex
HC

source_name: Hypocotyl Cortex

value: Hypocotyl Cortex


title: ChIP_PAX7+ prolif_myog_prog

library_source: genomic

molecule: genomic DNA

value: PAX7 (Developmental Studies Hybridoma Bank)


title: Emerging_Needles

description:
Gene expression in Emerging Needles
EN

source_name: Emerging Needles

value: Emerging Needles


title: Root_Vascular

description:
Gene expression in Root Vascular
RV

source_name: Root Vascular

value: Root Vascular


title: Root_Cortex

description:
Gene expression in Root Cortex
RC

source_name: Root Cortex

value: Root Cortex


title: Cotyledon_Vascular

description:
Gene expression in Cotyledon Vascular
CV

source_name: Cotyledon Vascular

value: Cotyledon Vascular


title: Young_Needles_Mesophyll

description:
Gene expression in Young Needles Mesophyll
YNM

source_name: Young Needles Mesophyll

value: Young Needles Mesophyll


title: Apical_Meristem

description:
Gene expression in Apical Meristem
AM

source_name: Apical Meristem

value: Apical Meristem


title: Hypocotyl_Vascular

description:
Gene expression in Hypocotyl Vascular
HV

source_name: Hypocotyl Vascular

value: Hypocotyl Vascular


title: CD24+/CD184 low tumor cells - biological replicate 2

city: Research Triangle Park

first: Rainer

last: Blaesius

state: NC

address: 21 Davis Drive

institute: Becton Dickinson Technologies

description:
D2
D2_L8.D704

data_processing:
Read filtering: Fastq-mcf version 1.04.636 was used to filter reads. Any read with the following parameters was removed: a single base at a frequency of at least 95%, at least 4 internal Ns, an average Q score below 25, nucleotides with a quality score below 7, Illumina sequencing adapter sequences, and Ns at the ends of reads were clipped, any read shorter than 25 nts after clipping.
Read alignment: Reads were aligned to the UCSC hg19 reference genome with lincRNAs from Ensembl added as well as the UCSC mm10 genome using the STAR aligner version: 2.4.
Read quantification: Reads were counted using RSEM version 1.2.14.
Genome_build: UCSC hg19 supplemented with lincRNAs from Ensembl and UCSC mm10.
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing either raw (counts), fpkm normalized (fpkm) or upper-quartile normalized (norm) gene and isoform counts.
Supplementary_files_format_and_content: *xls: Excel spreadsheets with log2 transformed normalized means, fold changes, un-adjusted P-values, and FDRs for each comparison made for both genes and isoforms.

source_name: Mouse PDX cohort of mixed ductal carcinoma; lung metastasis

growth_protocol: Female NOD/SCID/ILIIrg−/− (NSG) mice age 6–7 weeks were purchased from Jackson Laboratories with tumor material already implanted. All animal studies were performed under an IACUC approved protocol. Tumors were assessed weekly for growth and measured with a digital caliper. Tumor volume was estimated by the formula 0.5 x (length x width2). Once tumor size reached >500 mm3 (several weeks to several months), they were harvested for analysis. Mice were humanely euthanized and the tumor was immediately removed via blunt dissection and placed in cold PBS for dissociation and analysis.

extract_protocol:
A total of 80,000 or more cells chosen for a specific surface marker status were collected and processed for RNA extraction. RNA was extracted using the Qiagen AllPrep Kit (Qiagen catalog #80204). Quality assessments were determined using Agilent BioAnalyzer and NanoDrop readings.
Libraries were synthesized using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103). Total RNA samples were concentration normalized, and polyadenylated RNA was purified using oligo-dT attached to magnetic beads. Purified mRNA was fragmented using heat in the presence of divalent cations. Fragmented RNA was converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix. A single ‘A’ base was added to the cDNA and forked adaptors that include index, or barcode, sequences were attached via ligation. The resulting molecules were amplified via polymerase chain reaction (PCR). Final libraries were quantified, normalized and pooled prior to binding to the flow cell. For multiplex sequencing, the following sample-Illumina barcode combinations were used: A2-D701, A3-D705, B1-D702, B2-D710, B3-706, C1-711, C2-703, C3-D707_507, D1-D712, D2-D704, D3-D708_507.

treatment_protocol:
Excised tissue was weighed and then minced using a scalpel or scissors to a size not exceeding 1-2mm3. Tissue was then enzymatically dissociated into single cells as previously described in a 37 ̊C water bath for 30 minutes with frequent agitation. The enzymatic reaction was stopped by rinsing in PBS (Cellgro, Manassas, VA) and 1% Bovine Serum Albumin (Sigma-Aldrich, St. Louis, MO). Dissociated tissue was filtered through a 70um sieve and treated with ACK Buffer (Life Technologies, Grand Island, NY) to remove contaminating red blood cells. Cells were resuspended in PBS, without magnesium and calcium.
Before staining, single-cell suspensions were blocked for 30 minutes, on ice in FcR block (Miltenyi Biotec). For surface marker characterization, cells were diluted in PBS and distributed into wells of a 96-well plate containing viability dye (LIVE/ DEAD Fixable Near-IR or Aqua, Invitrogen) and Hoechst 33342 (Invitrogen; at 0.2 mg/mL) for viable nucleated cell identification. Cells were incubated with antibody solutions for 30 minutes at 4 C, in the dark, and then rinsed twice in PBS before acquisition on BD LSRII flow cytometer. For sorting, cells were stained using a four-color panel combining amine viability reagent, anti-mouse cocktail, and markers identified from the primary characterization plate. After staining, cells were rinsed, and resuspended in BD FACS Pre-Sort Buffer, filtered again through a 70 mm sieve, and populations of interest were sorted on the BD FACSAria II (BD Biosciences) at 20 p.s.i. using a 100-mm nozzle. Cell doublets or clumps were removed with electronic doublet discrimination gating.

tag: jackson labs tumor model

tag: cell population

value: CD24+/CD184 low tumor cells


title: diff_myo_rep2

value: H9 cells

value: dox-treated from (day 10 to 23)


title: diff_myo_rep3


title: s-4

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

country: China

institute: Zhejiang University

description: uterus single cell RNA-Seq counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
The final gene expression data was normalized using Cuffnorm and represented by TPM (tags per million)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts of each gene from each sample

organism: Mus musculus

source_name: uterus

extract_protocol:
Single cells were lysated, preamplified and library prepared accoring to the CEL-seq protocol (Science. 2014 Feb 14;343(6172):776-9.)
Single cells were lysated, preamplified and library prepared accoring to the CEL-seq protocol (Science. 2014 Feb 14;343(6172):776-9.)

treatment_protocol: 714 single CD326+ mice uterine epithelia from 5 developmental stages (post natal day 0, 7, 14, 28, 56)

tag: strain

value: ICR

value: uterus

tag: ages


title: CD24+/CD184 low tumor cells - biological replicate 1

description:
D1
D1_L8.D712


title: CD24+/CD184 high tumor cells - biological replicate 2

description:
C2
C2_L8.D703

value: CD24+/CD184 high tumor cells


title: prolif_nodox_rep3

source_name: Unsorted cells collected at day 23

value: untreated

value: day 23 of differentiation


title: diff_myo_rep1

value: day 30 of differentiation


title: CD24+/CD184 high tumor cells - biological replicate 1

description:
C1
C1_L8.D711


title: Bulk tumor cells depleted of mouse - biological replicate 3

description:
B3
B3_L8.D706

value: Human-only tumor cells depleted of mouse cells


title: CD24+/CD184 low tumor cells - biological replicate 3

description:
D3
D3_L1.D708_507


title: Bulk tumor cells depleted of mouse - biological replicate 1

description:
B1
B1_L8.D710


title: PAX7+ prolif_myog_rep5


title: CD24+/CD184 high tumor cells - biological replicate 3

description:
C3
C3_L1.D707_507


title: Unsorted bulk tumor cells - biological replicate 2

description:
A3
A3_L8.D705

treatment_protocol:
Excised tissue was weighed and then minced using a scalpel or scissors to a size not exceeding 1-2mm3. Tissue was then enzymatically dissociated into single cells as previously described in a 37 ̊C water bath for 30 minutes with frequent agitation. The enzymatic reaction was stopped by rinsing in PBS (Cellgro, Manassas, VA) and 1% Bovine Serum Albumin (Sigma-Aldrich, St. Louis, MO). Dissociated tissue was filtered through a 70um sieve and treated with ACK Buffer (Life Technologies, Grand Island, NY) to remove contaminating red blood cells. Cells were resuspended in PBS, without magnesium and calcium.
After dissociation, cells were held on ice in PBS until sorting of other populations was completed, then pelleted, the supernatant was aspirated, the samples were lysed with Qiagen RLT Plus and stored at -80C.

value: Unsorted tumor cells


title: PAX7+ prolif_myog_rep4


title: Estrogen+tamoxifen_2

city: Oslo

first: Shixiong

last: Wang

address: Gaustadalléen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

description:
analyzeRNA_SX_noadj.txt
analyzeRNA_SX_rpkm.txt

data_processing:
Library strategy: Gro-seq
Reads were first trimmed to remove 3´polyA with Homer 4.6
Trimmed reads were quality filtered with FASTX Toolkit 0.0.14 with options -v -q 10 -p 97 to have minimum 97% of reads with quality score greater than 10
Ribosome RNA reads were removed with Bowtie 1.12. Then filted reads were aligned to hg19 using Bowtie 1.12 with options v = 2, m = 3, k = 1.
Aligned files (sam files) were made into Tagdirectories with Homer 4.6. Raw reads counts calculated with analyzeRNA.pl command, option -noadj to specify raw counts. Normalized expression files were created also with analyzeRNA.pl command, with option -rpkm to specify the normalization.
Differential gene expression analysis was performed with edgeR 3.8.5
Genome_build: hg19
Supplementary_files_format_and_content: analyzeRNA_SX_noadj.txt tab-delimited text files include raw reads values for each sample, and analyzeRNA_SX_rpkm.txt  tab-delimited text files include RPKM values for each sample.

molecule: nuclear RNA

source_name: metastatic breast adenocarcinoma: pleural effusion

extract_protocol:
5 ×10^6 nuclei were used for each run-on reaction, 2 biological replicates were produced for both vehicle and estrogen treatments. Br-UTP was incorporated into on-going transcription by run-on reaction which was performed at 30 degree for 5 min. Total RNA was extracted with TRIzol and fragmented with RNA Fragmentation Reagent. Fragmented RNA was purified with P-30 column, which was followed by T4 polynucleotide kinase treatment to dephosphorylate the 3’ end of RNA fragments. Br-UTP labeled RNA was enriched twice with anti-BrdU beads and precipitated overnight.
PolyA tailing was done using E.coli Poly(A) Polymerase, followed by reverse transcription with oNTI-223-index: /5Phos/GATCGTCGGACTGTAGAACTCTGAAC/iSp18/TCAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTTVN which allows custom barcoding. Exonuclease I was used to remove excess oligo after reverse transcription. DNA-RNA duplex was purified with ChIP DNA Clean & Concentrator Kit followed by RNAse H treatment. cDNA was circularized amplified with oNTI-201: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG and oNTI-200: CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT(XXXXXX  is barcode used for specific sample) for 12 to 14 cycles. Final PCR product was purified by running 10% TBE gel and cleaned up.

value: mammary gland/breast

tag: tumor type

value: breast adenocarcinoma

tag: treatment

value: Estrogen+tamoxifen


title: Bulk tumor cells depleted of mouse - biological replicate 2

description:
B2
B2_L8.D702


title: PAX7+ prolif_myog_rep3

source_name: GFP+ sorted cells collected at day 23


title: mesod_nodox_rep4

source_name: Unsorted cells collected at day 14

value: day 14 of differentiation


title: Unsorted bulk tumor cells - biological replicate 1

description:
A2
A2_L8.D701


title: PAX7+_mesod_rep4

source_name: GFP+ sorted cells collected at day 14


title: mesod_nodox_rep3


title: prolif_nodox_rep1


title: Tamoxifen_1

value: Tamoxifen


title: PAX7+ prolif_myog_rep1


title: Vehicle_2

value: Vehicle


title: Estrogen_1

value: Estrogen


title: Estrogen_2


title: PAX7+_mesod_rep3

value: H9 cells


title: Tamoxifen_2


title: mesod_nodox_rep2


title: Vehicle_1


title: Estrogen+tamoxifen_1


title: PAX7+ prolif_myog_rep2

value: dox-treated from (day 10 to 23)


title: PAX7+_mesod_rep1


title: PAX7+_mesod_rep2


title: prolif_nodox_rep2


title: s-1

description: uterus single cell RNA-Seq counts.txt

value: ICR


title: H929 cells expressing FAM46CWTGFP for 72 hrs rep3_total RNA

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

data_processing:
base caling CASAVA v1.8.2
aligmnent STAR v2.4.0
further processing, filtering, counting, QC  - custom scripts emploing samtools v1.2-10, HTSeq v0.6.1, RSeQ v2.6.1, FastQC v0.11.3
differential expression analysis DESeq2 v1.8.2
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files (corected for total library size) and count tables (FPKM_count.py or htseq-count output files)

growth_protocol: Multiple myeloma cell line SKMM1 and H929 (ATCC; CRL-9068) were cultured in RPMI 1640 ATCC’s modified (Invitrogen) supplemented with 10% FBS (Invitrogen) and penicillin/streptomycin (Sigma; P4083) at 37°C in 5% CO2.

extract_protocol:
total RNA was extracted and RNA-seq libraries were prepared.  Replicate #3.
RNA isolation was performed with Trizol reagent (Invitrogen, 15596) according to the manufacturer’s instructions. Poly(A) fractionation was performed as previously described with the following modifications [Meijer, H.A. et al. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 35, e132 (2007)]. In brief, 80 µg of total RNA was mixed with 400 µl GTC buffer (4 M guanidine thiocyanate, 25 mM sodium citrate, pH 7.1, 2% β-mercaptoethanol) and 750 pmoles of biotinylated 5’biotin –TEG-oligo(dT)25 (Future Synthesis). 850 µl of “dilution buffer” (6× SSC, 10 mM Tris–HCl, pH 7.4, 1 mM EDTA, 0.25% SDS, 1% β-mercaptoethanol) was added, the mixture was incubated at 70°C for 5 minutes, and then it was centrifuged at 12 000 rpm for 10 min at RT. The resulting supernatant was mixed with 100 µl of M280 beads (Invitrogen; 60210) washed 3 times with 0.5x SSC buffer. After binding, samples were washed 3 times with 0.5x SSC buffer for 10 minutes. RNA fractions were eluted with decreasing concentrations of SSC buffer (from 0.2x SSC to 0.025x SSC) and the final elution was performed with water. RNA was precipitated and subjected to further analysis.
1 µg of total RNA was treated with Turbo-DNase (Life Technologies) according to the manufacturer’s instructions. Then, rRNA was removed from samples using a Ribo-Zero Kit (Epicentre), according to the manufacturer’s protocol, and samples were spiked-in with external RNA (ERCC RNA Spike-In Mix; Life Technologies). For libraries prepared from poly(A)+ fractions, the ribo-depletion step was omitted. Finally, RNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina) or a KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions. Quality of libraries was determined by chip electrophoresis performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: MM cells were transduced with lentiviruses carrying FAM46CWTGFP or FAM46CD90A,D92AGFP For lentivirus production, 2.6 x 106 HEK-293T cells were seeded into 10 cm dishes 24 hours prior to transfection in 10 mL of DMEM supplemented with 10% FBS (Invitrogen) and penicillin/streptomycin solution (Sigma). The lentiviruses encoding the gene of interest (GOI) were introduced to the packaging cells by calcium phosphate co-transfection with 8.6 µg of a GOI-containing vector HIV-SFFV and components of 2nd generation of packaging vectors, namely, 8.6 µg of psPAX2 packaging vector and 5.5 µg of pMD2.G envelope vector. The plasmids were resuspended in 450 µl of 300 mM CaCl2 and added dropwise to 450 μl of 2 × concentrated HEPES-buffered saline (280 mM NaCl, 20 mM HEPES, 1.5 mM Na2HPO4, 10 mM KCl and 12 mM D-glucose pH 7.2) by vortexing. The precipitate was immediately added to the cell culture medium with gentle swirling. The medium was replaced with 6 mL of fresh DMEM 16 hours post transduction.  Virus-containing supernatants were collected 24 hours later, centrifuged for 3 min at 300 x g, and filtered through 0.45 μm low-protein binding filters (Millipore) Then, the supernatants were concentrated 10 × by centrifugation (3000 x g, 16 hours, 4°C). The titer of viral particles was estimated using a Lenti-X p24 Rapid Titer Kit (Clontech) according to the manufacturer’s protocol. Multiplication of infection (MOI) was calculated by dividing the vector titer for the number of cells transduced. Efficiency of transduction was determined by flow cytometry for GFP-expressing cells using an Accuri C6 benchtop cytometer   (BD Biosciences). Additional staining with 2.5 µg/mL propidium iodide (Sigma-Aldrich) in PBS was performed to distinguish dead cells. If needed, to select GOI-expressing cells, sorting for GFP-positive cells using the Aria III cell sorter (BD Biosciences) was performed.

tag: cell line

value: Multiple myeloma cell line

tag: tranduced with

value: lentiviruses carrying FAM46CWTGFP for 72 hours


title: H929 cells expressing FAM46CWTGFP for 72 hrs rep4_total RNA

extract_protocol:
total RNA was extracted and RNA-seq libraries were prepared.  Replicate #4.
RNA isolation was performed with Trizol reagent (Invitrogen, 15596) according to the manufacturer’s instructions. Poly(A) fractionation was performed as previously described with the following modifications [Meijer, H.A. et al. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 35, e132 (2007)]. In brief, 80 µg of total RNA was mixed with 400 µl GTC buffer (4 M guanidine thiocyanate, 25 mM sodium citrate, pH 7.1, 2% β-mercaptoethanol) and 750 pmoles of biotinylated 5’biotin –TEG-oligo(dT)25 (Future Synthesis). 850 µl of “dilution buffer” (6× SSC, 10 mM Tris–HCl, pH 7.4, 1 mM EDTA, 0.25% SDS, 1% β-mercaptoethanol) was added, the mixture was incubated at 70°C for 5 minutes, and then it was centrifuged at 12 000 rpm for 10 min at RT. The resulting supernatant was mixed with 100 µl of M280 beads (Invitrogen; 60210) washed 3 times with 0.5x SSC buffer. After binding, samples were washed 3 times with 0.5x SSC buffer for 10 minutes. RNA fractions were eluted with decreasing concentrations of SSC buffer (from 0.2x SSC to 0.025x SSC) and the final elution was performed with water. RNA was precipitated and subjected to further analysis.
1 µg of total RNA was treated with Turbo-DNase (Life Technologies) according to the manufacturer’s instructions. Then, rRNA was removed from samples using a Ribo-Zero Kit (Epicentre), according to the manufacturer’s protocol, and samples were spiked-in with external RNA (ERCC RNA Spike-In Mix; Life Technologies). For libraries prepared from poly(A)+ fractions, the ribo-depletion step was omitted. Finally, RNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina) or a KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions. Quality of libraries was determined by chip electrophoresis performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).


title: mesod_nodox_rep1

tag: doxycycline-treatment

value: untreated


title: H929 cells expressing FAM46CWTGFP for 72 hrs rep2_total RNA

extract_protocol:
total RNA was extracted and RNA-seq libraries were prepared.  Replicate #2.
RNA isolation was performed with Trizol reagent (Invitrogen, 15596) according to the manufacturer’s instructions. Poly(A) fractionation was performed as previously described with the following modifications [Meijer, H.A. et al. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 35, e132 (2007)]. In brief, 80 µg of total RNA was mixed with 400 µl GTC buffer (4 M guanidine thiocyanate, 25 mM sodium citrate, pH 7.1, 2% β-mercaptoethanol) and 750 pmoles of biotinylated 5’biotin –TEG-oligo(dT)25 (Future Synthesis). 850 µl of “dilution buffer” (6× SSC, 10 mM Tris–HCl, pH 7.4, 1 mM EDTA, 0.25% SDS, 1% β-mercaptoethanol) was added, the mixture was incubated at 70°C for 5 minutes, and then it was centrifuged at 12 000 rpm for 10 min at RT. The resulting supernatant was mixed with 100 µl of M280 beads (Invitrogen; 60210) washed 3 times with 0.5x SSC buffer. After binding, samples were washed 3 times with 0.5x SSC buffer for 10 minutes. RNA fractions were eluted with decreasing concentrations of SSC buffer (from 0.2x SSC to 0.025x SSC) and the final elution was performed with water. RNA was precipitated and subjected to further analysis.
1 µg of total RNA was treated with Turbo-DNase (Life Technologies) according to the manufacturer’s instructions. Then, rRNA was removed from samples using a Ribo-Zero Kit (Epicentre), according to the manufacturer’s protocol, and samples were spiked-in with external RNA (ERCC RNA Spike-In Mix; Life Technologies). For libraries prepared from poly(A)+ fractions, the ribo-depletion step was omitted. Finally, RNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina) or a KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions. Quality of libraries was determined by chip electrophoresis performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).


title: H3K27me3_ChIPSeq LINC00173 knockdown #1

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

description: genomic DNA

data_processing:
Raw sequencing reads filtered for adapter contamination, low quality scores, and excluded reads in which more than 10% of bases were unknown.
Filtered ChIP-seq reads aligned to the human genome (hg19) using the software package BWA with standard parameters.
Peak calling performed using the software package MACS2 with options to detect broad peaks for histone modifications (--broad) and to filter sites with an adjusted q-value < 0.05 (--broad-cutoff 0.05).
The MACS2 routine bdgdiff was used to identify differentially methylated regions.
Annotations from the RefSeq database (http://www.ncbi.nlm.nih.gov/refseq/) were used to catalogue the locations of proximal promoter (-1kbp to TSS) and heatmaps were generated using the publicly available software seqMINER.
Genome_build: hg19

source_name: CD34+ HSPC cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library preparation was performed by BGI (Hong Kong) using a variation of the Illumina’s standard protocol. The workflow involves end repair of ChIP-enriched DNA using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase to generate blunt ended fragments. ‘A’ bases were added to the 3’ ends using Klenow fragments (3’ to5’ exo minus) to generate DNA fragments for ligation of adapters, which have a single ‘T’ base overhang at their 3’ end. Adapters were ligated to the DNA fragments using DNA ligase. Adapter-modified DNA fragments were amplified by PCR (15 cycles) and size selected (200 ± 25bp) by running PCR products on a 2% agarose gel and purifying using a QIAGEN Gel Extraction Kit (QIAGEN, #28704). The libraries were validated and clusters generated on flow cells, and sequenced using a HiSeq 2500 analyzer.

treatment_protocol: shRNA-miR knockdown of LINC00173

value: CD34+ HSPC cells

tag: shRNA

value: LINC00173 knockdown #1

tag: antibody

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_ChIPSeq LINC00173 knockdown #2

description: genomic DNA

value: LINC00173 knockdown #2


title: H929 cells expressing FAM46CWTGFP for 72 hrs rep1_total RNA

extract_protocol:
total RNA was extracted and RNA-seq libraries were prepared.  Replicate #1.
RNA isolation was performed with Trizol reagent (Invitrogen, 15596) according to the manufacturer’s instructions. Poly(A) fractionation was performed as previously described with the following modifications [Meijer, H.A. et al. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 35, e132 (2007)]. In brief, 80 µg of total RNA was mixed with 400 µl GTC buffer (4 M guanidine thiocyanate, 25 mM sodium citrate, pH 7.1, 2% β-mercaptoethanol) and 750 pmoles of biotinylated 5’biotin –TEG-oligo(dT)25 (Future Synthesis). 850 µl of “dilution buffer” (6× SSC, 10 mM Tris–HCl, pH 7.4, 1 mM EDTA, 0.25% SDS, 1% β-mercaptoethanol) was added, the mixture was incubated at 70°C for 5 minutes, and then it was centrifuged at 12 000 rpm for 10 min at RT. The resulting supernatant was mixed with 100 µl of M280 beads (Invitrogen; 60210) washed 3 times with 0.5x SSC buffer. After binding, samples were washed 3 times with 0.5x SSC buffer for 10 minutes. RNA fractions were eluted with decreasing concentrations of SSC buffer (from 0.2x SSC to 0.025x SSC) and the final elution was performed with water. RNA was precipitated and subjected to further analysis.
1 µg of total RNA was treated with Turbo-DNase (Life Technologies) according to the manufacturer’s instructions. Then, rRNA was removed from samples using a Ribo-Zero Kit (Epicentre), according to the manufacturer’s protocol, and samples were spiked-in with external RNA (ERCC RNA Spike-In Mix; Life Technologies). For libraries prepared from poly(A)+ fractions, the ribo-depletion step was omitted. Finally, RNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina) or a KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions. Quality of libraries was determined by chip electrophoresis performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

value: lentiviruses carrying FAM46CD90A,D92AGFP for 72 hours


title: H929 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep4_total RNA


title: H3K27me3_ChIPSeq scrambled/ctrl

description: genomic DNA

value: scrambled/ctrl


title: H929 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep2_total RNA


title: H929 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep3_total RNA


title: CAF strain_3 no treatment (DMSO vehicle)

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
trimming: Trimmomatic v.0.22
alignment: TopHat v.2.0.8b
expression levels: HTSeq package, release 0.5.4p1
genome build: hg19
processed data files format and content: tab-delimited text files include gene expression values (expressed in count) for each Sample

source_name: primary cancer associated fibroblasts

extract_protocol:
Total RNA was extracted using the directZol RNA miniprep kit (Zymo Research) with on-column DNase treatment. RNA quality was verified on the bioanalyzer (Agilent) with RIN > 8
Four (DEK004-6), 1 (DEK32-37) or 0.5 (DMSO_1-3, JX_1-3) ug of total RNA were used for library preparation using the Truseq Stranded Total RNA Sample Preparation kit (Illumina), with Ribo-Zero for DEK32-37 only.

tag: tissue

value: skin squamous cell carcinoma

value: primary cancer associated fibroblasts

tag: passage

tag: treated with

value: DMSO vehicle


title: SKMM1 cells expressing FAM46CWTGFP for 72 hrs rep2_polyA RNA

molecule: polyA RNA

extract_protocol:
total RNA was extracted and poly(A)+ RNA was fractionated in terms of length. Fraction 5 and 6 represents transcripts with longest poly(A) tails.
RNA isolation was performed with Trizol reagent (Invitrogen, 15596) according to the manufacturer’s instructions. Poly(A) fractionation was performed as previously described with the following modifications [Meijer, H.A. et al. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 35, e132 (2007)]. In brief, 80 µg of total RNA was mixed with 400 µl GTC buffer (4 M guanidine thiocyanate, 25 mM sodium citrate, pH 7.1, 2% β-mercaptoethanol) and 750 pmoles of biotinylated 5’biotin –TEG-oligo(dT)25 (Future Synthesis). 850 µl of “dilution buffer” (6× SSC, 10 mM Tris–HCl, pH 7.4, 1 mM EDTA, 0.25% SDS, 1% β-mercaptoethanol) was added, the mixture was incubated at 70°C for 5 minutes, and then it was centrifuged at 12 000 rpm for 10 min at RT. The resulting supernatant was mixed with 100 µl of M280 beads (Invitrogen; 60210) washed 3 times with 0.5x SSC buffer. After binding, samples were washed 3 times with 0.5x SSC buffer for 10 minutes. RNA fractions were eluted with decreasing concentrations of SSC buffer (from 0.2x SSC to 0.025x SSC) and the final elution was performed with water. RNA was precipitated and subjected to further analysis.
1 µg of total RNA was treated with Turbo-DNase (Life Technologies) according to the manufacturer’s instructions. Then, rRNA was removed from samples using a Ribo-Zero Kit (Epicentre), according to the manufacturer’s protocol, and samples were spiked-in with external RNA (ERCC RNA Spike-In Mix; Life Technologies). For libraries prepared from poly(A)+ fractions, the ribo-depletion step was omitted. Finally, RNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina) or a KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions. Quality of libraries was determined by chip electrophoresis performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).


title: HDF strain_2 si-ATF3 n°1

data_processing:
trimming: cutadapt 1.4.2
alignment: STAR v2.4.0j
expression levels: featurecounts 1.4.4
genome build: GRCh37
processed data files format and content: tab-delimited text files include gene expression values (expressed in count) for each Sample

source_name: primary dermal fibroblasts

value: abdomen skin

value: primary dermal fibroblasts


title: CAF strain_2 no treatment (DMSO vehicle)


title: HDF strain_2 si-ATF3 n°2


title: HDF strain_2 si-ctrl

value: si-ctrl


title: CAF strain_2 JQ1 treated (500 nM)

value: JQ1 treated (500 nM)


title: SKMM1 cells expressing FAM46CWTGFP for 72 hrs rep3_polyA RNA


title: CAF strain_1 no treatment (DMSO vehicle)


title: SKMM1 cells expressing FAM46CWTGFP for 72 hrs rep1_polyA RNA

extract_protocol:
total RNA was extracted and poly(A)+ RNA was fractionated in terms of length. Fraction 1 represents transcripts with shortest poly(A) tails.
RNA isolation was performed with Trizol reagent (Invitrogen, 15596) according to the manufacturer’s instructions. Poly(A) fractionation was performed as previously described with the following modifications [Meijer, H.A. et al. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 35, e132 (2007)]. In brief, 80 µg of total RNA was mixed with 400 µl GTC buffer (4 M guanidine thiocyanate, 25 mM sodium citrate, pH 7.1, 2% β-mercaptoethanol) and 750 pmoles of biotinylated 5’biotin –TEG-oligo(dT)25 (Future Synthesis). 850 µl of “dilution buffer” (6× SSC, 10 mM Tris–HCl, pH 7.4, 1 mM EDTA, 0.25% SDS, 1% β-mercaptoethanol) was added, the mixture was incubated at 70°C for 5 minutes, and then it was centrifuged at 12 000 rpm for 10 min at RT. The resulting supernatant was mixed with 100 µl of M280 beads (Invitrogen; 60210) washed 3 times with 0.5x SSC buffer. After binding, samples were washed 3 times with 0.5x SSC buffer for 10 minutes. RNA fractions were eluted with decreasing concentrations of SSC buffer (from 0.2x SSC to 0.025x SSC) and the final elution was performed with water. RNA was precipitated and subjected to further analysis.
1 µg of total RNA was treated with Turbo-DNase (Life Technologies) according to the manufacturer’s instructions. Then, rRNA was removed from samples using a Ribo-Zero Kit (Epicentre), according to the manufacturer’s protocol, and samples were spiked-in with external RNA (ERCC RNA Spike-In Mix; Life Technologies). For libraries prepared from poly(A)+ fractions, the ribo-depletion step was omitted. Finally, RNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina) or a KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions. Quality of libraries was determined by chip electrophoresis performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).


title: H929 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep1_total RNA


title: SKMM1 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep3_polyA RNA


title: SKMM1 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep1_polyA RNA


title: HDF strain_1 si-ATF3 n°2


title: HDF strain_1 si-ATF3 n°1


title: H929 cells expressing FAM46CWTGFP for 72 hrs rep3_polyA RNA


title: H929 cells expressing FAM46CWTGFP for 72 hrs rep2_polyA RNA


title: H929 cells expressing FAM46CWTGFP for 72 hrs rep1_polyA RNA


title: CAF strain_3 JQ1 treated (500 nM)


title: CAF strain_1 JQ1 treated (500 nM)


title: HDF strain_1 si-ctrl


title: Huh-6 (2HUH6HB)

description: embryonal cancer cell line

data_processing:
Trimming: cutadapt 1.4.2
Alignment: star 2.4.1a
Read counting: featureCounts (from Rsubreads 1.12.6 )
Genome_build: GRCh37
Supplementary_files_format_and_content: [.csv] Comma separated values text file countaing gene expression values (expressed in count) in a matrix, where columns correspond to sample fastq files and rows are gene (identified by ENSEMBL ids)

source_name: HB cell line

extract_protocol:
Cells pellets were collected, washed once with PBS and flash frozen on dry ice. RNA was extracted using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: Huh-6 embryonal cancer cell line


title: Huh-6 (1HUH6HB)

description: embryonal cancer cell line


title: Hep-U2 (2HepU2HB)

description: embryonal cancer cell line

value: Hep-U2 embryonal cancer cell line


title: H929 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep3_polyA RNA

value: Multiple myeloma cell line


title: RNA Pol2-siATF3 plus siCSL

description: 5ug Ab/1*10^6 cells

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner with default parameters
Peaks were called using MACS software version 2.1. The input sample H3K27ac-input has been used as control for all the other samples. In order to allow for the identification of the broad peaks from histone markers, the peak model building has been disabled (parameter --nomodel) and a global backgroud signal has been considered (parameter –nolambda).
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing the list of peaks identified by MACS

source_name: PolII ChIP-seq

extract_protocol:
Chromatin from 5 milions fixed cells was fragmented to a size range of 100–300 bases with a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibody against H3K27ac, H3K4m3e, H3K27me3 and  Polimerase-II. Antibody–chromatin complexes were pulled-down using magnetic beads, washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase.
ChIPed DNA was quantified by fluorometry on the Qubit system (Invitrogen). A total of 10 ng DNA were used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina, as recommended by the manufacturer.
NEBNext ChIP-seq Library kit (New England Biolabs)

tag: genotype/variation

value: siATF3 plus siCSL

tag: chip antibody

value: PolII (SantaCruz Cat.No.899)


title: RNA Pol2-siCSL

description: 5ug Ab/1*10^6 cells

tag: cell type

value: siCSL


title: H929 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep2_polyA RNA


title: Hep-U2 (1HepU2HB)

description: embryonal cancer cell line


title: Hep293TT (1Hep2TTHB)

description: fetal liver cancer cell line

value: Hep293TT fetal liver cancer cell line


title: H929 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep1_polyA RNA

value: lentiviruses carrying FAM46CD90A,D92AGFP for 72 hours


title: RNA Pol2-siCtrl

description: 5ug Ab/1*10^6 cells

value: siCtrl


title: Hep293TT (2Hep2TTHB)

description: fetal liver cancer cell line


title: H3K27me3-siCSL

description: 5ug Ab/1*10^6 cells

source_name: H3K27me3 ChIP-seq

value: H3K27m3e (Millipore Cat.No.07-449)


title: HepG2 (1HepG2HB)

description: fetal liver cancer cell line

value: HepG2 fetal liver cancer cell line


title: HepG2 (2HepG2HB)

description: fetal liver cancer cell line


title: HLF (2HLFHCC)

description: mesenchymal liver cancer cell line

source_name: HCC cell line

value: HLF mesenchymal liver cancer cell line


title: RNA Pol2-siATF3

description: 5ug Ab/1*10^6 cells

value: abdomen skin


title: H3K27me3-siATF3 plus siCSL

description: 5ug Ab/1*10^6 cells

value: primary dermal fibroblasts


title: H3K27me3-siATF3

description: 5ug Ab/1*10^6 cells


title: HLF (1HLFHCC)

description: mesenchymal liver cancer cell line


title: H3K27me3-siCtrl

description: 5ug Ab/1*10^6 cells


title: HLE (2HLEHCC)

description: mesenchymal liver cancer cell line

value: HLE mesenchymal liver cancer cell line


title: H3K4me3-siATF3 plus siCSL

description: 5ug Ab/1*10^6 cells

source_name: H3K4me3 ChIP-seq

value: H3K4m3e (Abcam Cat.No.8580)


title: H3K4me3-siCSL

description: 5ug Ab/1*10^6 cells


title: SKMM1 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep2_polyA RNA


title: H3K4me3-siATF3

description: 5ug Ab/1*10^6 cells


title: Hep-3B (2Hep3BHCC)

description: epithelial liver cancer cell line

value: liver

value: Hep-3B epithelial liver cancer cell line


title: Hep-3B (1Hep3BHCC)

description: epithelial liver cancer cell line


title: H3K4me3-siCtrl

description: 5ug Ab/1*10^6 cells


title: Huh-1 (3HUH1HCC)

description: epithelial liver cancer cell line

value: Huh-1 epithelial liver cancer cell line


title: HDF pIND-ATF3  doxy 500 ng/ml

data_processing:
trimming: Trimmomatic v.0.22
alignment: TopHat v.2.0.8b
expression levels: HTSeq package, release 0.5.4p1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene expression values (expressed in count) for each Sample

source_name: HDF pIND-ATF3 doxy

extract_protocol:
Total RNA was extracted using the directZol RNA miniprep kit (Zymo Research) with on-column DNase treatment. RNA quality was verified on the bioanalyzer (Agilent) with RIN > 8
Four ug of total RNA were used for library preparation using the Truseq kit (Illumina)

tag: infected with

value: 500 ng/ml doxyciclin for 3 days


title: H3K27ac-siCSL

description: 5ug Ab/1*10^6 cells

source_name: H3K27ac ChIP-seq

value: H3K27ac (Abcam Cat.No.4729)


title: HDF pIND-ATF3 doxy 100 ng/ml

value: 100 ng/ml doxyciclin for 3 days


title: H3K27ac-siCtrl

description: 5ug Ab/1*10^6 cells


title: H3K27ac-siATF3

description: 5ug Ab/1*10^6 cells


title: Huh-1 (2HUH1HCC)

description: epithelial liver cancer cell line


title: IA2-KO, Mn treatment rep1

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Genetically sensitized S2R+ cells (IA-2 KO) with 1mM MnCl2 treatment.
mRNA

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Drosophila r5.51) using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
We estimate the relative abundance (aka expression level) of genes and splice isoforms using Cufflinks (version 2.0.2) with default settings.
Genome_build: FlyBase genome annotation r5.51 (Release 5)
Supplementary_files_format_and_content: *_genes.csv: Comma-separated text files include FPKM values.

organism: Drosophila melanogaster

source_name: genetically sensitized S2R+ cells (IA-2 KO)

growth_protocol: Standard Drosophila cell culture media, 25 degree incubator.

extract_protocol:
RNA was extracted from cells using Trizol. We used poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>6.7 with no sign of RNA decay was required).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Supplementation to 1 mM followed by a 24 hr incubation.

value: 1 mM MnCl2 for 24 hr


title: IA2-KO, Mn treatment rep2


title: Input DNA [DEK008]

description: processed data file: pics_dek007-dek008_peaks.bed

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner with default parameters
peaks were called using MACS software version 1.4 with default parameter
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by MACS as output of the analysis

source_name: Input DNA

extract_protocol:
Chromatin from 10 milions fixed cells was fragmented to a size range of 100–300 bases with a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibody against ATF3. Antibody–chromatin complexes were pulled-down using magnetic beads, washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase.
ChIPed DNA was quantified by fluorometry on the Qubit system (Invitrogen). A total of 10 ng DNA were used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina, as recommended by the manufacturer.
NEBNext ChIP-seq Library kit (New England Biolabs)

value: none (Input DNA)


title: HLE (1HLEHCC)

description: mesenchymal liver cancer cell line


title: H3K27ac-input

description: 5ug Ab/1*10^6 cells


title: IA2-KO, no treatment rep1

description:
Genetically sensitized S2R+ cells (IA-2 KO).
mRNA

value: no metal treatment


title: Input DNA [DEK010]

description: processed data file: pics_dek009-dek010_peaks.bed


title: ZnT63-KO, Mn treatment rep2

description:
Genetically sensitized S2R+ cells (ZnT63C KO) with 1mM MnCl2 treatment.
mRNA

source_name: genetically sensitized S2R+ cells (ZnT63C KO)


title: IA2-KO, no treatment rep2


title: ZnT63-KO, Zn treatment rep2

description:
Genetically sensitized S2R+ cells (ZnT63C KO) with 1mM ZnCl2 treatment.
mRNA

value: 1 mM ZnCl2 for 24 hr


title: ZnT63-KO, Mn treatment rep1


title: endogenus ATF3 ChIPSeq [DEK007]

description:
5ug Ab/1*10^6 cells
processed data file: pics_dek007-dek008_peaks.bed

source_name: endogenus ATF3 ChIPSeq

value: ATF3 (Santa Cruz Cat.No. 188 C-19)


title: WT, Mn treatment rep2

description:
Wild type S2R+ cells with 1mM MnCl2 treatment.
mRNA

source_name: S2R+ cells

value: wild type


title: ZnT63-KO, no treatment rep1

description:
Genetically sensitized S2R+ cells (ZnT63C KO).
mRNA


title: WT, Mn treatment rep1


title: IA2-KO, Zn treatment rep2

description:
Genetically sensitized S2R+ cells (IA-2 KO) with 1mM ZnCl2 treatment.
mRNA


title: overexpressed ATF3 ChIPSeq [DEK009]

description:
5ug Ab/1*10^6 cells
processed data file: pics_dek009-dek010_peaks.bed

source_name: overexpressed ATF3 ChIPSeq

value: ATF3 (SantaCruz Cat.No.188 C-19)


title: H3K27ac-siATF3 plus siCSL

description: 5ug Ab/1*10^6 cells

value: abdomen skin

value: siATF3 plus siCSL


title: HDF pIND-ATF3 w/o doxy

source_name: HDF pIND-ATF3 w/o doxy

value: primary dermal fibroblasts


title: ZnT63-KO, no treatment rep2


title: IA2-KO, Zn treatment rep1


title: WT, no treatment rep2

description:
Wild type S2R+ cells.
mRNA


title: VRT rep2

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

description:
protocol: SMART-seq2
processed data file: Skin_domains_RNAseq_fpkm.txt

data_processing:
RSEM was used for alignment, mapping and quantification
Reads were not trimmed for adaptor sequence. Sequenced reads were aligned, mapped and quantified to the mouse genome (mm10/vM4) using RSEM v1.2.25 with standard parameters. (B. Li, C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 323 (2011).).
Genome_build: Gencode vM8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Ventral refractory telogen skin 2

extract_protocol:
Total RNA was isolated using the RNEasy Mini-Kit (Qiagen) as per manufacturer’s protocol with minor modifications (Qiagen). Optimal-quality RNAs were considered for cDNA library preparation (RIN>8.0).
100ng total RNA was reversed-transcribed, and resulting cDNA was pre-amplified for 10 cycles. Tagmentation was carried out on 10ng cDNA using the Nextera DNA Sample Preparation Kit (Illumina). The tagmentation reaction was carried out at 55°C for 5 minutes and purified using PCR Purification Kit (Qiagen). Transposed cDNA was utilized for limited cycle enrichment PCR using v2_Adx.x barcodes (IDT). Libraries were amplified for 12 continuous cycles and resulting libraries were purified with AMPure XP beads (Beckman Coulter). Library quantification was done using KAPA for Illumina Sequencing Platforms (Illumina)

value: skin

tag: tissue location

value: ventrum

tag: hair cycle stage

value: refractory telogen


title: LC rep1

description:
protocol: SMART-seq2
processed data file: Ear_pinna_RNAseq_fpkm.txt

source_name: Ear cartilage/muscle complex 1

value: cartilage/muscle

tag: strain

value: ear


title: LC rep3

source_name: Ear cartilage/muscle complex 3


title: LC rep2

source_name: Ear cartilage/muscle complex 2


title: VRT rep1

source_name: Ventral refractory telogen skin 1


title: VMA rep2

source_name: Ventral mid anagen skin 2

value: mid anagen


title: VMA rep1

source_name: Ventral mid anagen skin 1


title: ZnT63-KO, Zn treatment rep1


title: VLA rep2

source_name: Ventral late anagen skin 2

value: late anagen


title: VLA rep3

source_name: Ventral late anagen skin 3


title: VLA rep1

source_name: Ventral late anagen skin 1


title: VEA rep3

source_name: Ventral early anagen skin 3

value: early anagen


title: VEA rep2

source_name: Ventral early anagen skin 2


title: VCT rep3

source_name: Ventral competent telogen skin 3

value: competent telogen


title: VCT rep1

source_name: Ventral competent telogen skin 1


title: WT, Zn treatment rep2

description:
Wild type S2R+ cells with 1mM ZnCl2 treatment.
mRNA

source_name: S2R+ cells


title: VC rep1

source_name: Ventral catagen skin 1

value: ear rostral

value: catagen


title: VCT rep2

source_name: Ventral competent telogen skin 2


title: ERST rep2

source_name: Ear rostral skin telogen 2

value: telogen


title: ERST rep1

source_name: Ear rostral skin telogen 1


title: DRT rep2

source_name: Dorsal refractory telogen skin 2

value: dorsum


title: WT, Zn treatment rep1

value: wild type

value: 1 mM ZnCl2 for 24 hr


title: WT, no treatment rep1

description:
Wild type S2R+ cells.
mRNA

value: no metal treatment


title: DMA rep3

source_name: Dorsal mid anagen skin 3


title: DRT rep1

source_name: Dorsal refractory telogen skin 1


title: DMA rep2

source_name: Dorsal mid anagen skin 2


title: DMA rep1

source_name: Dorsal mid anagen skin 1


title: DLA rep2

source_name: Dorsal late anagen skin 2


title: DCT rep1

source_name: Dorsal competent telogen skin 1


title: DEA rep2

source_name: Dorsal early anagen skin 2


title: DCT rep2

source_name: Dorsal competent telogen skin 2


title: DEA rep1

source_name: Dorsal early anagen skin 1


title: DLA rep1

source_name: Dorsal late anagen skin 1


title: DC rep2

source_name: Dorsal catagen skin 2


title: DC rep1

source_name: Dorsal catagen skin 1


title: VEA rep1

source_name: Ventral early anagen skin 1


title: CRT rep1

source_name: Chin refractory telogen skin 1

value: chin


title: VC rep2

source_name: Ventral catagen skin 2

value: skin


title: CRT rep3

source_name: Chin refractory telogen skin 3


title: CRT rep2

source_name: Chin refractory telogen skin 2


title: CLA rep2

source_name: Chin late anagen skin 2


title: CLA rep1

source_name: Chin late anagen skin 1


title: CEA rep2

source_name: Chin early anagen skin 2


title: CCT rep2

source_name: Chin competent telogen skin 2


title: CEA rep1

source_name: Chin early anagen skin 1


title: CC rep3

source_name: Chin catagen skin 3


title: CCT rep1

source_name: Chin competent telogen skin 1


title: CC rep1

source_name: Chin catagen skin 1


title: DLA rep3

source_name: Dorsal late anagen skin 3


title: SKMM1 cells expressing FAM46CWTGFP for 72 hrs rep3_total RNA

value: Multiple myeloma cell line

value: lentiviruses carrying FAM46CWTGFP for 72 hours


title: SKMM1 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep3_total RNA

value: lentiviruses carrying FAM46CD90A,D92AGFP for 72 hours


title: SKMM1 cells expressing FAM46CWTGFP for 72 hrs rep2_total RNA


title: SKMM1 cells expressing FAM46CWTGFP for 72 hrs rep1_total RNA


title: SKMM1 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep2_total RNA


title: SKMM1 cells expressing FAM46CD90A,D92AGFP for 72 hrs rep1_total RNA


title: CMA rep2

source_name: Chin mid anagen skin 2


title: CMA rep1

source_name: Chin mid anagen skin 1


title: ChIP-seq_BRD3_Mutu_Replicate2

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

data_processing:
50 bp reads were mapped using Bowtie to an index containing both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes.
Parameters allowed for up to 2 mismatches and 2 alignments
Peaks were visualized after normalization to the background baseline
Formatted for uploading to Integrative Genomics Viewer (www.broadinstitute.org/igv/)
Genome_build: index contains both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes
Supplementary_files_format_and_content: Wigs are formatted for IGV. Genome file chrEBV(B95_8_Raji).fa is available from http://www.flemingtonlab.com/rnaseq.html.  Wig columns are chromosome, start, stop, counts per million mapped reads.

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: MutuI (EBV+ Burkitt lymphoma cell line)

growth_protocol: MutuI cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 in 5% CO2 with 10% (v/v) fetal bovine serum (Invitrogen)

extract_protocol:
DNA was prepared and ChIP performed as described in the paper
ChIP-seq libraries were prepared as described in the paper

treatment_protocol: Cells were not treated

value: MutuI

tag: pathogen

value: Epstein-Barr virus


title: B_TotalDNA-seq_AkataZta+Dox+RVX-208_Replicate3

data_processing:
Library strategy: DNA-seq
50 bp reads were mapped using Bowtie to an index containing both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes.
Parameters allowed for up to two mismatches and only considered reads that mapped to a unique sequence.
The percentage of EBV reads was calculated as a proportion of all reads that mapped
EBV genome abundance upon lytic induction and/or drug pretreatment was normalized to the vehicle control in each individual set of experiments
Genome_build: index contains both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes
Supplementary_files_format_and_content: Spreadsheet shows total reads, EBV reads, and EBV quantitation

source_name: Akata-Zta (EBV+ Burkitt lymphoma cell line)

growth_protocol: Akata-Zta cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 in 5% CO2 with 10% (v/v) Tet System Approved fetal bovine serum (Clontech)

extract_protocol:
EBV genome abundance was determined by deep sequencing of total DNA. Input chromatin was prepared as described in the paper.
Total DNA-seq libraries were prepared as described in the paper

treatment_protocol: Log phase cultures were pretreated for 1 hour with 1 μM JQ1 (EMD Millipore), I-BET/GSK525762A (EMD Millipore), RVX-208 (Cayman Chemical), or vehicle, then treated for 1 day with 500 ng/mL doxycycline (Sigma-Aldrich) or vehicle

value: Akata-Zta

tag: 1h pretreatment

tag: 1 day treatment

value: doxycycline


title: B_TotalDNA-seq_AkataZta+Dox+I-BET_Replicate1

tag: cell line

value: I-BET


title: B_TotalDNA-seq_AkataZta+Dox+I-BET_Replicate3


title: B_TotalDNA-seq_AkataZta+Dox+RVX-208_Replicate2


title: B_TotalDNA-seq_AkataZta+Dox_Replicate3

value: vehicle


title: ChIP-seq_BRD3_Mutu_Replicate1


title: ChIP-seq_BRD4_Mutu_Replicate1


title: B_TotalDNA-seq_AkataZta+Dox_Replicate2


title: B_TotalDNA-seq_AkataZta+RVX-208_Replicate2


title: B_TotalDNA-seq_AkataZta+Dox+I-BET_Replicate2


title: B_TotalDNA-seq_AkataZta+Dox_Replicate1


title: B_TotalDNA-seq_AkataZta+RVX-208_Replicate3


title: CC rep2

source_name: Chin catagen skin 2

value: catagen


title: ChIP-seq_H3K4me3_Mutu_Replicate1


title: ChIP-seq_H3K9ac_Mutu_Replicate2


title: ChIP-seq_H3K4me3_Mutu_Replicate2


title: B_TotalDNA-seq_AkataZta+Dox+RVX-208_Replicate1


title: H3K9me2_ChIPSeq_Untreated

city: San Francisco

first: Miguel

last: Ramalho-Santos

state: CA

address: 35 Medical Center Way

department: Eli and Edythe Broad Center of Regeneration Medicine

institute: UCSF

data_processing:
Paired-end sequenced reads were aligned to mm10 genome using BWA 0.5.7 and default parameters (for both aln and sampe steps). Aligned results were reported in the BAM format. Three reads partitions were merged followed by marking duplicated reads using PICARD 1.71 with default settings.
WIG files calculated by profiling paired fragment density after collapsing duplicated fragments and using mapping quality threshold of BWA q>=5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: WIG files contain ChIP-seq data processed as described.

source_name: embryonic stem cells, untreated, H3K9me2 ChIP

growth_protocol: Oct4-GiP ES cells were cultured on tissue culture plates coated with 0.1% gelatin in 2i medium, which consists of N2B27 base medium supplemented with the MEK inhibitor, PD0325901 (1 μM, Stemgent), the GSK3β inhibitor, CHIR99021 (3 μM, Selleck Chemicals), and with ESGRO leukemia inhibitory factor (LIF) at 1,000 U/ml (Millipore).

extract_protocol:
ChIP protocol: ES cells were crosslinked with 1% formaldehyde for 5 minutes at room temperature. Crosslinking was quenched with 125mM glycine. Crosslinked material was sonicated on a Covaris sonicator for 12 min at duty 5%, intensity 3, and bursts 200. ChIP was performed using the Diagenode LowCell# Kit. ChIP DNA was eluted, treated with RNase and Proteinase K, and reverse-cross-linked at 65°C for 4 hrs followed by purification with QIAquick kit.
Prior to library construction, sample volumes were adjusted to 35 ul with Qiagen EB buffer. All liquid handling steps were carried out on the Bravo liquid handling platform using VWorks Automation Control Software (Agilent Automation, Santa Clara, CA, USA). Enzyme mastermix dispenses and magnetic bead clean-up steps were performed using the Bravo configured with the 96LT pipetting head and 180μl disposable tips (Agilent Technologies, catalogue number 08585-002). End Repair and 5' Phosphorylation reaction (35uL DNA sample, 5uL of 10X NEB 2 buffer, 2uL of 25mM ATP, 2uL of 10mM dNTP, 10U T4 Polynucleotide Kinase, 4.5U T4 DNA Polymerase, 1U Klenow Large Fragment DNA Polymerase, and ultrapure water to a total reaction volume of 50uL (New England Biolabs Ipswich, MA, USA) was incubated for 30 minutes at room temperature. DNA samples were then purified using house-made magnetic bead solution (1M NaCL, 23% PEG, Sera-Mag Speedbeads (Fisher Scientific, Pittsburgh PA, USA)) with final PEG concentration of 13.87%. DNA was eluted from the beads in 35uL volume with Qiagen EB buffer. To enable ligation to the adaptors, a single dA overhang was added to the 3' ends of DNA fragments (35uL DNA, 5uL of 10X NEB 2 buffer, 1uL of 10mM dATP, 5U Klenow Fragment (3'→5 ' exo–), and ultrapure water to a total reaction volume of 50uL (New England Biolabs Ipswich, MA, USA)). A-addition reaction was incubated at 37C for 30 minutes. The product was then purified using house-made magnetic bead solution (1M NaCL, 23% PEG, Sera-Mag Speedbeads (Fisher Scientific, Pittsburgh PA, USA)) with final PEG concentration of 13.87%. DNA was eluted from the beads in 35uL volume with Qiagen EB buffer. Next, short adaptors containing sequences required downstream in the sequencing workflow were ligated to the dA-tailed DNA fragments (35uL DNA, 12uL of 5X Quick Ligation Buffer, 2000U Quick T4 DNA Ligase, 2uL of 0.5uM Illumina short sequencing adaptor, and ultrapure water to a total volume of 60uL). Ligation reaction was performed at room temperature overnight. To remove adaptor dimers and fragments below 200bp, the ligation product was then purified two times using house-made magnetic bead solution (1M NaCL, 20% PEG, Sera-Mag Speedbeads (Fisher Scientific, Pittsburgh PA, USA)) with final PEG concentrations of 8.89% and 10.91%, respectively. Adaptor-ligated DNA fragments were eluted from the beads with 35uL of Qiagen EB buffer. Adaptor ligated libraries were PCR amplified and barcoded by custom indexing primers in a 60 ul PCR reaction (35uL DNA, 12uL of 5X High fidelity buffer, 1uL of 10mM dNTPs, 1.5uL of DMSO, 1uL of 25uM PCR primer 1.0, 2uL of 12.5uM custom indexing primer (added separately to each well), 1U Phusion Hot Start II, and ultrapure water to a total volume of 60uL (Fisher Scientific, Pittsburgh PA)). PCR amplification was carried out with the following cycling conditions: 98C for 30 seconds, 10 cycles of (15 seconds at 98C (denaturation), 30 seconds at 65C (annealing), 30 seconds 72C (extension)), followed by 5 min at 72C. PCR amplified libraries were size selected to remove primer dimers with house-made magnetic bead solution (1M NaCL, 20% PEG, Sera-Mag Speedbeads (Fisher Scientific, Pittsburgh PA, USA)) with final PEG concentration of 9.19%. Final library product was eluted from the beads with 35uL of Qiagen EB buffer. The average size was determined by running 1uL of each final library product on the Agilent HS DNA assay chip. Libraries were quantified using Qubit HS DNA assay, pooled equal-molar and quantified for sequencing with Kapa Sybr Fast Complete Universal qPCR kit using manufacturer recommendations.

treatment_protocol: Vitamin C (L-ascorbic acid 2-phosphate, Sigma, A8960) was added on day 1 after seeding at 100 μg/ml. Cells were treated for 72 hours. Medium was replaced daily.

tag: strain/background

value: Oct4-GiP mES cells

tag: passages

tag: treatment

value: H3K9me2 (Abcam, ab1220)


title: input_DNA_Untreated

source_name: embryonic stem cells, untreated, input


title: input_DNA_VitC

source_name: embryonic stem cells, vitamin C, input

value: vitamin C


title: H3K9me2_ChIPSeq_VitC

source_name: embryonic stem cells, vitamin C, H3K9me2 ChIP


title: B_TotalDNA-seq_AkataZta+I-BET_Replicate2


title: B_TotalDNA-seq_AkataZta+RVX-208_Replicate1


title: B_TotalDNA-seq_AkataZta+I-BET_Replicate1


title: B_TotalDNA-seq_AkataZta+I-BET_Replicate3


title: B_TotalDNA-seq_AkataZta+vehicle_Replicate3


title: ChIP-seq_H3K9ac_Mutu_Replicate1


title: B_TotalDNA-seq_AkataZta+vehicle_Replicate1


title: A_TotalDNA-seq_AkataZta+Dox+JQ1_Replicate3


title: ChIP-seq_H3K27ac_Mutu_Replicate2


title: A_TotalDNA-seq_AkataZta+Dox+JQ1_Replicate2


title: A_TotalDNA-seq_AkataZta+Dox+JQ1_Replicate1


title: input_Mutu_Replicate2

value: none (input)


title: ChIP-seq_BRD2_Mutu_Replicate1


title: A_TotalDNA-seq_AkataZta+Dox_Replicate2


title: A_TotalDNA-seq_AkataZta+Dox_Replicate3


title: A_TotalDNA-seq_AkataZta+Dox_Replicate1


title: A_TotalDNA-seq_AkataZta+JQ1_Replicate3


title: input_Mutu_Replicate1


title: B_TotalDNA-seq_AkataZta+vehicle_Replicate2


title: A_TotalDNA-seq_AkataZta+JQ1_Replicate2


title: A_TotalDNA-seq_AkataZta+vehicle_Replicate3


title: A_TotalDNA-seq_AkataZta+JQ1_Replicate1


title: A_TotalDNA-seq_AkataZta+vehicle_Replicate1


title: TotalDNA-seq_MutuI+Ab+JQ1_Replicate1

treatment_protocol: Log phase cultures were pretreated for 1 hour with 1 μM JQ1 (EMD Millipore) or vehicle, then treated for 1 day with 10 μg/mL goat anti-human IgG, IgM, IgA secondary antibody (Thermo Scientific, PI31128) or vehicle

value: antibody


title: TotalDNA-seq_MutuI+Ab_Replicate1


title: ChIP-seq_BRD4_AkataZta_acy_JQ1_LGNFR-_Replicate2

data_processing:
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to 2 mismatches and 2 alignments
The number of hits at each base was counted and then normalized per million mapped reads.
Formatted for uploading to the Integrative Genomics Viewer (www.broadinstitute.org/igv)
Genome_build: hg19, EBV NC_007605.1
Supplementary_files_format_and_content: wig files

source_name: Akata-Zta cells

growth_protocol: Cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) Tet System Approved fetal bovine serum (Clontech) in 5% CO2 at 37°C.

extract_protocol:
18E6 cells were collected, and ChIP was performed as described in the paper.
Deep sequencing libraries were prepared by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).

treatment_protocol: Log-phase cultures were pretreated with 1) 200 μM acyclovir (Sigma-Aldrich) and 2) either 1 uM JQ1 or vehicle (DMSO) for 1 hr before induction with 500 ng/mL doxycycline (Sigma-Aldrich). After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotec).

value: Akata-ZTA


title: TotalDNA-seq_MutuI+Ab_Replicate3


title: TotalDNA-seq_MutuI+Ab+JQ1_Replicate2


title: B_RNA-seq_AkataZta+Dox+I-BET_Replicate3

data_processing:
50 bp reads were mapped using Bowtie to an index containing both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes.
Parameters allowed for up to two mismatches and only considered reads that mapped to a unique sequence.
The number of hits at each base was counted and then normalized per million mapped reads.
Formatted for uploading to Integrative Genomics Viewer (www.broadinstitute.org/igv/)
Genome_build: Index contains both the human hg19 and EBV [GenBank ID: NC_007605.1] reference genomes
Supplementary_files_format_and_content: Wigs are formatted for IGV. Genome file chrEBV(B95_8_Raji).fa is available from http://www.flemingtonlab.com/rnaseq.html.  Wig columns are chromosome, start, stop, counts per million mapped reads.

extract_protocol:
RNA was extracted and cDNA was prepared as described in the paper
RNA-seq libraries were prepared as described in the paper

treatment_protocol: Log phase cultures were pretreated for 1 hour with 1 μM JQ1 (EMD Millipore), I-BET/GSK525762A (EMD Millipore), or vehicle, then treated for 1 day with 500 ng/mL doxycycline (Sigma-Aldrich) or vehicle


title: TotalDNA-seq_MutuI+Ab_Replicate2


title: TotalDNA-seq_MutuI+JQ1_Replicate3


title: ChIP-seq_BRD2_Mutu_Replicate2


title: ChIP-seq_BRD4_AkataZta_acy_JQ1_LGNFR+_Replicate2


title: ChIP-seq_BRD4_Mutu_Replicate2


title: B_RNA-seq_AkataZta+Dox+I-BET_Replicate2


title: ChIP-seq_BRD4_AkataZta_acy_vehicle_LGNFR+_Replicate2


title: TotalDNA-seq_MutuI+Ab+JQ1_Replicate3


title: B_RNA-seq_AkataZta+Dox+I-BET_Replicate1


title: TotalDNA-seq_MutuI+JQ1_Replicate2


title: TotalDNA-seq_MutuI+JQ1_Replicate1


title: ChIP-seq_BRD4_AkataZta_acy_JQ1_LGNFR-_Replicate1


title: TotalDNA-seq_MutuI+vehicle_Replicate3


title: B_RNA-seq_AkataZta+I-BET_Replicate3


title: ChIP-seq_BRD4_AkataZta_acy_JQ1_LGNFR+_Replicate1


title: A_TotalDNA-seq_AkataZta+vehicle_Replicate2


title: B_RNA-seq_AkataZta+I-BET_Replicate2


title: TotalDNA-seq_MutuI+vehicle_Replicate2


title: ChIP-seq_BRD4_AkataZta_acy_vehicle_LGNFR-_Replicate1


title: B_RNA-seq_AkataZta+I-BET_Replicate1


title: A_RNA-seq_AkataZta+Dox+JQ1_Replicate3


title: TotalDNA-seq_MutuI+vehicle_Replicate1


title: RNA-seq_MutuI+Ab+JQ1_Replicate1

description: Sample name: 56

data_processing:
50 bp reads were mapped using Bowtie to an index containing both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes.
Parameters allowed for up to two mismatches and only considered reads that mapped to a unique sequence.
Wigs: The number of hits at each base was counted and then normalized per million mapped reads.
Wigs: Formatted for uploading to Integrative Genomics Viewer (www.broadinstitute.org/igv/)
Spreadsheet: Differential expression of human genes 28 upon drug treatment was calculated by comparing independent triplicate experiments where MutuI cells were treated with 1 μM JQ1 or vehicle for 1 day.
Spreadsheet: Adaptors and low-quality portions of reads were trimmed with Fastq-mcf, sequence quality control assessed with FastQC and RSeQC, and spliced and unspliced reads aligned to the hg19 reference human genome with Tophat 2.0.13 and Bowtie 2.2.4, respectively.
Spreadsheet: Reads were assigned to genes as annotated by Ensembl using featureCounts. Genes yielding counts per million expression below 0.5 or above 5000 in more than one sample were excluded for analysis.
Spreadsheet: Re-normalization of all other genes and calculation of differential expression p-values were performed with edgeR. The false discovery rate for each p-value was calculated using the Benjamini-Hochberg method with R. Pathway enrichment analysis was performed with GO-Elite 1.2.5 and a cut-off p-value of 0.05.
Genome_build: Index contains both the human hg19 and EBV [GenBank ID: NC_007605.1] reference genomes
Supplementary_files_format_and_content: Wigs are formatted for IGV. Genome file chrEBV(B95_8_Raji).fa is available from http://www.flemingtonlab.com/rnaseq.html.  Wig columns are chromosome, start, stop, counts per million mapped reads.

value: mutuI


title: ChIP-seq_BRD4_AkataZta_acy_vehicle_LGNFR+_Replicate1


title: RNA-seq_MutuI+Ab+JQ1_Replicate2

description: Sample name: 69


title: RNA-seq_MutuI+Ab+JQ1_Replicate3

description: Sample name: 83


title: ChIP-seq_BRD4_AkataZta_acy_vehicle_LGNFR-_Replicate2


title: A_RNA-seq_AkataZta+Dox+JQ1_Replicate2


title: TotalDNA-seq_Akata-Zta+acy+vehicle_LGNFR-_Replicate2

data_processing:
Library strategy: DNA-seq
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to one mismatch and only considered reads that mapped to a unique sequence.
The number of hits at each base was counted and then normalized per million mapped reads.
Formatted for uploading to the Integrative Genomics Viewer (www.broadinstitute.org/igv)
Genome_build: hg19, EBV NC_007605.1
Supplementary_files_format_and_content: wig files

extract_protocol:
DNA was isolated from 1 million cells each of LGNFR+ and LGNFR- using a Qiagen DNeasy Blood and Tissue kit.
Deep sequencing libraries were prepared by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).


title: A_RNA-seq_AkataZta+Dox+JQ1_Replicate1


title: TotalDNA-seq_Akata-Zta+acy+JQ1_LGNFR-_Replicate2


title: A_RNA-seq_AkataZta+Dox_Replicate3


title: RNA-seq_MutuI+Ab_Replicate3

description: Sample name: 85


title: A_RNA-seq_AkataZta+Dox_Replicate2


title: RNA-seq_MutuI+Ab_Replicate2

description: Sample name: 71


title: RNA-seq_MutuI+Ab_Replicate1

description: Sample name: 58


title: TotalDNA-seq_Akata-Zta+acy+JQ1_LGNFR-_Replicate1


title: A_RNA-seq_AkataZta+JQ1_Replicate3


title: TotalDNA-seq_Akata-Zta+acy+JQ1_LGNFR+_Replicate2


title: RNA-seq_MutuI+JQ1_Replicate3

description:
Sample name: 84
processed data file: Differential_Expression_GEO.xlsx


title: TotalDNA-seq_Akata-Zta+acy+JQ1_LGNFR+_Replicate1


title: A_RNA-seq_AkataZta+Dox_Replicate1


title: A_RNA-seq_AkataZta+JQ1_Replicate2


title: TotalDNA-seq_Akata-Zta+acy+vehicle_LGNFR-_Replicate1


title: RNA-seq_MutuI+JQ1_Replicate2

description:
Sample name: 70
processed data file: Differential_Expression_GEO.xlsx


title: A_RNA-seq_AkataZta+JQ1_Replicate1


title: TotalDNA-seq_Akata-Zta+acy+vehicle_LGNFR+_Replicate1


title: ChIP-seq_BRD4_Mutu_100E6_JQ1_Replicate2

extract_protocol:
Unless noted, 18E6 cells were collected for ChIP. For the Mutu cells treated with JQ1 or vehicle, 100E6 cells were collected for ChIP.
DNA was prepared and ChIP performed as described in the paper
ChIP-seq libraries were prepared as described in the paper

treatment_protocol: Unless noted, cells were not treated. For Mutu ChIPs with 100E6 cells, cells were treated with either 1 uM JQ1 or vehicle for 24 hours, and then cells were fixed for ChIP.


title: A_RNA-seq_AkataZta+vehicle_Replicate2


title: TotalDNA-seq_Akata-Zta+acy+vehicle_LGNFR+_Replicate2


title: A_RNA-seq_AkataZta+vehicle_Replicate3


title: ChIP-seq_BRD4_Mutu_100E6_JQ1_Replicate1


title: RNA-seq_MutuI+vehicle_Replicate2

description:
Sample name: 72
processed data file: Differential_Expression_GEO.xlsx


title: RNA-seq_MutuI+vehicle_Replicate3

description:
Sample name: 86
processed data file: Differential_Expression_GEO.xlsx


title: ChIP-seq_BRD4_Mutu_100E6_vehicle_Replicate1


title: RNA-seq_MutuI+vehicle_Replicate1

description:
Sample name: 59
processed data file: Differential_Expression_GEO.xlsx


title: Lympho RNA-seq

status: Public on Jun 29 2017

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
Data processing was performed using partek Flow build version 4.0.15.0702
Bases were trimmied on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign Bowtie2 version 2.1.0.
Quantification to transcriptome performed using Partek E/M algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: raw expression values

source_name: A representative LCL from healthy adult donors were obtained from the National Laboratory for the Genetics of Israeli Populations (NLGIP; http://nlgip.tau.ac.il) at Tel-Aviv University.

growth_protocol: Cells were maintained in optimal growth conditions as described (Oved K, Morag A, Pasmanik-Chor M, Rehavi M, Shomron N, Gurwitz D Genome-wide expression profiling of human lymphoblastoid cell lines implicates integrin beta-3 in the mode of action of antidepressants. Transl Psychiatry 3, e313, 2013)

extract_protocol:
RNA was extracted using TRI Reagent (T9242, Sigma-Aldrich, MO,USA) kit followed by mRNA libraries construction.
Customary Illumina TruSeq™ RNA Sample Prep Kit v2 protocol (catalog No. RS-122-2001)

value: Lympho

tag: tissue

value: lymphoblastoid cell line

value: wild-type


title: Ig1 RNA-seq

source_name: ADNP mutated LCL line (Ig1) was generated from peripheral blood lymphocytes donated by consenting patient and guardians/physicians (Professor Orly Elpeleg).

treatment_protocol: Cells were maintained in optimal growth conditions as described (Oved K, Morag A, Pasmanik-Chor M, Rehavi M, Shomron N, Gurwitz D Genome-wide expression profiling of human lymphoblastoid cell lines implicates integrin beta-3 in the mode of action of antidepressants. Transl Psychiatry 3, e313, 2013)

value: ADNP mutated lymphoblastoid cell line

value: ADNP mutated


title: SSC4121 RNA-seq

source_name: Two ADNP mutated LCLs were purchased from the Simon Simplex Collection, SSC04121 = ADNP (protein) p.Lys408Valfs*31, and SSC08311= p.Tyr719*


title: N709.N502

city: Oxford

first: Emma

last: Harvey

address: John Radcliffe Hospital

country: United Kingdom

institute: University of Oxford

description: Sample 3

data_processing:
Sequence reads were trimmed for adaptor sequences using TrimGalore v0.3.3 with parameters "-q 15 --stringency 3 --length 36 --paired"
Trimmed reads were mapped to the reference human genome using Bowtie v1.0.0 with parameters "-a --best --strata -m 100 -X 500 --chunkmbs 256"
Gene and transcript expression quantifications in log2(FPKM+1) units were obtained using MMSEQ v1.0.7 with default parameters (https://github.com/eturro/mmseq)
Differential gene and transcript expression were obtained using MMDIFF v.1.0.7 with default parameters (https://github.com/eturro/mmseq). Genes or transcripts not expressed in 2/3 samples of each ("Poor" and "Good") condition were discarded.
Genome_build: GRCh37.70/Ensembl v70
Supplementary_files_format_and_content: [.mmseq] Gene and transcript expression values
Supplementary_files_format_and_content: [Transcripts_up_good.txt] List of transcripts higher in samples 4-6 than in samples 1-3
Supplementary_files_format_and_content: [Transcripts_up_poor.txt] List of transcripts higher in samples 1-3 than in samples 4-6
Supplementary_files_format_and_content: [Genes_up_good.txt] List of genes higher in samples 4-6 than in samples 1-3
Supplementary_files_format_and_content: [Genes_up_poor.txt] List of genes higher in samples 1-3 than in samples 4-6

source_name: Cardiosphere derived cells, poor supporter of angiogenesis

growth_protocol: Cardiosphere derived cells were isolated from right atrial appendage cardic samples donated by patients undergoing elective coronary surgery. Cardiosphere derived cells were isolated using the Marban protocol and were cultured on fibronectin coated plates in IMDM (Life Technologies), 20% foetal bovine serum (FBS, Hyclone), 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin and 0.1mM 2-mercaptoethanol.

extract_protocol:
Total RNA from 6 CDC samples was isolated using RNeasy mini kits (QIAgen) according to the manufacturer’s instructions and treated with DNase I (Promega) to remove genomic DNA.
Smarter Clontech

treatment_protocol: Cardiosphere derived cells were tested for their supportive potential using a tubule assay based on co-culture with GFP labelled HUVECs. Cardiosphere derived cells were classifies as good or poor supporters of angiogenesis

value: Heart (right atrial appendage)

value: Cardiosphere derived cells

tag: supportive ability

value: Poor

tag: cell isolate number


title: N704.N501

description: Sample 6

source_name: Cardiosphere derived cells, good supporter of angiogenesis

value: Good


title: N701.N501

description: Sample 4


title: N702.N501

description: Sample 5


title: N707.N501

description: Sample 1


title: rna_135_run194_002_COG study 0447

city: Albuquerque

first: Ksenia

last: Matlawska

state: NM

address: 915 Camino de Salud

department: Pediatrics

institute: University of New Mexico

description:
135
RNA sequencing data from primary T-ALL samples at diagnosis

data_processing:
Illumina mRNA-seq data (fastq files) were mapped using StrongArm pipeline
genomic rearrangements were identified using CICERO, a novel algorithm identifying fusion transcripts (Illumina data)
Ion Proton data (BAM files) were aligned with STAR (bases calling: IonTorrent Base Caller)
aligned data were analyzed using customized scripts written in R (for Ion Proton data)
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing results of identified fusion transcripts

source_name: COG study 0447

growth_protocol: Derived from bone marrow in newly diagnosed T-ALL patients

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols (14 samples; Truseq RNA Library Preparation kit ) or standard Ion Proton protocols (3 samples; Xpress Plus Fragment Library kit), respectively.

treatment_protocol: COG study 9404/0434 (diagnostic samples)

tag: diagnosis

value: Newly diagnosed T-ALL patient

value: bone marrow


title: rna_133_run139__015_COG study 0448

description:
133
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0448


title: rna_117_run193_001_COG study 0446

description:
117
RNA sequencing data from primary T-ALL samples at diagnosis

source_name: COG study 0446


title: RNA-seq_MutuI+JQ1_Replicate1

description:
Sample name: 57
processed data file: Differential_Expression_GEO.xlsx

value: Epstein-Barr virus

value: vehicle


title: RiboMeth_trm734/rtt10D_2

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation Street

department: Biochemistry & Molecular Pharm

institute: UMass Medical School

description:
RiboMeth-seq
processed data files:
Chou_Table_S5.txt

data_processing:
Library strategy: RiboMeth-seq
Raw fastq reads were de-multiplexed and removed of adaptor sequence using homerTools function of HOMER package v4.6, with parameters "barcodes 5 -min 0.01" and "trim -5 2 -3 TGGAATTCTCGGGTGCCAAGG -mis 2 -minMatchLength 5", respectively.
De-multiplexed and adaptor-removed reads for RPF were mapped to S. cerevisiae rDNA and the mapping reads were discarded. The remaining RPF reads and RNA-seq reads were mapped to sacCer3 genome using TopHat v2.0.12 with parameters -p 4 -I 5000 --no-coverage-search
Uniquely mapping reads (filtered by samtools view function and parameter -q 10) in length of 27-34 nt (RPF) or >=27 nt (RNA-seq) were used for gene-level analysis, in which reads were quantified as raw counts or reads per kilobase of transcript per million mapped reads (RPKM) using HOMER package with open reading frame annotations downloaded from SGD.
Translational efficiency (TE) was calculated as relative ribosome footprint density (Ribo-rRPKM) divided by relative RNA abundance (RNA-rRPKM), with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch.
Global codon occupancy analysis was calculated as described in (Nedialkova and Leidel, 2015), with minor modifications. The P-site offset was calculated by examining the cumulative distribution of 28-31 nt reads aligning at start codons. After applying the respective offset to reads of each size, only in-frame reads were used. The first 15 and the last 5 codons of each transcript were removed from the reference. The frequency of each codon in ribosomal A, P, and E sites was calculated for normalization, and divided by the average frequency of the same codon in the three downstream codons from the A site
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (RPF or RNA-seq reads) and normalized codon frequencies per A/P/E site.
Supplementary_files_format_and_content: Chou_Table_S1.txt: RNA counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S2.txt: RPF counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S3.txt: relative Translational Efficiency values (RPF rRPKM/RNA rRPKM, with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch)
Supplementary_files_format_and_content: Chou_Table_S4.txt: A/P/E site normalized values
Supplementary_files_format_and_content: Chou_Table_S5.txt: RiboMeth-seq data with raw counts of 5' read starts

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: 100 mL of yeast cultures were grown to mid-log phase (OD600=0.5-0.6) in YPD (1% Yeast extract, 2% Peptone, 2% Dextrose) at 30°C

extract_protocol:
For RPF, cells were lysed by glass-bead beating in ice-cold lysis buffer, followed by RNase I treatment. Ribosomes were separated on 10-50% sucrose gradient and 80S monosome fractions were collected and RNA extracted. 27-34 nt ribosome footprints were isolated by denaturing PAGE.    For RNA-Seq, total RNA extracted using TRIZOL was depleted of rRNA using Ribo-Zero, followed by zinc-based fragmentation for 10 min at 70°C.
RPF and rRNA-depleted RNA are constructed into deep-sequencing libraries as described in (Heyer et al., 2015). Briefly, RNA 3’ ends were dephosphorylated, ligated with a preadenylated adaptor, and reverse transcribed. cDNA was precipitated and size selected by denaturing PAGE. The purified cDNA was circularized and PCR amplified prior to sequencing. For RiboMeth-seq, total RNAs were end-repaired with T4 PNK, Antarctic phosphatase, or Shrimp alkaline phosphatase for 3’-end dephosphorylation and with T4 PNK and ATP for 5’-end phosphorylation, followed by library construction using NEB Next Small RNA Library Prep kit. Amplified library was purified and subject to Illumina Nextseq 500 single-end sequencing with 75 cycles.

treatment_protocol: 30 sec of cycloheximide in a final concentration of 100 ug/mL in YPD at 30°C

tag: media

value: YPD

value: BY4741 with rtt10D::kanMX

value: Cycloheximide


title: RiboMeth_trm732D_2

value: BY4741 with trm732D::kanMX


title: RiboMeth_trm732D_1


title: ChIP-seq_BRD4_Mutu_100E6_vehicle_Replicate2

source_name: MutuI (EBV+ Burkitt lymphoma cell line)

value: MutuI

tag: chip antibody


title: A_RNA-seq_AkataZta+vehicle_Replicate1

source_name: Akata-Zta (EBV+ Burkitt lymphoma cell line)

value: Akata-Zta


title: RiboMeth_trm44D_2

value: BY4741 with trm44D::kanMX


title: RiboMeth_trm44D_1


title: RiboMeth_trm13D_1

value: BY4741 with trm13D::kanMX


title: RiboMeth_trm7D_1

value: BY4741 with trm7D::kanMX


title: RiboMeth_trm7D_2


title: RiboMeth_trm13D_2


title: RiboMeth_trm3D_1

value: BY4741 with trm3D::kanMX


title: RiboMeth_trm3D_2


title: SSC8311 RNA-seq

value: ADNP mutated lymphoblastoid cell line

tag: genotype/variation

value: ADNP mutated


title: RiboMeth_trm734/rtt10D_1


title: RiboMeth_BY4741_2


title: RiboMeth_trm3D_f20_rSAP


title: RiboMeth_trm3D_f20_AnP


title: RiboMeth_trm3D_f10_T4PNK


title: RiboMeth_BY4741_1


title: RiboMeth_trm3D_f10_rSAP


title: RiboMeth_trm7D_f10_AnP


title: RiboMeth_trm7D_f20_rSAP


title: RiboMeth_trm3D_f10_AnP


title: RiboMeth_trm7D_f10_rSAP


title: RiboMeth_trm7D_f20_T4PNK


title: RiboMeth_BY_f20_rSAP


title: RiboMeth_trm7D_f10_T4PNK


title: RiboMeth_BY_f20_AnP


title: RiboMeth_BY_f10_rSAP


title: RiboMeth_trm7D_f20_AnP


title: RiboMeth_BY_f10_AnP


title: RNA_cgi121D

description:
rRNA-depleted RNA
processed data files:
Chou_Table_S1.txt
Chou_Table_S3.txt

data_processing:
Raw fastq reads were de-multiplexed and removed of adaptor sequence using homerTools function of HOMER package v4.6, with parameters "barcodes 5 -min 0.01" and "trim -5 2 -3 TGGAATTCTCGGGTGCCAAGG -mis 2 -minMatchLength 5", respectively.
De-multiplexed and adaptor-removed reads for RPF were mapped to S. cerevisiae rDNA and the mapping reads were discarded. The remaining RPF reads and RNA-seq reads were mapped to sacCer3 genome using TopHat v2.0.12 with parameters -p 4 -I 5000 --no-coverage-search
Uniquely mapping reads (filtered by samtools view function and parameter -q 10) in length of 27-34 nt (RPF) or >=27 nt (RNA-seq) were used for gene-level analysis, in which reads were quantified as raw counts or reads per kilobase of transcript per million mapped reads (RPKM) using HOMER package with open reading frame annotations downloaded from SGD.
Translational efficiency (TE) was calculated as relative ribosome footprint density (Ribo-rRPKM) divided by relative RNA abundance (RNA-rRPKM), with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch.
Global codon occupancy analysis was calculated as described in (Nedialkova and Leidel, 2015), with minor modifications. The P-site offset was calculated by examining the cumulative distribution of 28-31 nt reads aligning at start codons. After applying the respective offset to reads of each size, only in-frame reads were used. The first 15 and the last 5 codons of each transcript were removed from the reference. The frequency of each codon in ribosomal A, P, and E sites was calculated for normalization, and divided by the average frequency of the same codon in the three downstream codons from the A site
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (RPF or RNA-seq reads) and normalized codon frequencies per A/P/E site.
Supplementary_files_format_and_content: Chou_Table_S1.txt: RNA counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S2.txt: RPF counts/RPKM per gene
Supplementary_files_format_and_content: Chou_Table_S3.txt: relative Translational Efficiency values (RPF rRPKM/RNA rRPKM, with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch)
Supplementary_files_format_and_content: Chou_Table_S4.txt: A/P/E site normalized values
Supplementary_files_format_and_content: Chou_Table_S5.txt: RiboMeth-seq data with raw counts of 5' read starts

value: BY4741 with cgi121D::kanMX


title: RNA_kti13D

value: BY4741 with kti13D::kanMX


title: RNA_bud32D

value: BY4741 with bud32D::kanMX


title: RNA_trm9D

value: BY4741 with trm9D::kanMX


title: RNA_gon7D

value: BY4741 with gon7D::kanMX


title: RiboMeth_BY_f10_T4PNK

value: YPD


title: RiboMeth_BY_f20_T4PNK


title: RNA_elp5D

value: BY4741 with elp5D::kanMX


title: RNA_BY4741_10

value: Cycloheximide


title: RiboMeth_trm3D_f20_T4PNK


title: RNA_tan1D

value: BY4741 with tan1D::kanMX


title: RNA_BY4741_9