title: APC ChIP-seq replicate 1

city: Columbus

first: Joanna

last: Groden

state: OH

address: 986 BRT 460 West 12th Ave.

department: Department of Cancer Biology and Genetics

institute: The Ohio State University, College of Medicine

description: ChIP-seq

data_processing:
Fastq files were analyzed for per base sequence quality.  97-98% of reads were confirmed to have passed quality control filters.
Burrows-Wheeler Aligner was used to perform alignment to the UCSC hg19 reference genome, generating bam files.
Bam alignment files were uploaded to Galaxy and peak calling was performed using the Model-based Analysis of ChIP-Seq version 2 (MACS2) tool, generating peak scores, p-values and false discovery rates (FDR).  Parameter tuning was performed to identify the p-value threshold (p < 0.001) at which input/background signal was lowest while positive control peaks in the AXIN2, DKK1 and MYC loci were still detected.  Peak regions were annotated using the RefGene database and distanes to transcription start sites were determined and used to assign peaks to
Overlapping peaks present in replicates 1 and 2 were identified using R software, defining overlapping peaks as those with a summit distance between them of 400 bp or less (the median of the peak width determined in the peak calling results).
Genome_build: hg19
Supplementary_files_format_and_content: Galaxy_APC_ChIP-seq_replicate_1.fasta and Galaxy_APC_ChIP-seq_replicate_2.fasta are track files useful for visualization of anti-APC ChIP-seq replicates 1 and 2 in a genome browser.  Annotated_peaks_APC_ChIP-seq_1.xlsx and Annotated_peaks_APC_ChIP-seq_2.xlsx are spreadsheets listing the genomic peaks identified in each anti-APC ChIP-seq replicate, along with the peak score, the identity of the nearest gene and the location of the peak relative to the transcription start site of that gene.  Overlapping_peaks_APC_ChIP-seq_replicates_1_2.xlsx is a spreadsheet listing the distance from the center of each peak in anti-APC ChIP-seq replicate 1 to the center of the closest corresponding peak in anti-APC ChIP-seq replicate 2.

source_name: APC wild-type, CTNNB1ΔSer45

growth_protocol: HCT-116 cells were purchased from the American Type Culture Collection (ATCC) and cultured in McCoy's 5A medium (GIBCO catalog #16600082) supplemented with 10% fetal bovine serum.  Cells had been cultured for fewer than 20 passages at the time of the experiment.

extract_protocol:
Two independent biological replicates were performed.  6 x 106 HCT-116 cells were initially seeded in each 150-mm dish.  Cells were crosslinked after 24 hrs. with 1% formaldehyde for 10 minutes before quenching by 0.125 M glycine.  Cells were washed and scraped into Dulbecco’s PBS, pelleted and resuspended in cold 10 mM HEPES pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100, 1 mM PMSF with mammalian protease inhibitor cocktail (Sigma-Aldrich) and incubated 10 minutes at 4oC with rotation.  Cells were again pelleted and resuspended in cold 10 mM HEPES pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 mM PMSF and protease inhibitors and rotated 10 minutes at 4oC.  Nuclei were pelleted and resuspended in 1 mL of cold 25 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.5% Sodium Deoxycholate, 1 mM PMSF with protease inhibitors.  Probe-based sonication at 4oC was performed using 30 pulses of 10-seconds each at 35% amplitude.  Fragment size was reduced by dividing the resulting supernatant into 300 μL aliquots and mixing each with 100 μL of 2 M sucrose, 320 mM KCl, 80 mM HEPES pH 7.5, 14 mM ATP, 24 mM CaCl2 and 4 µL of 50 U/µL micrococcal nuclease (Affymetrix, Inc.).  Digest was incubated 15 minutes at room temperature and quenched by mixing on ice with 45 µL of 200 mM EDTA, 20 mM EGTA.  An equal volume of 16.7 mM Tris-HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 1 mM PMSF, with protease inhibitors was added to each sample to dilute it.  Pre-clearing of input was performed using 2-hour incubation with 5 μg rabbit IgG antibody and 40 μL of pre-equilibrated Protein G Dynabead slurry (Thermo Fisher Scientific) at 4oC with rotation.  100 μL of the resulting supernatant was saved as “pre-cleared input”.  The remainder was used for anti-APC ChIP in combination with 10 μg of anti-APC antibody (a polyclonal antibody recognizing the C-terminal 50 amino acids of APC, catalog #A300-981A, Bethyl Laboratories, Inc.).  Immunoprecipitations were rotated overnight at 4oC and mixed with 40 μL of pre-equilibrated Protein G Dynabead slurry and rotated 3 hours at 4oC.  Beads were collected by magnet and washed twice with cold 50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40, 0.5% sodium deoxycholate, 1 mM PMSF, and protease inhibitors, twice with cold 50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40, 0.5% sodium deoxycholate, 1 mM PMSF, and protease inhibitors, twice with cold 50 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 1 mM PMSF, and protease inhibitors, and twice with cold 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 mM PMSF, and protease inhibitors.  All washes were accompanied by 5 minute rotation at 4oC.  Elution was performed by the addition of 210 μL room temperature Elution Buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) to the washed beads, and 45 minute incubation at 65oC with occasional gentle resuspension of beads.  Supernatant was isolated and crosslinks were reversed by mixing with 16 μL of 5M NaCl and incubation at 65oC for 12 hrs.  210 μL TE was added to ChIP reactions, while 300 μL TE was added tothe pre-cleared input samples.  8 μL of 10 mg/mL RNase A was mixed with each sample and incubated 2 hrs at 37oC.  4 μL of 25 mg/mL Proteinase K was mixed with each sample and followed by 2 hours incubation at 55oC.  Samples were extracted twice with phenol:chloroform:isoamyl alcohol (25:24:1), once with chloroform, and mixed with 1/10th volume of sodium acetate pH 5.2 and 60 μg glycogen for ethanol precipitation.  Yields from multiple parallel α-APC ChIP reactions were pooled to obtain the 10 ng required for ChIP-seq library preparation.  The PCR purification kit (QIAGEN) was used to clean up reactions prior to library preparation.
Library preparation for ChIP-seq was performed with the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina, using adaptors AD005 and AD019 (New England Biolabs) for the input and ChIP libraries, respectively.  Size selection was performed by E-gel (Life Technologies, Inc.) to obtain fragments ranging in size from 300-400 bp.  Next-generation sequencing (50 bp, single-end) was performed by the OSU Genomics Shared Resource using a HiSeq 2500 instrument (Illumina, Inc.).

treatment_protocol: 6 x 106 HCT-116 cells were seeded in each 150-mm dish.

value: colon carcinoma

tag: chip antibody

value: anti-APC (a polyclonal antibody recognizing the C-terminal 50 amino acids of APC, catalog #A300-981A, Bethyl Laboratories, Inc.)


title: Input ChIP-seq replicate 1

status: Public on May 24 2018

type: SRA

country: USA

description: ChIP-seq

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: Input ChIP-seq replicate 2

description: ChIP-seq


title: Vehicle Replicate  3

city: Bronx

first: Luis

last: Carvajal

state: NY

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

library_source: transcriptomic

data_processing:
Raw fastq files were created (demultiplexted and generated) using Picard tools ExtractIlluminaBarcodes and IlluminaBasecallsToFastq, respectively (see https://broadinstitute.github.io/picard/).
These initial raw fastq files only contained reads that passed the Illumina chastity filter.) Reads were next trimmed of flanking adapter sequences using trim galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Stats were generated using fastqc and fastq-screen (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ and https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
Each library (sample) was sequenced in two different lanes (sequenced twice) and then merged producing a single (larger) trimmed fastq file for each sample.
Trimmed fastq files were then aligned to the human genome (hg19 build b2_8) using the Star aligner (https://github.com/alexdobin/STAR and  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/)
Genome_build = hg19
Supplementary_files_format_and_content: The transcript counts (in the .ReadsPerGene.out.tab files) were generated by STAR.
Supplementary_files_format_and_content: rlog expression tab-delineated text files includes the -log expression values generated using DESeq 2.0 for each replicate. M13_6924_vs_vehicle.txt are the average normalized expression values for each condition.

molecule: total RNA

source_name: Moml13 AML cell line

extract_protocol:
Total mRNA was prepared from 5.0 x 10^5 cells using the QIAGEN Rneasy Micro Kit (cat#74004)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Myeloid Leukemia


title: APC ChIP-seq replicate 2

description: ChIP-seq


title: Vehicle Replicate 2


title: Vehicle Replicate 1


title: ALRN-6924 Replicate 1


title: ALRN-6924 Replicate 2


title: CM138 [RNA-Seq]

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
RNA-seq library from 12 cell lines were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment of the sequenced reads were perfromed using Tophat package
Differential expression analysis was perfomed using cufflink and cuffdiff packages
Exon usage analysis was perfromed using DEXSeq R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file contains FPKM values of 2 groups with P-value and fold changes for significant genes  (excel)

extract_protocol:
RNA was extracted from the cell lines using RNeasy Plus mini prep kit (QIAGEN, Limburg, Nether- lands), quantified using a Nanodrop (Thermo Scientific, Wilmington, DE)
Total RNA was isolated with RNeasy Mini Kit (Qiagen) following manufacturer’s protocol. Two rounds of RNase-free DNase I digestion (Qiagen) was performed to eliminate genomic DNA during the extraction process. RNA concentrations were determined using NanoDrop 2000 (Thermo Scientific). The quality and integrity of the RNA was determined using the RNA 6000 Pico chip on 2100 Bioanalyzer (Agilent Technologies). The median RNA integrity number (RIN) for the 12 samples was 8.0. RNA libraries were constructed using 1 µg of total RNA with TruSeq stranded mRNA Sample Preparation kit (Illumina, USA) following the manufacturer’s protocol.

value: Inducible PD-L1 melanoma cell line


title: Ima_150_056

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

data_processing:
Quality filtering of the NextSeq 500 fastq files was not required
Reads of the fastq files were aligned to the reference sequence using Tophat 2.0.14 combined with Bowtie 2.1.0 (yielding 93.4 - 95.7 % aligned reads/sample). The default mismatch rate of 2% was used (3 mismatches in a read of 150 bases). The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package.
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files. The amount of reads mapped on genes was 69.9-78.6 %/sample (as a % of all reads initially aligned to the genome).
Genome_build: Mus_musculus.GRCm38.dna.primary_assembly (.fa and .gtf files)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample).

organism: Mus musculus

source_name: liver

growth_protocol: In this study, we used female APOE*3Leiden.CETP mice mice (9 to 14 weeks of age) , as a well-established model for dyslipidemia and atherosclerosis, with a human-like lipoprotein metabolism and atherosclerosis development. During the study, mice were housed under standard conditions with a 12-h light-dark cycle and had free access to food and water.

extract_protocol:
Total RNA was extracted from liver tissue samples (8 per group) using RNA-Bee (Amsbio, Oxon, UK) and nucleospin RNA columns from Machery Nagel, according to manufacturer’s instruction.
The NEBNext Ultra RNA sample Prep Kit was used to further process the samples. The sample preparation was performed according the NEB protocol “Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module” (NEB #E7490)

treatment_protocol: Mice were fed a semi-synthetic diet, containing saturated fat from 15% (w/w) cacao butter and 0.15% cholesterol (Western-type diet [WTD]; Hope Farms, Woerden, The Netherlands). For the (cardio)vascular risk factor-atherosclerosis study, mice were randomized in 6 groups (n=15 per group, n=20 in control group) and received, based on the results of a PK study,  a daily oral gavage with the vehicle (5% carboxymethyl cellulose)(control group), nilotinib (10 or 30 mg/kg), ponatinib (3 or 10 mg/kg), or a twice daily gavage with imatinib (150 mg/kg).  All mice except the imatinib group received a second oral gavage with the vehicle.

tag: tissue

value: liver

tag: treatment-groupnr

value: Ima

value: mg/kg

value: 150 (mg/kg body weight) Imatinib (2x daily)

value: Diet T + 0.15% cholesterol – Imatinib          gavage


title: L-NA_0.2_055

value: L-NA

value: 0.12-0.20% L-NAME in drinkwater

value: Diet T + 0.15% cholesterol – vehicle gavage – L-NAME   in drinking water


title: L-NA_0.2_050


title: Nilo_30_054

value: Nilo

value: 30 (mg/kg body weight) Nilotinib (1x daily)

value: Diet T + 0.15% cholesterol – Nilotinib high      dose gavage


title: Ctrl_0_052

value: Ctrl

value: control

value: Diet T + 0.15% cholesterol - vehicle           gavage


title: Nilo_10_053

value: 10 (mg/kg body weight) Nilotinib (1x daily)

value: Diet T + 0.15% cholesterol – Nilotinib low dose      gavage


title: Pona_10_048

value: Pona

value: 10 (mg/kg body weight) Ponatinib (1x daily)

value: Diet T + 0.15% cholesterol – Ponatinib high dose     gavage


title: Ima_150_051

value: liver

value: Ima

value: mg/kg


title: Nilo_30_049


title: L-NA_0.2_045

value: L-NA


title: Nilo_10_043


title: Ctrl_0_046


title: Pona_3_047

value: 3 (mg/kg body weight) Ponatinib (1x daily)

value: Diet T + 0.15% cholesterol – Ponatinib low dose      gavage


title: Nilo_30_044

value: Nilo


title: Pona_10_042


title: Pona_3_041


title: ALRN-6924 Replicate 3

value: Myeloid Leukemia


title: Ctrl_0_040


title: Pona_10_035


title: Nilo_10_036


title: Ima_150_039

value: 150 (mg/kg body weight) Imatinib (2x daily)

value: Diet T + 0.15% cholesterol – Imatinib          gavage


title: L-NA_0.2_038

value: 0.12-0.20% L-NAME in drinkwater

value: Diet T + 0.15% cholesterol – vehicle gavage – L-NAME   in drinking water


title: Pona_3_034


title: Nilo_10_030

value: 10 (mg/kg body weight) Nilotinib (1x daily)


title: L-NA_0.2_032


title: Nilo_30_037

value: 30 (mg/kg body weight) Nilotinib (1x daily)

value: Diet T + 0.15% cholesterol – Nilotinib high      dose gavage


title: Ctrl_0_033

value: Ctrl

value: control

value: Diet T + 0.15% cholesterol - vehicle           gavage


title: Nilo_30_031

value: liver


title: Ima_150_027

value: Ima

value: mg/kg


title: Pona_3_029

value: Pona

value: 3 (mg/kg body weight) Ponatinib (1x daily)


title: Ctrl_0_028


title: Pona_10_024

value: 10 (mg/kg body weight) Ponatinib (1x daily)

value: Diet T + 0.15% cholesterol – Ponatinib high dose     gavage


title: Nilo_10_025

value: Nilo

value: Diet T + 0.15% cholesterol – Nilotinib low dose      gavage


title: L-NA_0.2_026

value: L-NA

value: 0.12-0.20% L-NAME in drinkwater


title: Nilo_30_020


title: Nilo_10_019

value: 10 (mg/kg body weight) Nilotinib (1x daily)


title: Pona_3_023

value: Diet T + 0.15% cholesterol – Ponatinib low dose      gavage


title: Ctrl_0_022


title: Pona_10_014


title: Ima_150_016

value: 150 (mg/kg body weight) Imatinib (2x daily)

value: Diet T + 0.15% cholesterol – Imatinib          gavage


title: Pona_10_018


title: Ima_150_021


title: Nilo_30_015

value: 30 (mg/kg body weight) Nilotinib (1x daily)

value: Diet T + 0.15% cholesterol – Nilotinib high      dose gavage


title: L-NA_0.2_010

value: liver

value: Diet T + 0.15% cholesterol – vehicle gavage – L-NAME   in drinking water


title: Ima_150_011

value: Ima

value: mg/kg


title: Pona_3_017

value: Pona

value: 3 (mg/kg body weight) Ponatinib (1x daily)


title: Pona_3_013


title: Pona_3_007


title: Nilo_10_009


title: Pona_10_002

value: 10 (mg/kg body weight) Ponatinib (1x daily)

value: Diet T + 0.15% cholesterol – Ponatinib high dose     gavage


title: L-NA_0.2_005


title: Nilo_10_003

value: Nilo

value: Diet T + 0.15% cholesterol – Nilotinib low dose      gavage


title: Ima_150_006


title: Nilo_30_004


title: Ctrl_0_012

value: Ctrl

value: control

value: Diet T + 0.15% cholesterol - vehicle           gavage


title: Pona_10_008


title: STM ProQ -CL rep3

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

description:
ProQ-bound RNA
background control sample

data_processing:
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Adapter trimming using cutadapt (Martin, 2011) version 1.5  or 1.7.1 (R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, R2: GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT), discard empty reads
Filtering of reads without mate via cmpfastq (http://compbio.brc.iop.kcl.ac.uk/software/cmpfastq.php)
Collapsing of identical reads and conversion to FASTA format using FastUniq (Xu et al. 2012)
Size filtering: discard read pairs with  at least one read longer than 25 nt
Size filtering: discard read pairs with at least one read shorter than 12 nt (READemption 0.3.7, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0 (READemption 0.3.7, Förstner et al., 2014)
Coverage calculation based on uniquely mapped reads (READemption 0.3.7, Förstner et al., 2014)
Calculation of size factors by applying the DESeq normalization method (Anders et al., 2010) to non-enriched nucleotide positions from coverage files (for details see associated publication)
Final coverage calculation during peak calling via PEAKachu (https://github.com/tbischler/PEAKachu, manuscript in preparation) based on previously calculated size factors
Genome_build: Salmonella Typhimurium SL1344 chromosome (NC_016810.1) and plasmids (NC_017718.1, NC_017719.1, NC_017720.1); E. coli K12 MG1655 (NC_000913.3)
Supplementary_files_format_and_content: wiggle

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella Typhimurium SL1344 ProQ::3xFLAG cells

growth_protocol: Salmonella Thyphimurium strain SL1344 or E. coli MG1655 containing a proQ::3xflag allele was grown from single colonies in 10 ml LB medium at 37°C for 16 hours. The cultures were diluted 1:100 into 200 ml fresh LB medium and continued to grow at 37°C until an OD600 of 2.0 was reached.

extract_protocol:
Bacteria were lysed and the FLAG-tagged proteins was immunoprecipitated using a monoclonal anti-FLAG antibody. The samples were treated with benzonase nuclease, calf intestine phophorylase, and polynucleotide kinase in the presence of radioactive gamma-ATP. Samples were separated with SDS-PAGE and followed by transfer to nitrocellulose membranes. Radioactively labelled RNA-protein complexes were eluted from membranes and treated with Proteinase K. RNA was purified with phenol:chloroform extraction and ethanol precipitation.
Purified RNA was used as input for library preparation using the NEB Next Small RNA Library kit according to the manufacturer’s instructions.

treatment_protocol: When the cultures reached an OD600 of 2.0, half of each culture was irradiated with UV light (254 nm, 800 mJ/cm2) while the other half was left untreated.

tag: clip antibody

value: M2 anti-FLAG monoclonal antibody attached to superparamagnetic iron impregnated agarose beads (Sigma-Aldrich, M8823)

tag: strain


title: STM ProQ +CL rep2

description:
ProQ-bound RNA
signal sample


title: STM ProQ +CL rep1

description:
ProQ-bound RNA
signal sample


title: STM ProQ +CL rep3

description:
ProQ-bound RNA
signal sample


title: Ctrl_0_001


title: STM ProQ -CL rep2


title: ECO ProQ +CL rep2

description:
ProQ-bound RNA
signal sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655 ProQ::3xFLAG cells


title: control2

city: Muenster

first: Katsuhiro

last: Kato

address: Roentgenstrasse 20

department: Department of Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

description: ribosome-associated RNA

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat-2 v2.0.13 with parameters -g 2
HTSeq was used to count the aligned reads on a per gene basis (Version: HTSeq-0.6.1). The count data were normalized, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: lung

extract_protocol:
Lungs were removed, flash frozen, and ribosome-associated RNA was immunoprecipitated with anti-HA antibody. Precipitated RNA was isolated with RNeasy Plus Micro kit(QIAGEN). Illumina TruSeq Stranded Total RNA Library Prep Kit (Cat#RS-122-2203) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: age

value: post natal day 8

tag: genotype

tag: rip antibody

value: anti-HA-tag mAb-Magnetic Beads (MBL, catalog# M180-11, lot# 002)


title: PCKO2

description: ribosome-associated RNA


title: PCKO1

description: ribosome-associated RNA


title: STM ProQ -CL rep1


title: ECO ProQ +CL rep1

description:
ProQ-bound RNA
signal sample


title: control3

description: ribosome-associated RNA


title: PCKO3

description: ribosome-associated RNA


title: ECO ProQ -CL rep2


title: control1

description: ribosome-associated RNA


title: Kras Usp22WT Rep1

city: Memphis

first: John

last: Crispino

state: Tennessee

address: 262 DANNY THOMAS PL

institute: St. Jude Children's Research

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC
Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered.
The cleaned reads were aligned to the Mus musculus genome (mm10) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for mm10 obtained from UCSC (University of California Santa Cruz; http://genome.ucsc.edu).
Differential expression was determined using DESeq2.  The cutoff for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: myeloid progenitors (cKit_Linlow/-)

extract_protocol:
Myeloid progenitors (cKit+Lin-/low) from 7-9 weeks old KM and KMUKO mice were isolated by sorting in a FACS Aria II flow cytometer. RNA was isolated using trizol (Invitrogen) following manufacturer’s instructions
RNA quality and quantity were determined with the Agilent Bioanalyzer 2100, accepting RNA integrity numbers (RIN) of > 7 and quantities of 100 nanograms or more per sample.  Directional mRNA libraries were prepared using Illumina TruSeq mRNA Sample Preparation Kits per manufacturer’s instructions.

value: Bone marrow myeloid progenitors

value: 7-9 weeks


title: HCT-116 cells transiently transfected with a pool of anti-APC siRNA

description: mRNA-seq

data_processing:
Initial data processing was performed by The Ohio State University Biomedical Informatics Shared Resource to generate .qseq files from base call files.
Files in .qseq format were sorted and filtered to generate sorted and export text files that could be analyzed using the CuffLinks software program.
The CuffLinks program was used to assign reads to transcripts, perform quantification and calculate statistical significance.  The output of the Cuffdiff program included transcript levels expressed in FPKM units and both p-values and (FDR-adjusted) q-values based on fold-changes.  The threshold for statistically significant differences between the anti-APC siRNA condition and either the scrambled siRNA or mock-transfected conditions was established as q-values less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: The files RNA-seq_RPKM_HCT-116_siAPC_vs_untreated_cuffDiff.txt and RNA-seq_RPKM_HCT-116_siAPC_vs_siScrambled_cuffDiff.txt are text files that each contain transcript abundance data expressed as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for two conditions.  The first compares transcript abundance in untreated vs. anti-APC siRNA-transfected HCT-116 cells, while the second compared transcript abundance in scrambled siRNA- vs. anti-APC siRNA-transfected cells.  Files were generated using the Cuffdiff program, and p- and q-values were calculated from fold-changes in order to estimate statistical significance.
Supplementary_files_format_and_content: In the file "RNA-seq_RPKM_HCT-116_siAPC_vs_siScrambled_cuffDiff.txt", q1 refers to the "siAPC" sample from column H, and q2 refers to the "siScrambled" or "siSCR" sample from column I.
Supplementary_files_format_and_content: In the file "RNA-seq_RPKM_HCT-116_siAPC_vs_untreated_cuffDiff.txt", q1 refers to the "siAPC" sample from column H, and q2 refers to the "untreated" or "none" sample from column I.

extract_protocol:
Cells were harvested by washing with Dulbecco’s PBS, addition of 500 μL Trizol (Life Technologies catalog # 15596-026), and scraping.  50 μg glycogen (RNase-free) was mixed into each sample.  A standard Trizol isolation protocol was then performed, with final resuspension in nuclease-free water.
Three single-read libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina catalog # RS-122-2001) according to Illumina's instructions.  Agilent Bioanlyzer was used to quantify libraries, and the OSU Genomics Shared Resource performed next-generation sequencing on an Illumina HiSeq instrument.

treatment_protocol: 1.0 x 105 HCT-116 cells were seeded in each well of a 6-well plate, 16-20 hours before transfection.  Transfections were performed on consecutive days either using no siRNA (mock transfection) or using pooled siRNA (Dharmacon) with scrambled sequence (non-targeting pool, D-001810-10-05), or targeting APC (L-003869-00-0005).  Transfections followed manufacturer's instructions for the transfection reagent (Dharmafect 2, T-2002-01) and used a combination of 4 μL of Dharmafect 2 and 5 μL of 10 μM siRNA stock solution.  Media changes were performed 6 hours after each transfection, and cell harvest was performed 48 hours after the second transfection.

value: colon carcinoma

tag: treatment

value: transfected with pooled anti-APC siRNA (twice)


title: Kras Usp22KO Rep2


title: long-reads preZGA

city: New York

first: Stuart

last: Sealfon

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

description: PacBio smart belt

data_processing:
Samples were run on the HiSeq2500 System, and base calling and Q-scoring was performed with Illumina’s Real-Time Analysis (RTA) version 1.18.64. bcl2fastq 1.8.3 was used to demulitplex and convert files to the fastq format
isoforms were quantified using kallisto
Genome_build: GRCz10

molecule: polyA RNA

organism: Danio rerio

growth_protocol: Zebrafish were maintained according to standard protocols and embryos were obtained during natural spawning of either AB, TAB14, or TAB5 WT adults. The IACUC committee of the Icahn School of Medicine at Mount Sinai approved all protocols.  Fertilized eggs were collected and staged based on morphological criteria to identify embryos at pre (256-cell stage) and post-ZGA

extract_protocol:
RNA was isolated from zebrafish embryos via standard Trizol protocol as described (Kent et al. 2016). Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT-PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix (Sigma). Annealing temperature was 58° C and extension time was 3 minutes. RT-qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2-Step SybrGreen™ kit using a fast 2-step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes.
For short read sequencing, RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo-Zero rRNA removal kit (Illumina)

treatment_protocol: The procedure for achieving suppression of ZGA is treatment of one-to-four-cell embryos by injection of 0.2nmol of the RNA Polymerase inhibitor α-amanitin. Pools of 15 embryos each for both untreated wild-type embryos and embryos injected with 0.2nmol α-amanitin to abolish zygotic transcription, as described previously (Zamir et al. 1997)

value: a-amanitin

tag: developmental stage

value: 6 hours post fertilization


title: HCT-116 cells transiently transfected with a pool of scrambled siRNA

description: mRNA-seq

value: transfected with pooled scrambled siRNA (twice)


title: short-reads postZGA

description: Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo-Zero rRNA removal kit (Illumina)

source_name: 5.25 hours post fertilization

value: untreated

value: 5.25 hours post fertilization


title: Kras Usp22KO Rep1


title: short-reads preZGA

source_name: 2.5 hours post fertilization

value: 2.5 hours post fertilization


title: long-reads postZGA

description: PacBio smart belt

source_name: epiboly


title: Kras Usp22WT Rep2


title: Positive for TB-HIV, with ART [IR-3-002]

status: Public on May 23 2018

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 south orange ave

department: Medicine

institute: Rutgers University

description:
IR-3-002
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx

data_processing:
Quality check was performed with the software FastQC. Low quality reads and adapters were trimmed with software Cutadapt.
Trimmed reads were mapped to the human genome GRCh38/hg19 with STAR.
Expression level for each gene was counted with HTSeq according to gene annotations from Ensembl.
The Bioconductor DESeq2 package was used to normalize counts and call differential expressions.
Genome_build: human genome GRCh38/hg19
Supplementary_files_format_and_content: normalizedCounts.xlsx: Excel spreadsheet contains a table where genes are in rows and samples are in columns. Each cell is normalized counts for a gene in a sample.

source_name: Whole blood

extract_protocol:
Whole blood was collected into PAXgene Blood RNA tubes, and RNA was isolated using the PAXgene Blood RNA Kit (Qiagen). Total RNA input was amplified using MessageAmp™ II aRNA Amplification Kit (ThermoFisher Scientific). 100ng of amplified RNA was used to prepare the library.
rRNAs were first removed from total RNAs using the Ribo-zero rRNA removal kit (Epiccenter, Applied Systems); after mRNA fragmentation, first strand cDNA synthesis was carried out using Super Script II (Invitrogen) reverse transcription system; after the second strand cDNA synthesis, the double strand (ds) cDNAs were repaired and their 3’ end adenylated for adapter ligation; after ligating multiple indexing adapters, the dsDNA library were enriched by PCR and validated; the qualified library was amplified. PCR amplicons were purified using AMPure XP beads and the library was quantified. This library was then used for RNA Sequencing on Illumina Hiseq2500. On average, 49-50 million basepair (bp) single-end reads were produced per sample.

value: blood

tag: disease status

value: TB-HIV

value: ART


title: Positive for TB-HIV, with ART [IR-3-001]

description:
IR-3-001
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-015]

description:
IR-2-015
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx

value: HIV

value: ART-naive


title: No TB but HIV+; ART-naïve [IR-2-012]

description:
IR-2-012
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: ECO ProQ -CL rep1

value: M2 anti-FLAG monoclonal antibody attached to superparamagnetic iron impregnated agarose beads (Sigma-Aldrich, M8823)


title: No TB but HIV+; ART-naïve [IR-2-001]

description:
IR-2-001
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-011]

description:
IR-2-011
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-004]

description:
IR-2-004
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-1-016]

description:
IR-1-016
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-006]

description:
IR-2-006
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-010]

description:
IR-2-010
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-008]

description:
IR-2-008
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: HCT-116 cells untransfected

description: mRNA-seq

value: transfected with reagent only (mock)


title: No TB but HIV+; ART-naïve [IR-2-009]

description:
IR-2-009
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-005]

description:
IR-2-005
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-013]

description:
IR-1-013
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx

value: HIV and TB


title: Positive for TB & HIV; ART-naïve [IR-1-014]

description:
IR-1-014
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-012]

description:
IR-1-012
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-011]

description:
IR-1-011
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-009]

description:
IR-1-009
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-016]

description:
IR-2-016
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-008]

description:
IR-1-008
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-007]

description:
IR-2-007
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-002]

description:
IR-2-002
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-010]

description:
IR-1-010
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-003]

description:
IR-1-003
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-005]

description:
IR-1-005
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-003]

description:
IR-2-003
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-006]

description:
IR-1-006
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: No TB but HIV+; ART-naïve [IR-2-013]

description:
IR-2-013
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: BL2Baff-3

city: Goettingen

first: Alexander

last: Wolff

state: Lower Saxony

address: Humboldtallee 32

department: Medical Statistics

institute: UMG

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
Alignment was performed with STAR RNA-Seq aligner version 2.4.0h, by mapping the reads against transcriptome, and counting was performed using RSEM v1.2.19.
The transcriptome was generated with RSEM from Ensembl reference genome version GRCh38.76.
Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: expected counts for each Sample

source_name: BL2 cells

growth_protocol: Cells were maintained in RPMI 160 supplemented with 10% fetal calf serum (FCS) and glutamine; peniciline; streptomycine at cell densities between 2x10^5 and 1x10^6 cells per ml.

extract_protocol:
RNA was isolated using Trizol reagent including a DNase I (Roche, Mannheim, Germany) digestion step.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. Accurate quantitation of cDNA libraries was performed using the QuantiFluor TM dsDNA System (Promega). The size range of nal cDNA libraries was determined applying the SS-NGS-Fragment 1-6000 bp Kit on the Fragment Analyzer from Advanced Analytical (320 bp). cDNA libraries were amplied and sequenced by using the cBot and the HiSeq2000 from Illumina.
Non stranded mRNA-Seq

treatment_protocol: For stimulation studies, cells were cultured in cell culture medium supplemented with 10 mM HEPES at 1 x 10^6 cells/ml and incubated with B-cell activating factor (BAFF) for up to 24 hrs.

value: Baff stimulated BL2 cell-line


title: BL2-3

value: unstimulated BL2 cell-line


title: Positive for TB & HIV; ART-naïve [IR-1-002]

description:
IR-1-002
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: Positive for TB & HIV; ART-naïve [IR-1-001]

description:
IR-1-001
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: BL2Baff-2


title: BL2Baff-1


title: BL2-1


title: BL2-2


title: Positive for TB & HIV; ART-naïve [IR-1-015]

description:
IR-1-015
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: NGP_nutlin_10

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

data_processing:
Gene expression quatification based on Kallisto v0.42.4 with Ensembl v85 index.
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: NGP cell line (neuroblastoma)

growth_protocol: NGP neuroblastoma cells grown in 6-well culture flasks.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen), quantified using Nanodrop-100, and quality controlled using FragmentAnalyzer (High Sensitivity RNA Analysis Kit, DNF-472-0500, Advanced Analytical).
100ng of total RNA was used for TruSeq stranded mRNA library prep (Illumina),

treatment_protocol: The cells were treated with either nutlin-3 (8µM racemic mixture) or vehicle (ethanol).

value: neuroblastoma

value: nutlin


title: NGP_nutlin_11


title: NGP_nutlin_3


title: NGP_nutlin_4


title: NGP_nutlin_8


title: NGP_nutlin_6


title: Positive for TB & HIV; ART-naïve [IR-1-004]

description:
IR-1-004
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx


title: NGP_nutlin_2


title: NGP_nutlin_1


title: NGP_ethanol_11

value: vehicle - ethanol


title: E16.5_Fgf8_3

city: New Orleans

first: Yiping

last: Chen

state: LA

address: 6400 Freret

department: CMB

institute: Tulane University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2
For each library, raw counts for each annotated gene were obtained using the featureCounts software.
Differential gene expression was identified using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: E14.5_Ctrl1.txt Raw count reads
Supplementary_files_format_and_content: E14.5_Ctrl2.txt Raw count reads
Supplementary_files_format_and_content: E14.5_Ctrl3.txt Raw count reads
Supplementary_files_format_and_content: E14.5_Fgf8_1.txt Raw count reads
Supplementary_files_format_and_content: E14.5_Fgf8_2.txt Raw count reads
Supplementary_files_format_and_content: E14.5_Fgf8_3.txt Raw count reads
Supplementary_files_format_and_content: E16.5_Ctrl1.txt Raw count reads
Supplementary_files_format_and_content: E16.5_Ctrl2.txt Raw count reads
Supplementary_files_format_and_content: E16.5_Ctrl3.txt Raw count reads
Supplementary_files_format_and_content: E16.5_Fgf8_1.txt Raw count reads
Supplementary_files_format_and_content: E16.5_Fgf8_2.txt Raw count reads
Supplementary_files_format_and_content: E16.5_Fgf8_3.txt Raw count reads
Supplementary_files_format_and_content: E14.5_Normalized_counts.txt Deseq2 normalized counts
Supplementary_files_format_and_content: E14.5_raw_counts.txt Raw count reads
Supplementary_files_format_and_content: E14.5_MT_vs_E14.5_Ctrl_DESeq2_result_files.txt Differential expression analysis results
Supplementary_files_format_and_content: E16.5_Normalized_counts.txt Deseq2 normalized counts
Supplementary_files_format_and_content: E16.5_raw_counts.txt Raw counts
Supplementary_files_format_and_content: E16.5_MT_vs_E16.5_Ctrl_DESeq2_result_files.txt Differential expression analysis results

source_name: Palate

extract_protocol:
The anterior palatal tissues were dissected out from E14.5 and E16.5 Shox2Cre;R26RFgf8 and control mice, respectively, and subjected to RNA extraction (RNeasy Micro Kit, Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic day 16.5

value: Shox2Cre; R26RFgf8


title: NGP_ethanol_10


title: NGP_ethanol_7


title: NGP_ethanol_6


title: E16.5_Fgf8_1


title: E16.5_Ctrl3

value: wild type


title: NGP_nutlin_7


title: E14.5_Ctrl3

value: Embryonic day 14.5


title: E14.5_Fgf8_3


title: NGP_nutlin_9


title: Positive for TB & HIV; ART-naïve [IR-1-007]

description:
IR-1-007
RNA fractions
RNA-seq, paired end, strand-specific.
Processed data file: normalizedCounts.xlsx

value: blood


title: NGP_ethanol_4


title: NGP_ethanol_12


title: NGP_ethanol_8


title: E16.5_Fgf8_2


title: NGP_ethanol_3


title: 30_HFT

city: Rochester

first: Yasuhiro

last: Ikeda

state: MN

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
Tophat 2.1.0 software with Bowtie 1.1.2 configuration was used to align reads
FeatureCounts 1.4.6-p5 software was used to quantify expression
Ensembl reference Mus_musculus.GRCm38.79.mod.gtf was used to define gene regions
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated
Genome_build: mm10
Supplementary_files_format_and_content: tsv file including the raw read count and RPKM values for each sample

source_name: pancreatic islet

growth_protocol: Mice were maintained on PicoLab Rodent Diet 20 (LabDiet) or OpenSource Diets D12331 58% fat diet (Research Diets). D12331 diet was maintained for at least 6 weeks prior to vector injection.

extract_protocol:
Pancreatic islets were extracted using standard pancreas perfusion with collagenase (VitaCyte). Islets were cultured in RPMI supplemented with 10% FBS, 50 U/ml penicillin, and 50 µg/ml streptomycin for approximately 48 hours, then total RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AAV was delivered via a single intraperitoneal injection. AAV was allowed to express for 2 weeks prior to islet isolation.

tag: diet

value: high fat diet

value: pancreatic islet


title: E16.5_Ctrl2


title: E16.5_Ctrl1


title: 23_NDC

value: normal diet

value: Control


title: E14.5_Fgf8_2


title: E14.5_Fgf8_1


title: NGP_ethanol_5


title: 31_HFC


title: G22_HFT


title: E14.5_Ctrl1


title: 11_NDC


title: D30_HFC


title: 1_HFT


title: E14.5_Ctrl2


title: ChIPseq for HP1g (Cbx3) in Adnp knock-out mES cells, rep2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument. Some samples were sequenced on two independent lanes and raw fastq files need to be pooled prior to mapping. These are indicated with "a" and "b" in the file name.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
RNAseq: Sequenced reads were aligned using Bowtie 1.0.0 ( -m1 --best –strata) or STAR 2.5.0a (--outFilterMultimapNmax 20 --outMultimapperOrder Random --outSAMmultNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000)
ChIPseq: Sequenced reads were aligned using Bowtie 1.0.0 (-m 1 —best –strata) or STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within )
For RNAseq and ChIPseq, QuasR was used to count aligned reads (qCount) and to generate depth normalized bigWig files (qExportWig). Differential expression analysis was perfored using EdgeR on the raw gene count tables generated by QuasR.
ATACseq data was mapped using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType Local --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within --outFileNamePrefix  --clip3pAdapterSeq CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using QuasR. Read counts were binned in 50bp intervals and normalized to average sequencing depth. For ATACseq, data was not binned and the bigwig files display the full sequencing reads normalized to 1 mio genome mapping reads. Bed files containing peak positions were generated from the .narrowPeak output file from MACS2.

source_name: embryonic stem cells, HP1g ChIP

growth_protocol: Mouse ES cells were grown under standard conditions in 2i medium containing LIF.

extract_protocol:
10^7 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 1% of chromatin was set aside as Input control. The chromatin was incubated with Streptavidin-coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ostapcuk et al, 2017.
Libraries were prepared using the NEB Next DNA library prep kit according to manufacturer's instructions. For barcodes, see sample characteristics.

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/6

tag: genotype/variation

value: Cbx3 FlagAvi, Adnp KO

value: Bio ChIP, Streptavidin Dynabeads (Thermofisher)


title: Input of ChIPseq for HP1g (Cbx3) in Cbx1 knock-out mES cells, rep1

source_name: embryonic stem cells, input

value: Cbx3 FlagAvi, Cbx1 KO


title: Input of ChIPseq for HP1g (Cbx3) in Cbx1 knock-out mES cells, rep2


title: Input of ChIPseq for H3K9me3 in wt mES cells, replicate 1

extract_protocol:
10^7 mES cells were crosslinked, chromatin was extracted and fragmented with micrococcal nuclease to mostly mono nucleosomes. 1% of chromatin was set aside as Input control. The chromatin was incubated with antibody over night, Protein A coupled Dynabeads were added for 2 hours and thereafter immunoprecipitated DNA was washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ostapcuk et al, 2017.
Libraries were prepared using the NEB Next DNA library prep kit according to manufacturer's instructions. For barcodes, see sample characteristics.

value: wt


title: Input of ChIPseq for HP1g (Cbx3) in Adnp knock-out mES cells, rep3


title: ChIPseq for H3K9me3 in wt mES cells, replicate 1

source_name: embryonic stem cells, H3K9me3 ChIP

value: anti-H3K9me3 (Abcam ab8898)


title: Input of ChIPseq for HP1g (Cbx3) in Adnp knock-out mES cells, rep1


title: ChIPseq for HP1g (Cbx3) in Adnp knock-out mES cells, rep3


title: ChIPseq for HP1g (Cbx3) in Adnp knock-out mES cells, rep1


title: ChIPseq for HP1b (Cbx1) in Cbx3 knock-out mES cells, rep2

source_name: embryonic stem cells, HP1b ChIP

value: Cbx1 FlagAvi, Cbx3 KO


title: ChIPseq for HP1g (Cbx3) in Cbx1 knock-out mES cells, rep2


title: ChIPseq for HP1b (Cbx1) in Cbx3 knock-out mES cells, rep1


title: ChIPseq for HP1g (Cbx3) in Cbx1 knock-out mES cells, rep1


title: 21_NDC


title: Input of ChIPseq for HP1g in wt mES cells, rep2

value: Cbx3 FlagAvi


title: Input of ChIPseq for HP1g in wt mES cells, rep3


title: Input of ChIPseq for HP1g in wt mES cells, rep1


title: ChIPseq for HP1b in wt mES cells, rep1

value: Cbx1 FlagAvi


title: Input of ChIPseq for HP1b (Cbx1) in Cbx3 knock-out mES cells, rep1


title: Input of ChIPseq for HP1b (Cbx1) in Cbx3 knock-out mES cells, rep2


title: ChIPseq for HP1g in wt mES cells, rep3


title: ChIPseq for HP1g in wt mES cells, rep1


title: ChIPseq for HP1g in wt mES cells, rep2


title: Input of ChIPseq for HP1g (Cbx3) in Adnp knock-out mES cells, rep2


title: ChIPseq for HP1b in wt mES cells, rep2


title: Input of ChIPseq for HP1b in wt mES cells, rep3


title: Input of ChIPseq for HP1b in wt mES cells, rep1


title: Input of ChIPseq for HP1b in wt mES cells, rep2


title: ChIPseq for HP1a in wt mES cells, rep2

source_name: embryonic stem cells, HP1a ChIP

value: Cbx5 FlagAvi


title: Input of ChIPseq for HP1a in wt mES cells, rep2


title: Input of ChIPseq for HP1a in wt mES cells, rep3


title: ChIPseq for Adnp in wt mES cells, rep3

source_name: embryonic stem cells, Adnp ChIP

value: Adnp FlagAvi


title: ChIPseq for HP1a in wt mES cells, rep1


title: ChIPseq for HP1a in wt mES cells, rep3


title: Input of ChIPseq for Adnp in wt mES cells, rep3


title: Input of ChIPseq for Adnp in wt mES cells, rep1


title: Input of ChIPseq for Adnp in wt mES cells, rep2


title: Input of ChIPseq for HP1a in wt mES cells, rep1


title: ChIPseq for HP1b in wt mES cells, rep3


title: RNAseq in Cbx1 Cbx3 Cbx5 triple knock-out mES cells, rep3

source_name: embryonic stem cells

extract_protocol:
Total RNA was isolated using the Absolutely RNA Microprep Kit (Stratagene) and ribosomal RNA was depleted using the Ribozero removal kit (Illumina) prior to library preparation.
Libraries were prepared using the Illumina ScriptSeq v2 kit according to the manufacturer's instructions.

value: Cbx1 KO, Cbx3 flox, Cbx5 flox


title: RNAseq in Cbx1 Cbx3 Cbx5 triple knock-out mES cells, rep1


title: RNAseq in Cbx1 Cbx3 Cbx5 triple knock-out mES cells, rep2


title: RNAseq in Cbx1 Cbx3 double knock-out mES cells, rep1

value: Cbx1 KO, Cbx3 flox


title: RNAseq in Cbx5/HP1a knock-out mES cells, rep2

value: Cbx5 flox


title: RNAseq in Cbx1 Cbx3 double knock-out mES cells, rep2


title: RNAseq in Cbx3/HP1g knock-out mES cells, rep3

value: Cbx3 flox


title: RNAseq in Cbx3/HP1g knock-out mES cells, rep2


title: RNAseq in Cbx5/HP1a knock-out mES cells, rep1


title: RNAseq in Cbx3/HP1g knock-out mES cells, rep1


title: ChIPseq for Adnp in wt mES cells, rep2


title: ChIPseq for Adnp in wt mES cells, rep1


title: RNAseq in Cbx1/HP1b knock-out mES cells, rep1

value: Cbx1 KO, Cbx5 flox


title: RNAseq in wt (Cbx3 flox) mES cells, rep2

value: embryonic stem (ES) cells


title: RNAseq in Adnp knock-out mES cells, rep3

value: hybrid 129-C57BL/6

value: Adnp flox


title: RNAseq in Adnp knock-out mES cells, rep2


title: RNAseq in wt (Cbx3 flox) mES cells, rep1


title: RNAseq in wt (Cbx3 flox) mES cells, rep3


title: RNAseq in wt (Adnp flox) mES cells, rep3


title: RNAseq in Cbx1/HP1b knock-out mES cells, rep2


title: RNAseq in wt (Adnp flox) mES cells, rep1


title: RNAseq in wt (Adnp flox) mES cells, rep2


title: RNAseq in Adnp knock-out mES cells, rep1


title: MEF_TSC2_neg

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

data_processing:
Number of transcripts per million reads mapped (TPM) were computed using kallisto (http://pachterlab.github.io/kallisto/)
Fold changes based on Kallisto TPM were computed using R (added 1 to all TPM values to avoid zero/infinite ratios)
Genome_build: mm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values (VKMJ-TSC2Effects_kallisto_abundance.txt) and transcript-based fold changes for MEF_TSC2_neg vs. MEF_TSC2_plus (VKMJ-TSC2Effects_fold_changes.txt).

source_name: Tsc2-/- p53-/- mouse embryonic fibroblasts

extract_protocol:
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc., San Diego, CA)

treatment_protocol: Cells were treated with diluent or 100 nM rapamycin for 18 hr in serum-free condition (DMEM supplemented with 0.1% BSA).

value: embryonic fibroblasts


title: TJ_Rap

source_name: Tsc2-null mouse kidney epithelial cells (TJ- tumor-derived from secondary tumor in C57BL6 mice from Jackson labs)

value: kidney epithelial cells_tumor derived

value: rapamycin


title: MEF_TSC2_plus

source_name: Tsc2+/+ p53-/- mouse embryonic fibroblasts


title: MKOC_Rap

source_name: Tsc2-null mouse kidney epithelial cells

value: kidney epithelial cells


title: TJ_Untreated


title: Watermelon-leaf-sample-3

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

description: small RNA

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequences whose lengths are greater than or equal to 18 bp (the 3' adapter sequences of reads had been removed by the sequencing facility)
Sort and remove repetitive sequences
Calculate the counts of unique sequences
The unique sequences were aligned to a self-assembled transcriptome with SOAP2
Supplementary_files_format_and_content: sequences and count values

organism: Citrullus lanatus

source_name: leaf

growth_protocol: The watermelon were grown in greenhouse, Kunming university of science and technology, Kunming, Yunnan, China

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Small RNA libraries were prepared by following the Illumina's protocol.

value: leaf


title: Watermelon-fruit-sample-4

description: small RNA

source_name: fruit

value: fruit


title: Watermelon-androecium-sample-1

description: small RNA

source_name: androecium

value: androecium


title: Watermelon-root-sample-2

description: small RNA

source_name: root

value: root


title: Watermelon-leaf-sample-1

description: small RNA


title: Watermelon-root-sample-1

description: small RNA


title: Watermelon-leaf-sample-2

description: small RNA


title: Watermelon-petal-sample-3

description: small RNA

source_name: petal

value: petal


title: Watermelon-fruit-sample-1

description: small RNA


title: Watermelon-fruit-sample-2

description: small RNA


title: Watermelon-petal-sample-2

description: small RNA


title: Acinetobacter baumannii  AbH12O-A2 grown in mice lung 3

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

description:
A2raton13
supplementary file: AbH12O_A2_ODvsADraton.tsv

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to Acinetobacter baumannii AbH12O-A2 and ATCC_17978 reference genomes using BWA mem aligner (http://bio-bwa.sourceforge.net/) allowing two  mismatches (n = 2).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: Acinetobacter baumannii MAR02 and  Acinetobacter baumannii ATCC_17978
Supplementary_files_format_and_content: Tables of raw counts, obtained from the BAM files of the samples in each comparative. These tables are in tab separated plain text format.

organism: Acinetobacter baumannii

source_name: mice lung

growth_protocol: Mice were subjected to pneumonia infection by intratraqueal inoculation

extract_protocol:
RNA was extracted from broncoalveolar lavages from the lung infection (RNAasy, Qiagen)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)


title: Acinetobacter baumannii ATCC 17978 grown  in mice lung 3

description:
ATCCraton11
supplementary file: ATCC_ODvsATCC_raton.tsv


title: Acinetobacter baumannii  AbH12O-A2 grown in LB medium 3

description:
A2OD103
supplementary file: AbH12O_A2_ODvsADraton.tsv

source_name: LB medium (control)


title: Acinetobacter baumannii AbH12O-A2 grown in LB medium 1

description:
A2OD101
supplementary file: AbH12O_A2_ODvsADraton.tsv


title: 103cell_siSTAT3

data_processing:
Number of transcripts per million reads mapped (TPM) were computed using kallisto (http://pachterlab.github.io/kallisto/)
Fold changes based on Kallisto TPM were computed using R (added 1 to all TPM values to avoid zero/infinite ratios)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample (VKMJ-STAT3_kallisto_abundance.txt) and transcript-based fold changes for 102siCtrl vs. 103siCtrl (VKMJ-STAT3_fold_changes.txt)

source_name: angiolipoma cells from LAM patient

treatment_protocol: For the rapamycin condition, cells were treated with 100 nM rapamycin for 18 hr in serum-free condition (DMEM supplemented with 0.1% BSA).  For downregulation of STAT3, 20mM siSTAT3 or NT (non targeting) siRNA was added to the cells in complete medium and incubated for 24 hours.  Medium was changed to DMEM containing 0.1% BSA, and cells were incubated overnight.

value: angiolipoma

tag: disease

value: Lymphangioleiomyomatosis

tag: cell line genotype

value: TSC2 re-expressed


title: Acinetobacter baumannii  AbH12O-A2 grown in mice lung 1

description:
A2raton11
supplementary file: AbH12O_A2_ODvsADraton.tsv


title: Acinetobacter baumannii AbH12O-A2 grown in LB medium 2

description:
A2OD102
supplementary file: AbH12O_A2_ODvsADraton.tsv


title: Acinetobacter baumannii ATCC 17978 grown in mice lung 1

description:
ATCCraton1
supplementary file: ATCC_ODvsATCC_raton.tsv


title: 103cell_Rap

value: Rapamycin


title: Watermelon-fruit-sample-3

description: small RNA


title: 103cell_siCtrl

value: siCtrl


title: Acinetobacter baumannii ATCC 17978 grown  in mice lung 2

description:
ATCCraton2
supplementary file: ATCC_ODvsATCC_raton.tsv


title: Acinetobacter baumannii ATCC 17978 grown in LB medium 3

description:
ATCCOD103
supplementary file: ATCC_ODvsATCC_raton.tsv


title: Watermelon-leaf-sample-4

description: small RNA


title: Acinetobacter baumannii ATCC 17978 grown in LB medium 2

description:
ATCCOD102
supplementary file: ATCC_ODvsATCC_raton.tsv


title: 102cell_Rap


title: Watermelon-leaf-degradome-sample-1

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Cut the first 20 nucleotides in the remaining reads
Sort and remove repetitive sequences
Calculate the counts of unique sequences
Supplementary_files_format_and_content: sequences and count values

growth_protocol: grown in greenhouse, Kunming university of science and technology, Kunming, Yunnan, China

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Degradome or PARE library was prepared by following the protocol reported in Li et al. 2010 (The Plant Journal 2010, 62:742-759).


title: Acinetobacter baumannii ATCC 17978 grown in LB medium 1

description:
ATCCOD101
supplementary file: ATCC_ODvsATCC_raton.tsv


title: 102cell_siSTAT3


title: Watermelon-petal-sample-1

description: small RNA


title: Acinetobacter baumannii  AbH12O-A2 grown in mice lung 2

description:
A2raton12
supplementary file: AbH12O_A2_ODvsADraton.tsv


title: 62.5 uM AA

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

description: Ribosomal RNA removed

data_processing:
Alignment (BOWTIE2)
Counts and direct comparison between samples (DESeq)
Genome_build: NC_008533
Supplementary_files_format_and_content: Text files with either counts/sample or relative counts between AA-treated and Untreated cells.

organism: Streptococcus pneumoniae D39

source_name: Whole cells

growth_protocol: Wild-type Streptooccus pneumoniae D39 cells were grown overnight on blood agar plates and then diluted into C+Y media at OD600 = 0.05.

extract_protocol:
Cells were collected and treated with Bacterial RNA protect (qiagen). Following lysis with mutanolysin and lysozyme, RNA was extracted with a Qiagen RNA mini kit on a QiaCube.
Illumina TruSeq Stranded Total RNA LT Sample Prep Kit

treatment_protocol: Sample 2 was supplmented with 62.5 uM AA, which resulted in a 15 minutes groth delay.

tag: agent

value: 62.5 uM AA


title: Resynthesized allopolyploid M. peregrinus replicate 4

city: Athens

first: Adam

middle: James

last: Bewick

state: GA

address: 120 East Green Street

department: Genetics

institute: University of Georgia

description: allc_resynthesized_allopolyploid_M_peregrinus.tsv.gz

data_processing:
Reads for M. guttatus and M. luteus were mapped to the genomes sequenced and annotated in the current study. For the hybrid and allopolyploids and mock genome of M. peregrinus was created by concatenating the genomes of M. guttatus and M. luteus. Reads for the hybrid and allopolyploids were mapped to this mock genome.
MethylC-seq analysis were performed as described in Schmtiz et al. (2013; Genome Research 23, 1663–1674)
Genome_build: Phytozome genome assembly of Mimulus guttatus (v2.0) was used for mapping M. guttatus.
Genome_build: all scaffolds in the M. luteus processed data files will be  included in the genome assembly filed submitted to CoGe
Genome_build: Natural allopolyploid M. peregrinus, resynthesized M. peregrinus and M.    robertsii are hybrids of M. guttatus x M. luteus. Genomes were not    sequenced for these hybrids, but rather artificial genomes were created by    concatenating the genome assembly files of M. guttatus and M. luteus.    Hence, all genome assembly data can be found in the M. guttatus Phytozome    and M. luteus CoGe genome assembly files.
Supplementary_files_format_and_content: Tab delimited text file. Please see metafile for column headers

organism: Mimulus peregrinus

source_name: genomic DNA

extract_protocol: MethylC-seq libraries were prepared according to the following protocol Urich et al. 2015 (Nature Protocols 10, 475–483)

value: Lab-generated


title: Mimulus guttatus replicate 1

organism: Erythranthe guttata

value: Wild-type


title: Mimulus luteus replicate 3

organism: Erythranthe lutea


title: Mimulus luteus replicate 4


title: Mimulus guttatus replicate 4


title: Mimulus guttatus replicate 2


title: Mimulus guttatus replicate 3


title: Resynthesized allopolyploid M. peregrinus replicate 3


title: Resynthesized allopolyploid M. peregrinus replicate 2


title: Mimulus luteus replicate 1


title: Resynthesized allopolyploid M. peregrinus replicate 1


title: Natural allopolyploid (Mimulus peregrinus) replicate 4

description: allc_natural_allopolyploid_M_peregrinus.tsv.gz


title: Natural allopolyploid (Mimulus peregrinus) replicate 3


title: Natural allopolyploid (Mimulus peregrinus) replicate 2


title: Untreated

description: Ribosomal RNA removed

value: Untreated


title: F1 hybrid M. x robertsii (M. guttatus x M. luteus) replicate 2

organism: Erythranthe lutea x Erythranthe guttata

value: Hybrid


title: F1 hybrid M. x robertsii (M. guttatus x M. luteus) replicate 1


title: ARPE19

status: Public on May 22 2018

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

description: animal-free and serum-free culture and cryopreservation system, GMP-standard

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Pair end RNA-seq data was pseudo-aligned to human reference transcriptome using Kallisto.
TPM value of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, and TPM table was then introduced into subsequent customized analysis.
Genome_build: hg19
Supplementary_files_format_and_content: TPM table (CSV table)

source_name: retinal pigmented epithelium

extract_protocol:
Cucumber leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: cell line

tag: passages


title: Fetal_RPE

value: 11 weeks of gestation

value: primate culture RPE cells


title: GMP4


title: GMP7

value: 12 weeks of gestation


title: Adult_RPE

value: over 18 years old


title: Mimulus luteus replicate 2


title: F1 hybrid M. x robertsii (M. guttatus x M. luteus) replicate 4


title: RatID9_TH_TRM_MBD-seq

city: Kuopio

first: Anssi

last: Lipponen

address: Neulaniementie 2

department: A. I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

description:
Processed data file: Thalamus_Repitools_gene_body_counts.txt
Processed data file: Thalamus_Repitools_exon_counts.txt
Processed data file: Thalamus_Repitools_promoter_counts.txt

data_processing:
Base calling was performed with OLBv1.8 software.
Reads were aligned to the rat genome (Rnor_5.0) using Spliced Transcripts Alignment to a Reference (STAR) (version 2.3.0e_r291).
Differentially methylated gene promoter, exons, and gene bodies were identified with Repitools R-package (R version 3.1.0).
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include count matrix.

organism: Rattus norvegicus

source_name: Ipsilateral thalamus, TBI

growth_protocol: Adult male rats (Sprague-Dawley, Harlan, Netherlands) weight 330-371g at a time of traumatic brain injury were housed in a controlled environment (21-23 °C, 12h dark/light cycle, 50-60% relative humidity) with drinking and feeding ad libitum.

extract_protocol:
Tissue was collected 3 months after TBI. For tissue collection, rats were anesthetized with isoflurane and decapitated. The brain was removed from skull, flushed with 0.9% cold sodium chloride, and two 2-mm-thick coronal slices (between -2.2 to -6.2 from the bregma) were cut with a slicing matrix. Perilesional cortex, thalamus, and dentate gyrus (including CA3c-b) were dissected under the magnifying glass on top of the light table. Samples were stored at -80oC until RNA extraction.
DNA extraction was done by using the DNeasy Blood & Tissue kit (Qiagen #69504) enrichment (Invitrogen). Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 13 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using the TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).

treatment_protocol: TBI was inducted with lateral fluid precussion (LFP) as described by McIntosh et al. (1989) and Kharatishvili et al. (2006). Animals were anesthetized with an intraperitoneal (i.p.) injection of a solution (6 ml/kg) containing sodium pentobarbital (58 mg/kg), chloral hydrate (60 mg/kg), magnesium sulphate (127.2 mg/kg), propylene glycol (42.8%) and absolute ethanol (11.6%) and placed in a Kopf stereotactic frame (David Kopf Instruments, Tujunga, CA, USA). The skull was exposed with a midline skin incision followed by extraction of the periosteum. The left temporal muscle was detached from the lateral ridge and then a circular craniectomy (diameter 5mm) was performed over the left parietal lobe midway between lambda and bregma keeping the dura mater intact. The edges of craniectomy were sealed with a modified LuerLock cap that was filled with saline while the calvaria was covered with dental acrylate (Selectaplus CN, Dentsply DeTrey GmbH, Dreieich, Germany). Lateral FPI was induced 90 min after the administration of anaesthesia by connecting the rat to a fluid-precussion device (AmScien Instruments, Richmond, VA, USA) via a female Luer-Lock fitting. In this study, the main of the impact was 3.32 +/- 0.01 atm. Control animals received anaesthesia and all surgical procedures but without lateral FPI.

tag: strain/background

value: Sprague-Dawley

tag: gender

value: Male

value: Adult

tag: tissue

value: Ipsilateral thalamus

value: TBI


title: RatID10_TH_TRM_MBD-seq

tag: age


title: GMP2


title: RatID8_TH_TRM_MBD-seq


title: RatID7_TH_TRM_MBD-seq


title: F1 hybrid M. x robertsii (M. guttatus x M. luteus) replicate 3

tag: genotype


title: RatID3_TH_SHM_MBD-seq

source_name: Ipsilateral thalamus, sham operated

value: sham operated


title: RatID6_TH_TRM_MBD-seq


title: RatID5_TH_SHM_MBD-seq


title: RatID2_TH_SHM_MBD-seq


title: effectory memory T cell [HD-47]

first: Andreas

last: Roller

address: Grenzacherstrasse 124

institute: Roche

description: effectory memory T cells from healthy donor

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to hg19 genome using gsnap with parameters -s Homo_sapiens.GRCh37.75.gsnap.splicesites.iit --nthreads=5 --batch=5. Mapped reads were assigned to human genes based on GRCh37.75 annotation.
Gene expression levels were computed as reads per kilobase per million mapped reads (RPKM) values [Mortazavi  et al., Nat Methods 2008] using in-house tools.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample

source_name: effectory memory T cells

extract_protocol:
High molecular weight RNA (> 200 bp) was extracted from 2.000–40.000 cells collected in XB buffer (Life Technologies) using the Arcturus Pico Pure RNA Isolation Kit (Life Technologies). During RNA extraction, residual genomic DNA was removed using the RNase free DNase set (Qiagen). RNA was quality controlled and quantity estimated from capillary electrophoresis on Eukaryote Total RNA pico chips (Agilent Technologies).
SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used to prepare and amplify cDNA from 500 pg of total RNA according to manufacturer’s instructions. The amplified cDNA was quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Then, 150 pg of amplified cDNA was subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies).

value: blood

value: effectory memory T cells

tag: donor id


title: effectory memory T cell [HD-55]


title: effectory memory T cell [HD-50]


title: Natural allopolyploid (Mimulus peregrinus) replicate 1


title: effectory memory T cell [HD-37]


title: RatID1_TH_SHM_MBD-Seq

tag: treatment


title: PD1-int CD8+ T cell [BS-423]

description: PD1+ (intermediate) CD45+ CD3+ CD14- CD19- CD56- CD4- CD8+ T cells from non-small cell lung cancer sample

source_name: CD8+ T cells

value: non-small cell lung cancer

value: CD8+ T cells


title: PD1-high CD8+  T cell [BS-423]

description: PD1+ (high) CD45+ CD3+ CD14- CD19- CD56- CD4- CD8+ T cells from non-small cell lung cancer sample


title: PD1-neg CD8+ T cell [BS-275]

description: PD1- CD45+ CD3+ CD14- CD19- CD56- CD4- CD8+ T cells from non-small cell lung cancer sample


title: PD1-int CD8+ T cell [BS-275]


title: PD1-high CD8+  T cell [BS-275]


title: RatID4_TH_SHM_MBD-seq


title: PD1-high CD8+  T cell [BS-488]


title: PD1-neg CD8+ T cell [BS-488]


title: PD1-high CD8+  T cell [BS-200]


title: PD1-int CD8+ T cell [BS-488]


title: PD1-neg CD8+ T cell [BS-200]


title: PD1-int CD8+ T cell [BS-200]


title: PD1-neg CD8+ T cell [BS-433]


title: PD1-int CD8+ T cell [BS-433]


title: PD1-high CD8+  T cell [BS-433]


title: PD1-int CD8+ T cell [BS-358]


title: PD1-neg CD8+ T cell [BS-358]


title: PD1-neg CD8+ T cell [BS-451]


title: PD1-int CD8+ T cell [BS-474]


title: PD1-neg CD8+ T cell [BS-423]


title: PD1-int CD8+ T cell [BS-451]


title: PD1-neg CD8+ T cell [BS-474]


title: PD1-high CD8+  T cell [BS-358]


title: PD1-int CD8+ T cell [BS-278]


title: PD1-neg CD8+ T cell [BS-278]


title: PD1-high CD8+  T cell [BS-451]


title: PD1-high CD8+  T cell [BS-278]


title: PD1-neg CD8+ T cell [BS-485]


title: PD1-int CD8+ T cell [BS-485]


title: PD1-high CD8+  T cell [BS-474]


title: PD1-neg CD8+ T cell [BS-483]


title: PD1-high CD8+  T cell [BS-485]


title: PD1-int CD8+ T cell [BS-483]


title: PD1-high CD8+  T cell [BS-483]


title: Agaricus bisporus  245 AMA-7 growth 39 days replicate 2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, reads with unknown bases (N) >10% and low quality reads (more than 50% of the bases with quality values<5%) were removed. Clean reads were mapped to the genome sequence using BWA/Bowtie (Langmead et al., 2009; Li and Durbin, 2010)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using RSEM tool (Li et al. 2009)
Genome_build: Agaricus bisporus var bisporus (H97) http://genome.jgi.doe.gov/Agabi_varbisH97_2/
Supplementary_files_format_and_content: Files include FPKM values for each sample.

organism: Agaricus bisporus

source_name: Mycelium colonized compost sample

growth_protocol: Compost is based of wheat straw, horse and chicken manure, gypsum and water, according to commercial practice at CNC (Coöperatieve Nederlandse Champignonkwekersvereniging, Milsbeek, The Netherlands). The composts were inoculated with 176 mL of wheat kernels (spawns) colonized by the different strains. The crates were incubated in a commercial composting tunnel for 17 d after which they were moved to mushroom breeding farm and covered by 5 cm of casing layer. The incubation was continued in a breeding chamber similar to large scale commercial mushroom production. Approximately 1 L samples were taken from the middle of the crates after 27 and 39 d from the introduction of the spawns into the compost and corresponding to pinning stage and the first flush, respectively.

extract_protocol:
Total RNA was extracted by using a CsCl gradient centrifugation (Patyshakuliyeva et al., 2014) from the duplicate compost samples of A. bisporus strains 065 BP-8, 219 30P, 245 AMA-7 and A15 collected at the primordial stage (27 d) and the first flush (39 d). RNA quantity and integrity were determined with RNA6000 Nano Assay (Agilent 2100 Bioanalyzer, Agilent Technologies, USA). Preparation of cDNA library and sequencing reactions were conducted in the BGI Tech Solutions Co., Ltd. (Hong Kong, China) as described previously (Patyshakuliyeva et al., 2015).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After reaching the specific time point, compost samples were immediately stored at -20°C.

tag: strain

tag: sampling time

value: 39 days

tag: sampling type

value: Mycelium colonized compost sample


title: Agaricus bisporus  219 30P growth 27 days replicate 1

value: 27 days


title: Agaricus bisporus  065 BP-8 growth 27 days replicate 2


title: Agaricus bisporus  A15 growth 39 days replicate 1


title: Agaricus bisporus  219 30P growth 27 days replicate 2


title: Agaricus bisporus  219 30P growth 39 days replicate 1


title: Agaricus bisporus  245 AMA-7 growth 27 days replicate 2


title: Agaricus bisporus  065 BP-8 growth 27 days replicate 1


title: Agaricus bisporus  219 30P growth 39 days replicate 2


title: Agaricus bisporus  A15 growth 27 days replicate 2


title: Agaricus bisporus  065 BP-8 growth 39 days replicate 2


title: Agaricus bisporus  065 BP-8 growth 39 days replicate 1


title: Agaricus bisporus  245 AMA-7 growth 39 days replicate 1


title: Agaricus bisporus  A15 growth 27 days replicate 1


title: ANP32e_ChIP-Seq TAC

first: Danish

last: Sayed

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

data_processing:
ChIP-Seq analysis done by Active Motif (Data Explan file attached in PdF format)
sequence analysis: The 75-nt sequence reads ("tags") identified by the sequencing service (using NextSeq 500) are mapped to the genome using BWA algorithm. Alignment information for each tag is stored in BAM format. Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
fragment density: Since the 5'-ends of the tags represent the end of a ChIP/IP-fragments, the tags are extended in silico (using Active motif software)at their 3' -ends to a length of 150-250 bp, depending on the average fragemtn length in the size selected library. To identify the density of fragemnts (extendend tags) along the genome, the genome is divided into 32 nt bins and the number of fragments in each bin is determined. This information is stored in a bigWig file that can be reviewed in a browser such as Affymetrix' Integrated Genome Browser (IGB).
peak finding: An interval is a discrete genomic region, defined by the chromosome number and a start and end coordinate. Intervals represent the locations of the fragment density peaks. Two main peak callers used by active motif are MACS and SICER. Both look for significant enrichments in the ChIUP/IP data file when compared to Input data file
active region: To compare peak metrics between two samples, overlapping intervals are grouped into"Active regions', which are defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval (=union of overlapping Intervals). In locations where only one sample has an interval, this interval defines the Active Region. Active regions are useful to consider because the location and the lenghts of the intervals are rarely exactly the same when comparing different samples.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: whole heart

extract_protocol: ChIP, Library construction and Illumina sequencing performed by Active Motif

treatment_protocol: C57Bl/6 mice (12wks, ~26gms, male) were subjecetd to transaortic coartation (standard protocol described in detail in related publication Sayed et al, 2013) for 4days before hearts were extracted for analysis.

tag: pathology

value: Hypertrophied heart

value: 12wk old

value: Transaortic coarctation (TAC) for 4days

tag: antibody

value: anti-ANP32e (Abcam ab5993)

tag: Sex

value: male


title: Input

value: Pooled heart


title: Agaricus bisporus  245 AMA-7 growth 27 days replicate 1


title: Agaricus bisporus  A15 growth 39 days replicate 2


title: ANP32e_ChIP_Seq Sham

value: Normal heart

value: Sham


title: H2Az_ChIP-Seq TAC

value: anti-H2A.Z (ActiveMotif 39113)


title: H2Az_ChIP-Seq Sham


title: GLUCOSE

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

country: United Kingdom

institute: University of Southampton

data_processing:
basecalling - bcl2fastq
filtering, alignment - STAR aligner (v2.5.0a)
digital gene expression - Drop_Seq_tools_v1.0
Genome_build: hg19
Supplementary_files_format_and_content: Digital gene expression matrix format. (A row for each gene, and a column for each cell barcode and a UMI count matrix)

source_name: mammosphere

growth_protocol: MDA-MB-231 cells were adapted to culture in 2D in DMEM containing either 25 mM glucose or 10 mM fructose, for 30 days.

extract_protocol:
Trypsin/ EDTA disaggregated mammospheres
PCR on bead then Nextera XT

treatment_protocol: Adapted cell cultures were plated on low attachment plates in conditioned media from their respective 2D cultures. Resultant mammospheres were cultured for 10 days

value: 25 mM glucose

tag: cell line


title: FRUCTOSE

tag: agent

value: 10 mM fructose


title: Kelly ATAC [Lab: Look]

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Raw reads were separately aligned using bowtie with parameters --sam --best -k 1 -m 1 -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Neuroblastoma

growth_protocol: Cells were cultured according to the suggested guidelines in RPMI media containing 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Libraries were generated using the Ad1 and Ad2.13–2.24 barcoded primers from and were amplified for 7–9 total cycles
DNA was simultaneously fragmented and tagged with sequencing adapters using the Nextera Tn5 transpoase kit

tag: cell type

value: Kelly


title: BE2C ATAC [Lab: Look]


title: BE2C GATA3 [Lab: Look]

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
Peaks were called using MACS 1.4 with parameters -p 1e-9 --keep-dup=auto and corresponding input control.
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.

tag: chip antibody

tag: antibody manu.

value: Thermo Fisher

tag: antibody catalog

tag: antibody lot


title: RatID8_TRM_HC_MBD-seq

description:
Processed data file: Hippocampus_Repitools_gene_body_counts.txt
Processed data file: Hippocampus_Repitools_exon_counts.txt
Processed data file: Hippocampus_Repitools_promoter_counts.txt

source_name: Ipsilateral hippocampus, TBI

tag: strain/background

value: Sprague-Dawley

tag: gender

value: Male

tag: age

value: Adult

tag: tissue

value: Ipsilateral hippocampus

value: TBI


title: BE2C MYCN [Lab: Look]

value: n-Myc

value: Abcam


title: BE2C TBX2 [Lab: Look]


title: RatID9_TRM_HC_MBD-seq

tag: treatment


title: BE2C ISL1 [Lab: Look]

value: DSHB


title: RatID10_TRM_HC_MBD-seq


title: Kelly ISL1 [Lab: Look]


title: Kelly GATA3 [Lab: Look]


title: BE2C PHOX2B [Lab: Look]

value: Santa Cruz


title: RatID5_SHM_HC_MBD-seq

source_name: Ipsilateral hippocampus, sham operated

value: sham operated


title: Kelly Input [Lab: Look]

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1


title: RatID6_TRM_HC_MBD-seq


title: Kelly HAND2_M19X [Lab: Look]


title: RatID2_SHM_HC_MBD-seq


title: BE2C Input [Lab: Look]


title: BE2C HAND2_M19X [Lab: Look]


title: RatID4_SHM_HC_MBD-seq


title: RatID1_SHM_HC_MBD-seq


title: NGP_ethanol_9

data_processing:
Gene expression quatification based on Kallisto v0.42.4 with Ensembl v85 index.
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: NGP cell line (neuroblastoma)

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen), quantified using Nanodrop-100, and quality controlled using FragmentAnalyzer (High Sensitivity RNA Analysis Kit, DNF-472-0500, Advanced Analytical).
100ng of total RNA was used for TruSeq stranded mRNA library prep (Illumina),

value: neuroblastoma

value: vehicle - ethanol


title: RatID_10_CX_TRM_MBD-seq

description:
Processed data file: Cortex_Repitools_gene_body_counts.txt
Processed data file: Cortex_Repitools_exon_counts.txt
Processed data file: Cortex_Repitools_promoter_counts.txt

source_name: Perilesional cortex, TBI

value: perilesional cortex


title: RatID_7_CX_TRM_MBD-seq


title: RatID_8_CX_TRM_MBD-seq


title: RatID_9_CX_TRM_MBD-seq


title: RatID7_TRM_HC_MBD-seq


title: RatID_6_CX_TRM_MBD-seq


title: RatID3_SHM_HC_MBD-seq


title: RatID_4_CX_SHM_MBD-seq

source_name: Perilesional cortex, sham operated


title: RatID_3_CX_SHM_MBD-seq


title: RatID_2_CX_SHM_MBD-seq


title: H3K4me3_V0

city: Beijing

first: Qing

last: Huan

address: No.20 Nanxincun Xiangshan, Haidian District

institute: Institute of Botany, Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 used for basecalling.
Clean reads from sequencing, after removing low quality reads and trimming for adaptor sequence, were mapped to unique locations in Brachypodium genome with Bowtie2 version 2.1.0, using default parameters.
EpiChIP was used to analyze the modification patterns of all the samples and calculate peak values. The normalized locus specific chromatin state values (NLCS) of each gene were used to indicate the level of histone modification.
Genome_build: Brachypodium distachyon (http://genome.jgi.doe.gov)
Supplementary_files_format_and_content: tab-delimited text files showing NLCS value for all the samples.

organism: Brachypodium distachyon

source_name: Seedling

growth_protocol: Brachypodium distachyon (L.) Beauv. diploid line ABR1 seeds were germinated on the wet sterile filter paper in petri dishes and grown at 24˚C for 14 days under long day (16 h light/8 h dark) condition.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed with antibodies from Upstate Biotechnology (MA, USA) (anti-H3K4me3: 17-614 and anti-H3K27me3: 17-622) following previously validated methods.
Samples were prepared for sequencing with the TruSeq ChIP Sample Preparation Kit as per the manufacturer instructions and quantified with a Qubit fluorometer.

treatment_protocol: The seedlings were transferred to 4˚C for 30 days for vernalization treatment (V30). Seedlings, grown 17 days after sowing without vernalization (with equivalent development stage of V30 seedlings), were regarded as non-vernalized seedlings (V0). To obtain the same stage of development (third-leaf stage), post-vernalized seedlings (V30N) were grown under long-day condition for 7 days, transferred to 4˚C for 30 days and brought back to normal condition for 7 days. The aerial part of seedlings were pooled and used for library construction.

tag: ecotype

value: seedling (aerial portion)

value: H3K4me3 (Millipore, 17-614)

value: no treatment


title: H3K4me3_V30N

value: vernalization and recovery treatment


title: H3K4me3_V0_2


title: H3K27me3_V0

value: H3K27me3 (Millipore, 17-622)


title: H3K4me3_V30

value: vernalization treatment


title: H3K27me3_V30


title: TAB-RRBS

city: Irvine

first: Xueguang

last: Sun

state: CA

address: 17062 Murphy Ave

institute: zymo research corp

data_processing:
Using this method, the 5hmC levels of various human tissues were mapped genome-wide.
Genome_build: hg19
Supplementary_files_format_and_content: big bed file

source_name: Brain Tissue

extract_protocol:
Genomic DNA from the source was purified via phenol::chloroform extraction
RRBS-derived
Mirror-seq library

value: brain


title: TAB-RRBS Negative control


title: DKO Mirror-Seq Negative Control

data_processing:
Using this method, the 5hmC levels of various human tissues and paired tumor liver tissues were mapped genome-wide.
Genome_build: hg19
Supplementary_files_format_and_content: big bed file

source_name: Cell line

value: Cell line


title: Tumor Liver

source_name: Liver Tumor Tissue

value: Liver Tumor Tissue


title: Kidney Mirror-Seq Negative Control

source_name: Kidney Tissue

value: Kidney Tissue


title: DKO


title: Notmal Liver

source_name: Adjacent Normal Liver Tissue

value: Adjacent Normal Liver Tissue


title: Spleen

source_name: Spleen Tissue

value: Spleen Tissue


title: RatID_5_CX_SHM_MBD-seq

value: Sprague-Dawley

value: Male

value: Adult


title: Liver

source_name: Liver Tissue

value: Liver Tissue


title: Kidney


title: RatID_1_CX_SHM_MBD-seq

value: perilesional cortex

value: sham operated


title: Liver Mirror-Seq Negative Control


title: H3K27me3_V30N

value: seedling (aerial portion)


title: Spleen Mirror-Seq Negative Control


title: 100ng

value: Brain Tissue


title: 400A Mirror-Seq Negative Control


title: 400B Mirror-Seq Negative Control


title: 200ng


title: mock 2 (SC1_Vehicle)

city: Orbassano

first: Elio

last: Grazio

address: Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10

country: Italy

institute: University of Turin

data_processing: Reads were mapped to the Rattus norvegicus rn5 reference assembly using TopHat v2.0.10 (D. Kim et al., 2013) ts were generated using htseq and the refseq transcriptome.  Genes with RPKM > 1 in all 3 replicates were considered expressed in each condition.

source_name: Schwann cells

growth_protocol:
Primary Schwann cells were routinely cultured on poly-L-lysine (PLL, Sigma)-coated plate, in complete medium consisting of DMEM (Sigma #D5671) supplemented with 10% heat-inactivated foetal bovine serum (FBS, Invitrogen), 100 units/mL penicillin, 0.1 mg/mL streptomycin, 1 mM sodium pyruvate, 2 mM L-glutamine, 63 ng/mL glial growth factor (GGF, #369-HB, R&D Systems) and 10 µM forskolin (Sigma) and incubated at 37°C in 5% CO2.
Confluent Schwann cells were starved overnight (18 hours) in "starving medium" consisting in: DMEM (Sigma #D5671) supplemented with 2% heat-inactivated foetal bovine serum, 100 units/mL penicillin, 0.1 mg/mL streptomycin, 1 mM sodium pyruvate, 2 mM L-glutamine, and 10 µM forskolin

extract_protocol: Deep RNA sequencing was performed on three mock samples and three stimulated samples obtained in three independent experiments. RNA quality was assessed on an Agilent 2100 Bioanalyzer. All samples had RIN ≥ 9. For RNA-Seq library preparation, approximately 2 μg of total RNA were subjected to poly(A) selection and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Sequencing was performed on the Illumina NextSeq 500 platform.

treatment_protocol: Starved Schwann cells were stimulated for 6 hours in "starving medium" containing  10 nM recombinant soluble NRG1β1 (#396-HB), purchased from R&D systems. Control mock samples were stimulated with the same volume of ligand resuspension buffer (PBS containing 1% bovine serum albumin, BSA, Sigma).

tag: strain

value: Wistar

value: adult

value: Schwann cells


title: RNAseq in Cbx1 Cbx3 double knock-out mES cells, rep3

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument. Some samples were sequenced on two independent lanes and raw fastq files need to be pooled prior to mapping. These are indicated with "a" and "b" in the file name.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
RNAseq: Sequenced reads were aligned using Bowtie 1.0.0 ( -m1 --best –strata) or STAR 2.5.0a (--outFilterMultimapNmax 20 --outMultimapperOrder Random --outSAMmultNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000)
ChIPseq: Sequenced reads were aligned using Bowtie 1.0.0 (-m 1 —best –strata) or STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within )
For RNAseq and ChIPseq, QuasR was used to count aligned reads (qCount) and to generate depth normalized bigWig files (qExportWig). Differential expression analysis was perfored using EdgeR on the raw gene count tables generated by QuasR.
ATACseq data was mapped using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType Local --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within --outFileNamePrefix  --clip3pAdapterSeq CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using QuasR. Read counts were binned in 50bp intervals and normalized to average sequencing depth. For ATACseq, data was not binned and the bigwig files display the full sequencing reads normalized to 1 mio genome mapping reads. Bed files containing peak positions were generated from the .narrowPeak output file from MACS2.

source_name: embryonic stem cells

extract_protocol:
Total RNA was isolated using the Absolutely RNA Microprep Kit (Stratagene) and ribosomal RNA was depleted using the Ribozero removal kit (Illumina) prior to library preparation.
Libraries were prepared using the Illumina ScriptSeq v2 kit according to the manufacturer's instructions.

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/6

tag: genotype/variation

value: Cbx1 KO, Cbx3 flox


title: mock 1 (SC31_Vehicle)


title: treated 3 (SC15_b10nM)


title: treated 1 (SC33_b10nM)


title: mock 3 (SC13_Vehicle)


title: 400A