title: Macrophage from EP2-KO mice_rep2

city: Taipei

first: Yuan-Yuan

last: Cheng

address: Academia road

country: Taiwan

institute: Academia Sinica

description: macrophage from EP2ko mice replicate 2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: macrophage from EP2ko mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol Purification procedure. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: macrophage isolation from LPS-induced wild-type and EP2-KO mice

value: macrophage

tag: gender

value: male


title: Macrophage from EP2-KO mice_rep1

status: Public on Jul 11 2018

type: RNA

description: macrophage from EP2ko mice replicate 1

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: cell type


title: ISConly_AL_rep2

type: SRA

city: Singapore

first: Joonki

last: Kim

address: 2 Medical drive, Blk MD9

department: Physiology, School Of Medicine

country: Singapore

institute: National University of Singapore

library_source: transcriptomic

data_processing:
Raw image data file from high-throughput sequencing (Illumina) was transformed to Sequenced Reads (Raw data or Raw reads) by CASAVA base recognition (Base calling).
Low quality reads was trimmed using command-line.
Alignment to reference genome was performed using TopHat2 (Kim et al., 2013).
FPKM (Fragments Per Kilo bases per Million reads) to estimate gene expression levels was performed according to Mortazavi et al. (2008).
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Excel files containing quantified 'FPKM' and 'Readcount' values of all 72 samples.

source_name: Brain

extract_protocol:
Total RNA was extracted from the frozen brain tissue samples using a micro-tube tissue homogenizer and EZ-10 DNAaway RNA extraction mini-prep kit following manufacturer's instruction. Samples with only RIN above 7 were seleted for the rest of the procedures.
Purified mRNA was used for library preparation for sequencing using standard Illumina protocols.

treatment_protocol: Feeding methods: (AD) Ad libitum diet feeding group which had free flow of food pellet 24 h per  day; EOD is every-other-day fasting group which had 24 h of fasting and consecutive 24 h free feeding day loop; IF12 is intermittent fasting 12 h group which had 12 h of fasting time every day. IF16 is intermittent fasting 16 h group which had 16 h of fasting time every  day.

tag: diet

value: Ad libitum

tag: strain

tag: tissue

value: Brain

tag: age

value: 7 months


title: ISConly_EOD_rep1

value: every-other-day fasting


title: 2afl/fl_4-OHT_brains

first: Bernice

middle: H

last: Wong

address: 8 College Road, Level 8

department: Cardiovascular and Metabolic Disorders

institute: Duke-NUS Medical School, Singapore

description: Gene expression data from brain

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix GeneChip® Mouse Genome 430 2.0 Array for 16hrs at 45ºC.

scan_protocol: GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). Scanning was done using the GeneChip®  Scanner 3000 7G (Affymetrix)

data_processing: CEL files were processed with Partek Genomics Suite 6.6 according to the gene expression workflow using RMA import settings.

label: biotin

source_name: postnatal day 8 Mfsd2afl/fl 4-OHT brains

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® 3' IVT PLUS Reagent Kit User Manual, Affymetrix)

growth_protocol: All mice were housed in colony cages on a 12hr light/12 hr dark cycle with controlled humidity and temperature at 23ºC. Mice were fed ad libitum on a normal chow diet (Global 18% Protein Rodent Diet from Harlan, Envigo) and have free access to water.  Pups were weaned at 3 weeks of age. Both male and female mice were used in all experiments and no gender differences were observed.

extract_protocol: Tissues were lysed in TRIzol (ThermoFisher Scientific) using a MagNA Lyser Instrument (Roche). Total RNAs were extracted according to protocol described by Untergasser Lab (Untergasser A. “RNAprep - Trizol combined with Columns” Untergasser's Lab. Winter 2008.). RNA concentration was quantified using Nanodrop.

value: brain

value: postnatal day 8


title: subject_231-Ascending colon-biopsy_407

city: New York

first: Eric

last: Schadt

address: 1425 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Gene expression were carried out using Affymetrix GeneChip HTHGU133+ (Affymetrix, Santa Clara, CA, USA Cat# 901262) according to the manufacturer’s protocol with the exception that dimethyl sulphoxide replaced the Tetramethylammonium Chloride Solution in the hybridization buffer.

scan_protocol: Arrays were washed and stained on the Affymetrix GeneChip Array Station then scanned on an HTAPS scanner.

data_processing: Array Studio software version 6.0 (OmicSoft Corp., St. Morrisville, NC) was used for data analysis. The microarray data were pre-processed and normalized using RMA. Log2 transformed data was used for statistical analysis.

label: NuGEN Encore Biotin Module

organism: Homo sapiens

source_name: Ascending colon

label_protocol: RNA samples were amplified by NuGEN Ovation RNA Amplification System V2 Whole Blood Solution (NuGEN, San Carlos, CA) and purified using Agencourt RNAClean magnetic beads.  Labeling was done using the NuGEN Encore Biotin Module (NuGEN). (Agencourt, Beverly, MA) on a Caliper SciClone robot.

extract_protocol: Total RNA including micro ribonucleic acids (miRNA) was isolated with PAXgene Blood RNA MDx Kit plus customized reagent BM3 (Cat#762431, lot 136237127) according to the manufacturer’s instructions (Qiagen Inc., Valencia, CA). Briefly, PAXgene Blood RNA Tubes were incubated at room temperature around 2 hrs before extraction. After centrifugation for 10 min at 3000–5000 x g, the pellet was re-suspended in 290 μl Buffer BR1 with 35 μl proteinase K. The remaining procedures were performed on a BioRobot Universal System using a customized protocol, PAXgene Blood RNA UNIV rcV73_miRNA Centocor.pro (Qiagen).

treatment_protocol: All blood samples were stored at −80 °C until RNA isolation was performed. Blood samples were hybridized by microarray for genome-wide mRNA expression profiling. Ileal, rectal, and colonic biopsies were collected at the screening visits from a sub-group of subjects who consented to this procedure. Biopsies were obtained from selected colonic sections, including the ascending, transverse, and descending colonic regions, and from both inflamed and non-involved areas. The inflamed regions were defined as the colonic segments with the most severe disease activity. Additional biopsies were collected from the terminal ileum and from the rectum (i.e., the distal 10 cm of the colon).

value: Ascending colon

value: FALSE

tag: Sex

value: F

tag: batch

tag: disease

value: Crohn's disease

tag: visit

value: Week 6

tag: inflammation

value: Non-involved area


title: Macrophage from wild-type mice_rep2

description: macrophage from wt mice replicate 2

source_name: macrophage from wt mice

value: wt


title: VDBR43b_C2CUGACXX_ACTGAT_L001

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

country: Australia

institute: CSL Limited / bio21 Institute

description:
technical replicate 1
Donor VDBR43 Blood neutrophils

data_processing:
Reads were mapped to Homo sapiens GRCh37.p10 genome, using TopHat (TopHat v2.0.8, bowtie v2.1.0; Trapnell et al.,2009).
Mapped reads were summaried on a gene level using Ensembl ID gene annotation (Ensembl Release 70 based on GRCh37.p10 genome build) and featureCounts (v1.4.6; Yang et al., 2014) software.
Summarised read counts in this submission were NOT normalised nor filtered. We recommend using Bioconductor edgeR package functions: i) calcNormFactors (TMM method) to normalise between samples based on library sizes,  and ii) rpkm function to normalise between genes within a sample based on gene lengths.
Genome_build: GRCh37.p10
Supplementary_files_format_and_content: All processed data files are in a tab delimited file format. They contain raw read counts summarised on a gene level according to Ensembl Release 70 annotation.

molecule: polyA RNA

source_name: Donor VDBR43 Blood neutrophils

extract_protocol:
RNA was extracted  using an Rneasy mini kit (Qiagen, catalog number 74034)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Neutrophils were isolated from peripheral blood and synovial fluid with EasySep Human Neutrophil Enrichment Kit (Stem Cell Technologies). Purified neutrophils were stored in RNAprotect (QIAGEN) for later use

value: Blood

value: neutrophils

tag: donor

value: M

tag: phenotype

value: Healthy

tag: medication

value: No


title: VDBR40b_C2CUGACXX_GGCTAC_L002

description:
technical replicate 2
Donor VDBR40 Blood neutrophils

source_name: Donor VDBR40 Blood neutrophils


title: Macrophage from wild-type mice_rep1

description: macrophage from wt mice replicate 1

value: macrophage

value: male


title: VDBR43b_C2CUGACXX_ACTGAT_L002

description:
technical replicate 2
Donor VDBR43 Blood neutrophils


title: ISConly_AL_rep1

value: Ad libitum

value: Brain

value: 7 months


title: Sham_IF16_rep3


title: VDBR40b_C2CUGACXX_GGCTAC_L001

description:
technical replicate 1
Donor VDBR40 Blood neutrophils


title: VDBR10b_C2CUGACXX_ATGTCA_L001

description:
technical replicate 1
Donor VDBR10 Blood neutrophils

source_name: Donor VDBR10 Blood neutrophils


title: Macrophage from EP2-KO mice_rep3

description: macrophage from EP2ko mice replicate 3


title: Macrophage from EP2-KO mice_rep4

description: macrophage from EP2ko mice replicate 4


title: Sham_IF16_rep2


title: 466b_C2CUGACXX_CCGTCC_L001

description:
technical replicate 1
Donor 466 Blood neutrophils

source_name: Donor 466 Blood neutrophils

value: Rheumatoid arthritis


title: Sham_IF16_rep1


title: 435b_C2CUGACXX_CTTGTA_L002

description:
technical replicate 2
Donor 435 Blood neutrophils

source_name: Donor 435 Blood neutrophils


title: 435b_C2CUGACXX_CTTGTA_L001

description:
technical replicate 1
Donor 435 Blood neutrophils


title: Sham_IF12_rep3


title: Macrophage from wild-type mice_rep3

description: macrophage from wt mice replicate 3


title: VDBR10b_C2CUGACXX_ATGTCA_L002

description:
technical replicate 2
Donor VDBR10 Blood neutrophils


title: 431b_C2CUGACXX_TAGCTT_L002

description:
technical replicate 2
Donor 431 Blood neutrophils

source_name: Donor 431 Blood neutrophils


title: 2aiECKO_brains

description: Gene expression data from brain

source_name: postnatal day 8 2aECKO brains

value: brain

value: Mfsd2afl/fl, Cdh5ERT2-cre

value: postnatal day 8


title: 466b_C2CUGACXX_CCGTCC_L002

description:
technical replicate 2
Donor 466 Blood neutrophils

value: F


title: Sham_IF12_rep2


title: Sham_IF12_rep1


title: Sham_EOD_rep3

value: every-other-day fasting


title: 431b_C2CUGACXX_TAGCTT_L001

description:
technical replicate 1
Donor 431 Blood neutrophils


title: Sham_EOD_rep1

source_name: sham


title: 416sf_C2CUGACXX_GTGAAA_L001

description:
technical replicate 1
Donor 416 Synovial fluid neutrophils

source_name: Donor 416 Synovial fluid neutrophils

value: Synovial fluid


title: 416sf_C2CUGACXX_GTGAAA_L002

description:
technical replicate 2
Donor 416 Synovial fluid neutrophils


title: 416b_C2CUGACXX_GTGGCC_L001

description:
technical replicate 1
Donor 416 Blood neutrophils

source_name: Donor 416 Blood neutrophils

value: Blood


title: Sham_AL_rep3


title: Sham_EOD_rep2


title: 396b_C2CUGACXX_AGTTCC_L002

description:
technical replicate 2
Donor 396 Blood neutrophils

source_name: Donor 396 Blood neutrophils

value: neutrophils


title: Sham_AL_rep1


title: 387b_C2CUGACXX_GTCCGC_L002

description:
technical replicate 2
Donor 387 Blood neutrophils

source_name: Donor 387 Blood neutrophils


title: Macrophage from wild-type mice_rep4

description: macrophage from wt mice replicate 4

value: wt


title: 387b_C2CUGACXX_GTCCGC_L001

description:
technical replicate 1
Donor 387 Blood neutrophils

value: Healthy


title: 332b_C2CUGACXX_AGTCAA_L001

description:
technical replicate 1
Donor 332 Blood neutrophils

source_name: Donor 332 Blood neutrophils

value: No


title: 396b_C2CUGACXX_AGTTCC_L001

description:
technical replicate 1
Donor 396 Blood neutrophils


title: Sham_AL_rep2

source_name: Brain


title: 416b_C2CUGACXX_GTGGCC_L002

description:
technical replicate 2
Donor 416 Blood neutrophils

value: M


title: D620N-rep3

city: Boise

first: Brad

middle: E

last: Morrison

state: ID

address: 1910 university dr., mail stop: 1515

department: Biological Sciences

institute: Boise State University

data_processing:
FASTX-toolkit to remove adapter sequences
Aligned to a reference genome (human hg19) with TopHat (v2.0.11)
Assembly from the mapped reads was performed using cufflinks (v2.2.1)
1.5 fold expression (FPKM) cutoff
Supplementary_files_format_and_content: junction.bed files, FPKM

source_name: SH-SY5Y cell line (obtained directly from ATCC)

growth_protocol: SH-SY5Y cells were grown in F12/DMEM (1:1) media with 15% FBS and pen/strep added. Cells were differentiated for 7 days with 10uM all-trans retinoic acid in the same growth media.

extract_protocol:
Qiagen RNEasy kit with DNAse on-column digestion per manufacturer's protocol
Standard processing with adapter sequences added

treatment_protocol: No treatments, just 7-day retinoic acid (10uM) differentiation

tag: cell line


title: D620N-rep2


title: D620N-rep1


title: 332b_C2CUGACXX_AGTCAA_L002

description:
technical replicate 2
Donor 332 Blood neutrophils


title: WT-rep3


title: WT-rep2


title: WT-rep1


title: 271b_C2CUGACXX_GAGTGG_L001

description:
technical replicate 1
Donor 271 Blood neutrophils

source_name: Donor 271 Blood neutrophils

value: Yes


title: 271b_C2CUGACXX_GAGTGG_L002

description:
technical replicate 2
Donor 271 Blood neutrophils


title: 271sf_C2CUGACXX_GTTTCG_L002

description:
technical replicate 2
Donor 271 Synovial fluid neutrophils

source_name: Donor 271 Synovial fluid neutrophils


title: 271sf_C2CUGACXX_GTTTCG_L001

description:
technical replicate 1
Donor 271 Synovial fluid neutrophils


title: 226sf_C2CUGACXX_CGTACG_L002

description:
technical replicate 2
Donor 226 Synovial fluid neutrophils

source_name: Donor 226 Synovial fluid neutrophils


title: RNA-Sequencing VapC11 overexpression Rep2

city: Chandigarh

first: Amar

last: Deep

state: Chandigarh

address: C/o Dr.krishan Gopal , IMTech

department: Protein Science and Engineering

country: India

institute: Institute of Microbial Technology

data_processing:
Data was subjected to quality control check bby fastqc_v0.11.7
Reads were mapped onto H37Rv by Tophat
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Functional annotation by DAVID

organism: Mycobacterium tuberculosis H37Rv

source_name: Microbe

growth_protocol: Mycobacterium tuberculosis cells harbouring either pTetR (vector only) or pTetR-vapC11 were grown in Middlebrook 7H9 medium at 37 degree C with contant shaking.

extract_protocol:
Expression of protein was induced using anhydro tetracycline (ATC) 50 ng/mL. 24 hour Post induction, pellets were resuspended in TRIzol and total RNA was extracted.
The purified RNA was shipped to Aggrigenome Labs Pvt Ltd (India). RNA integrity was checked using Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). Ribosomal RNA was removed from total RNA sample using Ribo-ZeroTM Magantic kit (Bacteria) as per manufacturer’s recommendations (Epicentre). RNA cleanup was performed using Agencourt RNACleanTM XP Beads (Beckman Coulter). RNA was fragmented followed by random priming for first strand cDNA synthesis and second strand synthesis.
Adapters were ligated and the library was cleaned up twice using Agencourt RNACleanTM XP Beads followed by 14 PCR amplification cycles. Amplified library was further cleaned up using AMPure XP Beads (Beckman Coulter Inc). The quality of library was checked using Standard Sensitivity NGS Fragment Analysis Kit on an Advanced Analytical Fragment Analyzer. Library was quantified using qPCR as per Illumina Sequencing Library qPCR quantification guide and sequencing was performed at Illumina HiSeq2000.

treatment_protocol: Above mentioned strains were sub-cultured in fresh 7H9 medium and allowed for further growth at 37 degree celcius. When optical density (OD 600nm)reached mid-log phase, the cultures were induced using Anhydro tetracycline (50 ng/mL).Post 24 hours treatment, cells were harvested.

tag: genotype/variation

tag: time point

value: 24 Hours post induction


title: RNA-Sequencing VapC11 overexpression Rep1


title: 226b_C2CUGACXX_GATCAG_L002

description:
technical replicate 2
Donor 226 Blood neutrophils

source_name: Donor 226 Blood neutrophils

tag: gender


title: 226b_C2CUGACXX_GATCAG_L001

description:
technical replicate 1
Donor 226 Blood neutrophils

tag: cell type


title: 226sf_C2CUGACXX_CGTACG_L001

description:
technical replicate 1
Donor 226 Synovial fluid neutrophils


title: up_papilla_2

city: Nagoya

first: Kazumi

last: Taguchi

address: Kawasumi-1, Mizuho-cho, Mizuho-ku

department: Nephro-urology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

data_processing:
Sequencing yielded ~682 million reads with an average read depth of 48 million reads/sample.
Reads were then aligned to the human genome and those that mapped uniquely to known mRNAs were used to assess differential expression.
We used DESeq2 to compare all the pairwise comparisons between cortex, papilla and medulla tissues, while controlling for variation that might be found between low, mid and upper sites.
Because the Cortex vs Papilla comparison had so many DE genes and such a strong change in expression in general, we created 4 heatmaps. One with all DE genes across all comparisons, and another three with the DE genes from just one pairwise comparison.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files including counts, volcano plots, heatmaps.

source_name: kidney

extract_protocol:
Tissue was obtained from a structurally normal kidney removed for severe, unilateral renal stone formation in a 23 year old male subject who elected for nephrectomy for debilitating stone disease. Immediately after kidney removal, needle core tissue biopsies were taken from the kidney and divided into three regions.
RNA libraries were prepared for sequencing using standard Illumina protocols (library kit: Illumina TruSeq mRNA stranded)

value: male

value: stone forming kidney


title: low_medula_1


title: up_cortex_2


title: mid_papilla_1


title: mid_medula_1


title: up_medula_2


title: mid_cortex_1


title: low_cortex_1


title: up_papilla_1


title: low_papilla_1


title: up_cortex_1


title: RNA-Sequencing Control Cells Rep2

value: pTetR Vector only


title: RNA-Sequencing Control Cells Rep1


title: up_medula_1


title: C. jejuni 12661 filament stationary phase replicate 2

status: Public on Jul 10 2018

city: Loughborough

first: Ian

middle: Frank

last: Connerton

state: Leicestershire

address: College Road, Sutton Bonington

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

data_processing:
Illumina CASAVA v1.8.2
Illumina bcl2fastq v1.8.4
CLC Genomics Workbench 10.1 Trim and Quality Filter
CLC Genomics Workbench 10.1 RNAseq strand specific abundance and normalisation recorded as TPM (Transcripts Per Kilobase Million) and RPKM (Reads Per Kilobase Million)
Genome_build: C. jejuni NCTC12661 NCBI Accession CP010906.1
Supplementary_files_format_and_content: tab-delimited text files include TPM and RPKM values for each gene location

organism: Campylobacter jejuni

source_name: Filamentous morphotype stationary phase

growth_protocol: Three independent biological replicates of C. jejuni 12661 were inoculated into 500 ml of sterile MEM (minimum essential medium without glutamine and phenol red; Catalogue number 51200-038; Life Technologies Ltd) with 10 mM sodium pyruvate, to a final density of approximately 10exp5 CFU/ml. The culture flasks were incubated in a shaking incubator at 100 rpm, at 37 °C under microaerobic conditions (approximately 7% O2, v/v) for 30 h.

extract_protocol:
Total RNA was isolated from the cell morphotypes using the Trizol Max Bacterial Isolation kit (Invitrogen) and purified using an RNeasy Mini kit (Qiagen) and the integrity was measured using a Bioanalyser 2100 (Agilent Technologies).
Ribosomal RNAs were depleted from the total RNAs using the Ribo-Zero™ Magnetic Kit for bacteria (Illumina) and used to prepare cDNA libraries using the NEBNext Ultra directional Prep Kit.

treatment_protocol: Short C. jejuni spiral cells were separated from filamentous cells using  a 0.8 µm sterile nitrocellulose membrane on a vacuum manifold.

tag: growth phase

value: Stationary

tag: cell morphology

value: Filamentous


title: C. jejuni 12661 filament stationary phase replicate 3

tag: strain


title: C. jejuni 12661 filament stationary phase replicate 1


title: C. jejuni 12661 spiral stationary phase replicate 1

source_name: Spiral morphotype stationary phase

value: Spiral


title: C. jejuni 12661 spiral exponential phase replicate 3

source_name: Spiral morphotype exponential phase

value: Exponential


title: C. jejuni 12661 spiral stationary phase replicate 3


title: C. jejuni 12661 spiral stationary phase replicate 2


title: C. jejuni 12661 spiral exponential phase replicate 2


title: C. jejuni 12661 spiral exponential phase replicate 1


title: HeLa_GWPBS-Cap-100 mM

city: Beijing

first: Liu

last: Fenglin

address: Courtyard 1, Beichen West Road

country: China

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
library strategy: GWPBS-Cap-seq
Illumina Casava1.7 software used for basecalling.
GWPBS-Cap-seq reads and MNase-seq reads were aligned to the hg19 genome assembly using the SOAP2 aligner, allowing up to 2 mismatches.
For GWPBS-Cap-seq, The resulting sequence read distribution was used to identify peaks. This was done by first separating forward (W) and reverse (C) strands, then connecting successive overlapping sequences on the W or C strand into continuous regions, and finally selecting the overlapping regions between the W and C strand. All these overlapping regions are considered to be peak regions. For MNase-seq, the peak calling procedure was finished with SICER (spatial clustering approach for the identification of ChIP-enriched regions) with a window size of 200 bp.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include peak information for each GWPBS-Cap group, MNase-seq group and FPKM values for each gene in Hela cells.

molecule: genomic DNA

growth_protocol: HeLa cells (from ATCC) were cultured in DMEM (HyClone, SH30243.01) supplemented with 10% FBS (Hyclone, SH30084.03) and 100 U ml-1 penicillin-streptomycin (HyClone, SV30010) and maintained in a incubator at 37˚C and 5% CO2.

extract_protocol:
For GWPBS-Cap samples, lysates were washed by cold NaCl Buffer containing different concentrations (50 mM,100 mM, 200 mM, 400 mM, 1000 mM or 2000 mM) of NaCl. After 2 hours’ rotation, nuclei were pelleted and resuspended in the same cold NaCl Buffer. Formaldehyde solution were added to cross-link protein and DNA and the complexes were sheared by sonication. Supernatants containing the solubilized chromatin DNA: protein complexes were clarified and added TCEP to reduce disulfide bonds of proteins. These complexes were isolated with active Amine-coated beads through sulfo-SMCC. For MNase-seq samples, lysates were clarified from MNase treated nuclei. For RNA-seq samples, total RNA was extracted using TRIzol and an aliquot of the RNA was reversed transcribed.
For GWPBS-Cap samples, DNA was end-repaired using T4 Polynucleotide Kinase. Phosphorylated 5' ends were treated with Lambda exonuclease and 3' single-stranded Sp6 adapters were ligated using T4 RNA Ligase 1. The DNA was extracted and double-stranded DNA was built using Klenow Fragment. DNA was added A-tail using dATP and Klenow Fragment (3'→5' exo-) and T7 double-stranded adapters were ligated to ends of DNA using T4 DNA Ligase. After adapter ligation DNA was PCR amplified with Sp6 and T7 primers for 20 cycles and library fragments of 80~120 bp (insert plus PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured and the paired-end sequencing was performed on Illumina Hiseq 4000 platform. For MNase-seq samples, The extracted 147 bp DNA bands were separated on agarose gel. The library  preparation and the high-throughput sequencing was performed on Illumina HiSeq 4000 platform. For RNA-seq samples, RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa

value: Cervical cancer cells

tag: nacl conc.


title: HeLa_Mnase-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
GWPBS-Cap-seq reads and MNase-seq reads were aligned to the hg19 genome assembly using the SOAP2 aligner, allowing up to 2 mismatches.
For GWPBS-Cap-seq, The resulting sequence read distribution was used to identify peaks. This was done by first separating forward (W) and reverse (C) strands, then connecting successive overlapping sequences on the W or C strand into continuous regions, and finally selecting the overlapping regions between the W and C strand. All these overlapping regions are considered to be peak regions. For MNase-seq, the peak calling procedure was finished with SICER (spatial clustering approach for the identification of ChIP-enriched regions) with a window size of 200 bp.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include peak information for each GWPBS-Cap group, MNase-seq group and FPKM values for each gene in Hela cells.


title: HeLa_GWPBS-Cap-2000 mM


title: HeLa_GWPBS-Cap-400 mM


title: HeLa_GWPBS-Cap-50 mM

value: 50 mM


title: HeLa_GWPBS-Cap-200 mM


title: m6A sample of MDD donor M_2 treated with Cort

city: Munich

first: Mareen

last: Engel

address: Kraepelinstr. 2-10

department: Stress Neurobiology and Neurogenetics

country: Germany

institute: Max-Planck-Institute of Psychiatry

description:
Sample name: MUC2065_M_2_C_m6A
Processed data files:
pheno_data.xlsx
MUC2065.bw
average_m6A_mdd_cort.bw
singlepeaks_M_2_C.bed
grouppeaks_mdd_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv

data_processing:
Basecalling, conversion and demultiplexing: Illumina RTA, bcl2fastq2
Alignment: to hg38 using STAR after Cutadapt
Peak-calling: per single m6A-input pair using exomePeak with window_width=100, sliding_step=10, minimal_peak_length=50
Consensus-peaks: Peaks from biological replicates were merged keeping only those ranges supported by a minimum of 2/3 of samples per group (using BEDTools with minimum length 50 nt and merging ranges with less than 50 nt distance, Quinlan and Hall, 2010): see grouppeaks_healthy_mock.bed, grouppeaks_healthy_cort.bed, grouppeaks_mdd_mock.bed, grouppeaks_mdd_cort.bed. For quantification with DiffBind (Ross-Innes et al., 2012) a consensus peak set was built with BEDTools including those ranges supported by either 2/3 of samples per group or 1/2 of samples of the entire experiment, furthermore filtered minimum abundancy (dba_score_rpkm_fold =2, dba_score_reads =25): finalpeaks_consensus_all_peaks.bed.
Quantitative analysis: For differential peak analysis m6A-RIP counts extracted from DiffBind (counts used: counts_in_peaks.csv) were compared with DESeq2 (Love et al., 2014) using a Treatment*Donor factorial model reporting two main effects (MainCort and MainDonor) and the Treatment*Donor interaction effect (Interaction) or a 4 group model for Posthoc comparisons of cortisol effect within each Donor group (Cortinhealthy and CortinMDD) (m6A_quantification.csv). Gene expression was analysed using the RNA input samples only employing  DESeq2 using the same models (counts used: RNA_counts.csv; analysis: RNA_quantification.csv). Significance cutoffs:  absolute fold change > 0.5 and Benjamini-Hochberg corrected P-value Q < 0.1. Peaks were annotated using ChIPseeker (Yu et al., 2015) and Biomart (Smedley et al., 2015). Peak bed-files are provided for all consensus peaks used for quantitaive analysis (finalpeaks_consensus_all_peaks.bed), and differential methylated peaks for the Cortisol main effect (finalpeaks_differential_mainCort_peaks.bed) and Cortisol*Donor interaction regulated peaks (finalpeaks_differential_interaction_peaks.bed).
Visualization: For visualization, bam files were normalised using deepTools (Ramírez et al., 2016) creating a single bigWigfile per sample (MUC2046.bw … MUC2070.bw). Biological replicates were merged using UCSC bigWigMerge and UCSC bedGraphToBigWig creating one m6A and one input RNA bigWigfile per condition: average_m6A_healthy_cort.bw, average_m6A_healthy_mock.bw, average_m6A_mdd_cort.bw, average_m6A_mdd_mock.bw, average_RNA_healthy_cort.bw, average_RNA_healthy_mock.bw, average_RNA_mdd_cort.bw, average_RNA_mdd_mock.bw
Genome_build: hg38
Supplementary_files_format_and_content: bed: peak ranges for single biological replicates (singlepeaks_*.bed), merged per group (grouppeaks_*.bed) or further processed see above (finalpeaks_*.bed); bw: normalized bigWig files per sample (MUC20*.bw) or merged per group/fraction (average_*.bw); csv: comma delimited files including raw counts used for DeSeq2 analysis and DeSeq2 (annotated) output.

source_name: immortalized B lymphocyte cell lines

growth_protocol: Human immortalized BLCLs derived from age-matched (33-53 y) male subjects either healthy or diagnosed with MDD were cultured in RPMI-1640 medium (Merck) supplemented with 10 % fetal calf serum at 37 °C with 5 % CO2. The cells were tested to be free of mycoplasma.

extract_protocol:
Total RNA was extracted  with Trizol (Invitrogen) and isopropanol precipitation. After removal of DNA (TurboDNA-free kit, Ambion), PolyA-RNA was enriched with the Genelute mRNA Prep Kit (Sigma), precipiated and diluted to 1ug/ul and fragmeneted using the fragmentation reagents (Life Technologies). 10 ug PolyA RNA fragments per samples were precipitated with 10ug anti-m6A antibody (SySy 202003). 10 ug PolyA RNA fragments mixed equimolar form all samples was precipiated with 10 ug IgG (Cell Signalling Technology 2729) and Protein A/G beads (Thermo Fisher Scientific) and recovered by Proteinase K elution.
Recovered immunoprecipitated fragments per sample or 100 ng of the input PolyA-RNA-fragments per samples were processed with the TruSeq non-stranded mRNA Sample Prep Kit and sequenced on a HiSeq4000 multiplexing all samples (16-57 Mio. raw reads).

treatment_protocol: Cells were treated with cortisol (Sigma-Aldrich, in ethanol, final concentration 0.1% v/v) or ethanol mock control, respectively, and harvested 1 h later.

value: MDD diagnosed male

tag: treatment

value: cortisol

tag: fraction

tag: rip antibody

value: Synaptic Systems anti-m6A Cat 202003 Lot 56

value: immortalized B lymphocyte cell lines


title: IgG mix sample

description:
Sample name: MUC2070_IgG
Processed data files:
pheno_data.xlsx
MUC2070.bw

value: mix

value: IgG

value: Cell Signalling Technology Normal Rabbit IgG Cat 2729 Lot 7


title: m6A sample of MDD donor M_3 treated with Mock

description:
Sample name: MUC2068_M_3_M_m6A
Processed data files:
pheno_data.xlsx
MUC2068.bw
average_m6A_mdd_mock.bw
singlepeaks_M_3_M.bed
grouppeaks_mdd_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv

value: mock


title: m6A sample of healthy donor H_3 treated with Mock

description:
Sample name: MUC2066_H_3_M_m6A
Processed data files:
pheno_data.xlsx
MUC2066.bw
average_m6A_healthy_mock.bw
singlepeaks_H_3_M.bed
grouppeaks_healthy_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv

value: healthy male


title: m6A sample of healthy donor H_3 treated with Cort

description:
Sample name: MUC2067_H_3_C_m6A
Processed data files:
pheno_data.xlsx
MUC2067.bw
average_m6A_healthy_cort.bw
singlepeaks_H_3_C.bed
grouppeaks_healthy_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of MDD donor M_3 treated with Cort

description:
Sample name: MUC2069_M_3_C_m6A
Processed data files:
pheno_data.xlsx
MUC2069.bw
average_m6A_mdd_cort.bw
singlepeaks_M_3_C.bed
grouppeaks_mdd_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of MDD donor M_2 treated with Mock

description:
Sample name: MUC2064_M_2_M_m6A
Processed data files:
pheno_data.xlsx
MUC2064.bw
average_m6A_mdd_mock.bw
singlepeaks_M_2_M.bed
grouppeaks_mdd_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: HeLa_GWPBS-Cap-1000 mM


title: input sample of MDD donor M_3 treated with Mock

description:
Sample name: MUC2056_M_3_M_input
Processed data files:
pheno_data.xlsx
MUC2056.bw
average_RNA_mdd_mock.bw
singlepeaks_M_3_M.bed
grouppeaks_mdd_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv

value: input


title: m6A sample of healthy donor H_2 treated with Cort

description:
Sample name: MUC2063_H_2_C_m6A
Processed data files:
pheno_data.xlsx
MUC2063.bw
average_m6A_healthy_cort.bw
singlepeaks_H_2_C.bed
grouppeaks_healthy_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of MDD donor M_1 treated with Mock

description:
Sample name: MUC2060_M_1_M_m6A
Processed data files:
pheno_data.xlsx
MUC2060.bw
average_m6A_mdd_mock.bw
singlepeaks_M_1_M.bed
grouppeaks_mdd_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: input sample of MDD donor M_3 treated with Cort

description:
Sample name: MUC2057_M_3_C_input
Processed data files:
pheno_data.xlsx
MUC2057.bw
average_RNA_mdd_cort.bw
singlepeaks_M_3_C.bed
grouppeaks_mdd_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: m6A sample of healthy donor H_1 treated with Cort

description:
Sample name: MUC2059_H_1_C_m6A
Processed data files:
pheno_data.xlsx
MUC2059.bw
average_m6A_healthy_cort.bw
singlepeaks_H_1_C.bed
grouppeaks_healthy_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of healthy donor H_2 treated with Mock

description:
Sample name: MUC2062_H_2_M_m6A
Processed data files:
pheno_data.xlsx
MUC2062.bw
average_m6A_healthy_mock.bw
singlepeaks_H_2_M.bed
grouppeaks_healthy_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of MDD donor M_1 treated with Cort

description:
Sample name: MUC2061_M_1_C_m6A
Processed data files:
pheno_data.xlsx
MUC2061.bw
average_m6A_mdd_cort.bw
singlepeaks_M_1_C.bed
grouppeaks_mdd_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of healthy donor H_1 treated with Mock

description:
Sample name: MUC2058_H_1_M_m6A
Processed data files:
pheno_data.xlsx
MUC2058.bw
average_m6A_healthy_mock.bw
singlepeaks_H_1_M.bed
grouppeaks_healthy_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: input sample of healthy donor H_3 treated with Cort

description:
Sample name: MUC2055_H_3_C_input
Processed data files:
pheno_data.xlsx
MUC2055.bw
average_RNA_healthy_cort.bw
singlepeaks_H_3_C.bed
grouppeaks_healthy_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of healthy donor H_2 treated with Mock

description:
Sample name: MUC2050_H_2_M_input
Processed data files:
pheno_data.xlsx
MUC2050.bw
average_RNA_healthy_mock.bw
singlepeaks_H_2_M.bed
grouppeaks_healthy_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of MDD donor M_1 treated with Mock

description:
Sample name: MUC2048_M_1_M_input
Processed data files:
pheno_data.xlsx
MUC2048.bw
average_RNA_mdd_mock.bw
singlepeaks_M_1_M.bed
grouppeaks_mdd_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of MDD donor M_2 treated with Cort

description:
Sample name: MUC2053_M_2_C_input
Processed data files:
pheno_data.xlsx
MUC2053.bw
average_RNA_mdd_cort.bw
singlepeaks_M_2_C.bed
grouppeaks_mdd_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of MDD donor M_2 treated with Mock

description:
Sample name: MUC2052_M_2_M_input
Processed data files:
pheno_data.xlsx
MUC2052.bw
average_RNA_mdd_mock.bw
singlepeaks_M_2_M.bed
grouppeaks_mdd_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of healthy donor H_1 treated with Cort

description:
Sample name: MUC2047_H_1_C_input
Processed data files:
pheno_data.xlsx
MUC2047.bw
average_RNA_healthy_cort.bw
singlepeaks_H_1_C.bed
grouppeaks_healthy_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of healthy donor H_1 treated with Mock

description:
Sample name: MUC2046_H_1_M_input
Processed data files:
pheno_data.xlsx
MUC2046.bw
average_RNA_healthy_mock.bw
singlepeaks_H_1_M.bed
grouppeaks_healthy_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: bisulphite converted DNA from paternal uniparental diplody 889

type: genomic

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

hyb_protocol: bisulphite or oxidative bisulphite converted DNA were amplified, fragmented and hybridised to Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Minfi package for the R statistical software and in-house R scripts
uthe non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: paternal uniparental diploidy 889 BS conversion

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted using standard phenol/chloroform extraction protocol

value: paternal uniparental diploidies (pUPDs)

tag: karyotype

value: paternal

tag: individual

tag: conversion

value: BS


title: Ts-1 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep1

city: Duesseldorf

first: Roxanne

last: van Rooijen

address: Universitaetsstrasse 1

country: Netherlands

institute: Heinrich Heine University

description: Ts-1 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep1

hyb_protocol: Per sample, 2.5 µg of the labelled ss-cDNA was hybridized onto an AraGene 1.1ST Array plate (Affymetrix, Santa Clara, CA, U.S.A.).

scan_protocol: Scanning was performed on a GeneTitan (Affymetrix, Santa Clara, CA, U.S.A.).

data_processing: Image analysis and extraction of raw expression data was performed with the Affymetrix Expression ConsoleTM v1.2.1. with “Gene-level Default: RMA-Sketch” settings. Raw data were analysed using the Bioconductor package and Limma package in the statistical programming language R.

organism: Arabidopsis thaliana

source_name: complete rosette

label_protocol: Labelling was performed with the EncoreTM Biotin Module (NuGEN Technologies, Inc., San Carlos, CA, U.S.A.).

growth_protocol: seeds were sown in a growth chamber, on rockwool automatically watered with nutrient solution, in a 10h/14hr day/night cycle, with the temperature set at 20/18°C (day/night), and relative humidity set at 70%. CO2 levels were ambient.

extract_protocol: Total RNA was extracted using the Direct-zol RNA mini-prep kit from Zymo Research (www.zymoresearch.com).

treatment_protocol: Under controlled conditions, plants in the light were kept at a constant, low, irradiance of 100 μmol m-2 s-1 (Philips 610 fluorescent tubes, MASTER TL5 HO, 80W). In the increased irradiance treatment, the irradiance was increased to 550 μmol m-2 s-1 at the onset of the photoperiod on the 25th day after sowing

tag: tissue

value: leaf

tag: genotype


title: Ga-0 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep3

description: Ga-0 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep3


title: Ga-0 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep1

description: Ga-0 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep1


title: Ts-1 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep3

description: Ts-1 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep3


title: Ts-1 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep3

description: Ts-1 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep3


title: Ga-0 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep2

description: Ga-0 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep2


title: oxidative bisulphite converted DNA from control leukocytes 15

source_name: leukocytes 15 oxBS conversion conversion

value: leukocytes

value: normal

value: oxBS


title: Ts-1 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep2

description: Ts-1 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep2


title: Ga-0 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep3

description: Ga-0 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep3


title: Ts-1 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep1

description: Ts-1 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep1


title: input sample of healthy donor H_3 treated with Mock

description:
Sample name: MUC2054_H_3_M_input
Processed data files:
pheno_data.xlsx
MUC2054.bw
average_RNA_healthy_mock.bw
singlepeaks_H_3_M.bed
grouppeaks_healthy_mock.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv

tag: donor

tag: cell line


title: Ga-0 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep1

description: Ga-0 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep1


title: Col-0 3.5 hours after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep3

description: Col-0 accession, 3.5 hours after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep3


title: bisulphite converted DNA from control leukocytes 2

source_name: leukocytes 2 BS conversion


title: input sample of healthy donor H_2 treated with Cort

description:
Sample name: MUC2051_H_2_C_input
Processed data files:
pheno_data.xlsx
MUC2051.bw
average_RNA_healthy_cort.bw
singlepeaks_H_2_C.bed
grouppeaks_healthy_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv


title: bisulphite converted DNA from control leukocytes 14

source_name: leukocytes 14 BS conversion


title: Ga-0 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep2

description: Ga-0 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep2


title: Col-0 3.5 hours after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep2

description: Col-0 accession, 3.5 hours after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep2


title: bisulphite converted DNA from paternal uniparental diplody 2705

source_name: paternal uniparental diploidy 2705 BS conversion


title: Col-0 3.5 hours after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep1

description: Col-0 accession, 3.5 hours after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep1


title: oxidative bisulphite converted DNA from control leukocytes 2

source_name: leukocytes 2 oxBS conversion conversion


title: input sample of MDD donor M_1 treated with Cort

description:
Sample name: MUC2049_M_1_C_input
Processed data files:
pheno_data.xlsx
MUC2049.bw
average_RNA_mdd_cort.bw
singlepeaks_M_1_C.bed
grouppeaks_mdd_cort.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_interaction_peaks.bed
finalpeaks_differential_mainCort_peaks.bed
RNA_counts.csv
RNA_quantification.csv

value: MDD diagnosed male


title: Col-0 3.5 hours after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep1

description: Col-0 accession, 3.5 hours after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep1


title: oxidative bisulphite converted DNA from control leukocytes 16

source_name: leukocytes 16 oxBS conversion conversion


title: oxidative bisulphite converted DNA from control leukocytes 13

source_name: leukocytes 13 oxBS conversion conversion


title: bisulphite converted DNA from control leukocytes 15

source_name: leukocytes 15 BS conversion


title: bisulphite converted DNA from maternal uniparental diplody 1407

source_name: maternal uniparental diploidy 1407 BS conversion

value: maternal uniparental diploidies (pUPDs)

value: maternal


title: m6A/m sample of WT 4

description:
Sample name: MUC4954_WT_4_m6A
Processed data files:
pheno_data.xlsx
MUC4954.bw
average_m6A_WT.bw
singlepeaks_WT_4.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv

data_processing:
Basecalling, conversion and demultiplexing: Illumina RTA, bcl2fastq2
Alignment: to mm10 using STAR after Cutadapt
Peak-calling: per single m6A/m-input pair using exomePeak with window_width=100, sliding_step=10, minimal_peak_length=50
Consensus-peaks: Peaks from biological replicates were merged keeping only those ranges supported by a minimum of 2/3 of samples per group (using BEDTools with minimum length 50 nt and merging ranges with less than 50 nt distance, Quinlan and Hall, 2010): see grouppeaks_WT.bed, grouppeaks_Mettl3_cKO.bed, grouppeaks_Fto_cKO.bed. For quantification with DiffBind (Ross-Innes et al., 2012) a consensus peak set was built with BEDTools including those ranges supported by either 2/3 of samples per group or 1/2 of samples of the entire experiment, furthermore filtered minimum abundancy (dba_score_rpkm_fold =2, dba_score_reads =15): finalpeaks_consensus_all_peaks.bed.
Quantitative analysis: For differential peak analysis m6A-RIP counts extracted from DiffBind (m6A_counts_in_peaks.csv) were compared with DESeq2 (Love et al., 2014) comparing Mettl3_cKO samples with WT samples or Fto_cKO samples with WT samples, respectively (m6A_analysis.csv). Gene expression was analysed using the RNA input samples only employing  DESeq2 (counts used: RNA_counts.csv; analysis: RNA_analysis.csv). Significance cutoffs:  absolute fold change > 0.5 and Benjamini-Hochberg corrected P-value Q < 0.1. Peaks were annotated using ChIPseeker (Yu et al., 2015) and Biomart (Smedley et al., 2015). Peak bed-files are provided for all consensus peaks used for quantitaive analysis (finalpeaks_consensus_all_peaks.bed), differential methylated peaks (finalpeaks_differential_Mettl3_cKO.bed, finalpeaks_differential_Mettl3_cKO.bed).
Visualization: For visualization, bam files were normalised using deepTools (Ramírez et al., 2016) creating a single bigWigfile per sample (MUC4915.bw … MUC4954.bw). Biolgical replicates were merged using UCSC bigWigMerge and UCSC bedGraphTobigWig creating one m6A and one input RNA bigWigfile per condition: average_m6A_WT.bw, average_m6A_Mettl3_cKO.bw, average_m6A_Fto_cKO.bw, average_RNA_WT.bw, average_RNA_Mettl3_cKO.bw, average_RNA_Fto_cKO.bw.
Genome_build: mm10
Supplementary_files_format_and_content: bed: peak ranges for single biological replicates (singlepeaks_*.bed), merged per group (grouppeaks_*.bed) or further processed see above (finalpeaks_*.bed); bw: normalized bigWig files per sample (MUC49*.bw) or merged per group/fraction (average_*.bw); csv: comma delimited files including raw counts used for DeSeq2 analysis and DeSeq2 (annotated) output.

source_name: cortex

extract_protocol:
Total RNA was extracted from freshly dissected and flash-frozen cortex with Trizol (Invitrogen) and isopropanol precipitation. After removal of DNA (TurboDNA-free kit, Ambion), PolyA-RNA was enriched with the Genelute mRNA Prep Kit (Sigma), precipiated and diluted to 1ug/ul and fragmented using the fragmentation reagents (Life Technologies). 7.5 ug PolyA RNA fragments per samples were precipitated with 10ug anti-m6A antibody (SySy 202003). 7.5 ug PolyA RNA fragments mixed equimolar form all samples was precipiated with 10 ug IgG (Cell Signalling Technology 2729) and Protein A/G beads (Thermo Fisher Scientific) and recovered by Proteinase K elution.
Recovered immunoprecipitated fragments per sample or 100 ng of the input PolyA-RNA-fragments per samples were processed with the TruSeq non-stranded mRNA Sample Prep Kit and sequenced on a HiSeq4000 multiplexing all samples(Average 50 Mio. raw reads).

treatment_protocol: Homecage group housed male adult animals with C57BL/6 background

value: cortex

value: WT

value: m6A/m RIP

tag: mouse line

value: Synaptic Systems anti-m6A Cat 202003 Lot 66


title: Col-0 1 hour after light onset on d 26 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep2

description: Col-0 accession, 1 hour after light onset on day 26 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep2


title: Col-0 23 hours before the irradiance increase (d 24 after sowing), bio rep1

description: Col-0 accession, 23 hours before the irradiance increase (day 24 after sowing), biological rep1


title: Col-0 23 hours before the irradiance increase (d 24 after sowing), bio rep3

description: Col-0 accession, 23 hours before the irradiance increase (day 24 after sowing), biological rep3


title: Col-0 23 hours before the irradiance increase (d 24 after sowing), bio rep2

description: Col-0 accession, 23 hours before the irradiance increase (day 24 after sowing), biological rep2


title: Col-0 1 hour after light onset on d 26 after sowing, in control light (100 μmol m-2 s-1), bio rep2

description: Col-0 accession, 1 hour after light onset on day 26 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep2


title: Col-0 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep2

description: Col-0 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep2


title: Col-0 3.5 hours after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep2

description: Col-0 accession, 3.5 hours after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep2


title: Col-0 1 hour after light onset on d 26 after sowing, in control light (100 μmol m-2 s-1), bio rep1

description: Col-0 accession, 1 hour after light onset on day 26 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep1


title: Col-0 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep3

description: Col-0 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep3


title: Col-0 1 hour after light onset on d 26 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep3

description: Col-0 accession, 1 hour after light onset on day 26 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep3


title: Col-0 1 hour after light onset on d 26 after sowing, in control light (100 μmol m-2 s-1), bio rep3

description: Col-0 accession, 1 hour after light onset on day 26 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep3


title: Col-0 1 hour after light onset on d 26 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep1

description: Col-0 accession, 1 hour after light onset on day 26 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep1


title: Col-0 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep3

description: Col-0 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep3


title: Col-0 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep1

description: Col-0 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep1


title: Ts-1 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep2

description: Ts-1 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep2


title: Col-0 3.5 hours after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep3

description: Col-0 accession, 3.5 hours after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep3


title: Col-0 1 hour after light onset on d 25 after sowing, in control light (100 μmol m-2 s-1), bio rep2

description: Col-0 accession, 1 hour after light onset on day 25 after sowing, in control light conditions (100 μmol m-2 s-1), biological rep2


title: Col-0 1 hour after light onset on d 25 after sowing, in increased irradiance (550 μmol m-2 s-1) since d 25, bio rep1

description: Col-0 accession, 1 hour after light onset on day 25 after sowing, in increased irradiance conditions (550 μmol m-2 s-1) since day 25, biological rep1


title: m6A/m sample of WT 2

description:
Sample name: MUC4952_WT_2_m6A
Processed data files:
pheno_data.xlsx
MUC4952.bw
average_m6A_WT.bw
singlepeaks_WT_2.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv


title: m6A/m sample of WT 3

description:
Sample name: MUC4948_WT_3_m6A
Processed data files:
pheno_data.xlsx
MUC4948.bw
average_m6A_WT.bw
singlepeaks_WT_3.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv


title: m6A/m sample of Mettl3 cKO 3

description:
Sample name: MUC4951_Mettl3_cKO_3_m6A
Processed data files:
pheno_data.xlsx
MUC4951.bw
average_m6A_Mettl3_cKO.bw
singlepeaks_Mettl3_cKO_3.bed
grouppeaks_Mettl3cKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv

value: Mettl3 cKO


title: m6A/m sample of Fto cKO 2

description:
Sample name: MUC4947_Fto_cKO_2_m6A
Processed data files:
pheno_data.xlsx
MUC4947.bw
average_m6A_Fto_cKO.bw
singlepeaks_Fto_cKO_2.bed
grouppeaks_FtocKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv

value: Fto cKO


title: m6A/m sample of Mettl3 cKO 2

description:
Sample name: MUC4949_Mettl3_cKO_2_m6A
Processed data files:
pheno_data.xlsx
MUC4949.bw
average_m6A_Mettl3_cKO.bw
singlepeaks_Mettl3_cKO_2.bed
grouppeaks_Mettl3cKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv


title: m6A/m sample of Fto cKO 3

description:
Sample name: MUC4953_Fto_cKO_3_m6A
Processed data files:
pheno_data.xlsx
MUC4953.bw
average_m6A_Fto_cKO.bw
singlepeaks_Fto_cKO_3.bed
grouppeaks_FtocKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv


title: oxidative bisulphite converted DNA from control leukocytes 14

source_name: leukocytes 14 oxBS conversion conversion


title: patient7-C

city: FuZhou

first: Li

last: meifeng

address: xueyuan road

institute: Fujian medical university

description: 2×150 paired-end sequence reads

data_processing:
Basecalls performed using Trimmomatic
RNA-seq reads were aligned to the reference genome (GRCh37) using hisat2
FPKM values of genes were computed to represent the expression levels of genes using StringTie
Genome_build: GRCH37
Supplementary_files_format_and_content: tab-delimited text files include gene counts and FPKM values for each Sample

source_name: epithelial cells

extract_protocol:
Total RNA was isolated from fresh frozen GC tissues using Trizol reagent (Invitrogen) according to the manufacture’s protocol.
The quality of RNA was assessed using Agilent 2200 TapeStation (Agilent technologies, US) to ensure high quality (RNA integrity number >6). Then, 1-2μg of total RNA was used for mRNA capture using NEBNext PolyA mRNA Magnetic Isolation Module and stranded RNA-seq libraries were constructed using a NEBNext Ultra Directional RNA Library Prep Kit.

value: stomach

tag: diagnosis

value: gastric cancer

tag: ptnm

value: IIIB

tag: age


title: patient7-B

description: 2×150 paired-end sequence reads


title: patient7-A

description: 2×150 paired-end sequence reads


title: m6A/m sample of Mettl3 cKO 1

description:
Sample name: MUC4943_Mettl3_cKO_1_m6A
Processed data files:
pheno_data.xlsx
MUC4943.bw
average_m6A_Mettl3_cKO.bw
singlepeaks_Mettl3_cKO_1.bed
grouppeaks_Mettl3cKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv


title: bisulphite converted DNA from control leukocytes 13

source_name: leukocytes 13 BS conversion

tag: cell type

value: BS


title: patient6-B

description: 2×150 paired-end sequence reads

value: IIA


title: patient6-C

description: 2×150 paired-end sequence reads


title: m6A/m sample of Fto cKO 1

description:
Sample name: MUC4939_Fto_cKO_1_m6A
Processed data files:
pheno_data.xlsx
MUC4939.bw
average_m6A_Fto_cKO.bw
singlepeaks_Fto_cKO_1.bed
grouppeaks_FtocKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv

tag: strain


title: patient6-A

description: 2×150 paired-end sequence reads


title: m6A/m sample of WT 1

description:
Sample name: MUC4944_WT_1_m6A
Processed data files:
pheno_data.xlsx
MUC4944.bw
average_m6A_WT.bw
singlepeaks_WT_1.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv


title: patient5-C

description: 2×150 paired-end sequence reads


title: patient5-A

description: 2×150 paired-end sequence reads


title: input sample of Fto cKO 3

description:
Sample name: MUC4933_Fto_cKO_3_input
Processed data files:
pheno_data.xlsx
MUC4933.bw
average_RNA_Fto_cKO.bw
singlepeaks_Fto_cKO_3.bed
grouppeaks_FtocKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv

value: input RNA


title: input sample of WT 4

description:
Sample name: MUC4934_WT_4_input
Processed data files:
pheno_data.xlsx
MUC4934.bw
average_RNA_WT.bw
singlepeaks_WT_4.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: input sample of WT 2

description:
Sample name: MUC4932_WT_2_input
Processed data files:
pheno_data.xlsx
MUC4932.bw
average_RNA_WT.bw
singlepeaks_WT_2.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: input sample of Mettl3 cKO 2

description:
Sample name: MUC4929_Mettl3_cKO_2_input
Processed data files:
pheno_data.xlsx
MUC4929.bw
average_RNA_Mettl3_cKO.bw
singlepeaks_Mettl3_cKO_2.bed
grouppeaks_Mettl3cKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: bisulphite converted DNA from control leukocytes 16

source_name: leukocytes 16 BS conversion

value: leukocytes

value: normal


title: input sample of Mettl3 cKO 3

description:
Sample name: MUC4931_Mettl3_cKO_3_input
Processed data files:
pheno_data.xlsx
MUC4931.bw
average_RNA_Mettl3_cKO.bw
singlepeaks_Mettl3_cKO_3.bed
grouppeaks_Mettl3cKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: patient4-C

description: 2×150 paired-end sequence reads

value: IIIA


title: input sample of WT 3

description:
Sample name: MUC4928_WT_3_input
Processed data files:
pheno_data.xlsx
MUC4928.bw
average_RNA_WT.bw
singlepeaks_WT_3.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: input sample of Fto cKO 2

description:
Sample name: MUC4927_Fto_cKO_2_input
Processed data files:
pheno_data.xlsx
MUC4927.bw
average_RNA_Fto_cKO.bw
singlepeaks_Fto_cKO_2.bed
grouppeaks_FtocKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: m6A/m sample of WT 5

description:
Sample name: MUC4940_WT_5_m6A
Processed data files:
pheno_data.xlsx
MUC4940.bw
average_m6A_WT.bw
singlepeaks_WT_5.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
m6A_counts_in_peaks.csv
m6A_analysis.csv


title: input sample of WT 1

description:
Sample name: MUC4924_WT_1_input
Processed data files:
pheno_data.xlsx
MUC4924.bw
average_RNA_WT.bw
singlepeaks_WT_1.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: patient4-A

description: 2×150 paired-end sequence reads


title: patient3-C

description: 2×150 paired-end sequence reads


title: input sample of Mettl3 cKO 1

description:
Sample name: MUC4923_Mettl3_cKO_1_input
Processed data files:
pheno_data.xlsx
MUC4923.bw
average_RNA_Mettl3_cKO.bw
singlepeaks_Mettl3_cKO_1.bed
grouppeaks_Mettl3cKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: patient3-B

description: 2×150 paired-end sequence reads


title: patient5-B

description: 2×150 paired-end sequence reads


title: input sample of WT 5

description:
Sample name: MUC4920_WT_5_input
Processed data files:
pheno_data.xlsx
MUC4920.bw
average_RNA_WT.bw
singlepeaks_WT_5.bed
grouppeaks_WT.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: patient3-A

description: 2×150 paired-end sequence reads


title: patient2-C

description: 2×150 paired-end sequence reads

value: IIIC


title: patient2-B

description: 2×150 paired-end sequence reads


title: input sample of Fto cKO 1

description:
Sample name: MUC4919_Fto_cKO_1_input
Processed data files:
pheno_data.xlsx
MUC4919.bw
average_RNA_Fto_cKO.bw
singlepeaks_Fto_cKO_1.bed
grouppeaks_FtocKO.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential_Mettl3_cKO.bed
finalpeaks_differential_Fto_cKO.bed
RNA_counts.csv
RNA_analysis.csv


title: IgG control

description:
Sample name: MUC4915_IgG
Processed data files:
pheno_data.xlsx
MUC4915.bw

value: mix

value: IgG

value: Cell Signalling Technology Normal Rabbit IgG Cat 2729 Lot 7


title: Fto cKO Rep5 after fear conditioning

description:
Sample name: MUC4067_Fto-Nex-CreERT2_751_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

data_processing:
Basecalling, convesion and demultiplexing: Illumina RTA, bcl2fastq2
Alignment: to mm10 using STAR after Cutadapt
Quantitative analysis: Gene expression was analysed employing  DESeq2 (counts used: raw_counts.csv; analysis: analysis.csv). Genes were considered differential with an absolute fold change > 0.5 and a Benjamini-Hochberg corrected P-value = Q < 0.1. Models run and contrasts extracted: 1) To asses basal genotype effects in unstressed animals: ~ mouse line * genotype on Box animals only: interaction effect="knockoutgene_dependent_genotypeeffect" followed up with postHoc effects extracted from 4 groups model on Box animals only: "Mettl3_genotypeeffect_in_basal" and "Fto_genotypeeffect_in_basal" ("Mettl3_genotype_effect_in_fearconditioned" and "Fto_genotype_effect_in_fearconditioned" are provided for completeness only). 2) To asses genotype-dependent transcriptome-regulation upon fear conditioning, ~ genotype * treatment models were run within each mouse line: interaction effects "Mettl3_genotype_dependent_feareffect" and "Fto_genotype_dependent_feareffect" followed up with postHoc effects extracted from 4 groups models: "Mettl3_feareffect_in_WT", "Mettl3_feareffect_in_cKO", "Fto_feareffect_in_WT", "Fto_feareffect_in_cKO".
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.csv, analysis.csv, pheno_data.csv

source_name: hippocampus CA1+CA3

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and isopropanol precipitation.
After removal of DNA (Turbo DNA-free kit, Ambion), mRNA-Seq libraries were prepared from 4 µg total RNA using the llumina TruSeq stranded mRNA protocol HT (Illumina). Libraries were sequenced on a HiSeq4000 multiplexing all samples (ave 46 Mio. raw reads).

treatment_protocol: Single housed male adult animals with C57BL/6 background. Brains were collected from 5 of each of the following: Mettl3 cKO and WT as well as Fto cKO and WT mice 24 h after fear conditioning (20 s of a 80 dB tone co-terminated with an 2s 0.7 mA electric foot shock) (FC) or comparable handling and exposure to the context box without fear induction or tone equaling baseline conditons (Box). CA1 and CA3 were cryopunched from flash-frozen brains.

value: cKO

value: FC

value: hippocampus CA1+CA3


title: patient2-A

description: 2×150 paired-end sequence reads


title: patient1-C

description: 2×150 paired-end sequence reads


title: Fto WT Rep4 baseline

description:
Sample name: MUC4068_Fto-Nex-CreERT2_769_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

value: WT

value: Box


title: patient4-B

description: 2×150 paired-end sequence reads

value: stomach

value: gastric cancer


title: patient1-A

description: 2×150 paired-end sequence reads


title: Fto WT Rep4 after fear conditioning

description:
Sample name: MUC4064_Fto-Nex-CreERT2_717_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Fto WT Rep5 after fear conditioning

description:
Sample name: MUC4065_Fto-Nex-CreERT2_733_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Fto cKO Rep5 baseline

description:
Sample name: MUC4066_Fto-Nex-CreERT2_749_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Fto WT Rep3 after fear conditioning

description:
Sample name: MUC4063_Fto-Nex-CreERT2_763_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: patient1-B

description: 2×150 paired-end sequence reads


title: DM_MOI100_Pol2_12hpi

city: Los Angeles

first: Arnold

middle: J

last: Berk

state: CA

address: 611 Charles E. Young Dr.

institute: UCLA

data_processing:
Reads were mapped to the HAd5 genome reference using Bowtie2 software.
Bedgraph files were generated using a custom algorithm and present the data as normalized tag density.
Genome_build: Custom build HAd5

growth_protocol: Human Bronchial/Tracheal Epithelial Cells (HBTEC, Lifeline Cell Technology Cat# FC-0035; lot# 02196) were grown at 37°C in BronchiaLife Medium Complete Kit (Lifeline Cell Technology catalog number: LL-0023) in a 5% CO2 incubator

extract_protocol:
1x10^7 low-passage HBTEC were infected with indicated Ad vector 3 days after reaching confluence. 24h p.i. cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and 2ug of anti-Pol2, -H3K27ac or 5uL of H3K18ac anti-rabbit sera. 50uL of protein A dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer.
ChIP sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the KAPA Hyper Prep Kit from KAPA Biosystems and NEXTflex ChIP-Seq barcodes purchased from Bioo Scientific.

treatment_protocol: HBTEC were grown until they reached confluence. Cells were then incubated 3 days more without addition of fresh media and were infected with the indicated Ad5-based vectors for 24h in the conditioned medium.

tag: Sex

value: Male

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

tag: infected with

value: an Ad5 mutant expressing E1A with multi-alanine substitutions in regions involved in p300 binding at an MOI of 100

tag: passage

tag: chip antibody

value: Mouse monoclonal anti-TBP Diagenode Cat#C15200002

tag: molecule subtype

value: genomic DNA and viral DNA


title: DM_MOI100_Pol2_18hpi


title: Fto cKO Rep4 after fear conditioning

description:
Sample name: MUC4061_Fto-Nex-CreERT2_747_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

tag: treatment


title: Fto WT Rep3 baseline

description:
Sample name: MUC4062_Fto-Nex-CreERT2_757_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: DM_MOI100_TBP_18hpi

value: Mouse monoclonal anti-Pol2 (8WG16) Santa Cruz sc-56767


title: DM_MOI100_TBP_12hpi


title: Fto cKO Rep4 baseline

description:
Sample name: MUC4060_Fto-Nex-CreERT2_741_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: DM_MOI100_H3K27ac_12hpi

value: Rabbit polyclonal anti-H3K27ac Active Motif Cat#39133  Lot#31814008


title: DM_MOI100_H3K27ac_18hpi


title: Fto cKO Rep3 baseline

description:
Sample name: MUC4059_Fto-Nex-CreERT2_729_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Fto cKO Rep2 baseline

description:
Sample name: MUC4058_Fto-Nex-CreERT2_773_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Fto WT Rep5 baseline

description:
Sample name: MUC4069_Fto-Nex-CreERT2_727_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: DM_MOI100_H3K18ac_18hpi

value: Rabbit polyclonal anti-H3K18ac (814) Grunstein/Kurdistani laboratories (Suka et al., 2001)


title: Fto WT Rep2 baseline

description:
Sample name: MUC4056_Fto-Nex-CreERT2_745_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: DM_MOI100_H3K9ac_18hpi

value: Rabbit polyclonal anti-H3K9ac Millipore 07-352 Lot#2631535


title: wt_MOI5_dl312_Pol2_18hpi

value: a mixture of the wt E1A-expressing vector at an MOI of 5 with an Ad5 mutant containing an E1A deletion (dl312) at an MOI of 95


title: DM_MOI100_H3K18ac_12hpi


title: wt_MOI5_dl312_TBP_12hpi


title: wt_MOI5_dl312_TBP_18hpi


title: wt_MOI5_dl312_Pol2_12hpi


title: wt_MOI5_dl312_H3K27ac_18hpi


title: Fto cKO Rep2 after fear conditioning

description:
Sample name: MUC4054_Fto-Nex-CreERT2_725_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

value: cKO


title: Fto cKO Rep1 after fear conditioning

description:
Sample name: MUC4053_Fto-Nex-CreERT2_771_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

value: FC


title: Fto cKO Rep1 baseline

description:
Sample name: MUC4052_Fto-Nex-CreERT2_755_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

value: hippocampus CA1+CA3


title: wt_MOI5_dl312_H3K27ac_12hpi


title: Fto WT Rep1 after fear conditioning

description:
Sample name: MUC4051_Fto-Nex-CreERT2_743_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

value: WT


title: Mettl3 WT Rep5 baseline

description:
Sample name: MUC4049_Mettl3-Nex-CreERT2_499_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

value: Box


title: Fto WT Rep1 baseline

description:
Sample name: MUC4050_Fto-Nex-CreERT2_737_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Mettl3 cKO Rep5 after fear conditioning

description:
Sample name: MUC4048_Mettl3-Nex-CreERT2_505_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI5_dl312_H3K18ac_18hpi


title: wt_MOI5_dl312_H3K18ac_12hpi


title: Mettl3 cKO Rep5 baseline

description:
Sample name: MUC4047_Mettl3-Nex-CreERT2_471_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI5_dl312_H3K9ac_18hpi


title: Mettl3 WT Rep5 after fear conditioning

description:
Sample name: MUC4046_Mettl3-Nex-CreERT2_445_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Mettl3 WT Rep4 baseline

description:
Sample name: MUC4045_Mettl3-Nex-CreERT2_415_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Fto WT Rep2 after fear conditioning

description:
Sample name: MUC4057_Fto-Nex-CreERT2_753_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI20_TBP_18hpi

value: an Ad5-based vector expressing wild-type E1A (wt) at an MOI of 20


title: Mettl3 WT Rep4 after fear conditioning

description:
Sample name: MUC4044_Mettl3-Nex-CreERT2_489_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI20_TBP_12hpi


title: DM_MOI100_H3K9ac_12hpi


title: Mettl3 WT Rep3 baseline

description:
Sample name: MUC4043_Mettl3-Nex-CreERT2_467_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Fto cKO Rep3 after fear conditioning

description:
Sample name: MUC4055_Fto-Nex-CreERT2_731_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI20_Pol2_12hpi


title: Mettl3 WT Rep3 after fear conditioning

description:
Sample name: MUC4040_Mettl3-Nex-CreERT2_421_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI20_Pol2_18hpi


title: Mettl3 cKO Rep4 baseline

description:
Sample name: MUC4041_Mettl3-Nex-CreERT2_427_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI20_H3K27ac_18hpi


title: Mettl3 cKO Rep3 baseline

description:
Sample name: MUC4039_Mettl3-Nex-CreERT2_513_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI20_H3K18ac_18hpi


title: Mettl3 WT Rep2 after fear conditioning

description:
Sample name: MUC4038_Mettl3-Nex-CreERT2_483_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: wt_MOI20_H3K27ac_12hpi


title: wt_MOI5_dl312_H3K9ac_12hpi


title: wt_MOI20_H3K9ac_18hpi


title: wt_MOI20_H3K18ac_12hpi


title: Mettl3 WT Rep2 baseline

description:
Sample name: MUC4037_Mettl3-Nex-CreERT2_451_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: uninfected THP-1_H3K4me3_ChIPSeq

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

institute: Bose Institute

data_processing:
Base calling was performed using CASAVA v1.7 software
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie with default parameters
Data was filtered with a p-value cut off of 0.01 and a high confidence fold enrichment using PeakAnalyzer v1.4
peaks were called using MACS2 with the following setting: ChIP threshold (>3), Enrichment Fold (>1).
Genome_build: hg19
Supplementary_files_format_and_content: Contains peaks obtained from MACS2 along with their -log10(pValue) and Fold Enrichment with respect to the uninfected sample

source_name: uninfected THP-1 cells

growth_protocol: Cells were maintained in complete RPMI (Gibco) medium with 10% Fetal Bovine Serum (Gibco).Passages were given after 48 h of culturing. PMA (Sigma) at a final concentration of 30ng/ml was used for 24hr to differentiate the THP-1 cells prior to Mtb infection. PMA was then washed out and cells were rested for 24h prior to infection.

extract_protocol:
Cells were dislodged  using Accutase (Himedia). Chromatin Immunoprecipitation (ChIP) was done using the Diagenode Ideal Chip seq kit and H3K4me3 specific antibody.
library preparation was performed according to the manufacturer’s protocol for the Illumina Hiseq 2000  platform

treatment_protocol: Cells were infected with Mycobacterium tuberculosis at an MOI of 10 for the indicated time periods.

value: THP-1 differentiated macrophage

value: none (uninfected control)

tag: passages

value: Passage 9

value: H3K4me3 (Abcam ChIP grade,ab8580)


title: Mettl3 cKO Rep2 baseline

description:
Sample name: MUC4035_Mettl3-Nex-CreERT2_405_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

tag: tissue


title: Mettl3 cKO Rep2 after fear conditioning

description:
Sample name: MUC4034_Mettl3-Nex-CreERT2_523_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

tag: genotype


title: wt_MOI20_H3K9ac_12hpi

value: Male

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)


title: MtbH37Rv infected (4hrs) THP-1_H3K4me3_ChIPSeq

source_name: MtbH37Rv infected (4hrs) THP-1 cells

value: Mtb H37Rv virulent strain


title: MtbH37Ra infected (4hrs) THP-1_H3K4me3_ChIPSeq

source_name: MtbH37Ra infected (4hrs) THP-1 cells

value: Mtb H37Ra avirulent strain

value: H3K4me3  (Abcam ChIP grade,ab8580)


title: Mettl3 WT Rep1 after fear conditioning

description:
Sample name: MUC4032_Mettl3-Nex-CreERT2_457_WT_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Mettl3 cKO Rep1 baseline

description:
Sample name: MUC4033_Mettl3-Nex-CreERT2_493_cKO_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: Mettl3 WT Rep1 baseline

description:
Sample name: MUC4031_Mettl3-Nex-CreERT2_433_WT_Box
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: input rep2

city: Boston

first: Thomas

last: Westerling

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer institute

data_processing:
base calling done by illumina 1.5 basecalling pipeline
BWA (bwa aln -q 5 -l 32 -k 2 -t 4| bwa samse |)
sam to bam format using samtools
peak calling using MACS2 (callpeak --SPMR -B -q 0.01 --keep-dup 1 --extsize=146 --nomodel -g hs)
Genome_build: hg19
Supplementary_files_format_and_content: .bw is the standard bigwig output of MACS2; .bed is the standard narrow peak calling peak file output of MACS2

growth_protocol: cells maintained in phenol red containing DMEM with 10% FBS, for experiments, cells are (hormone)starved for 3 day in phenol red free DMEM with 10% charcoal dextran treated DMEM. One day prior to treatment, fresh media (20ml) was changed on the plates

extract_protocol:
ChIP extraction done 1% SDS lysis buffer followed by Immunoprecipitation in a low detergent buffer (dilution 1/10 of original lysis buffer) using lab protocol on a sciclone ngs liquid handler with lab developed protocols with Santa Cruz HC-20 and the monoclonal ER Ab10 antibodies
libraries generated using standard protocol, end repair, AT overhang, oligo ligation, pippin prep size selection, PCR amplification, pippin prep size selection, Ethanol salt precipitation

treatment_protocol: 20ul of 10^-5M E2 was added to plate containing 20ml of growth media, after 45min media is aspirated and 10ml of 10% Formaldehyde fix is performed according to standard protocols.


title: Input rep1


title: ER ChIP rep2

source_name: Mcf7_ER ChIP

value: Santa Cruz HC-20 and the monoclonal ER Ab10 antibodies


title: Ribosome bound fragments of Stress 6

description:
Sample name: MUC2356_RPF_S6
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv

data_processing:
Library strategy: Ribo-Seq
Basecalling, convesion and demultiplexing: Illumina RTA, bcl2fastq2
Alignment: Reads were adapter- and quality-trimming with cutadapt (Martin et al., 2011) keeping only those reads with RA5 adapter present, insert length between 15 and 50 nt and a minimum Phred quality score of 15. After removing rRNA and tRNA sequences remaining sequences were aligned using Tophat/Bowtie1 (Langmead et al., 2009: Trapnell et al., 2009; at default settings to Gencode mm10/VM15).
Quantitative analysis: Translation efficiencies were calculated by dividing ribosome-bound CPM by input CPM after counting reads with HTSeq (Anders et al., 2015, only genes considered with minimum 25 counts per sample). Translation efficiencies were compared using T-tests with significantly regulated genes being defined with an absolute fold change  > 0.5 and a Benjamini-Hochberg corrected P-value=Q < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: cpm_normcounts.csv, quantification.csv

source_name: C57BL/6 cortex

extract_protocol:
Ribosome profiling libraries were prepared using the TruSeq Ribo Profile (Mammalian) Kit (Illumina, San Diego, CA) with the following adjustments: Flash-frozen cortex samples were homogenized in lysis buffer including cycloheximide Keeping 1/5 of the supernatent aside for input libraris, 4/5 of the supernatent were digested with nuclease for ribosome profiling and purified on a sucrose gradient.
Trizol LS purified ribosome protected fragments were processed as described in the TruSeq Ribo Profile Kit with rRNA depletion by RiboZero Gold (mammalian) and remaining fragments size-selected, purified and processed as described. cDNA was purified using a 2.5x AMPure clean-up. PCR was performed on undiluted circularized cDNA with 12 PCR cycles and PCR products on DNA-TBE PAGE. Sequencing was performed on each one lane for ribosome bound fractions and input fractions (indexed each 1-12) of an Illumina HiSeq4000 PE 2x100 (Illumina, San Diego, CA) using only the reverse read (R2).

treatment_protocol: Animals were treated with 15 min acute restraint stress and returned to their homecage (stress) or left in their homecage (basal) and sacrificed 4 h after.

value: acute stress

value: cortex

tag: fraction

value: ribosome bound fraction


title: Mettl3 cKO Rep4 after fear conditioning

description:
Sample name: MUC4042_Mettl3-Nex-CreERT2_477_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

value: cKO

value: FC

value: hippocampus CA1+CA3


title: Mettl3 cKO Rep1 after fear conditioning

description:
Sample name: MUC4030_Mettl3-Nex-CreERT2_411_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv


title: ER ChIP rep1

tag: cell line


title: Ribosome bound fragments of Stress 5

description:
Sample name: MUC2355_RPF_S5
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Ribosome bound fragments of Stress 3

description:
Sample name: MUC2353_RPF_S3
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Mettl3 cKO Rep3 after fear conditioning

description:
Sample name: MUC4036_Mettl3-Nex-CreERT2_441_cKO_FC
Processed data files:
pheno_data.csv
raw_counts.csv
analysis.csv

tag: mouse line


title: Ribosome bound fragments of Stress 4

description:
Sample name: MUC2354_RPF_S4
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Ribosome bound fragments of Stress 2

description:
Sample name: MUC2352_RPF_S2
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: UCLA4 Naïve Cobimetinib 0.5mM

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
UCLA4 Naïve Cobimetinib 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz

data_processing:
RNA sequencing library reads were mapped to the hg19 reference genome using TopHat v2.1.0 (Trapnell et al., 2009) with parameters set to '--b2-sensitive --no-novel-juncs --library-type fr-firststrand'.
The annotation of aligned reads with genomic features was prefomed using HTSeq v0.9.1 (Anders et al., 2014) with parameters set to '--type=exon --mode=union --minaqual=0 --stranded=reverse'.
For repetitive sequences, Repbase database annotations for ERV1, ERVK and ERVL superfamilies were used to intersect the alignment and generate TEs counts using the multiBamCov tool from Bedtools v.2.27 (Quinlan et al., 2010). Counts are reported in raw measurements.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Raw read counts for gene and repetitive element annotations for each samples

source_name: human embryonic stem cells

growth_protocol: Conventional human primed ESCs (WIBR3 cell line, DPE-OCT4GFP, UCLA1, UCLA3, UCLA4, UCLA5, UCLA9 and UCLA17 cell lines) were maintained on Matrigel (Corning) coated dishes in E8-medium (Stem Cell Technologies) and passaged using Versene solution (Life Technologies). For maintenance, cells were passaged every 4-5 days. Established naïve hESC lines were cultured on irradiated CF-1 MEFs (2.5x106 cells per 9.5 cm2) in 4i/LA medium with the indicated concentration of PD0325901 and passaged every 6-7 days. Cells were feeded daily with fresh medium. 5i/LAF medium contained a 50:50 mixture of DMEM/F-12 (Life Technologies) and Neurobasal medium (Life Technologies) containing 1x N2 supplement (Life Technologies), 1x B27 supplement (Life Technologies), 10 ng/mL bFGF (Peprotech), 1% nonessential amino acids (Life Technologies), 1mM GlutaMAX (Life Technologies), penicillin-streptomycin (Life Technologies), 0.1 mM beta-mercaptoethanol (Life Technologies), 50 μg/mL BSA (Life Technologies), 0.5 μM IM-12 (Axon Medchem), 0.5 μM SB590885 (Axon Medchem), 1 μM WH-4-023 (Axon Medchem), 10 μM Y-27632 (Axon Medchem), 20 ng/mL Activin A (Peprotech), 20 ng/mL rhLIF (Peprotech), 0.5% KSR (Life Technologies) and 0.5 or 1 μM PD0325901 (Axon Medchem)

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen). RNA was eluted from the columns using RNase-free water and quantified using a Nanodrop ND-1000.
RNA sequencing libraries were prepared using Ribo-Zero rRNA Removal Kit (H/M/R) (Illumina Cat#: MRZH11124) and NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#: E7420).  The total RNA input amount for the RiboZero kit was 1 m total.  The rRNA input for library construction was 50 ng total.  Libraries were amplified for 14 cycles.  Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit.  Libraries were quantified using the Kapa Biosystems Library Quantification kit (Catalog Number KK4828) and the BioRad CFX96 instrument.

treatment_protocol: Cells were harvested following acutase treatment and processed for total RNA extraction

value: naive hESCs


title: UCLA9 Naïve PD03 1mM

description:
UCLA9 Naïve PD03 1mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: UCLA4 Naïve Refametinib 0.5mM

description:
UCLA4 Naïve Refametinib 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: UCLA5 Naïve PD03 0.5mM

description:
UCLA5 Naïve PD03 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: UCLA9 Naïve PD03 0.5mM

description:
UCLA9 Naïve PD03 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: UCLA4 Naïve t2iLGoY

description:
UCLA4 Naïve t2iLGoY
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: UCLA4 Naïve TAK-733 0.5mM

description:
UCLA4 Naïve TAK-733 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Ribosome bound fragments of Control 6

description:
Sample name: MUC2350_RPF_C6
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv

value: basal


title: Ribosome bound fragments of Control 4

description:
Sample name: MUC2348_RPF_C4
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Ribosome bound fragments of Control 3

description:
Sample name: MUC2347_RPF_C3
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Ribosome bound fragments of Stress 1

description:
Sample name: MUC2351_RPF_S1
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: UCLA5 Naïve PD03 1mM

description:
UCLA5 Naïve PD03 1mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Ribosome bound fragments of Control 1

description:
Sample name: MUC2345_RPF_C1
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: UCLA4 Naïve PD03 1mM

description:
UCLA4 Naïve PD03 1mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: UCLA4 Naïve PD03 0.5mM

description:
UCLA4 Naïve PD03 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Total RNA of Stress 6

description:
Sample name: MUC2344_total_S6
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv

value: input RNA


title: Total RNA of Stress 5

description:
Sample name: MUC2343_total_S5
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Total RNA of Stress 4

description:
Sample name: MUC2342_total_S4
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: UCLA1 Naïve PD03 1mM

description:
UCLA1 Naïve PD03 1mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: WIBR3 Naïve PD03 0.5mM

description:
WIBR3 Naïve PD03 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: WIBR3 Naïve PD03 1mM

description:
WIBR3 Naïve PD03 1mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Total RNA of Stress 3

description:
Sample name: MUC2341_total_S3
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Total RNA of Stress 2

description:
Sample name: MUC2340_total_S2
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: UCLA5 Primed

description:
UCLA5 Primed
HTSeq-counts.txt.gz
TE-counts.txt.gz

value: primed hESCs


title: UCLA9 Primed

description:
UCLA9 Primed
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Total RNA of Stress 1

description:
Sample name: MUC2339_total_S1
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Ribosome bound fragments of Control 5

description:
Sample name: MUC2349_RPF_C5
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: UCLA4 Primed

description:
UCLA4 Primed
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Ribosome bound fragments of Control 2

description:
Sample name: MUC2346_RPF_C2
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Total RNA of Control 5

description:
Sample name: MUC2337_total_C5
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Total RNA of Control 4

description:
Sample name: MUC2336_total_C4
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: Total RNA of Control 6

description:
Sample name: MUC2338_total_C6
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: UCLA1 Naïve PD03 0.5mM

description:
UCLA1 Naïve PD03 0.5mM
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Total RNA of Control 1

description:
Sample name: MUC2333_total_C1
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv


title: WIBR3 Primed

description:
WIBR3 Primed
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: UCLA1 Primed

description:
UCLA1 Primed
HTSeq-counts.txt.gz
TE-counts.txt.gz


title: Total RNA of Control 2

description:
Sample name: MUC2334_total_C2
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv