title: U5

city: guangzhou

first: liu

state: State...

address: guangdong

institute: sysu

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 10

data_processing:
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.  D1/D2/D3/D4/D5 columns represents the miRNA pattern of DBTRG treated with dbcAMP at 0/6/12/24/48h（FPKM）.U1/U2/U3/U4/U5 columns represents the miRNA pattern of U87 treated with dbcAMP at 0/6/12/24/48h（FPKM).

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
RNA-seq for Sample 1-10:Total RNA was isolated from cultured cell lines. We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample 1-5 were the RNA-seq data of DBTRG-05MG treated with dbcAMP at 0/6/12/24/48 hours. Sample 6-10 were the RNA-seq data of U87 treated with dbcAMP at 0/6/12/24/48 hours.

tag: cell line

value: 1mM dbcAMP_48h

tag: time point


title: Cow 72 PA embryo #1 ED

status: Public on Mar 03 2020

type: SRA

city: Wilrijk

first: Karolien

middle: LJ

last: Desmet

state: Antwerpen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

library_source: transcriptomic

data_processing:
RNAseq read pairs were mapped against the Bos Taurus UMD3.1 genome using CLC Genomics Workbench (version 9, Qiagen). Read pairs uniquely mapping to genes were used to obtain a gene count table for further processing.
Differential analysis was then performed using the DESeq2 R package version 1.10.1 .
Four samples were excluded from further analysis as they were identified as strong outliers in a preliminary principle component analysis on the normalized DESeq2 data. These four samples had a poor sequencing quality measures according to the quality control results from the sequencing run, each with more than 50% uncalled bases and less than 1 million mapped reads. Embryos where the ED could not be dissected from EXT were not included in the RNAseq analysis as well. This was limited to the spherical embryos.
Differential expression within the remaining samples was established in a DESeq2 model based on a Negative Binomial distribution. The samples were divided by origin, namely ED and EXT for further analysis. Gene dispersion estimates were based on all samples of each origin, regardless of treatment or morphology. Genes with less than one average read per sample were excluded from the analysis.
An FDR of 10% was used as a cut-off for differential expression and reported P-values were Benjamini-Hochberg corrected.
Genome_build: Bos Taurus UMD3.1 genome
Supplementary_files_format_and_content: abundance measurements

molecule: total RNA

organism: Bos taurus

source_name: bovine day 14 embryo

growth_protocol: A total of 2141 embryos were produced among the three treatment groups (7 replicates). Grade I cumulus-oocyte complexes (COCs) were matured in groups of 50-60 in 500 μl serum-free maturation medium (containing TCM199 supplemented with 0.75% w/v FA-free BSA, 0.4 mM glutamine, 0.2 mM sodium pyruvate, 0.1 mM cysteamine, 50 mg/ml gentamycin and 20 ng/ml murine epidermal growth factor) in 4-well plates for 24 h in humidified air with 5% CO2 at 38.5°C. Oocytes were randomly divided in equal groups between treatment-specific maturation media. After IVM, COCs were co-incubated in groups of 100-120 with spermatozoa at a final concentration of 106/ml for 22 h at 38.5°C in 500 μl fertilization medium (containing 114 mM NaCl, 3.1 mM KCl, 0.3 mM Na2HPO4, 2.1 mM CaCl2-2H2O, 0.4 mM MgCl2-6H2O, 25 mM bicarbonate, 1 mM sodium pyruvate, 36 mM sodium lactate, 2 μl/ml phenol red, 6 mg/ml FA-free BSA, 50 μg/ml gentamycin and 0.72U/ml heparin) in 4-well plates in a humidified 5% CO2 incubator at 38.5°C. Presumptive zygotes were cultured in groups of 25 ± 4 in 75 μl droplets of modified synthetic oviductal fluid (mSOF) medium supplemented with 5% fetal bovine serum in 96-well plates in a modular incubator (5% CO2, 5% O2 and 90% N2 at 38.5 °C) until the day of transfer. Cows were randomly assigned to receive embryos from the BASAL and HIGH PA treatment group following a crossover design. Cows were synchronized in groups of four. Two cows received embryos from the BASAL group and two cows received HIGH PA embryos. One of the cows was used once for CONTROL embryos. Embryo transfer (ET) was performed into the uterine horn ipsilateral to the CL on day 7.7. Equal proportions of normal and expanded blastocysts (n = 8 blastocysts per recipient cow), per treatment and per replicate, were transferred to the synchronized cows. At day 14 p.i., conceptuses were transcervically flushed and recovered, morphologically assessed and dissected into ED and EX. A total of 53 samples (EX and ED) were used for RNA/DNA extraction, representative for the pool of recovered day 14 embryos, the embryo morphology, the recipient cows (embryos from one of the eight cows were excluded for RNA sequencing) and replicates.

extract_protocol:
Total RNA was isolated from individual ED and EXT samples using the Allprep DNA/RNA micro and mini kit (Qiagen), respectively, according to the manufacturer’s protocol.
Sequencing libraries were prepared using the TruSeq® Stranded mRNA HT Sample Preparation kit (Illumina, California, US), following the manufacturer's Low Sample protocol.
12 samples per lane, 2x 50BP paired end

treatment_protocol: oocytes were exposed during IVM to the following conditions: i) CONTROL: FA-free and solvent-free medium, ii) BASAL: physiological NEFA concentrations (72 μM total NEFA containing 28 μM SA, 23 μM PA, and 21 μM OA) in 0.45 % absolute ethanol, iii) HIGH PA: a combination of physiological concentrations of SA (28 µM) and OA (21 µM) and an elevated concentration of PA equivalent to that measured in follicular fluid during lipolytic conditions (150 μM) in 0.45 % absolute ethanol.

tag: individual

tag: tissue

value: embryonic disc

tag: treatment

value: HIGH PA

tag: developmental stage

value: day 14 embryo

tag: morphology

value: ovoid

tag: Sex

value: female


title: Cow 12 BASAL embryo #1 ED

value: BASAL


title: 4 Control mouse

type: RNA

city: morgantown

first: Anna

middle: A

last: Shvedova

state: WV

address: 1095 willowdale Rd

department: HELD

country: USA

institute: CDC/NIOSH

hyb_protocol: Array hybridization was done using the NimbleGen 12x135K microarray followed by washing with the NimbleGen wash buffer kit

scan_protocol: Array scanning was done using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing:
Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.
The Gene level (*_RMA.calls) files generated after normalization were imported into Agilent GeneSpring GX software (version 12.1) for further analysis.
All Targets Value (Entities where at least 5 out of 10 samples having values greater than or equal to Lower cut-off: 50.0) were only considered from the whole array. Differentially expressed genes with statistical significance between two groups were identified through Volcano Plot filtering

organism: Mus musculus

source_name: control_Left Lung

label_protocol: Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit;

extract_protocol: Total RNA was isolated from whole lung tissues of control and MWCNT exposed mice 56 days post exposure (n=5 for MWCNT group, n=4 for controls). The RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy MiniKits (Qiagen, Mississauga, ON, Canada) as described by the manufacturer.

tag: strain

value: vehicle control

value: 56 days post exposure

value: left lung


title: stage4_AB rep1

city: cologne

first: Udhaya

last: Ponraj

state: NRW

department: Department of chromosome biology

country: Germany

institute: Max Planck Institute for Plant Breeding research

description: 1X150 bp single end

data_processing:
NGS analysis package: CLC genomics server 9.1.1 was used for processing and mapping reads. Data was further analysed using CLC genomics workbench 12.0
data-filtering: FASTQC was used to assess quality of reads. CLC genomics server was used to trim low quality sequences and ambiguous nucleotides using following parameters- Ambiguous trim = Yes, Ambiguous limit = 2, Quality trim = Yes, Quality limit = 0.05
read mapping: Reads were mapped to the latest annotation of the Arabis alpina genome V5 with the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Maximum number of hits for a read = 10.
adundance measurement: reads counts were normalised for differences in gene and library size using RPKM
differential expression analysis: Fold change between the two developmental stages of buds was calculated in CLC genomics workbench. The resulting candidate list was filtered for genes with statistically significant difference in expression of atleast two-fold at FDR adjusted p-value <0.05
Genome_build: Arabis alpina genome http://arabis-alpina.org/refseq.html/Arabis_alpina.MPIPZ.V5.chr.all.fasta.gz
Supplementary_files_format_and_content: excel file including geneIds, total mapped reads, normalised counts RPKM, TPM, CPM, average counts, DE test results including Fold Chnage, logFold change, FDR

organism: Arabis alpina

source_name: Axillary bud

growth_protocol: All the experiments were performed using A. alpina Pajares accession (Wang et al., 2009). A. alpina seeds were stratified on wet filter paper for 4 days at 4°C in dark and then transferred to soil in a Bronson growth chamber (LD) with day-time temperature of 24°C and a night-time temperature of 18°C. Cold treatments were performed at 4°C in LD condition (16h light, 8h darkness) for seven weeks. Young buds with single leaf primordium and their corresponding shoot apical meristem including one leaf primordium were harvested. For each sample three biological replicates were prepared except for stage1_AB (two replicates). 120-150 buds and SAMs were harvested per replicate.

extract_protocol:
Total RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma Aldrich), following protocol A and on-column DNase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Pajares

value: Axillary bud

value: after seven weeks of cold treatment


title: TSS_TAP_untreated1

city: Daejeon

first: Yongjae

last: Lee

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description:
Sample 3
TSS.txt

data_processing:
Library strategy: dRNA-seq
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome. Also, the random 3’-overhanging (N2) sequences in reads of Term-seq library were trimmed.
The reads were aligned to the S. avermitilis genome (BA000030) with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
The 3' end position of Term-Seq reads located within intergenic regions including up to 10 bp downstream to gene were regarded as potential transcription termination sites (TTS). The positions were clustered together based on the distance from adjacent positions (< 10 bp). Within each cluster, the read count of each position was assumed to follow normal distribution and read count enriched positions were deduced by calculating modified z-score. Z(x)=(r(x)-μ(r(x)))/(σ(x)), where, μ(r(x))=1/(N(x)-1)(-r(x)+∑_(y∈C(x))▒r(y) ), σ(x)=√(μ(〖r(x)〗^2 )-〖μ(r(x))〗^2 ). Z(x) is modified z-score at position x, r(x) is the read count of evaluated position x. μ(r(x)) and σ(x) is the mean and standard deviation of read counts of other positions in the cluster except the evaluated position, respectively. N(x) is the length of the cluster containing position x and C(x) is the set of positions within the cluster containing position x. The positions with read count less than 3 or modified z-score less than 3 were discarded. All the procedures above were conducted separately for each biological replicate. Among the remaining potential TTSs, the reproducible positions with the highest read count within the intersecting region of clusters from two biological replicate was selected as TTS. For example, if genomic positions from 3 to 25 were clustered together for one replicate and genomic positions from 13 to 42 were clustered together for another replicate, potential TTS with highest read count within the genomic positions from 13 to 25 was selected as TTS.
Genome_build: BA000030
Supplementary_files_format_and_content: tab-delimited text files include TSS, TTS or normalized expression values for each sample

organism: Streptomyces avermitilis

source_name: cell culture

growth_protocol: The mycelium of S. avermitilis MA4680 was maintained in 25% glycerol. Cells were first recovered in 50 mL R5- media with 8 g glass beads (3 ± 0.3 mm diameter) at 30 oC, 250 rpm. R5- medium consists of 5.73 g/L TES (pH 7.2), 103 g/L sucrose, 10 g/L glucose, 5 g/L yeast extract, 10.12 g/L MgCl2∙6H2O, 0.25 g/L K2SO4, 0.1 g/L casamino acids, 0.08 mg/L ZnCl2, 0.4 mg/L FeCl3∙6H2O, 0.02 mg/L CuCl2∙2H2O, 0.02 mg/L MnCl2∙4H2O, 0.02 mg/L Na2B4O7∙10H2O, and 0.02 mg/L (NH4)6Mo7O24∙4H2O. The inoculum was then transferred to fresh R5- media with 8 g glass beads for main culture. Cells were harvested at 13, 17, 19.5 and 33.5 hours after inoculation for early exponential phase (E), transition phase (T), late-exponential phase (L) and stationary phase (S), respectively.

extract_protocol:
Harvested cells were washed with polysome buffer (20 mM Tris-HCl pH 7.5, 140 mM NaCl, 5 mM MgCl2), and then resuspended with lysis buffer (0.3 M sodium acetate pH 5.2, 10 mM EDTA, 1% Triton X-100). The cell suspension was then frozen with liquid nitrogen, and lysed by grinding using mortar and pestle. The cell lysate was centrifuged at 4 oC for 10 minutes at 16,000 g and the supernatant was stored at -80 oC until used for RNA extraction. RNA was extracted by mixing with equal volume of phenol:chloroform:isoamyl alcohol = 25:24:1 solution. The mixture was then centrifuged and upper aqueous phase was recovered. The RNA was purified with ethanol precipitation. The purified RNA was treated with DNase I (New England Biolabs) to remove any genomic DNA contamination. Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit Bacteria (Epicentre) according to the manufacturer's instructions.
About 700 ng of rRNA-depleted RNA was incubated in 1x RNA 5' polyphosphatase (TAP) (Epicentre) reaction buffer and 1 U of SUPERase-In (Invitrogen) at 37 oC for 1 hour without TAP. After ethanol precipitation, 5 pmol of 5' RNA adaptor (5'-ACACUCUUUCCCUACACGACGCUCUUCCGAUCU-3') was ligated to the purified RNA with T4 RNA ligase (Thermo) in 1x RNA ligase buffer and 0.1 mg/mL BSA by incubating at 37 oC for 90 minutes. The adaptor-ligated RNA was then purified using Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. The purified product was reverse-transcribed using SuperScript III Reverse Transcriptase (Invitrogen) and purified using Agencourt AMPure XP beads. The purified cDNA was amplified and indexed using Phusion High-Fidelity DNA Polymerase (Thermo) for the Illumina sequencing. The amplification step was monitored on a CFX96 Real-Time PCR Detection System (Bio-Rad) to be stopped before the PCR reaction was fully saturated. Finally, the amplified library was purified using Agencourt AMPure XP beads, and the concentration of the library was measured with Qubit 2.0 fluorometer (Invitrogen). The size distribution of the library was checked with gel electrophoresis on 2% agarose gel.


title: SvenRibo_S2

first: Soonkyu

last: Hwang

address: 291 Daehakro, Yuseong-gu

department: Biological Sciences

description:
treated RNA
Sven_Ribo_ETLS_readcount.txt

data_processing:
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
Raw reads were mapped to PhiX control sequence (NCBI Genbank accession number : NC_001422) to eliminate the PhiX control reads with the following parameters; Mismatch cost : 2, Insertion cost : 3, Deletion cost : 3, Length fraction : 0.9, Similarity fraction 0.9, non-specific matches were randomly mapped.
The adaptor sequence was trimmed before being aligned to the genome.
The reads were aligned to the S. griseus or S. venezuelae genome and megaplasmid with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
Genome_build: NC_010572 for S. griseus, NZ_CP013129 for S. venezuelae
Supplementary_files_format_and_content: Sgri_Ribo_ETLS_readcount.txt, and Sven_Ribo_ETLS_readcount.txt : tab-delimited txt files that raw mapped read count within each gene and normalized expression of each gene in each sample.

organism: Streptomyces venezuelae

source_name: Mycelium cells from liquid culture

growth_protocol: The cells were inoculated from its 20% glycerol stock of spores to 50 ml of R5- liquid complex medium with 8 g of glass beads (3 ± 0.3 mm diameter) in 250 ml of a baffled flask, and grown at 30 °C, 250 rpm

extract_protocol:
Thiostrepton (Sigma) was added to cultures to a final concentration of 20 μM to stall the translating ribosomes, and the cultures were incubated for 5 min at 30 °C, and subsequently harvested for the construction of ribosome profiling libraries. Lysate for all samples were prepared by resuspended at polysome buffer and grinding in liquid nitrogen
The mycelium treated by thiostrepton was collected by centrifugation at 4 °C for 10 min at 3,000 g, and the cell pellet was washed with 2 ml polysome buffer composed of 20 mM Tris-HCl (pH 7.5), 140 mM NaCl, and 5 mM MgCl2 with 20 μM thiostrepton. The washed pellet was resuspended in 1 ml lysis buffer composed of 950 μl of polysome buffer and 50 μl of 20% triton X-100 with 20 μM thiostrepton. The resuspended cells were dripped into a mortar filled with liquid nitrogen and then ground with pestle. The cell debris was removed by centrifugation at 4 °C for 5 min at 3,000 g. The supernatant was further clarified and collected by centrifugation at 4 °C for 10 min at 16,000 g. To digest RNA, MNase was treated to the samples. Then, the samples were loaded onto illustra MicroSpin S-400 HR Columns. The ribosome-protected RNA fragments (RPF) between 26 and 34 bp were separated by electrophoresis for 65 min at 200 V using 15% polyacrylamide TBE-urea gel (Invitrogen), and eluted in 400 μl of RNA gel extraction buffer.
Ribosome profiling

value: Streptomyces venezuelae ATCC15439

tag: sampling time

value: Stationary phase (S)

tag: sequencing

value: Ribosome profiling

tag: cell sample

value: thiostrepton


title: U4

country: China

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 9

organism: Homo sapiens

value: 1mM dbcAMP_24h


title: 2 Control mouse


title: Cow 13 BASAL embryo #1 ED

value: embryonic disc

value: tubular


title: degron background wt 80 min spiked input rep1

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

library_source: genomic

data_processing:
FASTQ files were generated by Illumina basespace   (https://basespace.illumina.com/home/index).
The resulting sequences were aligned to S. cerevisiae reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) and to S. pombe (Downloaded from https://www.pombase.org/downloads/genome-datasets (9/4/2018)) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Unaligned reads from S. cerevisiae were aligned to S. pombe genome and unaligned reads from S. cerevisiae were aligned to S. pombe genome to aquire unique reads using samtools (http://samtools.sourceforge.net/) and bowtie2  (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):
BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks.
The data then was sorted into 50 bp bins and used for meta data analysis using custom made R programs
H2AP enrichment data over H2AP was normalized by multiplying each value by OR= Enrichment over input in S. cerevisiae genome/enrichment over input in S. pombe genome
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Genome_build: Schizosaccharomyces pombe (pombase (9/4/2018))
Supplementary_files_format_and_content: wig files contained normalised realtive H2AP enrichment over H2A

molecule: genomic DNA

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

growth_protocol: Sacchamromyces cerevisiae top2-td cell cultures for alpha factor release experiments were prepared as described previously -S. A. Schalbetter, S. Mansoubi, A. L. Chambers, J. A. Downs, J. Baxter, Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proceedings of the National Academy of Sciences. 112, E4565-70 (2015).  Schizosaccharomyces pombe cells were induced for 2h as described in  Adam T. Watson, Petra Werler, Antony M. Carr, Regulation of gene expression at the fission yeast Schizosaccharomyces pombe urg1 locus, Gene, Volume 484, Issues 1-2, 2011, Pages 75-85, ISSN 0378 1119, https://doi.org/10.1016/j.gene.2011.05.028.

extract_protocol:
S. cereviseae pellets from 50 ml culture were resuspended in 500 μl SDS buffer (1% SDS, 10 mM EDTA, 5M Tris HCl, cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)). Aliquots of S. pombe cell pellets were resuspended in 250 µl SDS buffer, and 1/1000 volume of the original S. cerevisiae culture (corresponding to 1:10 S. pombe to S. cerevisiae ratio) was added to each S. cerevisiae samples.  Cells were lysed in a FASTPREP machine, 5 rounds of 1 min at 6.5 power, with 200 μl of 0.5 mm silica beads. Lysate was spun out and IP buffer (0.1% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7 mM TRIS HCl (pH8), cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)) was added to a final volume of 1 ml. Samples were sonicated using the Focused-Ultrasonicator (Covaris, M220) (Average incident power - 7.5 Watts, Peak Incident Power - 75 Watts, Duty Factor - 10 %, Cycles/Burst - 200, Duration - 20 min). The sample was centrifuged for 20 min at 13,000 rpm at 4°C. Supernatant was then diluted to 1:10 (5 ml total).  50 μl protein A Dynabeads (Invitrogen, 10002D) and 50 μl protein G Dynabeads (Invitrogen, 10004D), were washed 3 times in IP buffer followed by adding to the sample and incubating for 2 h at 4°C. Supernatant was split, with 2X 2 ml being taken to 15 ml Falcon tubes, and 1 ml being kept at -20°C as an input sample. To the two 2 ml samples antibody was added, either H2A 1:500 (active motif) or 1.6 μg/ml yH2A (Abcam), and these were placed on a rotating wheel at 4°C for 15 - 20 h.   A preparation of Dynabeads (Invitrogen), Protein A (30 μl) and Protein G (30 μl), was washed 3 times in IP buffer. This was added to each sample and incubated at 4°C for 4 h. Supernatant was removed and beads were washed at 4°C for 6 min in TSE-150 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 150 mM NaCl), followed by TSE-500 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 500 mM NaCl), followed by LiCl wash (0.25 M LiCl, 1% NP-40, 1% dioxycholate, 1 mM EDTA, 10 mM Tris HCl (pH8)) and finally Tris-EDTA (TE pH8). Elution was carried out in 400 μl elution buffer, for 30 min at room temperature. At the same time 50 μl from the input sample was added to 150 μl of elution buffer. 20 μl of 5 M NaCl and 10 μl of 10 mg/ml proteinase K (Invitrogen) was then added to the input, and 40 μl and 20 μl to the IP samples respectively. These were incubated at 65°C overnight. Then 10 μl of DNase-free RNase (Roche) was added to the input and 20 μl to the IP samples, and they were left at 37°C for 30 min. All DNA was purified with a Qiagen PCR pufirication kit and eluted in 50 μl. DNA amount was measured using the Qubit 2.0 Fluorometer (Life technologies) as per the manufacturer’s instructions.
Libraries were prepared using the NEBnext Ultra II library kit (NEB) as per the manufacturers instructions. PCR enrichment required 13 cycles. PCR purification was carried out using AMPure XP beads.

treatment_protocol: Cultures were fixed at 25°C  in  YP  + 1%  formaldehyde  (Sigma)  for  45  min. 125 mM glycine was then added for 5 min. Cells were washed with PBS before being pelleted and frozen in liquid nitrogen.

tag: s. cerevisiae strain

tag: s. cerevisiae genotype

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3  pRS316

tag: s. pombe strain

tag: s. pombe genotype

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1

tag: time

value: 80 min after alpha factor release

tag: chip antibody


title: 1 Control mouse

value: female

tag: time point


title: U3

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 8

tag: cell line

value: 1mM dbcAMP_12h


title: SvenRibo_S1

tag: treatment


title: Cow 07 BASAL embryo #1 ED

tag: individual

tag: tissue

value: BASAL

tag: developmental stage

value: day 14 embryo

value: male


title: Cow 66 BASAL embryo #1 ED

tag: morphology

value: ovoid

tag: Sex


title: SvenRibo_L2

tag: strain

tag: sampling time

value: Late-exponential phase (L)


title: U2

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 7

value: 1mM dbcAMP_6h


title: U1

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 6

value: 1mM dbcAMP_0h


title: Cow 13 PA embryo #2 ED

value: HIGH PA


title: SvenRibo_T1

value: Streptomyces venezuelae ATCC15439

value: Transition phase (T)

tag: sequencing

value: Ribosome profiling

tag: cell sample

value: thiostrepton


title: SvenRibo_T2


title: D5

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 5

value: 1mM dbcAMP_48h


title: SvenRibo_E2

value: Early-exponential phase (E)


title: D3

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 3


title: degron background wt 80 min spiked yH2A rep2

tag: s. cerevisiae strain

tag: s. cerevisiae genotype

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3  pRS316

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1

value: 80 min after alpha factor release

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: Cow 07 PA embryo #5 ED

value: embryonic disc

value: day 14 embryo


title: SvenRibo_L1


title: Cow 813 BASAL embryo #3 ED

value: BASAL

value: tubular

value: female


title: SvenRibo_E1


title: mRNA_MCMV_72hr

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
mrna_MCMV_Smith_72h_mouse_rpkm.xlsx
mrnamrna_MCMV_Smith_72h_viral_rpkm.xlsx

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v1.1.2 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Next, remaining reads were aligned to the human or mouse and and the matching herpesvirus genome.
All remaining reads were aligned to the human/ mouse transcriptome (canonical known genes).
Wig files were then generated by summing the numbers of reads obtained from each position in the human/mouse genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: hg19 + NC_006273.2 + mm10 + NC_004065.1

molecule: polyA RNA

organism:
Mus musculus
Murid betaherpesvirus 1

source_name: Mouse embryonic fibroblast

extract_protocol:
Cells were lysed and RNA was extracted using Tri Reagent (Sigma).
mRNA was isolated using polyA selection kit (Ambion) and then fragmented. Fragments were then dephosphorylated, ligated with a 3' barcoded adapter, reverse transcribed and ligated with a 5' barcoded adapter. The resulting barcoded cDNA was PCR amplified.

tag: cells

value: primary

value: Smith


title: D4

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 4

value: 1mM dbcAMP_24h


title: Cow 72 PA embryo #2 ED

value: HIGH PA

value: ovoid

value: male


title: stage1_AB rep1

description: 1X150 bp single end

tag: cultivar

value: Pajares

value: Axillary bud

value: four weeks old plant


title: stage2_AB rep1

description: 1X150 bp single end

value: eight weeks old plant


title: stage3_AB rep2

description: 1X150 bp single end

value: after four weeks of cold treatment


title: stage2_AB rep2

description: 1X150 bp single end


title: stage3_AB rep3

description: 1X150 bp single end


title: stage1_AB rep2

description: 1X150 bp single end


title: stage3_AB rep1

description: 1X150 bp single end


title: Cow 813 PA embryo #3 ED


title: stage2_AB rep3

description: 1X150 bp single end


title: D1

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 1

value: 1mM dbcAMP_0h


title: D2

description:
mRNA_Time course of DBTRG treated with dbcAMP
Sample 2

value: 1mM dbcAMP_6h


title: MCF7RBPlus-Control-b2

status: Public on Mar 02 2020

city: Buffalo

first: Ram

middle: Mohan

last: Nambiar

state: NY

address: 665 Elm Street

institute: Roswell Park

data_processing:
The adaptors of the sample files were removed using Trimmomatic in Single End (SE) mode and. Trimmomatic also removes leading and trailing low quality bases (below quality 3),reads who’s average quality score per base falls below 15 for 4 base wide sliding window and those reads who’s length is below 20.
After the Fastq files are preprocessed, they were aligned to the Human genome(hg38) using tophat2 with default parametrs(i.e read-mismatch=2,read-gap-length=2) for each samples to create a bam file
Finally, the corresponding bam files are collected and sorted using samtools sort and the number of reads for each genes in each samples are computed using HTSeq.
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq Counts

source_name: mammary gland, breast

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using the RNeasy kit from Quiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO(0.1%) and Palbociclib(250nM+0.1% DMSO) upto 48 hrs

value: mammary gland, breast

tag: genotype

value: wild type

tag: agent

value: DMSO


title: MCF7RBPlus-Control-a2

tag: cell line


title: MCF7RBPlus-PD-a2

value: Palbociclib


title: MCF7RBPlus-PD-b2


title: MCF7RB-PD-a2

value: RB Knockout


title: MCF7RB-PD-b2


title: 3 Mouse exposed to 40 µg of MWCNT

source_name: MWCNT_Left Lung

value: female

tag: treatment

value: 40 µg of MWCNT

tag: time point

value: 56 days post exposure

value: left lung


title: MCF7RB-Control-b2

tag: tissue


title: MCF7RB-Control-a2


title: TIGE9_P4

city: Nagakute

first: Yohei

last: Okada

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Neural iPSC Research, Institute for Medical Science of Aging

country: Japan

institute: Aichi Medical University

data_processing:
Sequenced reads were mapped to hg38 whole genome using STAR v.2.7.1a with parameters -twopassMode
Reads counts of transcripts (feature counts) were calculated using FeatureCounts of the Rsubread package.
Ensembl gene annotation (Homo_sapiens.GRCh38.96.chr.gtf) was used for the transcripts counts.
Normalized feature counts were calculated using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Ensembl_ENSG_ID and normalized feature counts for each sample

source_name: iPSC derived motor neurons

growth_protocol: iPSC derived motor neurons were cultured in motor neuron medium as previously reported (PMCID: PMC4666063) for 4 weeks.

extract_protocol:
Total RNA was obtained from 4 control and 4 SBMA motor neurons. Each group include NT and P4 fraction. The RNA was extracted using RNeasy mini kit followed by the generation of mRNA libraries using Illumina TruSeq protocols for poly-A selection, fragmentation, and adaptor ligation according to the manufacturer’s instructions (illumina, TruSeq RNA Sample Prep Kit v2)
TruSeq RNA Sample Prep Kit v2

value: iPSC derived motor neurons

tag: disease state

value: control


title: YFE16_P4


title: YFE19_P4


title: EKA_P4


title: SBMA4E_P4

value: spinal and bulbar muscular atrophy (SBMA)


title: SBMA3E_NT


title: YFE16_NT


title: TIGE9_NT


title: 3 Control mouse

value: vehicle control


title: SBMA2E_P4


title: SBMA4E_NT


title: SBMA1E_NT


title: SBMA1E_P4


title: RNA-Seq_Ctrl_RepB

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

institute: Goethe University Frankfurt

data_processing:
RNA-Seq: Reads were trimmed with Cutadapt and mapped to the mouse genome mm10 using STAR with default parameters.
Ribo-Seq: RiboSeq reads were trimmed with Cutadapt and reads were mapped to rRNAs using Bowtie2. Unmapped reads were kept and aligned to the mouse genome mm10 using STAR with default parameters.
Genome_build: mm10

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37?C with 5% CO2.

extract_protocol:
Ribosome profiling experiments were performed according to Ingolia et al., 2011. The final RiboSeq libraries were sequenced on an Illumina HiSeq2000 instrument (single end reads).
For RNA-Seq, total RNA was subjected to poly(A)+ selection and Illumina library preparation following standard procedures. RNA-Seq libraries were sequenced on an Illumina NEXTSeq2500 instrument (single-end 75-nt reads; 50 million reads per replicate).

treatment_protocol: For Ribo-Seq, For RiboSeq, cells were pre-treated with 100 µg/ml cycloheximide (Sigma) in culture medium for 1 min at room temperature and washed with ice-cold PBS containing 100 µg/ml cycloheximide. PBS was quickly removed and culture dishes were immediately flash frozen on dry ice.

tag: genotype/variation

value: WT


title: RNA-Seq_Ctrl_RepA


title: Bcl6f/fPrx1cre P25 22degC sample 5

city: San Francisco

first: Yixuan

last: Wu

state: CA

address: 555 Mission Bay Boulevard South

department: Physiology

institute: University of California, San Francisco

data_processing:
Raw sequence data were pseudoaligned to the mouse transcriptome (mm10, UCSC annotation) using Kallisto (Bray et al. 2016).
Differential expression analysis was performed with DESeq2 (Love et al. 2014) and exported as count tables.
Genome_build: mm10
Supplementary_files_format_and_content: count tables

source_name: Ingunal white adipose tissue

extract_protocol:
Inguinal white adipose tissue was harvested and flash frozen in liquid nitrogen. RNA was isolated via homogenization in Trisure followed by phase separation with 1-bromo-3-chloropropane and precipitation with isopropanol.
Libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina), with 4 μg total RNA as starting material.

value: ingunal white adipose tissue

tag: age

value: Bcl6-flox Prx1-cre

tag: temperature

value: 22 deg C


title: Bcl6f/fPrx1cre P25 22degC sample 7


title: Bcl6f/fPrx1cre P25 22degC sample 6


title: RNA-Seq_SRSF7_OE_RepB

value: SRSF7-GFP OE


title: Bcl6f/fPrx1cre P25 22degC sample 4


title: 2 Mouse exposed to 40 µg of MWCNT

tag: strain

tag: Sex


title: RNA-Seq_SRSF7_OE_RepA


title: 5 Mouse exposed to 40 µg of MWCNT


title: 4 Mouse exposed to 40 µg of MWCNT


title: Bcl6f/fPrx1cre P25 22degC sample 2


title: Bcl6f/fPrx1cre P25 22degC sample 3


title: Bcl6f/fPrx1cre P25 22degC sample 1


title: SBMA3E_P4


title: EKA_NT


title: Bcl6f/f P25 22degC sample 7


title: YFE19_NT


title: 1 Mouse exposed to 40 µg of MWCNT


title: Bcl6f/f P25 22degC sample 4


title: Bcl6f/f P25 22degC sample 5


title: Bcl6f/f P25 22degC sample 6


title: Bcl6f/f P25 22degC sample 1


title: Bcl6f/fPrx1cre P25 22degC sample 8


title: Bcl6f/f P25 22degC sample 2


title: 6TGT3

city: 长春市

first: 昊

last: 李

address: 新竹路1977号

institute: 吉林大学

description: mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM values for each Sample.

source_name: Breast cancer cells

growth_protocol: The breast cancer cells MCF-7 were cultured in DMEM (Gibco, high glucose, USA) supplemented with 10% fetal bovine serum (BI, Israel), 1% MEM Non-Essential Amino Acids (Gibco, USA), 1% GluMAX and 1% Penicillin-Streptomycin Solution (Gibco, USA).

extract_protocol:
Total RNA was extracted from MCF-7 breast cancer cells using TRIzol reagent (Invitrogen) according to the instruction. The RNA was reverse transcribed to cDNA with TransScript All-in-One First-Strand cDNA Synthesis SuperMix for qPCR (TRAN, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 6μM 6-TG treated MCF-7 cells for 48h.

tag: cell type

value: Breast cancer cell line

tag: drug treatment

value: Thioguanine (Selleck, US)


title: 6TGT4

description: mRNA


title: 6TGT2

description: mRNA


title: MCF7N1

description: mRNA


title: MCF7N3

description: mRNA


title: MCF7N4

description: mRNA


title: NCH644_KDM7A_sh2_dox_RNA

city: Heidelberg

first: Jan-Philipp

last: Mallm

address: Im Neuenheimer Feld 267

institute: DKFZ

description:
strand-specific RNA, shRNA
Differential_expression_GIC_wt_KDM7A_KD

data_processing:
alignment to the human genome with bowtie /STAR
peak calling with MACS for ChIP and differential expression analysis with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: bed / raw counts

growth_protocol: Cells were cultured as neuronal spheres in Neuronal Base medium supplemented with BIT9500 (Provitro), basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) at 20 ng/µl (both Biomol) and hLIF produced in COS-7 cells.

extract_protocol:
For each sample, 1 x 10'6 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). For histone modifications, chromatin was sheared by sonication to mononucleosomal fragments. Total RNA was extracted using Trizol. Prior to library preparation, RNA was digested with DNaseI.
Libraries were prepared according to NEB protocols with external barcodes for both ChIP-seq and RNA-seq. For RNA-seq rRNA was depleted with RiboZero and strand-specific libraries were prepared.

treatment_protocol: For differentiation, cells were cultured in presence of 500 nM retinoic acid and serum. For KDM inhibition, GICs were treated with 2.5 mM DMOG for up to five days. SHRNA induction was achieved by putting the cells in medium containing 2 μg ml−1 doxycycline for at least 6 days.

tag: Stage

value: GIC

value: dox

tag: tag

value: neurosphere cell line


title: NCH644_KDM7A_sh1_RNA

description:
strand-specific RNA, shRNA control
Differential_expression_GIC_wt_KDM7A_KD

value: untreated


title: SBMA2E_NT


title: NCH644_KDM7A_sh2_RNA


title: 6TGT1

description: mRNA


title: NCH644_KDM4C_sh4_dox_RNA

description:
strand-specific RNA, shRNA
Differential_expression_GIC_wt_KDM4C_KD


title: NCH421k_diff_RNA_DMOG, 1

description:
strand-specific RNA
Differential_expression_GIC_wt_diff

value: differentiated GIC

value: ATRA + DMOG


title: NCH421k_diff_RNA_DMOG, 2


title: NCH644_KDM4C_sh1_RNA

description:
strand-specific RNA, shRNA control
Differential_expression_GIC_wt_KDM4C_KD


title: NCH421k_diff_RNA, 2

description:
strand-specific RNA
Differential_expression_GIC_wt_DMOG

value: ATRA


title: NCH644_KDM4C_sh1_dox_RNA


title: NCH644_KDM4C_sh4_RNA


title: NCH421k_diff_RNA, 1


title: NCH441_RNA, 1

value: nonGIC


title: NCH421k_RNA_DMOG, 2

value: DMOG


title: Bcl6f/f P25 22degC sample 3


title: NCH421k_RNA, 2


title: NCH441_H3

tag: antibody

value: ab1791, abcam #lot GR103864


title: NCH421k_RNA_DMOG, 1


title: NCH421k_diff_H3_DMOG

value: ATRA+DMOG


title: NCH421k_RNA, 1


title: NCH644_KDM7A_sh1_dox_RNA


title: NCH644_H3


title: NCH644_H3K4me3

value: ab8580, abcam #lot GR95388


title: NCH644_H3K9ac


title: NCH644_H3K4me1

value: ab8895, abcam #lot GR149140


title: NCH441_H3K9ac


title: NCH644_H3K27ac

value: ab4729, abcam #lot GR133922


title: NCH441_H3K4me1


title: MCF7N2

description: mRNA


title: NCH441_RNA, 2


title: NCH421k_H3K4me3_DMOG


title: NCH441_H3K4me3


title: NCH421k_H3K9ac_DMOG


title: NCH421k_H3K9ac


title: NCH421k_H3K4me3


title: NCH421k_H3_DMOG


title: NCH421k_H3


title: NCH421k_H3K27ac


title: NCH421k_H3K4me1_DMOG


title: NCH421k_H3K4me1


title: NCH421k_H3K27ac_DMOG


title: NCH441_H3K27ac


title: NCH421k_diff_H3K4me1


title: NCH421k_diff_H3K4me1_DMOG


title: NCH421k_diff_H3


title: Adh_NCH421k_H3K9ac

value: adherent cell line


title: NCH421k_diff_H3K4me3


title: NCH421k_diff_H3K27ac_DMOG


title: Adh_NCH421k_H3K4me3


title: NCH421k_diff_H3K9ac


title: BS_LS5

city: Cincinnati

first: Latha

last: Satish

state: OH

address: 3229 Burnet Avenue

department: Research

institute: Shriners Hospitals for Children

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Burn Eschar-Derived Pericytes

extract_protocol:
Total RNA was extracted from normal skin pericytes, burn eschar pericytes and normal skin fibroblasts using RNeasy Mini Kit from Qiagen Inc,. RNA quality was determined by Capillary electrophoresis using an Agilent 2100 Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue source

value: discarded burn eschar tissue

value: Pericytes


title: BS_LS4


title: Adh_NCH421k_H3K4me1


title: BS_LS6


title: Adh_NCH421k_H3


title: NS_LS3

source_name: Normal Skin-Derived Pericytes

value: discarded human skin tissue


title: NS_LS2


title: CF3

source_name: Normal Skin Fibroblasts

value: Fibroblasts


title: CF1


title: CF2


title: NCH421k_diff_H3K9ac_DMOG

value: neurosphere cell line


title: wild-type_Oxarol [S15062]

city: Yokohama

first: Hidehiro

last: FUKUYAMA

state: Kanagawa

address: 1-7-22, Suehirocho, Tsurumi-ku

department: IMS

institute: RIKEN

data_processing:
Read alignment: TopHat2 v2.0.8 and Bowtie2 v2.1.0 with default settings
expression level: Cufflinks v2.1.1 with default settings
FPKM (Fragments per Kirobase per Million reads) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Ear skin tissues were lysed in TRIzol LS reagent (Thermo Fisher Scientific) and total RNA was extracted.
cDNA library preparation for RNA-Seq analysis using an NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: 100mg of Oxarol ointment containing 2.5g of the active ingredient Maxacalcitol was applied to the ear

value: 8-12 weeks

tag: genotype

value: wild-type

tag: stimulus

value: 1 day after Oxarol

value: skin


title: wild-type_Oxarol [S15041]


title: K5-Cre;VDR f/f _Oxarol [S15068]

source_name: K5-Cre;VDR f/f _Oxarol

value: K5-Cre;VDR f/f


title: K5-Cre;VDR f/f _Oxarol [S15060]


title: NCH421k_diff_H3K27ac

value: differentiated GIC

tag: treatment

value: ATRA


title: wild-type_Oxarol [S15039]


title: K5-Cre;VDR f/f _Oxarol [S15069]


title: wild-type_PBS [S15061]

value: 1 day after PBS


title: wild-type_PBS [S15035]


title: wild-type_No treatment [S15031]

source_name: wild-type_No treatment

value: No


title: Adh_NCH421k_H3K27ac

value: nonGIC

value: untreated


title: wild-type_PBS [S15034]


title: wild-type_No treatment [S15059]


title: wild-type_No treatment  [S15030]


title: NS_LS1


title: GAS_sRNA_IP_LFD3

city: München

first: Raffaele

last: Teperino

address: Ingolstädter Landstraße 1

department: Institute of Experimental Genetics (IEG)

institute: Helmholtz Zentrum München

description: small RNA

data_processing:
trimming for adaptor and read quality. Aligned using STAR to mm10 genome built with  --sjdbOverhang 35 --outFilterIntronMotifs --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.16 . star output to htseq-count with --minaqual 10 and --nonunique none
Genome_build: mm10
Supplementary_files_format_and_content: count files from htseq-count

extract_protocol:
tissues were dissected and flash frozen. Plasma collected and filtered through a 22um spin-filter. RNA from plasma was extracted Tri reagent BD, RNA from tissues was extracted using NucleoZOL
CATS small RNA library kit from Diaganode cat #C05010048
single ended 75bp

value: GAS

tag: in/pd

value: Pull-down


title: GAS_sRNA_IP_LFD2

description: small RNA

tag: tissue


title: GAS_sRNA_IP_LFD1

description: small RNA


title: NCH421k_diff_H3K4me3_DMOG

value: ATRA+DMOG

value: ab8580, abcam #lot GR95388


title: GAS_sRNA_IN_LFD2

description: small RNA

value: Input


title: GAS_sRNA_IN_LFD3

description: small RNA


title: Tet1_wildtype_2iL_GTB6_rep1

city: Leuven

first: Kian

last: Koh

address: Herestraat 49, O&N IV - box 804

department: KU Leuven Department of Development and Regeneration

institute: KULeuven

description: biological replicate_1

data_processing:
Demultiplexed fastq files were aligned to UCSC mm10 genome reference using bowtie2 (v2.26) with default arguments.
The generated BAM files were then analyzed using MACS2 (v2.1.0) with the following settings and the corresponding controls to identify significant binding peaks enriched in the target proteins: Tet1 ChIP-seq in WT and Tet1GT/GT C57BL/6 2iL-cultured ESCs: the MACS2 settings were “--nomodel --extsize 200 -q 0.01”; Oct4 ChIP-seq in WT and Tet1tm1Koh B6129S6F1 hybrid EpiLCs: the MACS2 settings were “-q 0.05”; Oct4 ChIP-seq in WT and Tet1GT/GT C57BL/6 EpiLCs: the MACS2 settings were “-q 0.05”.
The BAM files were first summarized and transformed into BigWig files with bamCompare command from deepTools2 (v3.3.1) using the following settings: --scaleFactorsMethod None --normalizeUsing RPKM --ignoreDuplicates
Genome_build: mm10
Supplementary_files_format_and_content: bigWig fiels provide peak tracks information

source_name: 2iL cultured Tet1 gene-trap (GT) ESC

growth_protocol: Differentiation toward EpiLCs was performed as previously described but without activin A supplementation (Buecker et al. 2014). Briefly, feeder-depleted ESCs were first adapted at least 5 passages in defined media referred as 2iL media, which is composed of N2B27 basal media supplemented with 1 µM MEK inhibitor PD0325901 (Cat#Axon 1386, Axon Medchem BV), 3 µM GSK3 β inhibitor CHIR99021 (Cat#Axon 1408, Axon Medchem BV) and 1000 U/ml ESGRO LIF (Cat#ESG1107, Millipore). The N2B27 basal media is prepared as a 1:1 mixture of DMEM-F12 (Cat#11320-074, Invitrogen) and Neurobasal medium (Cat#21103-049, Invitrogen) supplemented with 1 x N2 (Cat#17502-048, Invitrogen), 1 x B27 (Cat#17504-044, Invitrogen), 1 mM L-glutamine, 0.1 mM 2-mercaptoethanol and 100:100 units:g/ml penicillin:streptomycin. 2iL-adapted ESCs were seeded at 2-3 x 105 cells per 10-cm2 on dishes coated with 5 g/10 cm2 fibronectin and differentiated for 2 days in N2B27 basal media supplemented with 1% knockout serum replacement KSR (Cat#10828-028, Invitrogen) and 12 ng/ml bFGF (Cat#100-18C, Peprotech).

extract_protocol:
Cells were trypsinized and chemically cross-linked with 1% methanol-free formaldehyde (Cat#04018, Polysciences) for 10 min at room temperature, then quenched with 0.125 M glycine. Fixed cells were lysed sequentially in lysis buffer I (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 0.25% Triton X-100, 0.5% NP-40, 10% glycerol, 1 mM  EDTA), lysis buffer II (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), followed by lysis buffer III (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin fractions were sheared to 200–500 bp using Bioruptor® Plus sonicator under high power setting for 20 cycles (30 seconds ON, 30 seconds OFF). The sheared DNA was measured on an Agilent 2100 Bioanalyzer using High Sensitivity DNA Analysis Kits (Agilent, Cat#5067-4626). The high-size fragments (> 500 bp), if detected, was then removed with size-selection using Agencourt AMPure XP beads (Cat#A63881, Beckman Coulter). The sheared DNA then was incubated using appropriate antibodies (and the same amount of control IgG for ChIP-qPCR) overnight and then precipitated with Protein G Dynabeads (Cat#10004D, Thermo Scientific). Precipitates were washed sequentially using the following washes for 5 minutes each: low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8.0, 500mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), 1X LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40) and twice in 1X TE buffer + 50 mM NaCl. Chromatin-antibody-beads were eluted in 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and de-cross-linked in 5 M NaCl solution at 65°C overnight. Sheared DNA was purified using the Zymo ChIP DNA Clean & Concentrator kit (Cat#D5201, Zymo) for ChIP–seq library preparation.
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer’s instructions.

value: 2iL cultured ESC

tag: chip antibody


title: Tet1_wildtype_2iL_GTB6_rep2

description: biological replicate_2


title: Tet1_Tet1KO_2iL_GTB6_rep1

description: biological replicate_1


title: Tet1_Tet1KO_2iL_GTB6_rep2

description: biological replicate_2


title: CD4+T_9h_IN_2_S6

city: Montpellier

first: Monsef

last: Benkirane

address: 141 rue de la cardonille

country: France

institute: CNRS

description: MNASE-seq

data_processing:
TRIM ADAPTER SEQUENCES + READS FILTERING AND QUALITY CONTROL (Trim Galore version: 0.5.0; cutadapt 1.8.3; FastQC_v0.11.7  python-2.7.2)
trim_galore -q 20 --stringency 5 --fastqc_args "--nogroup --outdir path/to/fastqc/trimmed_fqc" -o path/to/fastq/trimmed_fq --paired path/to/fastq/sample_example_R1.fq.gz path/to/fastq/sample_example_R2.fq.gz
READS INDEX (bwa-0.7.15)
bwa aln -t 8 path/to/NL4_3/NL4_3_vDNA.fasta path/to/fastq/trimmed_fq/sample_example_R1_val_1.fq > path/to/SAI/sample_example_R1_val_1.sai
READS ALIGNMENT (MNase-seq librairies were constructed using the NEXTflex Rapid DNA-Seq kit2.0 (BIOO SCIENTIFIC). To capture library DNAs containing HIV-1 sequence, MNase-seq libralies were hybridized with Custom Design SureSelect XT Capture Libraries (Agilent).)
bwa sampe path/to/NL4_3/NL4_3_vDNA.fasta path/to/SAI/sample_example_R1_val_1.sai path/to/SAI/sample_example_R2_val_2.sai path/to/fastq/trimmed_fq/sample_example_R1_val_1.fq path/to/fastq/trimmed_fq/sample_example_R2_val_2.fq > path/to/SAM/sample_example.sam
ALIGNED READS FILTERING (samtools-1.8)
samtools view -bS -F 1540 -q 0 path/to/SAM/sample_example.sam -o path/to/BAM_filt/sample_example_non_uniq_filt.bam
ALIGNED READS SORTING (samtools-1.8)
samtools sort path/to/BAM_filt/sample_example_non_uniq_filt.bam -o path/to/BAM_sort/sample_example_non_uniq_filt_sort.bam
REMOVE DUPLICATES IN ALIGNED READS (picard-tools/picard-2.18.2 MarkDuplicates)
MarkDuplicates I=path/to/BAM_sort/sample_example_non_uniq_filt_sort.bam REMOVE_DUPLICATES=true O=path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam M=path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.txt
ALIGNED READS INDEXING (samtools-1.8)
samtools index path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam
FILTERING BY FRAGMENT LENGTH AND MNASE SIGNAL PROCESSING (python-3.4.3 / deepTools-3.0.2)
bamCoverage Option Mnase -> center on Nucleosome center (for MNASE-seq samples only)
bamCoverage  --bam path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam --MNase --minFragmentLength 130 --maxFragmentLength 190 --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 9709 -o path/to/BIGWIG_rmMarkDup/sample_example_non_uniq_filt_sort_rmMarkDup_MnaseOpt_Frag130_160_RPGC.bw
bamCoverage Option extendReads -> extend signal to nucleosome size (for MNASE-seq samples only)
bamCoverage --bam path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam --extendReads 148 --minFragmentLength 130 --maxFragmentLength 190 --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 9709 -o path/to/BIGWIG_rmMarkDup/sample_example_non_uniq_filt_sort_rmMarkDup_ExtReads_Frag130_160_RPGC.bw
Genome_build: NL4-3; https://www.ncbi.nlm.nih.gov/nuccore/12831134
Supplementary_files_format_and_content: Bigwig files containing mnase-seq reads coverage after fragment length filtering and coverage processing

source_name: T-cell

growth_protocol: CD4+ T cells were cultured in RPMI-1640 supplemented with 10% heat-inactivated FBS, 1X MEM Non-Essential Amino Acids Solution, 2 mM ultraglutamine, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 mg/mL streptomycin. After 3 hours incubation at 37°C under 5% (vol/vol) CO2, CD4+ T cells were stimulated with 0.5 µg/ml phytohaemagglutinin (PHA, Sigma) and 50 U/ml interleukin 2 (IL-2, Roch).

extract_protocol:
(Samples treated with MNase) Chromatin extracted from cells infected with HIV were treated with MNase. DNA was then extracted by phenol–chloroform extraction, followed by ethanol precipitation. (Samples treated with sanication) DNA, extracted from cells using DNeasy Blood & Tissue Kit, were sonicated using Bioruptor Pico.
MNase-seq librairies were constructed using the NEXTflex Rapid DNA-Seq kit2.0 (BIOO SCIENTIFIC). To capture library DNAs containing HIV-1 sequence, MNase-seq libralies were hybridized with Custom Design SureSelect XT Capture Libraries (Agilent).

treatment_protocol: CD4+ T cells were infected with HIV obtained from pNL4-3 WT or IND116A. Cells were collected at 9 or 48 hours post-infection.

value: T-cell lymphoma cell line

value: CD4+ T

value: WT

tag: passages

tag: agent

value: HIV


title: GAS_total_IN_LFD1

description: total RNA

value: Total


title: GAS_sRNA_IP_HFD1

description: small RNA


title: GAS_sRNA_IN_HFD3

description: small RNA


title: GAS_sRNA_IN_HFD1

description: small RNA


title: GAS_sRNA_IN_LFD1

description: small RNA


title: GAS_total_IN_LFD3

description: total RNA


title: GAS_total_IN_HFD3

description: total RNA


title: VsWAT_total_IN_LFD2

description: total RNA

value: VsWAT


title: CD4+T_9h_IN_1_S2

description: MNASE-seq


title: VsWAT_total_IN_LFD3

description: total RNA


title: CD4+T_48h_WT_2_S7

description: MNASE-seq

value: IN mut


title: GAS_sRNA_IP_HFD3

description: small RNA


title: CD4+T_48h_WT_1_S3

description: MNASE-seq


title: CD4+T_9h_WT_2_S5

description: MNASE-seq


title: GAS_total_IN_LFD2

description: total RNA


title: GAS_sRNA_IN_HFD2

description: small RNA


title: VsWAT_total_IN_HFD3

description: total RNA


title: JurKat_9h_sonic_IN-2_S4

description: sonicated

data_processing:
TRIM ADAPTER SEQUENCES + READS FILTERING AND QUALITY CONTROL  Trim Galore version: 0.5.0 cutadapt 1.8.3 FastQC_v0.11.7 python-2.7.2 trim_galore -q 20 --stringency 5 --fastqc_args "--nogroup --outdir path/to/fastqc/trimmed_fqc" -o path/to/fastq/trimmed_fq --paired path/to/fastq/sample_example_R1.fq.gz path/to/fastq/sample_example_R2.fq.gz
READS INDEX   bwa-0.7.15   bwa aln -t 8 path/to/NL4_3/NL4_3_vDNA.fasta path/to/fastq/trimmed_fq/sample_example_R1_val_1.fq > path/to/SAI/sample_example_R1_val_1.sai
READS ALIGNMENT  MNase-seq librairies were constructed using the NEXTflex Rapid DNA-Seq kit2.0 (BIOO SCIENTIFIC). To capture library DNAs containing HIV-1 sequence, MNase-seq libralies were hybridized with Custom Design SureSelect XT Capture Libraries (Agilent).   bwa sampe path/to/NL4_3/NL4_3_vDNA.fasta path/to/SAI/sample_example_R1_val_1.sai path/to/SAI/sample_example_R2_val_2.sai path/to/fastq/trimmed_fq/sample_example_R1_val_1.fq path/to/fastq/trimmed_fq/sample_example_R2_val_2.fq > path/to/SAM/sample_example.sam
ALIGNED READS FILTERING  samtools-1.8   samtools view -bS -F 1540 -q 0 path/to/SAM/sample_example.sam -o path/to/BAM_filt/sample_example_non_uniq_filt.bam
ALIGNED READS SORTING  samtools-1.8   samtools sort path/to/BAM_filt/sample_example_non_uniq_filt.bam -o path/to/BAM_sort/sample_example_non_uniq_filt_sort.bam
REMOVE DUPLICATES IN ALIGNED READS  picard-tools/picard-2.18.2 MarkDuplicates   MarkDuplicates I=path/to/BAM_sort/sample_example_non_uniq_filt_sort.bam REMOVE_DUPLICATES=true O=path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam M=path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.txt
ALIGNED READS INDEXING  samtools-1.8   samtools index path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam
FILTERING BY FRAGMENT LENGTH AND MNASE SIGNAL PROCESSING  python-3.4.3 / deepTools-3.0.2
bamCoverage Option Mnase -> center on Nucleosome center (for MNASE-seq samples only)    bamCoverage  --bam path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam --MNase --minFragmentLength 130 --maxFragmentLength 160 --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 9709 -o path/to/BIGWIG_rmMarkDup/sample_example_non_uniq_filt_sort_rmMarkDup_MnaseOpt_Frag130_160_RPGC.bw
bamCoverage Option extendReads -> extend signal to nucleosome size (for MNASE-seq samples only)    bamCoverage --bam path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam --extendReads 148 --minFragmentLength 130 --maxFragmentLength 160 --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 9709 -o path/to/BIGWIG_rmMarkDup/sample_example_non_uniq_filt_sort_rmMarkDup_ExtReads_Frag130_160_RPGC.bw
bamCoverage default Option (for Sonicated samples)    bamCoverage --bam path/to/BAM_MarkDup/sample_example_non_uniq_filt_sort_rmMarkDup.bam --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 9709 -o path/to/BIGWIG_rmMarkDup/sample_example_non_uniq_filt_sort_rmMarkDup_RPGC.bw
Genome_build: NL4-3
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/12831134
Supplementary_files_format_and_content: Bigwig files containing mnase-seq reads coverage after fragment length filtering and coverage processing + sonicated reads sample as describe
Supplementary_files_format_and_content: mnase-seq processing centered on nucleosome
Supplementary_files_format_and_content: mnase-seq processing extended fragment on nucleosome
Supplementary_files_format_and_content: sonic processing

growth_protocol: Jurkat cells were routinely maintained in RPMI 1640 Medium (Lonza) supplemented with 10% (v/v) heat-inactivated fetal calf serum (Lonza), 1000 U.mL-1 penicillin/streptomycin (Lonza).

treatment_protocol: Jurkat cells were infected with HIV obtained from pNL4-3 WT or IND116A. Cells were collected at 9 or 48 hours post-infection.

tag: cell line

value: JurKat


title: CD4+T_9h_WT_1_S1

description: MNASE-seq


title: JurKat_48h_Sonic_S4

description: sonicated


title: VsWAT_total_IN_HFD1

description: total RNA

tag: strain


title: GAS_total_IN_HFD1

description: total RNA


title: Plasma_sRNA_IP_LFD2

description: small RNA

value: Plasma


title: Plasma_sRNA_IP_LFD1

description: small RNA


title: JurKat_48h_sonic_WT-2_S6

description: sonicated


title: Plasma_sRNA_IP_HFD1

description: small RNA


title: JurKat_9h_Sonic_S3

description: sonicated


title: JurKat_48h_sonic_WT-1_S5

description: sonicated


title: JurKat_9h_sonic_WT-2_S2

description: sonicated


title: JurKat_9h_IN-2_S4

description: MNASE-seq


title: VsWAT_sRNA_IP_LFD3

description: small RNA


title: Plasma_sRNA_IN_HFD2

description: small RNA


title: Plasma_sRNA_IN_LFD1

description: small RNA


title: Plasma_sRNA_IN_LFD2

description: small RNA


title: JurKat_48h_Mnase_S2

description: MNASE-seq


title: JurKat_48h_WT-1_S5

description: MNASE-seq


title: JurKat_48h_WT-2_S6

description: MNASE-seq


title: JurKat_9h_IN-1_S3

description: MNASE-seq


title: VsWAT_total_IN_HFD2

description: total RNA


title: Plasma_sRNA_IN_HFD1

description: small RNA


title: VsWAT_total_IN_LFD1

description: total RNA


title: JurKat_9h_sonic_IN-1_S3

description: sonicated


title: JurKat_9h_Mnase_S1

description: MNASE-seq


title: VsWAT_sRNA_IP_HFD3

description: small RNA


title: JurKat_9h_WT-2_S2

description: MNASE-seq


title: VsWAT_sRNA_IP_LFD1

description: small RNA


title: VsWAT_sRNA_IP_HFD1

description: small RNA


title: VsWAT_sRNA_IP_HFD2

description: small RNA


title: JurKat_9h_WT-1_S1

description: MNASE-seq


title: VsWAT_sRNA_IP_LFD2

description: small RNA


title: VsWAT_sRNA_IN_LFD3

description: small RNA


title: CN8

city: Shanghai

first: Fangbin

last: Zhou

address: Siping Road 1239

institute: Tongji University School of Medicine

data_processing:
The raw sequencing reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the dataset was then further processed using an in-house program, ACGT101-miR (LC Sciences, Houston, TX, United States) to remove adapter dimers, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), repeats in the NCBI GenBank1, Repbase2, and Rfam3) databases.
the remaining non-annotated sequences were mapped to specific species precursors in miRbase 21.04 by BLAST searches to identify known miRNAs.
On the basis of sequence similarity to human genome, these miRNA sequences were classified into subgroups 1a, 1b, 2a, 2b, and 3 with high-to-mid confidence in order
All non-annotated reads with lengths of 18–25 nt were mapped to the reference genome sequences using the Bowtie package; only perfectly matched sRNAs were used in further analyses.
Novel miRNAs were identified using the MIREAP software based on their precursors, and the hairpin RNA structures containing sequences were predicated from the flanking 120 nt sequences using RNAfold software.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample

source_name: colorectal cancer adjacent  tissue

extract_protocol:
Total RNA enriched in small RNA population was extracted using miRNeasy kit (Qiagen) as per the manual’s protocol.
RNA libraries were constructed for sequencing using standard Illumina protocols

value: adjacent tissue


title: JurKat_9h_sonic_WT-1_S1

description: sonicated


title: CN6


title: VsWAT_sRNA_IN_LFD2

description: small RNA


title: CN5


title: VsWAT_sRNA_IN_HFD3

description: small RNA


title: CN3


title: CN4


title: Liver_sRNA_IP_LFD1

description: small RNA

value: Liver


title: Liver_sRNA_IP_LFD3

description: small RNA


title: CT6

source_name: colorectal cancer tissue

value: cancer tissue


title: CN7


title: Liver_sRNA_IP_HFD3

description: small RNA

value: Pull-down


title: VsWAT_sRNA_IN_LFD1

description: small RNA


title: Liver_sRNA_IP_HFD1

description: small RNA


title: Liver_sRNA_IN_LFD3

description: small RNA


title: CT7


title: VsWAT_sRNA_IN_HFD1

description: small RNA


title: CT8


title: CT5


title: Liver_sRNA_IP_HFD2

description: small RNA


title: CT3


title: Kidney_mRNA_IP_LFD2

description: mRNA

value: Kidney


title: Liver_sRNA_IN_HFD1

description: small RNA


title: Kidney_mRNA_IP_LFD1

description: mRNA


title: Kidney_mRNA_IP_HFD3

description: mRNA


title: HS2_hop_tm

city: MADRID

first: M.

middle: MAR

last: CASTELLANO

address: Crta. de la Coruña, km 7,5

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA (CBGP)

data_processing:
TopHat (version 2.1.0)
HTSeq
DESeq2 R package (version 1.1.14)
Genome_build: Arabidopsis thaliana EnsemblGenomes release 27
Supplementary_files_format_and_content: XLS With counts and differential expression values

organism: Arabidopsis thaliana

source_name: HS rep2_hop_tm

growth_protocol: 7 day old Arabidopsis seedlings from wt and hop1 hop2 hop3 triple mutant

extract_protocol:
Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen)
TrueSeq Stranded mRNA library Prep Kit

treatment_protocol: Grown under control conditions or challenged at 38ºC for the last 3 hours

tag: developmental stage

value: 7 day-old seedlings

tag: genotype/variation

value: hop1 hop2 hop3 triple mutant

value: HS


title: HS1_hop_tm

source_name: HS rep1_hop_tm


title: CC3_Col-0

source_name: CC rep3_wt

value: wt

value: CC


title: CC2_hop_tm

source_name: CC rep2_hop_tm


title: Liver_sRNA_IN_HFD2

description: small RNA

value: Input


title: CC1_Col-0

source_name: CC rep1_wt


title: CT4


title: Liver_sRNA_IN_HFD3

description: small RNA


title: Liver_sRNA_IN_LFD2

description: small RNA


title: VsWAT_sRNA_IN_HFD2

description: small RNA


title: Liver_sRNA_IN_LFD1

description: small RNA


title: CC1_hop_tm

source_name: CC rep1_hop_tm


title: HS3_Col-0

source_name: HS rep3_wt


title: Kidney_mRNA_IP_HFD2

description: mRNA


title: CC3_hop_tm

source_name: CC rep3_hop_tm


title: GAS_total_IN_HFD2

description: total RNA

value: GAS


title: Kidney_mRNA_IP_HFD1

description: mRNA


title: Kidney_mRNA_IN_LFD2

description: mRNA


title: HS2_Col-0

source_name: HS rep2_wt


title: HS1_Col-0

source_name: HS rep1_wt


title: Kidney_mRNA_IN_HFD3

description: mRNA


title: Kidney_mRNA_IN_HFD2

description: mRNA


title: Kidney_mRNA_IN_HFD1

description: mRNA


title: Liver_mRNA_IP_LFD3

description: mRNA

source_name: Liver mRNA


title: D21 UI w/ 1% DMSO rep1

city: Farmington

first: Efthymios

last: Motakis

state: CT

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

description:
TPMs_ControlvsDMSO_upload.xlsx
RME725

data_processing:
Sequenced reads were trimmed for adaptor sequence by Trimmomatic
Fastqc deduplication was done with FastUniq
Kallisto v43 was used for transcript quantification
tximport R package was used to convert transcript-to-gene expression
Genome_build: mm12
Supplementary_files_format_and_content: Excel files where spreadsheet 'Kallisto TPMs' includes Kallisto's TPM-normalised counts for each sample and spreadsheet 'Experimental Design' includes the detailed infomation of the experimental design (SampleID, Condition, Replicate, Day of the experiment)

source_name: Mouse embryonic fibroblasts

growth_protocol: Cells were grown with StemPro34 SFM supplemented with 10ng/mL FGF2, 50ng/mL FGF10 and 5ng/mL VEGF

extract_protocol:
Cells were washed onece with PBS and subsequently lysed on tissue culture plate with trizol. RNA was purified with Direct-zol RNA kits from Zymo Research according to manufacturer's protocol
Library preperation was performed using TruSeq RNA Library Prep Kit from Illumina according to manufacturer's protocol

treatment_protocol: Cells were either untreated or treated with 1% DMSO

value: Myh6-promoter driven mCherry

tag: develpmental stage

value: Embryonic E12.5-13.5

value: UI w/ 1percent DMSO

tag: time point

tag: cell type

value: Mouse embryonic fibroblasts


title: D21 UI w/ 1% DMSO rep2

description:
TPMs_ControlvsDMSO_upload.xlsx
RME727


title: D21 UI w/ 1% DMSO rep3

description:
TPMs_ControlvsDMSO_upload.xlsx
RME729


title: Liver_mRNA_IP_LFD1

description: mRNA


title: D21 UI rep1

description:
TPMs_ControlvsDMSO_upload.xlsx
RME724

value: UI


title: D21 UI rep2

description:
TPMs_ControlvsDMSO_upload.xlsx
RME726


title: Liver_mRNA_IP_HFD2

description: mRNA


title: Liver_mRNA_IP_LFD2

description: mRNA


title: D7 UI w/ 1% DMSO rep3

description:
TPMs_ControlvsDMSO_upload.xlsx
RME723


title: D7 UI w/ 1% DMSO rep2

description:
TPMs_ControlvsDMSO_upload.xlsx
RME721


title: D7 UI rep3

description:
TPMs_ControlvsDMSO_upload.xlsx
RME722


title: Liver_mRNA_IP_HFD1

description: mRNA


title: D7 UI w/ 1% DMSO rep1

description:
TPMs_ControlvsDMSO_upload.xlsx
RME719


title: Liver_mRNA_IN_LFD3

description: mRNA


title: Kidney_mRNA_IN_LFD1

description: mRNA


title: D7 UI rep2

description:
TPMs_ControlvsDMSO_upload.xlsx
RME720


title: D7 UI rep1

description:
TPMs_ControlvsDMSO_upload.xlsx
RME718


title: Plasma_sRNA_IP_HFD2

description: small RNA

value: Plasma


title: D21 UI rep3

description:
TPMs_ControlvsDMSO_upload.xlsx
RME728


title: Liver_mRNA_IN_HFD2

description: mRNA

value: Liver


title: D2 UI w/ 1% DMSO rep1

description:
TPMs_ControlvsDMSO_upload.xlsx
RME713


title: D21 GHMT w/ 1% DMSO rep3

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF856

value: GHMT w/ 1percent DMSO


title: D2 UI w/ 1% DMSO rep2

description:
TPMs_ControlvsDMSO_upload.xlsx
RME715


title: m4_YFPneg_IgL

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 using TopHat2 and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to fragments per kilobase per million (FPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 3 reads per million in all samples for at least one group.
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing FPKM normalized read counts for all ENTREZ genes.

source_name: GC B cell

extract_protocol:
Cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v3 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Mice were infected with 1,000 pfu of MHV68-H2bYFP intranasally and tissues harvested 18 days post infection.

tag: Sex

value: Female

tag: infection status

value: negative

tag: sorting markers

value: Spleen


title: Liver_mRNA_IP_HFD3

description: mRNA

value: Pull-down


title: D2 UI rep2

description:
TPMs_ControlvsDMSO_upload.xlsx
RME714


title: m3_YFPpos_IgL

source_name: MHV68 infected GC B cell


title: m3_YFPpos_IgK


title: m3_YFPneg_IgL


title: D21 GHMT rep2

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF849

value: GHMT


title: Liver_mRNA_IN_HFD3

description: mRNA


title: Liver_mRNA_IN_LFD2

description: mRNA


title: D2 UI w/ 1% DMSO rep3

description:
TPMs_ControlvsDMSO_upload.xlsx
RME717


title: m2_YFPpos_IgL


title: HS3_hop_tm

source_name: HS rep3_hop_tm

value: 7 day-old seedlings

value: hop1 hop2 hop3 triple mutant

value: HS


title: m4_YFPpos_IgL


title: D7 GHMT w/ 1% DMSO rep3

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF854


title: CC2_Col-0

source_name: CC rep2_wt

value: wt

value: CC


title: D2 UI rep1

description:
TPMs_ControlvsDMSO_upload.xlsx
RME712

value: Myh6-promoter driven mCherry

value: Embryonic E12.5-13.5


title: m2_YFPneg_IgL


title: D7 GHMT rep3

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF853

value: Mouse embryonic fibroblasts


title: D7 GHMT rep2

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF847


title: D7 GHMT w/ 1% DMSO rep1

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF842


title: m1_YFPpos_IgK


title: D7 GHMT rep1

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF841


title: D21 GHMT w/ 1% DMSO rep2

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF850


title: m3_YFPneg_IgK


title: D2 UI rep3

description:
TPMs_ControlvsDMSO_upload.xlsx
RME716

value: UI


title: m4_YFPpos_IgK


title: Liver_mRNA_IN_HFD1

description: mRNA

value: Input


title: D21 GHMT w/ 1% DMSO rep1

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF844


title: D2 GHMT w/ 1% DMSO rep3

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF852


title: m1_YFPneg_IgK


title: D21 GHMT rep1

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF843


title: m2_YFPpos_IgK


title: m1_YFPneg_IgL


title: D7 GHMT w/ 1% DMSO rep2

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF848


title: D2 GHMT rep3

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF851


title: D21 GHMT rep3

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF855


title: D2 GHMT rep2

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF845


title: D2 GHMT w/ 1% DMSO rep1

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF840


title: m2_YFPneg_IgK


title: m4_YFPneg_IgK


title: input_Tet1KO_EpiLC_GTB6_rep1

description: biological replicate_1

source_name: Tet1 gene-trap (GT) EpiLC

value: EpiLC

tag: genotype

value: input


title: Oct4_wildtype_EpiLC_GTB6_rep1

description: biological replicate_1


title: D2 GHMT rep1

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF839


title: input_wildtype_EpiLC_GTB6_rep1

description: biological replicate_1


title: D2 GHMT w/ 1% DMSO rep2

description:
TPMs_GMTHvsDMSO_upload.xlsx
RMF846

value: GHMT w/ 1percent DMSO


title: Oct4_Tet1KO_EpiLC_Tet1tm1Koh_rep2

description: biological replicate_2

source_name: Tet1tm1Koh EpiLC

value: C57BL/6J x 129S6 F1 hybrid


title: Oct4_wildtype_EpiLC_Tet1tm1Koh_rep2

description: biological replicate_2


title: Oct4_Tet1KO_EpiLC_Tet1tm1Koh_rep1

description: biological replicate_1


title: input_wildtype_EpiLC_Tet1tm1Koh_rep1

description: biological replicate_1


title: Oct4_Tet1KO_EpiLC_GTB6_rep1

description: biological replicate_1


title: Oct4_wildtype_EpiLC_Tet1tm1Koh_rep1

description: biological replicate_1


title: input_Tet1KO_EpiLC_Tet1tm1Koh_rep2

description: biological replicate_2


title: input_Tet1KO_EpiLC_Tet1tm1Koh_rep1

description: biological replicate_1


title: input_wildtype_EpiLC_Tet1tm1Koh_rep2

description: biological replicate_2


title: ATACseq_Rmt_EpiLC_GTB6_rep2

description: biological replicate_2

data_processing:
Demultiplexed fastq files were analyzed using automated ENCODE ATAC-seq pipeline (http://doi.org/10.5281/zenodo.156534) developed by Anshul Kundaje’s laboratory with default arguments.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig fiels provide peak tracks information

source_name: Tet1 gene-trap (GT) EpiLC rescued with catalytic mutant Tet1(Rmt)

growth_protocol: Differentiation toward EpiLCs was performed as previously described but without activin A supplementation (Buecker et al. 2014). Briefly, feeder-depleted ESCs were first adapted at least 5 passages in defined media referred as 2iL media, which is composed of N2B27 basal media supplemented with 1 µM MEK inhibitor PD0325901 (Cat#Axon 1386, Axon Medchem BV), 3 µM GSK3 β inhibitor CHIR99021 (Cat#Axon 1408, Axon Medchem BV) and 1000 U/ml ESGRO LIF (Cat#ESG1107, Millipore). The N2B27 basal media is prepared as a 1:1 mixture of DMEM-F12 (Cat#11320-074, Invitrogen) and Neurobasal medium (Cat#21103-049, Invitrogen) supplemented with 1 x N2 (Cat#17502-048, Invitrogen), 1 x B27 (Cat#17504-044, Invitrogen), 1 mM L-glutamine, 0.1 mM 2-mercaptoethanol and 100:100 units:g/ml penicillin:streptomycin. 2iL-adapted ESCs were seeded at 2-3 x 105 cells per 10-cm2 on dishes coated with 5 ug/10cm2 fibronectin and differentiated for 2 days in N2B27 basal media supplemented with 1% knockout serum replacement KSR (Cat#10828-028, Invitrogen) and 12 ng/ml bFGF (Cat#100-18C, Peprotech).

extract_protocol:
50,000 freshly isolated cells were washed once with 100 ul PBS and resuspended in ice-cold 50 ul lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) for 3 min. The suspension of nuclei was then centrifuged for 10 min at 500 g at 4°C, followed by one wash with lysis buffer without Tween-20 and Digitonin. The visible pellets were incubated with 50 ul transposition reaction mix (25 l 2x TD buffer, 2.5 ul (or 5 ul) Tn5 Transposase, 16.5 ul PBS, 0.5 l 1% Digitonin, 0.5 ul 10% Tween-20 and nuclease-free H2O) (Cat#FC-121-1030, Illumina) at 37°C for 30 min with 500×g mixing. DNA was isolated using Zymo DNA clean and concentrator-5 kit (Cat#D4014, Zymo).
Library amplification was done by two sequential PCR reactions (5 and 8 cycles, respectively) using NEBNext High-Fidelity 2X PCR Master Mix (Cat#M0541S, New England BioLabs).


title: ATACseq_Rmt_EpiLC_GTB6_rep1

description: biological replicate_1


title: E18.5_DRG_F10_L6_S1_15766

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

data_processing:
Base calls were performed using Off-Line Base Caller (OLB) v1.9.4
FASTQ libraries were quality checked using FASTX toolkit version 0.0.14 and were aligned to the mm9 Ensembl 67 genome retaining uniquely mapping reads only. Samples were aligned with package Subread v1.18 under R v3.2.1 with max indels = 5, max mismatches = 5
Raw reads were counted and annotated against Ensembl v67 genes using featureCounts function of package Subread v1.20.6 under R v3.2.2
Gene counts were normalized using the “Voom” method of limma package v3.26.9 under R v3.2.2 with additional TMM library size adjustment using edgeR package v3.12.1 and further transformation to produce RPKM log2 abundance measures
Genome_build: mm9 (GRCh37.p7)
Supplementary_files_format_and_content: TAB-separated values, Ensembl Gene v67 annotated TMM RPKM log2 normalized abundance measures

source_name: dorsal root ganglion

extract_protocol:
Qiagen RNeasy Plus Micro Kit (Qiagen, Australia)
Total RNA was amplified to create double stranded cDNA using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer's protocol. cDNA concentrations were measured using the Qubit dsDNA BR assay, with cDNA size determined by using a DNA 1000 Chip. Libraries were then prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocol. The concentration of the pool is optimized to acquire at least 15-20 million reads per sample.

value: dorsal root ganglion

tag: region

value: sacral

tag: age

value: Female


title: WT 9wk 4degC sample 4

source_name: Ingunal white adipose tissue

tag: tissue

value: ingunal white adipose tissue

value: 9 weeks

tag: temperature

value: 4 deg C


title: E18.5_DRG_F9_L6_S1_15764


title: ATACseq_Rwt_EpiLC_GTB6_rep1

description: biological replicate_1

source_name: Tet1 gene-trap (GT) EpiLC rescued with wildtype Tet1(Rwt)


title: E18.5_DRG_F9_L4_L5_15763

value: lumbar


title: ATACseq_wildtype_2iL_GTB6_rep1

description: biological replicate_1

source_name: 2iL cultured Tet1 gene-trap (GT) ESC

value: 2iL cultured ESC


title: ATACseq_Tet1KO_2iL_GTB6_rep2

description: biological replicate_2


title: ATACseq_wildtype_EpiLC_GTB6_rep2

description: biological replicate_2


title: ATACseq_Tet1KO_EpiLC_GTB6_rep2

description: biological replicate_2


title: ATACseq_Tet1KO_2iL_GTB6_rep1

description: biological replicate_1


title: ATACseq_Tet1KO_EpiLC_GTB6_rep1

description: biological replicate_1


title: ATACseq_wildtype_2iL_GTB6_rep2

description: biological replicate_2


title: ATACseq_wildtype_EpiLC_GTB6_rep1

description: biological replicate_1


title: E18.5_DRG_F8_L6_S1_15762


title: WT 9wk 4degC sample 3


title: E18.5_DRG_F8_L4_L5_15761


title: WT 9wk 4degC sample 2


title: E18.5_DRG_F10_L4_L5_15765


title: E18.5_DRG_F7_L4_L5_15759


title: WT 9wk 4degC sample 1


title: E18.5_DRG_F3_L6_S1_15758


title: E18.5_DRG_F3_L4_L5_15757


title: WT 9wk 22degC sample 4

value: 22 deg C


title: WT 9wk 22degC sample 2


title: Bcl6f/fPrx1cre 9wk 4degC sample 3

value: Bcl6-flox Prx1-cre


title: E18.5_DRG_M8_L6_S1_15739

value: Male


title: ATACseq_Rwt_EpiLC_GTB6_rep2

description: biological replicate_2


title: E18.5_DRG_M8_L4_L5_15738


title: WT 9wk 22degC sample 1


title: Bcl6f/fPrx1cre 9wk 4degC sample 4


title: E18.5_DRG_M7_L4_L5_15736


title: Bcl6f/f 9wk 4degC sample 3


title: Bcl6f/f 9wk 4degC sample 4


title: Bcl6f/fPrx1cre 9wk 4degC sample 2


title: E18.5_DRG_M3_L6_S1_15733


title: E18.5_DRG_M5_L4_L5_15734


title: E18.5_DRG_M5_L6_S1_15735


title: Liver_mRNA_IN_LFD1

description: mRNA

value: Liver

tag: in/pd


title: E18.5_DRG_M3_L4_L5_157232


title: E18.5_DRG_M1_L6_S1_15731


title: E18.5_DRG_M7_L6_S1_15737


title: E18.5_DRG_F7_L6_S1_15760


title: Bcl6f/fPrx1cre 9wk 4degC sample 1


title: Bcl6f/f 9wk 4degC sample 2


title: WT 9wk 22degC sample 3


title: TrkAf/fTHcre P28 22degC sample 4

value: TrkA-flox Th-cre


title: E18.5_DRG_M1_L4_L5_15730


title: Bcl6f/f 9wk 4degC sample 1


title: Female_337_338_L6_S1_15438

value: 6-8 weeks

value: Homozygous Trpv1tm2Bbm


title: TrkAf/fTHcre P28 22degC sample 3


title: TrkAf/fTHcre P28 22degC sample 2


title: WT P28 30degC sample 4

value: 30 deg C


title: TrkAf/fTHcre P28 22degC sample 1


title: WT P28 30degC sample 3


title: Female_328_330_L6_S1_15439


title: Female_328_330_L4_L5_15444


title: Female_309_311_L4_L5_15445


title: Female_269_278_L4_L5_15446


title: WT P28 30degC sample 1


title: GAS_sRNA_IP_HFD2

description: small RNA

value: GAS

value: Pull-down


title: Female_246_247_L4_L5_15447

value: dorsal root ganglion


title: WT P28 22degC sample 3


title: WT P28 22degC sample 2


title: WT P28 22degC sample 4


title: WT P28 30degC sample 2


title: Male_347_349_L4_L5_15433


title: Male_347_349_L6_S1_15428

value: sacral


title: genomic DNA at diagnosis from BCP-ALL patient ALL_47

type: genomic

city: Uppsala

first: Yanara

last: Marincevic-Zuniga

address: Husargatan 3, BOX 1432, Biomedicinskt Centrum (BMC)

department: Medical Sciences

country: Sweden

institute: Uppsala University

description: raw data not available due to patient consent issues

hyb_protocol: not provided

scan_protocol: not provided

data_processing: LogR ratios and B-allele fractions (BAF) were calculated in GenomeStudio (Illumina) followed by copy number detection using the Tumor Aberration Prediction Suite (TAPS) and Integrative Genomics Viewer (IGV). LogR files  with the extension ".cn" are submitted to GEO and can be visualized in IGV.

label: Cy5 and Cy3

source_name: ALL patient sample

label_protocol: Standard Illumina Protocol

growth_protocol: primary cells

extract_protocol: genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN) or the QIAamp DNA Blood Mini Kit (QIAGEN)

treatment_protocol: patients were treated according to the Nordic Society of Pediatric Hematology and Oncology (NOPHO) ALL92 or ALL2000 protocols

tag: disease state

value: ALL diagnosis

tag: immunophenotype

value: BCP-ALL

value: primary acute lymphoblastic leukemia


title: Male_316_318_L4_L5_15434

value: lumbar

tag: strain


title: Male_316_318_L6_S1_15429


title: genomic DNA at diagnosis from BCP-ALL patient ALL_689


title: WT P28 22degC sample 1

value: ingunal white adipose tissue


title: genomic DNA at diagnosis from BCP-ALL patient ALL_707


title: Female_337_338_L4_L5_15443

value: Female


title: Male_274_280_L4_L5_15435


title: Female_309_311_L6_S1_15440


title: Male_274_280_L6_S1_15430


title: genomic DNA at diagnosis from BCP-ALL patient ALL_604


title: genomic DNA at diagnosis from BCP-ALL patient ALL_613


title: Male_273_275_L6_S1_15431


title: Female_269_278_L6_S1_15441


title: genomic DNA at diagnosis from BCP-ALL patient ALL_501


title: Male_243_245_L6_S1_15432


title: genomic DNA at diagnosis from BCP-ALL patient ALL_458


title: genomic DNA at diagnosis from T-ALL patient ALL_559

value: T-ALL


title: Female_246_247_L6_S1_15442


title: genomic DNA at diagnosis from BCP-ALL patient ALL_390


title: Adult_DRG_Sacral_Female_12

data_processing:
Base calls were performed using Real Time Analysis (RTA) v1.18.66.3 on data processed by HiSeq Control Software (HCS) v2.2.68
FASTQ libraries were quality checked using FASTX toolkit version 0.0.14 and were aligned to the mm9 Ensembl 67 genome retaining uniquely mapping reads only. Batch 1 samples aligned with package Subread v1.18 under R v3.2.1 with max indels = 5, max mismatches = 5. Batch 2 samples aligned with package Subread v1.20.6 under R v3.2.2 with same settings.
Raw reads were counted (merged Batch 1 and 2 BAM files as input) and annotated against Ensembl v67 genes using featureCounts function of package Subread v1.20.6 under R v3.2.2
Gene counts were normalized using the “Voom” method of limma package v3.26.9 under R v3.2.2 with additional TMM library size adjustment using edgeR package v3.12.1 and further transformation to produce RPKM log2 abundance measures
An observed technical batch effect between the 2 experimental batches (5 samples from Batch 1 and 19 samples from Batch 2) was corrected on the RPKM log2 expression data using removeBatchEffect function of limma package v3.26.9
Genome_build: mm9 (GRCh37.p7)
Supplementary_files_format_and_content: TAB-separated values, Ensembl Gene v67 annotated TMM RPKM log2 normalized abundance measures

tag: experimental batch

value: Batch 1


title: Adult_DRG_Sacral_Female_13


title: Adult_DRG_Sacral_Female_11


title: Silvestrol rep3

city: Montreal

first: Jerry

last: Pelletier

state: Quebec

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill university

data_processing:
The adapater sequence (AGATCGGAAGAGCGTCGTGTAG) was removed with Cutadapt
Removal of the first 13 nucleotides from R1 reads with custom python script. This includes barcodes (CCTATAT,ATCTTCT,TGCTATT,TATACTT) that identifes treatement. Note owing to the short length of some of the reads, the reverse complement of these barcodes and of the adapter sequence are also found on some the R2 reads.
Alignment of R1 reads to rRNA with Bowtie (version 1.1)
Alignment of R1 reads to RefSeq Catalog (version 80) with Bowtie
Reads that ambiguously mapped to transcripts derived from different gene loci were removed using a custom python script.
Supplementary_files_format_and_content: Processed files show the number of mapped reads assigned to different mRNA categories, (5'leader, coding,3'UTR, ncRNA, transcript, Pseudogene and LINC RNA)

source_name: Silvestrol rep3

growth_protocol: DMEM supplemented with 10% FBS (Wisent), 100 U/mL penicillin/streptomycin, and 2 mM L-glutamine at 37 °C and 5% CO2

extract_protocol:
Extraction was performed as described in Van. Nostrand et al (2016) PMID 27018577
Libraries were constructed as described in Van. Nostrand et al (2016) PMID 27018577

treatment_protocol: Cells were treated with vehicle, 20 nM CR-1-31-B or 20 nM Silvestrol for 1 hour prior to UV crosslinking (254 nm, 400 mJ/cm2, Hoefer UVC 500)

tag: rip antibody

value: Anti-FLAG

tag: treatment

value: Silvestrol (20 nM)

tag: cell line

value: HEK 293T


title: Adult_DRG_Lumbar_Female_11

value: 6-8 weeks


title: CR-1-31-B rep2


title: CR-1-31-B rep3


title: Silvestrol rep2

source_name: Silvestrol rep2


title: Adult_DRG_Lumbar_Female_2345

value: Batch 2


title: Silvestrol rep1

source_name: Silvestrol rep1


title: DMSO rep3

source_name: DMSO rep3

value: Vehicle


title: Adult_DRG_Sacral_Female_2261


title: DMSO rep2

source_name: DMSO rep2


title: Input rep2

source_name: Input rep2


title: Adult_DRG_Lumbar_Female_2245


title: Adult_DRG_Lumbar_Female_2145


title: Adult_DRG_Lumbar_Female_2045


title: Adult_DRG_Sacral_Female_2161


title: Adult_DRG_Sacral_Female_1961


title: RNA_seq_PP2-LSDi-inh-early_r3

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Homer
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build with bowtie2 using the parameters: --very-sensitive -p 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Fragments were normalized to 1e7 bases of library size using Homer
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

source_name: Early LSD1 inhibition PP2 replicate 3

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012).

extract_protocol: Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)

tag: cell type

value: differentiated hESCs

tag: developmental stage

value: Early pancreatic progenitor cells


title: DMSO rep1

source_name: DMSO rep1


title: CR-1-31-B rep1


title: Adult_DRG_Lumbar_Female_1945

value: dorsal root ganglion

tag: Sex


title: Male_273_275_L4_L5_15436

value: Homozygous Trpv1tm2Bbm

value: Male


title: Adult_DRG_Lumbar_Female_12


title: ChIP-Seq_LSD1_GT_r1

source_name: PP1 Control replicate 1


title: ChIP-Seq_RXR_PP1_r1


title: ChIP-Seq_LSD1_GT_r2

source_name: PP1 Control replicate 2


title: Adult_DRG_Sacral_Male_1561

value: sacral


title: Adult_DRG_Sacral_Male_1461


title: Adult_DRG_Lumbar_Male_1445

value: lumbar


title: ChIP-Seq_GATA6_PP1_r2


title: ChIP-Seq_HNF6_PP1_r2


title: ChIP-Seq_HNF6_PP1_r1


title: Adult_DRG_Sacral_Male_1261


title: Adult_DRG_Lumbar_Male_1345


title: ChIP-Seq_GATA4_PP1_r2


title: ChIP-Seq_GATA6_PP1_r1


title: ChIP-Seq_GATA4_PP1_r1


title: Adult_DRG_Sacral_Male_1161


title: Adult_DRG_Lumbar_Male_1245


title: ChIP-Seq_FOXA2_PP1_r1


title: ChIP-Seq_FOXA1_PP1_r1


title: WT KLRG1-negative 3 ILC

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

institute: National Jewish Health

data_processing:
Raw sequence data was demultiplexed and FASTQ files were generated using the Illumina bcl2fastq converter (version 2.17).
Nextera TruSight adapters were trimmed with skewer (version 0.2.2), which by default removes reads with a remaining length of less than 18 nt, using parameter -q 3.
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the GRCm38 (mm10) assembly of the mouse genome using gene annotations from Ensembl version 90. (http://aug2017.archive.ensembl.org/).
Reads mapping to each gene of the Ensembl 90 annotation were counted with the featureCounts program from the Subread software package (v1.5.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: counts per gene (Ensembl 90 mouse annotation) for each sample (gzipped output from featureCounts program)

source_name: Lung

extract_protocol:
KLRG1neg and KLRG1high ILCs from WT Il44get mice were sorted to >90% purity into a solution of 50% FCS 50% PBS and 20 U RNAase inhibitor on a BD FACSAria Fusion. RNA was isolated (RNeasy Micro Kit; Qiagen)
Libraries were constructed by SMARTer 1st strand cDNA synthesis (SMARTer® Ultra™ Low Input RNA Kit v4; Clontech) and full-length dscDNA amplification by LD-PCR, followed by purification and validation. Samples were then fragmented, tagged, indexed (Nextera XT) and sequenced on a HiSeq 2500.

treatment_protocol: 500ng recombinant IL-33 (Biolegend) was injected i.p. for 4 days and mice were euthanized on day 5.

value: Lin-, CD90-positive, KLRG1-negative ILC

value: day 5 after IL-33 administration

tag: reporter mouse

value: IL-4-4get GFP reporter mouse


title: WT KLRG1-positive 3 ILC

value: Lin-, CD90-positive, KLRG1-Postive ILC2


title: WT KLRG1-positive 1 ILC


title: WT KLRG1-positive 2 ILC


title: Adult_DRG_Lumbar_Male_1145


title: WT KLRG1-negative 1 ILC


title: WT KLRG1-negative 2 ILC


title: Adult_DRG_Sacral_Male_1361


title: chcc_source2 rep3

city: Hørsholm

first: Yun

last: Chen

address: Bøge Alle 10

department: Health & Nutrition

country: Denmark

institute: Chr Hansen A/S

data_processing:
Eurofins performed basecalling
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low-quality base pairs (bp) from the reads. The first 5 bps from the 5’end of both paired reads were also trimmed due to the observation of biased quality scores and nucleotide composition.
Spades with the “—careful” setting was used for performing de novo assembly.
Judged by contig coverage distribution, contigs with read coverage lower than 32 folds were removed from downstream analysis
Genome_build: de novo
Supplementary_files_format_and_content: de novo assemblies

organism: Lacticaseibacillus rhamnosus

source_name: whole organism

extract_protocol:
DNA was extracted using DNeasy Blood & Tissue Minikit (Qiagen)
Eurofins genomics - 4GLI-000100 shotgun library preparation
Eurofins genomics - 4GLI-000100 final quantification of library pool

value: GG

tag: growth

value: Original stock


title: chcc_source2 rep1


title: stock1994_rep2

growth_protocol: Freeze-dried product Lactobacillus rhamnosus GG from Chr Hansen were used. Overnight cultures and isolates were grown in MRS pH 6.5-broth and incubated at 37 degrees anaerobically.

extract_protocol:
DNA was extracted  using DNeasy Blood & Tissue Minikit (Qiagen)
Eurofins genomics - 4GLI-000100 shotgun library preparation
Eurofins genomics - 4GLI-000100 final quantification of library pool

treatment_protocol: No further treatment was applied

tag: growth conditions

value: Year 1994 stock


title: chcc_source1_rep3


title: stock1994_rep1


title: chcc_source1_rep2


title: chcc_source1_rep1


title: ChIP-Seq_FOXA2_PP1_r2


title: ChIP-Seq_FOXA1_PP1_r2


title: FD2B_Batch3

value: Freeze-dried product

tag: second time fermentation batch

tag: freeze-dried batch

value: Non-overnight-culture


title: FD2B_Batch3_ON

value: Overnight culture of freeze-dried product

value: Grown in MRS 6.5 broth


title: RNA-seq_EN-LSD1-inh-early_RA-late_r2

description: hESC-derived pancreatic cells

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Homer
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build with bowtie2 using the parameters: --very-sensitive -p 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Fragments were normalized to 1e7 bases of library size using Homer
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated

source_name: Early LSD1 inhibition + late RA treatment EN replicate 2

growth_protocol: Primary cells were cultured in 1640 RPMI e medium supplemented with 10% FBS, 8.3mM glucose and, antibiotic  at 37˚C and 5% CO2

extract_protocol:
Total RNA was extracted by RNARNeasy Mini Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina®  KAPA Kit (ChIP-seq)

treatment_protocol: Islets were dissociated and reaggreate, transfected with lentivirus. Total RNA was prepared 72 hours post-transfection.

value: differentiated hESCs

value: Pancreatic endocrine cells


title: RNA-seq_EN-LSD1-inh-early_RA-late_r1

description: hESC-derived pancreatic cells

source_name: Early LSD1 inhibition + late RA treatment EN replicate 1


title: FD2B_Batch2


title: RNA-seq_EN-LSD1-inh-early_r2

description: hESC-derived pancreatic cells

source_name: Early LSD1 inhibition EN replicate 2


title: Adult_DRG_Lumbar_Male_1545

source_name: dorsal root ganglion

value: Batch 2

tag: tissue

value: dorsal root ganglion

tag: region

tag: age

value: 6-8 weeks


title: stock1994_rep3