title: BY_5k

city: Pleasanton

first: Preyas

last: Shah

address: 7068 Koll Center Pkwy #401

institute: 10x Genomics

data_processing:
The Cell Ranger ATAC Software Suite (version 1.0.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the transposase made cuts
Regions of enriched accessibility, i.e. peaks were identified along the genome
Barcodes likely associated with whole cells were identified by analyzing the number of fragments mapped near TSS regions and a peak-barcode matrix is defined
Genome_build: hg19

organism:
Homo sapiens
Mus musculus

source_name: ATCC

growth_protocol: Human (GM12878) and Mouse A20 (ATCC TIB-208) B Lymphocytes were acquired and cultured according to guidelines from Coriell and ATCC, respectively. Fresh PBMCs, GM12878, and A20 cells were frozen according to the instructions outlined here: https://assets.ctfassets.net/an68im79xiti/18T8YsKiwKcGUakQmc8U22/086d0daa06444314fb757e35828f3c08/CG000169_DemonstratedProtocol_NucleiIsolation_ATAC_Sequencing_RevA.pdf. Healthy volunteer PBMC and BM samples were obtained from AllCells or the Stanford Blood Center (SBC).

extract_protocol:
All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are  available here: https://support.10xgenomics.com/single-cell-atac. The isolation, washing, and counting of nuclei suspensions were performed according to the Demonstrated Protocol: Nuclei Isolation for Single Cell ATAC Sequencing (10x Genomics). Briefly, anywhere from 100,000 to 1,000,000 cells were added to a 2 ml microcentrifuge tube and centrifuged (300 rcf for 5 min at 4°C). The supernatant was removed without disrupting the cell pallet and 100 µl chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) was added then pipette mixed 10 times. The microcentrifuge tube was then incubated on ice, with the length of time optimized for each cell type: GM12878 and A20 cell lines were 5 min; PB and BM cells were 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and the resulting solution and pipette mixed 5 times. Nuclei were centrifuged (500 rcf for 5 min at 4°C) and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and desired final nuclei concentration, an appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics; 2000153) was used to resuspend nuclei. The resulting nuclei concentration was determined using a Countess II FL Automated Cell Counter. Nuclei were then immediately used to generate single cell ATAC-seq libraries as described below.
scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 Rev A). Briefly, the desired number of nuclei were combined with ATAC Buffer (10x Genomics; 2000122) and ATAC Enzyme (10x Genomics; 2000123/2000138), to form a Transposition Mix which was then incubated for 60 min at 37°C. A Master Mix comprising of Barcoding Reagent (10x Genomics; 2000124), Reducing Agent B (10x Genomics; 2000087) and Barcoding Enzyme (10x Genomics; 2000125/2000139) was then added to the same tube as Transposed Nuclei. The resulting solution was loaded onto a Chromium Chip E (10x Genomics; 2000121) in a Chip Holder (10x Genomics; 330019). Vortexed Chromium Single Cell ATAC Gel Beads (10x Genomics; 2000132) then Partitioning Oil (10x Genomics; 220088) were also loaded onto the same Chromium Chip E before attaching a 10x Gasket (10x Genomics; 370017/3000072) and placing into on a ChromiumTM Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA). Resulting single-cell GEMs were collected at the completion of the run (~7 min) and linear amplification was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; 1851197): 72°C for 5 min, 98°C for 30 s, cycled 12 x: 98°C for 10 s, 59°C for 30 s and 72°C for 1 min. Emulsions were coalesced using tje Recovery Agent (10x Genomics; 220016) then subjected to Dynabeads (2000048) and SPRIselect reagent (Beckman Coulter; B23318) bead clean-ups. Indexed sequencing libraries were constructed by combining the barcoded linear amplification product with a Sample Index PCR Mix comprising of SI-PCR Primer B (10x Genomics; 2000128), Amp Mix (10x Genomics; 2000047/2000103) and Chromium i7 Sample Index (10x Genomics; 3000262). Amplification was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98°C for 45 s, cycled variable amounts depending on cell load: 98°C for 20 s, 67°C for 30 s, 72°C for 20 s with a final extension of 72°C for 1 min. The barcode sequencing libraries were subjected to a final bead clean-up SPRIselect reagent and quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms; KK4824).
Sequencing libraries were loaded on an Illumina sequencer with 2 × 50 paired-end kits using the following read length: 50 bp Read 1N, 8 bp i7 Index, 16 bp i5 Index and 50 bp Read 2N.

treatment_protocol: Fresh BCC biopsies were digested in 5 mL DMEM/F12 media + 250 ug/mL Liberase TL and 200 U/mL DNAse I with the gentleMACS Octo system at 37C for 3 hours at 20 rpm. After tissue pieces were fully digested, 50 uL of 500 mM EDTA was added and samples were collected by centrifugation at 300xg for 5 minutes. Single-cell suspensions were filtered through 70 um mesh and pelleted by centrifugation at 300xg at 4C for 10 minutes. Finally, cells were then resuspended in 1 mL of RPMI media and cryopreserved in FBS supplemented with 10% DMSO.Cells were gently thawed at 37C for 5 min and resuspended in media prior to FACS. Cells were stained with anti-CD45 V500 (clone HI30, cat. no. 560779, BD Biosciences), anti- CD3 FITC (clone OKT3, cat. no. 11-0037-41, Invitrogen), anti-CD8 Pacific Blue (clone 3B5, cat. no. MHCD0828, Invitrogen), anti-PD-1 APC/Cy7 (clone EH12.2H7, cat. no. 329921, BioLegend), and anti-HLA-DR eVolve 605 (clone LN3, cat. no. 83-9956-41, Affymetrix-Ebioscience). All antibodies were used at a 1:200 dilution, with the exception of anti-CD45 and anti-HLA-DR antibodies, which were used at a 1:100 dilution. Propidium iodine (cat. no. P3566, Invitrogen) was used for live/dead staining at a final concentration of 2.5 g/mL. PI-negative live cells were sorted as T cells (CD45+CD3+), non-T immune cells (CD45+CD3-), or tumor/stromal cells (CD45-CD3-). Cells were processed following 10x  Demonstrated Protocol (https://assets.ctfassets.net/an68im79xiti/18T8YsKiwKcGUakQmc8U22/086d0daa06444314fb757e35828f3c08/CG000169_DemonstratedProtocol_NucleiIsolation_ATAC_Sequencing_RevA.pdf) for PBMCs and Low Cell Input Nuclei Isolation protocol was followed for samples with cell count < 100,000. Isolated nuclei were further processed for scATAC-seq.

value: mixture of GM12878 and A20 cells


title: BY_500

status: Public on Apr 16 2019

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: treatment


title: BY_1k


title: BY_10k


title: siControl-Veh_RNAseq

status: Public on Apr 17 2019

city: Toronto

first: Carolyn

middle: L

last: Cummins

state: Ontario

address: 144 College St.

country: Canada

institute: University of Toronto

library_source: transcriptomic

data_processing:
Splicing analysis: Detailed description of the analysis pipeline can be found in [Irimia et al. Cell 159, 1511-1523 (2014)]. A summary of the main steps is provided here. An RNA-Seq dataset is first aliged to the genome using Bowtie. Reads that map to the genome are discarded from further analysis since exon-exon junctions (EEJs) are absent from genomic sequence. Reads that failed to align to the genome are aligned to a custom library of EEJs using Bowtie. To quantify splicing, the combination of EEJs that define each splicing event was created. For the case of single exon skipping events, we generated EEJs for C1A, AC2 and C1C2 (A represents the alternative exon and C1 and C2 represent the neighboring constitutive exons), requiring a minimum of eight positions from each exon. For multi-exon events we generated all possible forward combinations from C1 to C2 exons. If multiple alternative 5’ and/or 3’ splice sites were associated with any alternative, C1 or C2 exons, they were also included in the combinations. Read counts for each EEJ were then used to calculate the Percent Spliced In (PSI) of each event. A  simplified format of the formula is: PSI = 100% * (reads supporting inclusion / total reads).
Gene expression analysis (cRPKM): RNA-seq reads were aligned back to the mouse genome (Ensembl release 67) and transcript levels were quantified as reads per kilobase (of target gene) per million (of total reads) and corrected for transcript length and sequence redundancy (cRPKM)
Genome_build: mm9
Supplementary_files_format_and_content: 2014-03-13_cassette_all.txt, 2014-03-13_5altSS_all.txt, and 2014-03-13_3altSS_all.txt: 3 tab delimited text files summarizing the splicing analysis in N2a cells, where the tables contain, cassette exon, 5 prime splice site, and 3 prime splice site events, respectively. For all tables, each row corresponds to a unique splicing event. The table has the following columns: GENE - gene ID, EVENT - unique event ID containing the ENSEMBL gene ID, COORD - genomic coordinates of the alternative exon, LENGTH - nucleotide length of the alternative exon, FullCO - genomic coordinates of alternative exon as well as the coordinates of the last and first base pairs of the upstream and downstream exons, respectively, COMPLEX - refers to type of splicing event (S/C1/C2/C3: alternative cassette exon > 15 nucleotides, ME: mutually exclusive exons, Alt3: alternative 3´ splice site, Alt5: alternative 5´ splice site, MIC: alternative micro cassette exon ≤ 15 nucleotides), siArg_Dex_R1 - PSI in cells treated with siArglu1 + 100nM Dexamethasone, SiArg_Veh_R1 - PSI in cells treated with siArglu1 + Vehicle (ethanol), siCon_Dex_R1 - PSI in cells treated with control siRNA + 100nM Dexamethasone, siCon_Veh_R1 - PSI in cells treated with control siRNA + Vehicle (ethanol), siArg_Dex.Q + siArg_Veh.Q + siCon_Dex.Q + siCon_Veh.Q - quality scores for the corresponding PSI values, see  [Irimia et al. Cell 159, 1511-1523 (2014)] for details.
Supplementary_files_format_and_content: 2014-03-13_cRPKMs_all.txt: tab delimited text file summarizing gene expression analysis in N2a cells. Each row corresponds to a single gene. The table has the following columns: Gene - gene ID, external_gene_id - ENSEMBL gene ID, description – full gene name, cRPKM_siCon_Dex_R1 - cRPKMs in cells treated with control siRNA + 100nM Dexamethasone, cRPKM_siCon_Veh_R1 - cRPKMs in cells treated with control siRNA + Vehicle (ethanol), cRPKM_siArg_Dex_R1 - cRPKMs in cells treated with siArglu1 + 100nM Dexamethasone, cRPKM_siArg_Veh_R1 - cRPKMs in cells treated with siArglu1 + Vehicle (ethanol), reads_siCon_Dex_R1 - reads in cells treated with control siRNA + 100nM Dexamethasone, reads_siCon_Veh_R1 - reads in cells treated with control siRNA + Vehicle (ethanol), reads_siArg_Dex_R1 - reads in cells treated with siArglu1 + 100nM Dexamethasone, reads_siArg_Veh_R1 - reads in cells treated with siArglu1 + Vehicle (ethanol), see  [Labbéet al. Stem Cells 30, 1734–1745 (2012)] for details.

molecule: polyA RNA

organism: Mus musculus

source_name: Neuro-2a cells

growth_protocol: Monolayer growth in DMEM with 10% FBS

extract_protocol:
Total RNA was extracted from cultured cells using RNA-STAT60 reagent (Tel-Test Inc)
mRNA enriched Illumina TruSeq V2 RNA libraries were constructed using standard illumina protocol following DNAse treatment.

treatment_protocol: siRNA transfection with Lipofectamine RNAiMax (Life Technologies)

tag: cell line

value: Neuro-2a; N2a

value: neuroblastoma cell line

tag: transfected with

value: non-targeting control siRNAs for 48 hrs

tag: treated with

value: Vehicle (EtOH) for 4 hrs


title: HiChIP_Pax3_nodox

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
library strategy: HiChIP
ChIP-seq analysis. Each sample’s reads were aligned to the mouse (mm10) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. Similar results were obtained by performing peak calling using QESEQ with the following parameters: -s 100 -c 15 -p 0.01. Peak analysis was performed using bedtools. For triplicate experiments, peaks called in 2 of the 3 replicates were further considered. For duplicate experiments, common peaks between the 2 replicates were further considered. In addition, the peak lists were filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and in the mouse ChIP-seq black-list. Density maps were generated with SeqMiner using the enrichment file enr.sgr produced by QESEQ. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS  using the Kent tool Wig-to-BigWig.
HiChIP analysis. Paired-end samples were processed using the HiC-Pro pipeline. Contact matrices were generated for 10Kb bin pairs using default parameters in HiC-Pro to map the reads to the mm10 genome, remove duplicate reads, assign reads to Mbol restriction fragments, and acquire valid interactions. Statistically significant bin pairs and number of contacts were determined using the Fit-Hi-C contact caller using default settings and interaction distance less than 2 Mb.   Generation of Contact Matrix Heat Maps. Raw contact matrices from the HiC-Pro pipeline were normalized by read depth. The resulting normalized matrices were used to generate heat maps. The matrix acquired for the condition with no addition of doxycycline (non-induced) was subtracted from the matrices for 1-day and 6-day in doxycycline conditions. This enhanced the visualization of the heat maps for contacts specific to the manipulated condition. Similarly, the matrix for the Ldb1 knockdown sample was subtracted from the shSCR matrix to emphasize loss of contacts with the knockdown of Ldb1. R Bioconductor package “HiTC” was used to assist the generation of the contact heat maps.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: processed files represent author-curated list of peaks obtained by removing Encode blacklist and peaks detected in non-induced samples or input
Supplementary_files_format_and_content: HiChIP: processed files represent .hic matrix

growth_protocol: Mouse ES cell differentiation was achieved by diluting 40000 cells/ml in EB differentiation medium and incubation in an orbital shaker at 80 RPM. EB differentiation medium: IMDM supplemented with 15% FBS , 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol. Trangene induction was achieved by adding doxycycline (Sigma-Aldrich) to day 3 EBs cultures (final concentration 1µg/ml), and then maintained throughout the differentiation protocol by replacing the media (including dox) every two days. At day 5, EBs were disgregated and single cells were incubated for 20 minutes with PDGFRα-PE and FLK1-APC conjugated antibodies. PDGFRα+FLK1- cells were sorted using FACSAriaII (BD biosciences) and replated on gelatin coated dishes using serum- or serum-free EB differentiation media supplemented with 1µg/ml doxycycline and 10ng/ml mouse basic-FGF.

extract_protocol:
ChIP-seq: D4 EBs (1-day induced and control Pax3 mouse cells) were trypsin-treated at 37°C for 1 minute with gentle shacking and reaction was inhibited by adding 10%FBS/PBS. 1-day induced Pax3 NIH3T3 cells and 6-day induced Pax3 mouse cells growing in monolayer were harvested by incubation with trypsin for 1-2 minutes. Single cells were washed once with PBS, resuspended in 10%FBS/PBS and supplemented with formaldehyde (final concentration 1%) for crosslinking of protein-DNA complexes (10 minutes at RT) followed by quenching with glycine and staining with PDGFRα-PE antibody. PDGFRα+ cells were sorted using FACSAriaII, snap-frozen in liquid nitrogen and stored at -80°C if not processed immediately. Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated. Cells were sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF to achieve an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. 10-15µg (histone mark) or 25-40µg (Ldb1, Smc1, Ctcf) of chromatin were diluted to 250µl and 500µl, respectivley, and then precleared for 4h at 4°C with 20µl of BSA-blocked Protein A (or Protein G)-conjugated sepharose beads (GE healthcare). Samples were supplemented with 1/10 volume of 10% Triton X-100 and incubated overnight with the indicated antibody. Immune complexes were recovered by incubation with 20µl of BSA-blocked Protein G-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
ChIP-seq libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program. Libraries from Ldb1, histone marks in 6-day induced cells and H3K4me1 in dTAD and dTAD-Ldb1 immunoprecipitations were generated using the NEBNext DNA library prep kit (NEB).
HiChIP libraries. Long range interactions involving Pax3 binding sites were analyzed following the detailed protocol described by the Chang group. Briefly, non-induced, 1-day and 6-day Pax3-induced cells (respectively mesoderm, paraxial mesoderm precursors and myogenic progenitors) and 6-day+shSCR and 6-day+shLdb1 cells were harvested using trypsin for 1-2 min followed by inactivation with PBS/10%FBS, centrifuged 5 min at 400g, washed with PBS twice and then counted. 13 million cells, diluted to 1million/ml in PBS, were crosslinked for 15 min using methanol-free formaldehyde (Pierce – Thermoscientific). In situ contact generation was performed by digesting chromatin with MboI (NEB) followed by blunting with dNTP mix containing biotin-dATP (Thermo Fisher, 19524016) and ligation using T4 DNA ligase (NEB). After centrifugation, nuclei were resuspended in 880μL in Nuclear Lysis Buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, Complete Protease inhibitor - Roche), transferred in a Millitube and sonicated using a Covaris S220 (parameters: fill level = 10, duty cycle = 5, PIP = 140, cycles/burst = 200, time = 4 min). Chromatin was cleared by centrifugation, diluted 1:2 in ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 7.5, 167 mM NaCl), precleared for 4h at +4°C with 75µl of Protein G-conjugated magnetic beads and then incubated with 30µg of anti-Pax3 and anti-Ldb1 antibodies overnight at +4°C. Immune complexes were recovered by incubation with 60µl of BSA-blocked Protein G-conjugated sepharose beads for 5h at +4°C, then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Due to the sample volume during the Pax3 IP, Protein-G:Pax3-chromatin bound beads were splitted in two 1.5ml tubes during the previous procedure. Immunoprecipitated chromatin was recovered by incubating beads with 200µl/tube of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 30 minutes at 65°C. ChIP samples and Input (equivalent to 1% of starting material) were reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Following 30 minutes centrifuge at 16000g, pellets were washed with 75% ethanol, air dried and the combined DNA pellet were dissolved in 40µl H2O. Before proceeding with the biotin capture and transposase mediated library generation, ChIP samples were analyzed by qPCR to ensure enrichment at Pax3 sites vs control region. Samples were quantified using Pico-green (Invitrogen), resuspended in binding buffer and then incubated with 20µl of Streptavidin T1-conjugated magnetic beads (Invitrogen). After washing, DNA-bound streptavidin beads were incubated with 1.5µl of Tn5 transposase in a final volume of 50µl for 10 minutes at 55°C. This amount of transposase was selected based on the picogreen results of the ChIP, which yielded 25ng of DNA. Following quenching and washing, transposed DNA was incubated 5 minutes at 65°C with activated NEBNext UltraII QS Taq (+Illumina adaptor/barcodes) to allow primer extension and then amplified for 5 cycles (15 seconds 98°C followed by 1.5 minutes at 65°C). Additional cycles for library amplification were determined by qPCR using T5-T7 primer

value: differentiating mES cells

tag: time

value: day4 of differentiation

tag: purification

value: PDGFRα+FLK1- sorted

tag: doxycycline-treatment

value: not treated

tag: antibody


title: Input

city: Strasbourg

first: Irwin

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: Input DNA from melanoma tumors

extract_protocol:
Epigenetic profiling experiments were performed on native Mnase-digested chromatin isolated from BrafV600E Pten-/- mouse melanoma tumors. PolII occupancy profiling was performed on 0,4% PFA-fixed chromatin (Input data) isolated from BrafV600E Pten-/- mouse melanoma tumors according to standard protocols as previously described (Laurette et al., 2014). Up to 60 ug of chromatin was subjected to immunoprecipation with a specific antibody.
The libraries were sequenced on the Illumina Hiseq 4000 as single-end 50 base reads following Illumina’s instructions

tag: strain

tag: genotype

value: BrafV600E Pten-/-

tag: tissue

value: Melanoma

tag: chip antibody

value: none (input)


title: PolII_CHIP-seq

source_name: Chipped DNA from melanoma tumors


title: H3K27ac_CHIP-seq

value: Active Motif 39133


title: HiChIP_Ldb1_1day_dTAD_Ldb1_rep2

value: day9 of differentiation

value: ab96799 (Abcam)


title: ompcre_rad21ko_HiC_rep2

status: Public on Apr 15 2019

city: San Francisco

first: Daniele

last: Canzio

state: CA

address: 555 Mission Bay Boulevard South

department: Neurology

institute: University of California San Francisco

description: HiC-Seq, Paired End

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All mouse samples were aligned to mm10, human samples aligned to hg19. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: mOSNs with Rad21 KO

growth_protocol: HEK293T cells were purchased from ATCC and cultured in DMEM supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. Cells were maintained at 37°C in a 5% (vol/vol) CO2 incubator.

extract_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: mOSNs


title: tetotet3iresgfp_omptta_HiC_rep1

description:
HiC-Seq, Paired End
Processed data file includes data for both rep1 and 2

source_name: mOSNs overexpressing Tet3


title: H3K27me3_CHIP-seq

value: Millipore 07-449


title: HiChIP_Ldb1_nodox_dTAD_Ldb1


title: HEK_a12eCBS_dCas9-VPR_sorted_HiC_rep1

description:
captureHiC-Seq, Paired End
Processed data file includes data for rep1, 2 and 3

organism: Homo sapiens

source_name: HEK293T cells

value: HEK293T cells

value: HEK293T cells positively transfected with dCas9-VPR targeting the eCBS of Pcdha12


title: ompcre_rad21ko_HiC_rep1

description: HiC-Seq, Paired End


title: icam1_HiC

description: HiC-Seq, Paired End

data_processing:
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.
For ChiP-Seq experiments, raw FASTQ files were aligned using Bowtie2 using hg19 reference genome upon adapter sequences removal using CutAdapt. Uniquely aligning reads were selected using Samtools and reads with alignment quality below 30 (-q 30) were removed. The HOMER software package was used to generate signal tracks.
For in situ Hi-C experiments, raw FASTQ files were processed through use of the Juicer Tools Version 1.76 pipeline (Durand et al., 2016)  with one modification. Reads were aligned to hg38 using BWA 0.7.17 mem algorithm and specifying the -5 option implemented specifically for in situ Hi-C data.
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: icam1 positive cells from mouse olfactory epithelium

growth_protocol: SK-N-SH cells were purchased from ATCC and cultured in RPMI-1640 supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. HEK293T cells were purchased from ATCC and cultured in DMEM supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. Cells were maintained at 37°C in a 5% (vol/vol) CO2 incubator.

value: genomic DNA


title: HEK_a12pCBS_dCas9-VPR_sorted_HiC_rep1

value: HEK293T cells positively transfected with dCas9-VPR targeting the pCBS of Pcdha12


title: SKNSHadel1_HiC

description: captureHiC-Seq, Paired End

source_name: SK-N-SH heterozygous for the Pcdha cluster

value: SK-N-SH neuroblastoma cells


title: Lmnb1_KD_MLE12_RNA_seq_rep1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
Raw RNA-seq reads were trimmed with Reaper (http://www.ebi.ac.uk/~stijn/reaper/reaper.html) using the following parameters: -geom no-bc -3pa -clean-length 20 -qqq-check 53/10 -trim-length 150 –nozip. Trimmed reads were mapped to the reference genome mm10 (UCSC assembly) using STAR software (Dobin et al., 2013) with parameters (--outFilterMismatchNoverLmax 0.1 --chimSegmentMin 18 --chimScoreMin 12). Differential expression (Log2FC [fold change] ≥1, false discovery rate [FDR] <0.05, BaseMean ≥2 for upregulated genes, Log2FC ≤ −1, FDR <0.05, BaseMean ≥2 for downregulated genes) was quantified and normalized by the use of DESEq2.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file to visualize
Supplementary_files_format_and_content: Lmnb1_MLE12_RNA_seq_DEseq2_diffe_expression.xlsx

source_name: Lmnb1 KD MLE12 cells

growth_protocol: Control and Lmnb1 KD MLE-12 cells were cultured in DMEM/F12 medium supplemented with 10% fetal calf serum (FCS), penicillin/streptomycin/glutamine (PSG) and 2 µg/ml puromycin.

extract_protocol: RNA was isolated using RNeasy Microarray kit (Qiagen; no. 73304).For RNA-Seq of control and Lmnb1 KD MLE12 cells 1µg RNA was used for mRNA isolation using the Dynabeads®  mRNA DIRECT™  Micro Kit (Cat. no. 61021). RNA libraries were prepared using Ion Total RNA-Seq Kit v2 and sequenced on Ion Torrent V2 Chip.

value: Lung epithelial cells

tag: sample description

value: RNA-Seq of Lmnb1 KD MLE12 cells


title: Lmnb1_ctrl_MLE12_RNA_seq_rep2

source_name: control MLE12 cells

value: RNA-Seq of Control MLE12 cells


title: SKNSH_HiC

description: captureHiC-Seq, Paired End

source_name: SK-N-SH WT cells


title: HiChIP_Ldb1_1day_dTAD_Ldb1_rep1

value: differentiating mES cells

value: PDGFRα+FLK1- sorted


title: HEK_a12eCBS_dCas9.a12_HiC_rep3

description: captureHiC-Seq, Paired End

value: HEK293T cells transfected with dCas9 targeting the eCBS of Pcdha12


title: Lmnb1_ctrl_MLE12_RNA_seq_rep1

value: RNA-Seq of control MLE12 cells


title: 5C GFP-

status: Public on Apr 14 2019

city: Guangzhou

first: xiao

last: yang

address: 190 Kaiyuan Ave.

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

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
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

molecule: total RNA

source_name: Mouse embryonic fibroblast

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse embryonic fibroblast

tag: passages

tag: sorted fraction

value: GFP-


title: 5C GFP+ (naive)

value: GFP+ (naive)


title: 5C GFP+ (primed)

value: GFP+ (primed)


title: 5C GFP+

value: GFP+


title: R1 ESC_naive

source_name: Mouse embryonic stem cell

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit_Cat#FC-122-1001 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell


title: ICR MEF

value: ICR

value: embryonic fibroblast


title: OG2 MEF


title: Lmnb1_KD_MLE12_RNA_seq_rep2


title: mES GFP-


title: mES GFP+


title: G-R-_rep2

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
tophat -p 8 --library-type fr-firststrand -G hg19_exon.gtf -o ./ hg19.fa D7G1R1_1.clean.fq D7G1R1_2.clean.fq
featureCounts -t exon -g gene_name -s 1   -a hg19_exon.gtf -o Joe_Zhang_mRNA.txt *.bam
Genome_build: hg19
Supplementary_files_format_and_content: text tables. Raw gene counts and DESeq2 processed normalized expression levels.

source_name: iPSC

growth_protocol: Small molecule based cardiac differentiation

extract_protocol: NEBNext® Ultra™ RNA Library Prep Kit

value: TBX5-Clover2-/NKX2-5-TagRFP- subpopulation at D8 of post-differentiation


title: G+R-_rep2

value: TBX5-Clover2+/NKX2-5-TagRFP- subpopulation at D8 of post-differentiation


title: G-R+_rep2

value: TBX5-Clover2-/NKX2-5-TagRFP+ subpopulation at D8 of post-differentiation


title: G-R+_rep1

value: TBX5-Clover2-/NKX2-5-TagRFP+ subpopulation at D7 of post-differentiation


title: G-R-_rep1

value: TBX5-Clover2-/NKX2-5-TagRFP- subpopulation at D7 of post-differentiation


title: G+R-_rep1

value: TBX5-Clover2+/NKX2-5-TagRFP- subpopulation at D7 of post-differentiation


title: G+R+_rep2

value: TBX5-Clover2+/NKX2-5-TagRFP+ subpopulation at D8 of post-differentiation


title: R1 ESC (primed)

value: Mouse embryonic stem cell


title: G+R+_rep1

value: TBX5-Clover2+/NKX2-5-TagRFP+ subpopulation at D7 of post-differentiation


title: cde-1 (mj414) rep2 [5' independent]

status: Public on Apr 12 2019

city: Cambridge

first: Tomas

last: Di Domenico

address: Gurdon Institute, Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambirdge

data_processing:
Basecalling was performed by the Illumina BaseSpace website
Illumina TruSeq smallRNA 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was removed with cutadapt v1.9. Command line:”cutadapt --discard-untrimmed --minimum-length 20 -a TGGAATTCTCGGGTGCCAAGG -o <outfname> <infname>”
Adaptor-trimmed reads were aligned to the Ensembl WBcel235 genome using STAR v2.5.1b. Command line: “STAR --alignEndsType Local --outSAMtype BAM SortedByCoordinate --runThreadN 6 --outFilterMultimapNmax 1 --alignIntronMax 1 --readFilesCommand gunzip -c --scoreInsOpen -10000 --scoreDelOpen -10000 --outFilterMismatchNmax 0 --genomeDir <genome_index_path> --readFilesIn <infnames> --outFileNamePrefix <outfprefix>”
Smal RNA reads mapping to the worm genome (wrnas) and mapping to the Orsay virus genome (virnas) where counted and analysed using custom scripts. Details available at https://github.com/tdido/cde-1_analysis.
For the WT and CDE-1 (tm1021) non-phosphatase treated samples, small RNA reads mapping to microRNAs as annotated in the Ensembl WBcel235.78 gtf file where assigned to features using featureCounts v1.5.0-p1. Command line: featureCounts -T 12 -M --fraction -a Caenorhabditis_elegans.WBcel235.78.miRNA.gtf -o featureCounts_WT-cde-1_tm1021-miRNAs.out <sample files>
Counts assigned to microRNAs in the WT and CDE-1 (tm1021) samples were then processed with DEseq2.
Genome_build: WBcel235
Supplementary_files_format_and_content: virnas_tailing.json.bz2 and wrnas_tailing.json.bz2: list of untemplated tails and total read counts for each smallRNA category for viRNAs and wRNAs, in JSON format. counts_vrna_types.csv.bz2: viRNAs counts for several smallRNA categories, in CSV format. featureCounts_WT-cde-1_tm1021-miRNAs.out.bz2: featureCounts output for miRNA counts in WT and CDE-1 (tm1021), TSV format. deseq2_WT-cde-1_tm1021-miRNAs-vsd.out.bz2: DEseq2 output for miRNA differential expression between WT and CDE-1 (1021).

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Approximately 200 animals (strain as indicated) were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological duplicates.

extract_protocol:
Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines.
Purified RNA was either directly used for library preparation (5’ dependent libraries) or was first submitted to 5’ polyphosphatase treatment (5’ independent libraries) as in Ashe, et al. 2013. sRNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (with size selection between 20 and 35 nt, adapters excluded) and deep sequencing was produced with an Illumina HiSeq machine (single read 36)

treatment_protocol: Orsay virus infection as described above.

value: 5' independent

tag: hiseq run

tag: index


title: cde-1 (tm1021) ; rde-1 (ne219) rep2 [5' independent]

tag: treatment


title: cde-1 (tm1021) ; rde-1 (ne219) rep1 [5' independent]


title: cde-1 (tm1021) rep1 [5' independent]


title: cde-1 (tm1021) rep2 [5' independent]


title: dcl3b knockdown mutant rice replicate3

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

description:
dcl3b rep3
dcl3b-rp3
Oryza Sativa subsp. Japonica
mRNA
Strand-specific RNA-seq
processed data file: dcl3b_upregulated.xls
processed data file: dcl3b_downregulated.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean reads were acquired from initial pair-end reads after trimming low quality (Q < 20) and adaptor sequences by SeqPrep version 1.1.
Reads aligned to rice genome by TopHat version 2.1.0 with no more than two mismatches.
Differentially expressed genes were identified with the edgeR package. Classic model of edgeR was used for the differential expression analysis with false discovery rate (FDR) of 0.05 and two-fold change of Fragments Per Kilobase of gene per Million mapped reads (FPKM) as significant cutoffs.
Functional enrichment analysis was performed using GOstats. With the hypergeometric test p-value less than 0.05 as threshold.
Clean reads of siRNA samples aligned to rice genome using Bowtie version 1.1.2 with no mismatches. With FDR less than 0.05 and expression level fold change more than five as threshold, we got the siRNA different expression regions.
Genome_build: Oryza sativa Genome Annotation Project Release 7
Supplementary_files_format_and_content: dcl3b_upregulated.xls, dcl3b_downregulated.xls: Excel files of FPKM values and annotation for DEGs.
Supplementary_files_format_and_content: dcl3b_21nt_siRNA_DER.xls, dcl3b_24nt_siRNA_DER.xls: Excel files include differentially expressed regions generated from the small RNA-seq samples.

organism: Oryza sativa Japonica Group

source_name: young panicles before heading date, dcl3b knockdown

growth_protocol: Rice plants were grown in the paddy field.

extract_protocol:
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (Ambion) for removing DNA contamination.
Libraries were constructed through applying TruSeq Small RNA sample preparation and TruSeq Stranded mRNA kits (Illumina, San Diego, CA, USA) for small RNA sequencing and RNA sequencing, respectively, in accordance with the manufacturer’s instruction.

tag: genotype/variation

value: dcl3b knockdown mutant

value: young panicles


title: Wild type rice small RNA sample

description:
WT siRNA
WT
Oryza Sativa subsp. Japonica
Small RNA
processed data file: dcl3b_21nt_siRNA_DER.xls
processed data file: dcl3b_24nt_siRNA_DER.xls

source_name: young panicles before heading date, WT

value: Wild type


title: rde-1 (ne219) rep1 [5' independent]


title: drh-1 (ok3495) rep1 [5' independent]


title: Wild type rice replicate2

description:
WT rep2
WT-rp2
Oryza Sativa subsp. Japonica
mRNA
Strand-specific RNA-seq
processed data file: dcl3b_upregulated.xls
processed data file: dcl3b_downregulated.xls


title: Wild type rice replicate1

description:
WT rep1
WT-rp1
Oryza Sativa subsp. Japonica
mRNA
Strand-specific RNA-seq
processed data file: dcl3b_upregulated.xls
processed data file: dcl3b_downregulated.xls


title: WT rep1 [5' independent]

value: WT


title: Wild type rice replicate3

description:
WT rep3
WT-rp3
Oryza Sativa subsp. Japonica
mRNA
Strand-specific RNA-seq
processed data file: dcl3b_upregulated.xls
processed data file: dcl3b_downregulated.xls


title: rde-1 (ne219) rep2 [5' independent]


title: drh-1 (ok3495) rep2 [5' independent]


title: dcl3b knockdown mutant rice replicate2

description:
dcl3b rep2
dcl3b-rp2
Oryza Sativa subsp. Japonica
mRNA
Strand-specific RNA-seq
processed data file: dcl3b_upregulated.xls
processed data file: dcl3b_downregulated.xls


title: cde-1 (tm1021) ; drh-1 (ok3495) rep1 [5' independent]


title: WT rep2 [5' independent]


title: cde-1 (tm1021) ; drh-1 (ok3495) rep2 [5' independent]


title: CNV 2

status: Public on Apr 13 2019

type: RNA

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description: lncRNA and mRNA expression data from samples of laser-induced CNV mice.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl of 10 × blocking agent and 1 μl of 25 × Fragmentation Buffer, then heating the mixture to 60 °C for 30 min, finally adding 25 μl of 2 × GE Hybridization buffer to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated in an Agilent Hybridization Oven for 17 hours at 65°C.

scan_protocol: The hybridized arrays were washed, fixed and scanned with the Agilent G2505C DNA Microarray Scanner.

data_processing: Acquired array images were analyzed by Feature Extraction software (Agilent Technologies,version 11.0.1.1).Quantile normalization and subsequent data processing were performed by using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs which at least 3 out of 6 samples signed with Present or Marginal flags(“All Targets Value”) were chosen for further data analysis.

source_name: RPE-choroid-sclera complexes

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random primers according to manufacturer’s protocol (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified using RNeasy Mini Kit (Qiagen,Genman). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured with NanoDrop ND-1000.

growth_protocol: The animals were maintained in cages in temperature-controlled rooms featuring a 12-h light/12-h dark cycle.

extract_protocol: Total RNA was isolated from the RPE-choroid-sclera complexes using Trizol RNA extraction kit(Invitrogen life technologies). RPE-choroid-sclera complexes from 4 eyes were used as one sample.

treatment_protocol: The photocoagulation was applied in eyes of mice around the optic disc using a 532-nm diode laser (100 mW, 0.1 s duration, 50 μm).  Twenty-five spots were burned on each eye, and the eyes were enucleated at 7 days after the laser photocoagulation. Age-matched mice without laser photocoagulation treatment were used as controls.

value: RPE-choroid-sclera complexes from laser-induced CNV eye (7 days after the laser photocoagulation)

tag: age

value: Seven to eight-week-old

tag: Sex

value: male


title: dcl3b knockdown mutant rice replicate1

description:
dcl3b rep1
dcl3b-rp1
Oryza Sativa subsp. Japonica
mRNA
Strand-specific RNA-seq
processed data file: dcl3b_upregulated.xls
processed data file: dcl3b_downregulated.xls


title: CNV 1


title: cde-1 (mj414) rep2 [5' dependent]

value: 5' dependent


title: Control 3

description: lncRNA and mRNA expression data from samples of normal mice.

value: RPE-choroid-sclera complexes from normal eye


title: Control 2


title: Control 1


title: cde-1 (mj414) rep1 [5' dependent]


title: cde-1 (tm1021) rep1 [5' dependent]

description:
featureCounts_WT-cde-1_tm1021-miRNAs.out.bz2
deseq2_WT-cde-1_tm1021-miRNAs-vsd.out.bz2


title: cde-1 (tm1021) ; rde-1 (ne219) rep2 [5' dependent]


title: drh-1 (ok3495) rep2 [5' dependent]


title: cde-1 (tm1021) ; rde-1 (ne219) rep1 [5' dependent]


title: cde-1 (mj414) rep1 [5' independent]


title: WT rep2 [5' dependent]


title: dcl3b knockdown mutant rice small RNA sample

description:
dcl3b siRNA
dcl3b
Oryza Sativa subsp. Japonica
Small RNA
processed data file: dcl3b_21nt_siRNA_DER.xls
processed data file: dcl3b_24nt_siRNA_DER.xls


title: cde-1 (tm1021) rep2 [5' dependent]


title: rde-1 (ne219) rep1 [5' dependent]


title: drh-1 (ok3495) rep1 [5' dependent]


title: rde-1 (ne219) rep2 [5' dependent]


title: RNA-seq-WT2

status: Public on Apr 11 2019

city: Los Angeles

first: Douglas

middle: Edmund

last: Feldman

address: 2011 Zonal Avenue

department: Pathology

institute: USC Keck School of Medicine

data_processing:
For ChIP-seq, DIP-seq and RNA-seq, raw reads were trimmed to remove adapters and low-  quality reads using Trim Galore (v0.3.5). Bowtie (v0.12.8) was used to obtain reads mapped  uniquely to the mouse genome (mm10). ChIP and DIP peak candidates were identified with  MACS (v2.1.1) using input as the control data set. To remove nonspecific signals, IgG samples  were processed similarly and their normalized read density (RPKM) values were subtracted  from modification-specific peaks. For DIP, the empirical FDR was estimated by exchanging the  DIP and IgG control samples and identifying peaks in the control sample using the same set of  parameters used for the DIP sample. Called peaks were annotated with Gencode M1 and  Cistrome CEAS (Shin et al., 2009) . Normalized read density plots centered on annotated  elements downloaded from ENCODE were generated using NGSPLOT (Shen et al., 2014) .  Peak overlap statistics were calculated using Fisherbed. For RNA-seq, Cufflinks (v 2.2.1.0) was  used to assemble transcripts, estimate their abundances and test for differential transcript  expression. All GO analyses used DAVID (http://david.abcc.ncifcrf.gov).
Genome_build: mm10
Supplementary_files_format_and_content: bam files were mapped using TopHat, FPKM values calculated with CuffLinks

source_name: mouse ES cells

growth_protocol: Co-derived wild-type and Srap1 KO mouse ES cells were cultured on gelatin-coated plates in high-glucose DMEM containing 15% FBS, 1x non-essential amino acids, 2 mM L-glutamine, 100 mM beta-mercaptoethanol, 1x nucleosides (Millipore), 1000U/ml leukemia inhibitory factor (StemRD) and 2i (selective GSK3β & Mek 1/2 inhibitors; Millipore), 25 mg/ml L-ascorbic acid.

extract_protocol: ChIP, MeDIP and RNA library preparation  For ChIP, strain-matched wild-type or Mettl4 KO mouse ES cells (C57BL/6N x 129/Sv  background) were fixed in 1% paraformaldehyde for 10 min at 37°C, followed by quenching with  125 mM glycine for 5 min. Cells were lysed and processed using the MAGnify ChIP system (Life  Sciences). Lysates were sonicated using an ultrasonic processor (Cole Parmer) at power  setting 3 in 30 s pulses followed by 1 min on ice, for a total of 6 min sonication. Nucleoprotein  complexes were immunoprecipitated the indicated antisera (2.5 g) equivalent amounts of  isotype-matched control IgG per sample. For MeDIP experiments, genomic DNA was isolated  from ES cells using the DNeasy Blood & Tissue DNA kit and sonicated for a total of 6 min.  Samples were processed using the hMeDIP kits (Active Motif) according to the manufacturer’s  protocol. For RNA-seq, total RNA was extracted from mouse ES cells using the Zymo RNA  Clean & Concentrator (Zymo Research), followed by mRNA enrichment and cDNA preparation  using the KAPA Stranded RNA-Seq Kit. Library preparations were performed using the Kapa  HyperPrep kit, followed by 12 cycles of PCR amplification with Kapa HiFi HotStart polymerase.  Amplified libraries were pooled, purified twice with 0.9X Ampure XP beads and analyzed on an  Illumina HiSeq2000 or NextSeq500.

treatment_protocol: WT and strain-matched Mettl4 KO ESCs

tag: cell type

value: cultured mouse ES cells

value: passages 3-5


title: KO-O-NAcGlc

value: cultured ES cells

value: Santa Cruz  O-GlcNAc CTD110.6, Lot G0715


title: RNA-seq-KO1


title: RNA-seq-KO2


title: cde-1 (tm1021) ; drh-1 (ok3495) rep2 [5' dependent]


title: RNA-seq-WT1


title: WT rep1 [5' dependent]


title: cde-1 (tm1021) ; drh-1 (ok3495) rep1 [5' dependent]


title: KO-H2AK119Ub

value: Cell Signaling H2A-K119Ub D27C4 Lot 07/2016


title: WT-H2AK119Ub


title: KO-BAP1

value: Santa Cruz BAP1 C-4, Lot B2117


title: mEpiSC1000

city: Beijing

first: Yusi

last: Fu

address: biopic,PKU

institute: PKU

data_processing:
Base-calling performed by RTA v1.9 and CASAVA v1.8.2
filter reads that have too many N, of too low quality or with the adaptor sequence
align reads with Bowtie 2 version 2.0.0-beta7, default setting
peak-calling with MACS 1.4.1 20110622 with  --keep-dup all --bw 180
Genome_build: mm9
Supplementary_files_format_and_content: wig file is generated by MACS

source_name: 1000 mEpiSCs

extract_protocol:
use microfludic chip to do DNA extraction, MNase digestion and ChIP
The reagents for library preparation were provided by Illumina and were used according to the manufacturer’s protocol with appropriate modifications as described below. We purified DNA from the ChIP assay by AMPure XP beads and eluted the DNA by 20 μl Resuspension Buffer. The DNA suspension was concentrated from 20μl to 5μl by evaporation. Then, 4 μl of End Repair Mix and 1 μl Resuspension Buffer were added to the 5 μl of cleaned up DNA suspension before incubating at 30 ºC for 30 minutes and inactivating at 75 ºC for 15 minutes for end repairing. Adenylation of  3’ ends is performed by adding 8.4 μl thawed A-Tailing Mix and 1.6 μl Resuspension Buffer and incubating at 37 ºC for 30 minutes. We ligated adapters by adding 1.7 μl of DNA Ligase Mix, 3.1 μl Resuspension Buffer, and 0.2 μl Adapter Index. 30 ºC for 10 minutes is the duration for adapters ligation. We added 1 μl DNA which contains 100 ng of 5k size.= then purified DNA twice by AMPure XP Beads. Enrichment of DNA was achieved by PCR for 15 cycles. Polyacrylamide gel electrophoresis was followed another purification by AMPure XP Beads and we separated DNA with the length of 250-700bp. We extracted DNA from PAGE gel and purified it by a QIAGEN gel extraction kit.

tag: development stage

tag: ChIP


title: embryo_exp2

source_name: 1000 E6.5 epiblasts

value: E6.5 embryo


title: mEpiSCbulk

source_name: 1 million mEpiSCs


title: embryo_exp1


title: KO-Asxl1

tag: antibody

value: Santa Cruz ASXL1 6E2, Lot J0316


title: KO-IgG

tag: strain

value: lnvitrogen Mouse IgG 10005292, lot V017.


title: WT-Asxl1


title: WT-input


title: E17.5 Control female lung 2

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

data_processing:
Cutadapt 1.13
Trimmomatic 0.35
RNA-star 2.5.2b
Htseq-count 0.6.1p2
EdgeR 3.16.5
Genome_build: gencode v24 m11
Supplementary_files_format_and_content: 27Oct16_C_v_M_DE_Annotated.xls: annotated counts and RPKM data
Supplementary_files_format_and_content: AlignmentStatistics.xls: total read counts from processing

source_name: E17.5 Control female lung

extract_protocol:
Embryonic lungs were isolate from E17.5 embryos in cold PBS. Esophagus, trachea ancd bronchi were removered. Total RNA was extracted with Trizon and isolated with  RNA-mini Qiagen colums. Samples were treated with DNAse before transcriptome profiing analysis
Illumina TruSeq v2

treatment_protocol: Activation of TGF-beta signaling pathway in the murine embryonic lung epithelium

tag: strain background

tag: developmental stage

tag: gender

value: female

value: control

value: whole embryonic lung


title: E17.5 Control male lung 2

source_name: E17.5 Control male lung

tag: tissue


title: WT-IgG

tag: passages


title: E17.5 Control male lung 1


title: WT mouse ES cells 6mA DIP

tag: medip antibody

value: Active Motif 6mA antibody Catalog No: 61495 Lot W034


title: E17.5 Mutant male lung 2

source_name: E17.5 Mutant male lung

value: expressing the constitutive active form of the Tgf-b receptor 1


title: WT mouse ES cells control IgG DIP

value: Invitrogen mouse IgG 10005292, lot V017.


title: WT-O-NAcGlc


title: WT-BAP1


title: E17.5 Mutant female lung 1

source_name: E17.5 Mutant female lung


title: E17.5 Control female lung 1


title: E17.5 Mutant male lung 1

value: male


title: ERY-DKO2

city: CHCAGO

first: BAOBING

last: ZHAO

state: IL

address: 303 E CHICAGO AVENUE

institute: NORTHWESTERN UNIVERSITY

data_processing:
Standard Illumina adapters were removed from fastq files using cutadapt (version 1.13).
Trimmed reads were then aligned to the mouse reference genome mm10 using STAR (version 2.5.2a).
Raw read counts were determined using htseq-count as part of HTSeq (version 0.6.1pl).
Differential expression was performed using DESeq2 (version 1.14.1).
Genome_build: mm10
Supplementary_files_format_and_content: Text Document  include Raw read counts for each Sample

source_name: Erythroblast

extract_protocol:
Total RNA was extracted with the TRIzol reagent. RNA quality and quantity was checking using an Agilent Bio-analyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols. Libraries were QC-ed and quantitated using an Agilent bio-analyzer.

treatment_protocol: TER119 positive cells were directly purified from JAK2V617F/+ Plek2+/+ and JAK2V617F/+ Plek2-/- bone marrow. C-kit+ cells were purified from  JAK2V617F/+ Plek2+/+ and JAK2V617F/+ Plek2-/- bone marrow lineage negative cells.

tag: genotype


title: HSPC-VF1

source_name: Hematopoietic stem / progenitor cells


title: HSPC-VF2


title: HSPC-DKO1


title: KO-input


title: ERY-DKO1


title: CNV 3

value: RPE-choroid-sclera complexes from laser-induced CNV eye (7 days after the laser photocoagulation)

value: Seven to eight-week-old


title: ERY-VF1


title: 2.WT36_mRNA_PolyRNASeq

status: Public on Apr 10 2019

city: Leuven

first: Kim

last: De Keersmaecker

address: Herestraat 49

department: Oncology

country: Belgium

institute: KU Leuven

description:
2-WT36
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

data_processing:
rRNA and tRNA contamination was computationally removed by mapping reads to tRNA and rRNA references by Bowtie2 and collecting only unaligned reads
Preprocessed ribosome footprints were mapped to the mm10 reference genome using Tophat v.2.0.11 with the following parameters: --b2-sensitive –no-novel-juncs –transcriptome-index Mus_musculus.GRCm38.76.chr. High quality uniquely mapped ribosome footprints were kept, using samtools view -b -F 256 -q 10
Gene expression was estimated counting exon-aligned reads using HTSeq-count in union mode.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 normalized counts for each sample

source_name: isogenic Ba/F3_WT form of human RPL10_mRNA_polyRNAseq

extract_protocol:
RNA extraction was performed using the phenol/chloroform method with inclusion of an extra washing step with 70% ethanol.
Next generation sequencing libraries were generated from total RNA and polysomal RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina)

value: mouse lymphoid Ba/F3 cells

value: isogenic Ba/F3 cells engineered to express the WT form of human RPL10

tag: replicate

value: Replicate 2, RPL10 WT clone #36

tag: molecule subtype

value: polyA RNA


title: 3.WT29_mRNA_PolyRNASeq

description:
3-WT-29
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

tag: genotype/variation

value: Replicate 3, RPL10 WT clone #29


title: 3.WT36_mRNA_PolyRNASeq

description:
3-WT36
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 3, RPL10 WT clone #36


title: 2.WT28_mRNA_PolyRNASeq

description:
2-WT28
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 2, RPL10 WT clone #28


title: 2.R98S13_mRNA_PolyRNASeq

description:
2-R98S13
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

source_name: isogenic Ba/F3_R98S mutant form of human RPL10_mRNA_polyRNAseq

value: isogenic Ba/F3 cells engineered to express the R98S mutant form of human RPL10

value: Replicate 2, RPL10 R98S clone #13


title: 3.R98S13_mRNA_PolyRNASeq

description:
3-R98S13
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 3, RPL10 R98S clone #13


title: 3.WT28_mRNA_PolyRNASeq

description:
3-WT28
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 3, RPL10 WT clone #28


title: 3.R98S35_mRNA_PolyRNASeq

description:
3-R98S35
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 3, RPL10 R98S clone #35


title: 2.R98S11_mRNA_PolyRNASeq

description:
2-R98S11
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 2, RPL10 R98S clone #11


title: 1.WT29_mRNA_PolyRNASeq

description:
1-WT29
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 1, RPL10 WT clone #29


title: 1.WT28_mRNA_PolyRNASeq

description:
1-WT28
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 1, RPL10 WT clone #28


title: E17.5 Mutant female lung 2

value: female

value: expressing the constitutive active form of the Tgf-b receptor 1

value: whole embryonic lung


title: HSPC-DKO2


title: 1.R98S35_mRNA_PolyRNASeq

description:
1-R98S35
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: mouse lymphoid Ba/F3 cells

value: Replicate 1, RPL10 R98S clone #35


title: 1.R98S13_mRNA_PolyRNASeq

description:
1-R98S13
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 1, RPL10 R98S clone #13

value: polyA RNA


title: 1.R98S11_mRNA_PolyRNASeq

description:
1-R98S11
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 1, RPL10 R98S clone #11


title: ERY-VF2


title: 3.WT36_PolyRNASeq

description:
Poly_3.WT36
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

source_name: isogenic Ba/F3_WT form of human RPL10_polyRNAseq

value: isogenic Ba/F3 cells engineered to express the WT form of human RPL10

value: Replicate 3, RPL10 WT clone #36

value: polysome associated mRNA


title: 3.R98S35_PolyRNASeq

description:
Poly_3.R98S35
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

source_name: isogenic Ba/F3_R98S mutant form of human RPL10_polyRNAseq

value: isogenic Ba/F3 cells engineered to express the R98S mutant form of human RPL10


title: 3.WT29_PolyRNASeq

description:
Poly_3.WT29
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

value: Replicate 3, RPL10 WT clone #29


title: 3.WT28_PolyRNASeq

description:
Poly_3.WT28
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

value: Replicate 3, RPL10 WT clone #28


title: 3.R98S13_PolyRNASeq

description:
Poly_3.R98S13
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

value: Replicate 3, RPL10 R98S clone #13


title: 3.R98S11_mRNA_PolyRNASeq

description:
3-R98S11
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 3, RPL10 R98S clone #11


title: 2.WT29_PolyRNASeq

description:
Poly_2.WT29
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

value: Replicate 2, RPL10 WT clone #29


title: 3.R98S11_PolyRNASeq

description:
Poly_3.R98S11
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq


title: 2.R98S13_PolyRNASeq

description:
Poly_2.R98S13
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

value: Replicate 2, RPL10 R98S clone #13


title: 2.WT29_mRNA_PolyRNASeq

description:
2-WT29
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq


title: 2.R98S35_mRNA_PolyRNASeq

description:
2-R98S35
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingPolySeq

value: Replicate 2, RPL10 R98S clone #35


title: 2.R98S35_PolyRNASeq

description:
Poly_2.R98S35
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq


title: 1.R98S13_PolyRNASeq

description:
Poly_1.R98S13
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq


title: 1.R98S35_PolyRNASeq

description:
Poly_1.R98S35
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq


title: 1.WT29_PolyRNASeq

description:
Poly_1.WT29
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

value: Replicate 1, RPL10 WT clone #29


title: R98S35_mRNA_Suppl

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were preprocessed by trimming the first nucleotide from the 5′ end of each read, as it usually is a untemplate addition by the reverse transcriptase
rRNA and tRNA contamination was computationally removed by mapping reads to tRNA and rRNA references (Mus_musculus.GRCm38.ncrna.fa) by Bowtie2 and collecting only unaligned  reads
Preprocessed reads were mapped to the mm10 reference genome using Tophat with the following parameters: --b2-sensitive –no-novel-juncs –transcriptome-index Mus_musculus.GRCm38.76.chr. High quality uniquely mapped ribosome footprints were kept, using samtools view -b -F 256 -q 10
Features count was performed using HTSeq with the following parameters:  -i gene_name -f sam -a 0 -m union -t exon -s no
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 normalized counts for each sample

source_name: isogenic Ba/F3_R98S mutant form of human RPL10_mRNA_Suppl

extract_protocol:
RNA was isolated using the Maxwell 16 LEV simplyRNA Cells Kit (promega)
Next generation sequencing libraries were generated from total RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina)

treatment_protocol: Cells were treated with cycloheximide (CHX, 100 μg/ml) for 5 min and pelleted by centrifugation

value: mouse lymphoid Ba/F3 cells

tag: rpl10 form

tag: clone

value: RPL10 R98S clone #35


title: WT36_mRNA_Suppl

source_name: isogenic Ba/F3_WT form of human RPL10_mRNA_Suppl

tag: cell type

value: RPL10 WT clone #36


title: 1.R98S11_PolyRNASeq

description:
Poly_1.R98S11
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq


title: WT28_mRNA_Suppl

value: RPL10 WT clone #28


title: WT28_mRNA_RiboSeq

description:
wt28_RNA_RPF
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingRiboSeq

data_processing:
Illumina Casava1.7 software used for basecalling.
For both ribosome footprinting and RNA-Seq libraries, reads were trimmed to remove the first nucleotide from the 5’.  Additionally,  adaptor sequences were removed from reads from ribosome footpriniting libraries and only clipped reads of a minimum length of 20 nct were kept.
rRNA and tRNA contamination was computationally removed by mapping ribosome footprints to tRNA and rRNA references by Bowtie2 and collecting only unaligned  ribosome footprints
Preprocessed  reads were mapped to the mm10 reference genome using Tophat v.2.0.11 with the following parameters: --b2-sensitive –no-novel-juncs –transcriptome-index Mus_musculus.GRCm38.76.chr. High quality uniquely mapped reads were kept, using samtools view -b -F 256 -q 10
Features count was performed for reads from ribosome footprinting libraries considering only those aligned to the CDS and excluding those aligned to the first 15 and last 5 codons due to the accumulation of ribosomes at these sites (PMIDs: 22056041, 25159147).  For reads from RNA-Seq instead, features count was performed considering those aligned to exons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 normalized counts for each sample

source_name: isogenic Ba/F3_WT form of human RPL10_RNAseq

extract_protocol:
Ribosome footprinting libraries. RNA fragments  were purified using Trizol. RNA-Seq libraries. RNA was isolated using the Maxwell 16 LEV simplyRNA Cells Kit (Promega)
Ribosome footprinting libraries. RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30 to 33 nucleotides was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 PNK (New England Biolabs) for 4 hrs at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England Biolabs) for 2.5 hrs at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 hrs at 22°C. To deplete ribosomal RNAs (rRNA), the resulting fragments were incubated with a biotinylated rRNAs oligo pool (10 μM each) for 10 min at 37°C, upon short denaturation at 95-100 °C for 1 min. rRNA depletion was carried on using MyOne Streptavidin C1 DynaBeads (ThermoFisher Scientific). The resulting rRNA-depleted fragments were reverse transcribed using the SuperScript III cDNA synthesis kit. Samples were PCR-amplified for 15 cycles and the products were multiplexed and sequenced on an Illumina HiSeq 2000 platform in single read 50 nucleotides mode. RNA-Seq libraries. Libraries were generated from total RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina)

treatment_protocol: Ribosome footprinting libraries. Cells were treated with CHX (100 μg/ml) for 5 min and lysed in buffer containing 20 mM Tris-HCl, pH 7.8, 100 mM KCl, 10 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 μg/ml CHX, and 1X complete protease inhibitor. Lysates was treated as following: centrifugation (5,000 rpm), RNAse I digestion of the supernatant (2 U/μl of RNase I, Thermo Scientific, 40 min, room temperature), fractionation on a linear sucrose gradient (7% to 47%) using the SW-41Ti rotor at 36,000 rpm for 2 hrs; pooling of fractions enriched in ribosomes; proteinase K (Roche) in a 1% SDS solution. RNA-Seq libraries. Cells were treated with cycloheximide (CHX, 100 μg/ml) for 5 min and pelleted by centrifugation.


title: WT29_mRNA_RiboSeq

description:
wt29_RNA_RPF
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingRiboSeq

value: RPL10 WT clone #29


title: WT29_mRNA_Suppl

value: isogenic Ba/F3 cells engineered to express the WT form of human RPL10


title: R98S35_mRNA_RiboSeq

description:
R98S35_RNA_RPF
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingRiboSeq

source_name: isogenic Ba/F3_R98S mutant form of human RPL10_RNAseq


title: WT36_mRNA_RiboSeq

description:
wt36_RNA_RPF
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingRiboSeq


title: R98S13_mRNA_Suppl

value: RPL10 R98S clone #13


title: R98S11_mRNA_RiboSeq

description:
R98S11_RNA_RPF
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingRiboSeq

value: RPL10 R98S clone #11


title: WT29_RiboSeq

description:
wt29_RPF
ribosome footprinting
processed data file: NormalizedCountsByDESeq2_RiboSeq

source_name: isogenic Ba/F3_WT form of human RPL10_RiboSeq


title: WT36_RiboSeq

description:
wt36_RPF
ribosome footprinting
processed data file: NormalizedCountsByDESeq2_RiboSeq


title: R98S13_mRNA_RiboSeq

description:
R98S13_RNA_RPF
RNA-Seq
processed data file: NormalizedCountsByDESeq2_RNASeqMatchingRiboSeq

value: isogenic Ba/F3 cells engineered to express the R98S mutant form of human RPL10


title: R98S35_RiboSeq

description:
R98S35_RPF
ribosome footprinting
processed data file: NormalizedCountsByDESeq2_RiboSeq

source_name: isogenic Ba/F3_R98S mutant form of human RPL10_RiboSeq


title: R98S11_mRNA_Suppl


title: R98S13_RiboSeq

description:
R98S13_RPF
ribosome footprinting
processed data file: NormalizedCountsByDESeq2_RiboSeq


title: R98S11_RiboSeq

description:
R98S11_RPF
ribosome footprinting
processed data file: NormalizedCountsByDESeq2_RiboSeq


title: 2.WT28_PolyRNASeq

description:
Poly_2.WT28
polysomal RNA sequencing
processed data file: NormalizedCountsByDESeq2_PolySeq

value: Replicate 2, RPL10 WT clone #28

value: polysome associated mRNA


title: WT HSPC sample_2

status: Public on Apr 09 2019

city: New York

first: Timothy

middle: Cragin

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie2 and Tophat 2.0.4.
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: Xlsx file with raw counts for each gene

source_name: C57BL/6 mouse  bone marrow

extract_protocol:
Total RNA was isolated from sorted 2,000 Hematopoetic Stem and Progenitor Cells (HSPCs) using the ARCTURUS PicoPure RNA isolation kit (Life Technologies).
cDNA was amplified using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories),
Libraries were constructed using the Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions.

value: hematopoetic stem and progenitor cells


title: WT HSPC sample_3


title: Hdc-/- HSPC sample_4

source_name: Hdc-/- mouse (C57BL/6 background) bone marrow


title: WT HSPC sample_4


title: Hdc-/- HSPC sample_3

value: stem and progenitor cells


title: Hdc-/- HSPC sample_2


title: Hdc-/- HSPC sample_1


title: Peripheral whole blood_ health _ rep2

first: Yu-Jin

last: Zhu

address: FuXing Road, Haidian District

institute: Chinese PLA General Hospital

data_processing:
in-house perl scripts
Bowtie v2.0.6
TopHat v2.0.9.
Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010)
Cuffdiff (v2.1.1) was used to calculate FPKMs
Genome_build: hg19
Supplementary_files_format_and_content: excel,FPKM

source_name: Peripheral whole blood

growth_protocol: 2ml Peripheral blood was isolated from each sample and saved

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5x). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNaseH-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

tag: group

value: Control

tag: disease

value: healthy


title: Peripheral whole blood_ health _ rep3


title: Peripheral whole blood_ health _ rep1


title: Peripheral whole blood_ high IgE _ rep1

value: high IgE

value: eosinophilic asthmatics


title: Peripheral whole blood_ high IgE _ rep4


title: Peripheral whole blood_ high IgE _ rep2


title: Peripheral whole blood_ high IgE _ rep3


title: WT28_RiboSeq

description:
wt28_RPF
ribosome footprinting
processed data file: NormalizedCountsByDESeq2_RiboSeq

value: mouse lymphoid Ba/F3 cells


title: Peripheral whole blood_ low IgE _ rep3

value: low IgE


title: Peripheral whole blood_ low IgE _ rep1


title: WT HSPC sample_1


title: m7_Brain

status: Public on Apr 06 2019

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina).
FASTQ-formatted sequence data was analyzed using a standard TopHat-Cufflinks workflow. RNA-Seq sequence reads (FASTQ format) were aligned to the reference human genome assembly (Feb. 2009, GRCh37/hg19) using TopHat software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. FPKM values were utilized for downstream analysis steps.
Processed data are Cufflinks output files and contain Gene_Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: Feb. 2009, GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol (Ensembl ID), FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks gene-level output files.

source_name: H1_DL2 human melanoma xenograft cells

growth_protocol: H1_DL2 cells were grown in DMEM supplemented with 10% heat-inactivated newborn calf serum, four times the prescribed concentration of non-essential amino acids, 2% L-glutamine, penicillin (100 IU/ml), and streptomycin (100 ul/ml) (BioWhittaker, Verviers, Belgium). The cells were kept in a standard tissue culture incubator at 37°C (100% humidity, 5% CO2). The growth medium was exchanged twice a week. H1_DL2 xenograft tumors were then generated by performing intracardiac injections of cells in seven mice (5x10^5 H1_DL2 cells suspended in 0.1 mL PBS). Whole-body bioluminescence imaging (BLI) was performed weekly to monitor metastasis formation using a Xenogen Ivis 100 Small Animal Molecular Imager (Xenogen Corporation). At seven weeks, 150 mg/kg D-luciferin Firefly (Gold Biotechnology) was injected, the mice were sacrificed 10 minutes later, ex vivo BLI performed in order to evaluate organ involvement in detail. All animals invariably developed metastases in their brain, adrenals, ovaries, and femurs, and these organs from five animals were then dissociated using Liberase TM Research Grade (Roche Applied Science). Cell sorting for metastatic GFP-positive tumor cells from each organ was then performed with a BD Influx high-speed cell sorter (BD Biosciences). The GFP-positive cell samples were collected in 1% FBS medium, pelleted by centrifugation, snap-frozen, and stored in a -80C freezer.

extract_protocol:
Total cellular RNA was isolated from snap-frozen cell pellets (73,942- 433,703 cells) using the TRIzol reagent (Life Technologies) and a modified protocol that incorporatesd an additional extraction with phenol/chloroform/isoamyl alcohol (25:24:1, pH 4.3).  RNA quantity and quality were assessed on a NanoDrop spectrophotometer (Thermo Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
RNA-Sequencing (RNA-Seq) libraries were prepared from 1 ug total RNA using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s protocol.  Briefly, poly-adenylated mRNA was purified from total RNA and ribosomal RNA removed by two rounds of binding to magnetic poly-T beads. This was followed by RNA fragmentation by incubation in the presence of divalent cations at 94C for 5 minutes.  Double-stranded cDNA was then generated by random-primed first-strand synthesis with SuperScript II reverse transcriptase and subsequent second strand synthesis with RNase H and DNA Polymerase I.  The cDNA was then blunt-ended with T4 and Klenow DNA polymerases to remove the 3'-overhangs and fill in 5'-overhangs, phosphorylated with T4 PNK, and then 3'-A tailed by incubation with Klenow Fragment (3´→5´ exo–) and dATP.  Illumina paired-end (PE) adapters were then ligated, followed by purification wit AMPure XP beads.  The library was then enriched by high-fidelity PCR amplification (15 cycles) with Phusion DNA Polymerase (Finnzymes Oy) and adapter-specific primers.

value: H1_DL2 metastasis to brain

tag: description

value: H1 subline generated by lentiviral transduction with Dendra (a GFP variant) and luciferase genes


title: m3_Bone

value: H1_DL2 metastasis to bone


title: m7_Adrenals

value: H1_DL2 metastasis to adrenals


title: m7_Ovaries

value: H1_DL2 metastasis to ovaries


title: m4_Bone


title: m6_Ovaries


title: m4_Brain


title: Betula luminifera degradome

status: Public on Apr 08 2019

city: beijing

first: junhong

last: zhang

address: Xiangshan Road

institute: Chinese Academy of Forestry

data_processing:
The raw reads of sRNA library were subjected to the Illumina pipeline filter (Solexa 0.3), The dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Raw sequencing reads of degradome library were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. The extracted sequencing reads were stored in _fileSampleA_RawData.txt and were then used in the standard data analysis, a Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: tab-delimited text files include reads for Sample
Supplementary_files_format_and_content: miRNA_targets_Betula.txt:
Supplementary_files_format_and_content: The Cleaveland column names for the 5 columns are position,raw reads,position normalized reads,mutiply hits, and category, respectively.

organism: Betula luminifera

source_name: roots, stems, and leaves

extract_protocol:
Total RNA was extracted from the samples using Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions.
Equal quantities of total RNA from roots, stems, and leaves were pooled to generate a sRNA library (LC Sciences, Hangzhou, China) using the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA). Approximately 20 ug of total RNA were used to prepare Degradome library. Approximately 150 ng of poly(A) RNA was used as input RNA and annealing with Biotinylated Random Primers

value: The roots, stems, and leaves from 2-month-old tissue culture seedlings


title: m1_Bone


title: m1_Brain


title: m1_Ovaries


title: Peripheral whole blood_ high IgE _ rep6


title: m1_Adrenals


title: hiPSCs differentiated to spinal cord motor neurons on matrigel day 30

city: Tel-Aviv

first: Irit

last: Gat-Viks

address: Tel-Aviv

department: Department of Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

data_processing:
Illumina HiSeq 2500 used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.87 whole genome using Tophat2 with parameters --b2-sensitive --no-coverage-search --min-intron-length 70 --max-intron-length 500000 -p 4 -N 3  Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.87 whole genome using Tophat2 with parameters --b2-sensitive --no-coverage-search --min-intron-length 70 --max-intron-length 500000 -p 4 -N 3
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: Homo Sapiens
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hiPSCs

growth_protocol: iPCSs were mainted in nutristem and were taken after 4 days grow on matrigel or inside omentum. Cardiomyocyte differentiation: Cells were differentiated as previously described (Lian et al 2012). Briefly; Growth media (NutriStem®)was changed daily until achieving 100% confluence, at this point (day 0 implants) medium was changed to RPMI (Biological Industries) supplemented with 0.5% glutamine (Biological Industries), B27 minus Insulin (Invitrogen, Carlsbad, California) and 10 µM CHIR-99021 (Tocris,Bristol, UK). Medium was changed every other day. At day 2, CHIR-99021 was removed. At day 4, 5µM IWP-2 (Tocris) was added and removed on day 6. At day 8, contracting implants were observed and medium was changed to medium supplemented with 0.5% glutamine, B27 minus retinoic acid (Invitrogen), and 1µM retinoic acid (Sigma). After day 10 medium was changed to M-199 (Biological Industries), supplemented with 0.1% penicillin/streptomycin, 5% FBS (Biological Industries), 0.6 mM CuSO4•5H2O, 0.5 mM ZnSO4•7H2O, 1.5 mM vitamin B12 (Sigma). Endotheilal cell differentiation: Cells were differentiated as previously described (Patsch et al 2015) with modifications. Briefly: after achieving ~90% confluence, medium was changed to 50% (v/v) Neurobasal (Invitrogen) 50% (v/v) DMEM/F12 (Biological Industries), supplemented with 1% penicillin/streptomycin, 1% glutamine, B27 minus retinoic acid, N2 supplement (Invitrogen), 1% non-essential amino acids (Invitrogen), 10 µM β-mercaptoethanol (Gibco, Welltham, Massachusetts), 8 µM CHIR- 99021(Tocris), BMP4 20 ng/ml (R&D, Minneapolis, Minnesota). On day 3 medium was changed to EGM-2 ™ (Lonza, Basel, Switzerland) and was changed every other day. Adipocyte differentiation: Cells were differentiated as previously described (Yang et al 2016). Briefly, upon achieving ~90% confluence medium was changed to Knockout/DMEM (Invitrogen), supplemented with 15% Knockout Serum (Invitrogen), 1% penicillin/streptomycin, 0.5% glutamine, 1% non essential amino acids, 10 µM β-mercaptoethanol. At day 2, medium was replaced and supplemented with 1µM retinoic acid and 20 ng/ml ascorbic acid (Sigma). Medium was replaced at day 5. On day 7, cells were treated with adipogenic cocktail containing: 3 nM T3 (Sigma), 20 nM ascorbic acid, 0.5 µg/ml rosiglitazone (Sigma), 0.5 µg/ml insulin (R&D). Medium was changed every 2-3 days. On days 15-20, medium was supplemented with 20 nM ascorbic acid, 0.5 µg/ml rosiglitazone, 20 µg/ml insulin, 0.5 µM IBMX (Sigma), 0.1 µM dexamethasone (Sigma) and 0.06 mM indomethacin (Sigma). On days 21-27 medium was supplemented with 3 nM T3, 20 nM ascorbic acid, 0.5 µg/ml rosiglitazone, 10 µg/ml insulin. On day 27 cells and/or patches were stained using Oil red-O (Abcam) to asses lipid presence. Spinal cord motor neurons and deep layers cortical neurons differentiation: Cells were differentiated as previously described (Shimojo et al 2015) with modifications according to Edri et al 2015. Briefly, after achieving ~90% confluence medium was changed to Knockout/DMEM, supplemented with 15% Knockout Serum, 1% penicillin/streptomycin, 0.5% glutamine, 1% non-essential amino acids (Invitrogen), 10 µM β-mercaptoethanol, 10 mM SB-431542 (Tocris), 1 µM LDN-193189 (Tocris), 3 µM CHIR-99021 and was gradually changed every 3 days to DMEM/F12 supplemented with N2. On days 4 and 6 motor neuron media was supplemented with 1 µM retinoic acid  and 1 µM purmorphamine (Tocris). On day 8, both cortical and spinal media were supplemented with 30 ng/ml sonic hedgehog (R&D). After day 10 medium was changed every 3 days, supplemented with 5 µg/ml BDNF (R&D) and 100 µM ascorbic acid for both neuron types. In addition, for cortical neurons 30 ng/ml sonic hedgehog (R&D) and 50 ng/ml FGF8 (R&D) were added, and for motor neurons 125 ng/ml sonic hedgehog with 1 µM retinoic acid were added. Between day15-18, 2.5 µM DAPT (Tocris) were added until day 30.

extract_protocol:
Cells were suspended inside qiazole (Qiagene) and RNA was extracted using miRNeasy kit (Qiagen) and treated with DNAse.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: Omentum hiPSCs

tag: chip antibody


title: hiPSCs differentiated to spinal cord motor neurons insdie omentum hydrogel day 30


title: Peripheral whole blood_ low IgE _ rep2


title: hiPSCs differentiated to cortical neurons insdie omentum hydrogel day 30


title: hiPSCs differentiated to cardiac cells on matrigel day 30


title: hiPSCs differentiated to cortical neurons on matrigel day 30


title: hiPSCs day 4 on matrigel

value: hiPSCs day 4 on matrigel


title: hiPSCs differentiated to endothelial cells on matrigel day 8


title: hiPSCs differentiated to endothelial cells insdie omentum hydrogel day 7


title: hiPSCs day 4 inside omentum hydrogel

value: hiPSCs day 4 inside omentum hydrogel


title: hiPSCs differentiated to cardiac cells insdie omentum hydrogel day 30


title: RNA-Seq CTCF KO 2

status: Public on Apr 05 2019

city: London

first: Nathalie

last: Berube

address: 800 Commissioners Road East

institute: Children's Health Research Institute

data_processing:
RNA-Seq reads were aligned to mouse genome version mm10 using STAR version 2.5.3.a with default settings and GENCODE M11 primary annotations.
Count matrices were generated using the R GenomicAlignments package and normalized using DeSeq2
Low expressing genes (counts less than 2% of the average of all samples) were removed
Genes with an average fold change of 1.5 fold or greater between control and knockout were considered changed
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file containing normalized read counts and fold changes

source_name: Telencephalon

extract_protocol:
Tissue was preserved in RNAlater and sent to Otogenetics for extraction
cDNA was prepared using the Clontech Smart cDNA kit and Illumina libraries were prepared.

treatment_protocol: Telencephalon were dissected from E14 embryos. RNAlater was added and the samples shipped to Otogenetics for RNA isolation, library constructions and RNA seuqencint

tag: developmental stage

value: Embryonic day 14

tag: strain

value: Ctcf floxed; NestinCre


title: RNA-Seq Control 2

value: Ctcf floxed;


title: RNA-Seq CTCF KO 1


title: m3_Adrenals

tag: tissue


title: ChIP-seq telencephalon input

data_processing:
For telencephalon samples, base calling was performed with the Illumina pipeline 1.8.1, for MGE samples base calling and adapter trimming were performed by Illumina BaseSpace
ChIP-seq reads were aligned to mouse genome version mm10 using Bowtie2 version 2.3.2 with default settings.
Peak calling was perfomed using MACS2 version 2.1.1.20160309 with P=0.01 (MGE) or P=0.001 (Tel)
Genome_build: mm10
Supplementary_files_format_and_content: Peak files contain a list of ChIP-seq peaks in .bed format with a track line to enable viewing in the UCSC Genome Browser

extract_protocol:
Chromatin was sonicated to an average size of 500 bp, then 1/25 of total chromatin was set aside (input). The rest of the chromatin was incubated overnight with rabbit anti-CTCF antibody (Cell Signaling Technology) or rabbit IgG, as a control. CTCF-bound chromatin fragments were then purified using magnetic Dynabeads (Invitrogen), and crosslinking was reversed.
For telencepalon samples, libraries were prepared following New England Biolabs NEB ChIP-Seq Library Prep Kit for Illumina, for MGE libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: E13.5 MGE was dissected and pipetted up and down in DMEM to create a single cell suspension.

value: telencephalon


title: RNA-Seq Control 1


title: ChIP-seq telencephalon CTCF

value: rabbit anti-CTCF antibody (Cell Signaling Technology


title: ChIP-seq MGE CTCF

source_name: MGE

value: medial ganglionic eminence


title: ChIP-seq MGE input


title: Betula luminifera miRNA


title: H48BHISG_rep1

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Clostridiaceae difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v2
HtSeqCount was used for counting genes with default parameters
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied with the 48h BHISG value as a reference for reporting the expression data of 48h BHISG with Deoxycholate 240µM.
Genome_build: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts and Normalized Counts (48H BHISG with and withoutDeoxycholate 240µM), Normalized Counts, Statistics (FC, pvalue, Significant)

organism: Clostridioides difficile

source_name: Wild type strain 630_H48BHISG

growth_protocol: Strains were grown aerobically in BHISG at 37°C for 48 H

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols; Truseq stranded RNA seq kit

value: wild type

tag: growth condition

value: aerobically in BHISG at 37°C for 48hrs


title: H48D240_rep3

source_name: Wild type strain 630_H48D240

value: aerobically in BHISG at 37°C for 48hrs with 240 µM Deoxycholate


title: H48BHISG_rep2


title: CKC_15

city: Poznań

first: Michal

last: Kabza

address: ul. Fredry 10

country: Poland

institute: Poznan University of Medical Sciences

data_processing:
Short reads were trimmed using BBDuk2 version 36.32
Read mapping and methylation calling at each CpG site were performed using Bismark version 0.18.1
Differential methylation analysis was performed using DSS package version 2.14.0
Nearest gene for each differential methylation region was identified using BEDTools version 2.26.0
Genome_build: GRCh38
Supplementary_files_format_and_content: bedGraph files created by Bismark software and containing methylation percentage information for every CpG–context cytosine covered by at least one read

source_name: Cornea

extract_protocol:
The corneas were preserved in an Eusol-C solution (Alchimia, Ponte S. Nicolò, Italy) directly after corneal button excision during the surgical procedure, and stored at 4°C until DNA extraction. Genomic DNA samples from the corneas were extracted using the Cells and Tissue DNA Isolation Kit (Norgen Biotek, Thorold, ON, Canada) according to the manufacturer’s protocol.
RRBS libraries were performed using the NEXTflex Bisulfite Library Preparation Kit (Bioo Scientific, Austin, TX, USA) according to manufacturer’s instruction. In brief, 500 ng of high molecular weight genomic DNA was used for MspI digestion (New England Biolabs, Ipswich, MA, USA) followed by DNA purification using Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA). Purified fragmented DNA samples with 5′-CG-3′ overhangs were subject into end repair, adenylation and adaptor ligation reactions Bisulfite conversion was performed using the EZ DNA Lightning Kit (Zymo Research, Irvine, CA, USA), according to manufacturer’s instructions and followed by PCR amplification. The PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter). Prior to sequencing RRBS libraries were quantified using Qubit instrument (ThermoFisher Scientific, Waltham, MA USA) and qualified using Agilent 2100 Bioanalyzer High Sensitivity chips (Agilent Technologies, Santa Clara, CA, USA).

tag: condition

value: KTCN


title: H48D240_rep2


title: CKR_02

value: non-KTCN


title: CKC_18


title: CKR_11


title: CKR_92


title: CKC_19


title: SH-SY5Y_Pol2_rep2

status: Public on Apr 04 2019

city: Boston

first: John

middle: G

last: Flanagan

state: MA

address: 200 Longwood Ave, Building C2, Room 523

department: Cell Biology

institute: Harvard Medical School

data_processing:
ChIP-seq data quality was evaluated by using FASTQC (Andrews, 2010), and if required, reads were trimmed with Cutadapt (v1.4.2) (Martin, 2011).
High quality sequencing reads were mapped to the human genome UCSC build hg19 using Bowtie2 2.2.8 (Langmead and Salzberg, 2012). Alignments (BAM files) were filtered to retain only reads with a unique mapping to the genome.
Peaks were called with MACS2 2.1.1 (Zhang et al., 2008) using default parameters, and a narrow peak cutoff of P<0.001.
To assess the reproducibility of peaks across replicates, samples were run through the IDR pipeline (Babu et al., 2011), in which peak consistency was validated by use of pooled pseudo-replicates.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain genomic coordinates for peaks that were identified as reproducible, per the IDR analysis. BigWig files were generated from BAM files using Deeptools within the Galaxy platform (v1.0.4).

source_name: SH-SY5Y cells

growth_protocol: For ChIP-seq, two biological replicates from independent experiments were used for each condition. HepG2 and SH-SY5Y cells were maintained in EMEM or a 1:1 mixture of EMEM and F-12 medium, respectively. Medium was supplemented with 10% final concentration of fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37˚C.

extract_protocol:
Lysates were clarified from sonicated nuclei and IR-DNA or Pol2-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using Thruplex DNAseq kit (Rubicon) according to manufacturer’s instruction.

treatment_protocol: For serum starvation, medium was removed, cells were washed three times with PBS, and medium supplemented with 0.1% BSA was added to cells for 16h. Cells were stimulated with 10 nM insulin for 20min.

value: rabbit, anti-Pol2, CST_2629


title: CKC_17


title: CKC_16


title: SH-SY5Y_input_rep2


title: CKR_93


title: CKR_94


title: Peripheral whole blood_ high IgE _ rep5

value: high IgE

value: eosinophilic asthmatics


title: SH-SY5Y_Pol2_rep1


title: SH-SY5Y_IRb_rep1

value: rabbit, anti-IR_beta, sc-711


title: HepG2_IRb_input_rep1

description: input used for IRb rep-1 sample

source_name: HepG2 cells


title: HepG2_input_rep2

description: input used for all (starve and insuin-treated) rep-2 samples


title: HepG2_Pol2_rep1


title: H48D240_rep1


title: H48BHISG_rep3


title: HepG2_Pol2_rep2