title: mesc_hmc_500_R2

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

data_processing:
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a mouse genome (mm10 build), minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include coverage per CG

source_name: Embryonic stem cells

growth_protocol: mESCs were grown on 0.1% gelatin coated dishes in the presence of 1000 U/ml LIF and 15% FBS

extract_protocol:
Standard DNA phenol-chloroform extraction
5hmC in sonicated  genomic DNA was glycosylated with 6-azide-glucose. After ligation of adapters as described previously (Stasevskij et al., 2017),  the alkyne-bearing oligodeoxyribonucleotide with biotin was attached to the azide moiety of the modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads and subsequently used in a DNA priming reaction from the tethed oligonucleotide. Primed DNA library was amplified, size-selected and subjected to Ion Proton sequencing. uTOP-seq libraries were prepared as described in Stasevskij et al, 2017.

tag: modification


title: mesc_ucg_300_R3

status: Public on Apr 17 2020

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

value: unmodified CG sites


title: mesc_ucg_300_R1


title: mesc_ucg_300_R2


title: HUDEP2_r1

city: Guangzhou

first: Peng

last: Huang

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

country: China

institute: Guangzhou Medical University

description: processed data file: 2338_2343_nor.bigwig

data_processing:
library strategy: Capture-C
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with the normalized Capture-C interaction signals

organism: Homo sapiens

growth_protocol: HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.

extract_protocol: Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).

treatment_protocol: HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.

tag: cell line

tag: tissue

value: Immortalized Human Erythroid Progenitor

tag: cell type

value: Erythroid cells

tag: differentiation

value: Differentiated for 5 days


title: Control_6hr_Replicate1 [24_6_rep1]

city: Aubière

first: Said

last: Mouzeyar

address: 1 Impasse Amélie Murat

department: Biology

country: France

institute: Université Clermont Auvergne

library_source: transcriptomic

data_processing:
basecalling Illumina RTA 1.18.64
demultiplexing software bcl2fastq-1.8.4.  Sequences are demultiplexed according to the 2x8 bp index code with 1 mismatch allowed.
Mapping of reads to the reference genome using BWA-MEM (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1)
Raw read counts created using featureCounts on a Galaxy web server (Galaxy Tool Version: 1.4.6.p5) with default parameters and feature type filter = gene. The annotation version 3.3 of P. patens genome (file Ppatens_318_v3.3.gene.gff3 was downloaded from http://plants.ensembl.org).
Genome_build: Ppatens_318_v3 (https://genome.jgi.doe.gov/)
Supplementary_files_format_and_content: featureCounts.  gene level expression estimates; tab-delimited text

molecule: total RNA

organism: Physcomitrium patens

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 24 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 6H.

extract_protocol:
Total moss RNA was extracted from 100 mg of P. patens 7-day protonemal tissues from control or heat-treated samples using Nucleospin® RNA plant (Macherey-Nagel-Germany).
Sequencing was carried out by Eurofin (Germany) using one channel and Illumina Illumina HiSeq 2500 2x 100 bp paired-end. RNA libraries were prepared for sequencing using standard Illumina protocols
strand-specific cDNA libraries; RNA selection using polyA selection. RNAseq

tag: strain

value: Gransden

value: protonema

tag: treatment


title: mesc_hmc_500_K2


title: mesc_hmc_500_R1


title: Primary_erythroblast_input

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome hg38 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: hg38;
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks

growth_protocol: Human CD34+ HSPCs were cultured using a three-phase protocol. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 50 ng/mL IL3, 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin. For Phase II medium, the IL3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Libraries were prepared using TruSeq ChIP-seq Sample Preparation Kit (Part# IP-202-1012) according to Illumina's instructions.

value: Adult peripheral blood

value: CD34+ derived erythroblasts

value: Day 11


title: HUDEP2_BCL11A+55KO_input

treatment_protocol: The ATF4 binding motif at the BCL11A +55 enhancer was disrupted using a CRISPR-Cas9-mediated approach in pooled HUDEP2 cells.

value: Undifferentiated


title: HUDEP2-ATF4-r2

tag: chip antibody

value: ATF4 (Cell Signaling Technology, 11815S, lot 4)


title: Control_1hr_Replicate1 [24_1_rep1]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 24 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 1H.


title: Experienced SP3 4

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

description: Gene expression data from SP19-experienced animal subsequently infected with SP3.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

label: biotin

source_name: whole lung homogenate

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Mice were euthanized by isoflurane overdose, and lungs were perfused through the right ventricle with 5 mL of PBS for exsanguination.  Excised lung lobes were digested in a solution containing type 2 collagenase (1 mg/ml), DNase I (150 mg/ml), and CaCl2 (2.5mM) in PBS while shaking at 37°C for 1 hour before being passed through a 70-mm cell strainer (Fisher, Grand Island, NY).  Erythrocytes were removed using red blood cell lysis buffer (Sigma, St Louis, MO), and single-cell suspensions were counted using a cell counter.

extract_protocol: RNA was extracted from the samples of sorted cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Alveolar macrophages were collecetd by cell sorting. After Fc receptor blocking (FcBlock αCD16/CD32, eBioscience) to reduce non-specific binding, cells were incubated with combinations of monoclonal antibodies for 30 min on ice in the dark, and then washed with PBS containing FBS and EDTA.  Fluorochrome-conjugated monoclonal antibodies used in the study included but were not limited to CD11c-PE/Cy7 (clone HL3, BD Bioscience) and SiglecF-APC/Cy7 (clone E50-2440, BD Bioscience), and alveolar macrophages were defined as double-positive for those 2 surface markers.

value: whole lung homogenate

value: alveolar macrophage

tag: sp19 exposure

value: experienced


title: HUDEP2-ATF4-r1

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
human samples: Mapping to reference genome hg38 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: hg38;
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks


title: mesc_hmc_500_K1


title: mesc_hmc_50_R2


title: Experienced SP3 2


title: HUDEP2_input

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Genome_build: hg38;
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks


title: mesc_hmc_50_R1


title: mesc_hmc_50_K1


title: mesc_hmc_50_K2


title: SHED, 72h-Biodentine

city: Dongdaemun-gu

first: Hosun

last: Lee

state: Seoul

address: 26, Kyungheedae-ro

country: South Korea

institute: School of Dentistry, Kyung Hee University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: primary dental teeth

growth_protocol: To isolate and culture Stem cells from human exfoliated primary teeth (SHED), Pulp tissue was removed from the teeth using a barbed broach, placed in Dulbecco’s phosphate-buffered saline (PBS) solution (WELGENE, Gyeongsan-si, Geyongsangbuk-do, Korea). The removed tissue was then washed three times with PBS, and cut into small fragments band before preservation in alpha minimum essential medium (α-MEM, Gibco Invitrogen, Grand Island, NY, USA) including 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 mg/mL streptomycin. Cells were incubated at 37°C in a humidified atmosphere containing 5% carbon dioxide (CO2). When cells had grown enough to cover cell plates, trypsin was added and a new batch of subculture was initiated. SHED at passage 3 to 5 were used for experiments.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: passages

value: 3 to 5

value: BD

tag: time


title: SHED, 72h-Theracal LC

value: Stem cells from human exfoliated primary teeth (SHED)

value: TC


title: SHED, 72h-MTA

value: MTA


title: Experienced SP3 1


title: SHED, 24h-Theracal LC


title: mesc_hmc_5_R2


title: Experienced Control 3

description: Gene expression data from SP19-experienced animal subsequently treated with saline.

value: saline control


title: mesc_hmc_5_R1


title: SHED, 24h-Biodentine


title: Experienced Control 4


title: Experienced Control 1


title: Experienced Control 2


title: Naive SP3 4

description: Gene expression data from SP19-naive animal subsequently infected with SP3.

value: naive


title: mesc_hmc_5_K1


title: mesc_hmc_5_K2


title: Naive SP3 1


title: Naive SP3 3


title: TTA16_D5_scRNAseq

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

data_processing:
Data was demultiplexed using CellRanger
Fastq files were mapped using CellRanger
Count matrices were generated using CellRanger
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Genomics CellRanger output for scRNAseq 3’ V2 kit

source_name: Human postnatal thymus

extract_protocol:
Pediatric thymus from children undergoing cardiac surgery were obtained and used according to and with the approval of the Medical Ethical Commission of Ghent University Hospital (Belgium). The thymus tissue was mechanically disrupted to obtain a single cell suspension. CD34+ thymocytes were enriched using MACS with CD34 microbeads (Miltenyi Biotec) according to the instructions of the manufacturer.
10X Genomics Chromium V2 kit – Manufacturers recommendations were followed

value: CD44+ Thymocytes

tag: donor


title: SHED, 24h-MTA


title: 231.ctrl.capMNase.SonicationFragment

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
Reads were filtered based on a mean base quality score >20.
Reads were mapped to hg19 genome using Bowtie 0.12.8 (with the following parameters: -I 0 -X 1000 -m 1) allowing only uniquely mapped hits. All paired-end reads were converted to a single fragment, and fragment midpoint and endpoint were extracted for the metaplot analysis. Mapped reads, midpoints, or endpoints were converted to bedGraph format with genomeCoverageBed from BEDtools and then to bigWig with UCSC utility bedGraphToBigWig. Mapped reads were also normalized to 18 million reads and generated bigWig files (indicated as 18M in the file names).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

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

extract_protocol: Libraries were prepared according to BIOO SCIENTIFIC instruction. RNA probes were obtained from Agilent. 750 ng of MNase-seq libraries were used to enrich targeted GATA3 peaks following the instruction in the SureSelect kit.

value: MDA-MB-231 with empty vector


title: 833: control 6 (saline at pnd 7)

city: Aurora

first: Tim

last: Benke

state: CO

department: Pediatrics

institute: University of Colorado School of Medicine

data_processing:
Trim galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim raw reads for adaptors and quality.
Trimmed reads were aligned to the Ensembl Rattus norvegicus 6.0 annotated transcriptome(Aken et al. 2017) and quantitated using RNAseq by Expectation Maximization (RSEM)(Li and Dewey 2011).
Subsequent to quality assessments on each sample, the data set was analyzed for differential expression analyses using DESeq2(Love et al. 2016).
RNA sequencing data were aligned to the Ensembl Norway Rat reference genome 6.0 using SamTools(Li et al. 2009).  The GATK pipeline for variant calling and filtering(Piskol et al. 2013) was used to generate variant calling files for each sample.
Quantification of splice variants for AMPA-R were determined using MISO(Katz et al. 2010).
RNAseq was performed in two separate rounds of hippocampal CA1 mRNA processed from 8 litter matched P14 control and KA-ELS rats per round.  The first round of sequencing was performed on HiSeq2500 platform, and the second round on the HiSeq4000 platform.  The average number of paired end reads per sample ranged from 25 to 86 million (Supplemental Table 2). There were no significant differences (p = 0.959, Mann-Whitney Rank sums) in the number of reads per sample in the first round of sequencing (55444299 ± 8006362 reads) as compared to the second round of sequencing (50280352 ± 1301910 reads).  The original read lengths differed between batches, 125 and 150 base-paired reads for the first and second batches, respectively.  The sequencing produced high quality data with mean Phred scores of 33 and 39 from the first and second rounds of sequencing, respectively, indicating > 99.9% accuracy of base calling.
Genome_build: Ensembl Norway Rat reference genome 6.0
Supplementary_files_format_and_content: DESeq2 output to excel spreadsheet

organism: Rattus norvegicus

source_name: dorsal CA1 hippocampus

extract_protocol:
P14 rats (seven days post KA-ELS) were decapitated without anesthesia and the brain rapidly removed.  Dorsal hippocampal slices were prepared by slicing the brain into parasagittal slices (400 μm) on a Leica VT 1200 microtome in ice cold solution containing (in mM) 206 Sucrose, 2.8 KCl, 1.25 NaH2PO4, 26 NaHCO3, 10 Glucose, 10 MgSO4, 2 NaAscorbate, 0.4 CaCl2, and 2.5 N-acetyl L-cysteine.  Scalpel cuts were made to remove CA3 while retaining the CA1 region of the hippocampus with the overlying cortex and dentate gyrus intact during recovery.  All slices from every animal were uniformly recovered for 60 min at room temperature in a submersion chamber in standard artificial Cerebral Spinal Fluid (aCSF), containing (in mM) 124 NaCl, 26 NaHCO3, 1.2 NaH2PO4, 10 D-glucose, 3 KCl, 2 NaAscorbate, 1 MgSO4, 2 CaCl2, and 2.5 N-acetyl L-cysteine) prior to all experiments in order to correlate to previous studies.  All solutions were oxygenated with 95% O2 - 5% CO2.  After recovery, the CA1 region of the hippocampus was further isolated from the slices for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male Sprague-Dawley rats were subcutaneously injected with KA (Tocris, Bristol, UK) (2 mg/kg) or saline on P7(Cornejo et al. 2007).  KA injection at this age induces discontinous seizure activity characterized by generalized tonic-clonic jerks, or “swimming” 30 min post injection that lasts nearly 3 hrs.  All of the rats used in these experiments seized uniformly.  Mortality rate for this study was 0%.

value: sprague dawley

value: dorsal CA1 hippocampus

tag: age

value: postnatal day 14


title: MC9 IP

city: Atlanta

first: Nicole

middle: M.

last: Baran

state: GA

address: 1510 Clifton Rd NE

department: Department of Psychology

institute: Emory University

data_processing:
Raw FASTQ files were processed using cutadapt to trim adapter sequences from the SmartSeq kit, Illumina TruSeq Indexed adapter, both poly-A and poly-T contamination and to exclude sequences shorter than 25bp.
Sequence reads were then aligned to the Metriaclima zebra (Malawi cichlid) reference genome UMD2A using HiSat2 and default parameters.
Transcripts were quantified using StringTie.
A pseudocount of 1 was added to all reads and differential expressional analyses were performed using DESeq2 using the default settings.
We compared transcript abundance in whole-brain input RNA to pS6-IP RNA from two species (MC & PC) exposed to either a mirror or control stimulus using three models in DESeq2. We considered the following three models.
Model 1: Differential Expression in Input versus IP samples ~ Batch + Condition + Species + SampleType, with a likelihood ratio test to evaluate the effect of SampleType
Model 2: Differential expression in IP samples in the Mirror Test ~ Batch + SampleType + Condition + Species + SampleType:Condition, with a likelihood ratio test to evaluate the effect of the SampleType:Condition interaction term
Model 3: Differential expression in IP samples in the Mirror Test by Species ~ Batch + SampleType + Condition + Species + SampleType x Condition + Sampletype:Condition:Species, with a likelihood ratio test to evaluate the effect of the three-way Sampletype:Condition:Species interaction term
Genome_build: M_zebra_UMD2a
Supplementary_files_format_and_content: Raw Read Counts from StringTie, Three tab-delimited text files (one per model) of DeSeq2 differential expression analysis output (baseMean, log2FoldChange, lfcSE, stat, pvalue, padj) all merged on gene_id with information from GTF file

organism: Mchenga conophoros

source_name: brain

extract_protocol:
Whole brains were removed, flash frozen, and stored at -80C. Frozen brains were homogenized in 2mL homogenization buffer on ice [10 mM HEPES, 150mM KCl, 5mM MgCl2 in RNAse-free water, plus 5uL of 1M DTT, 1/2 EDTA-free protease inhibitor tablet (Roche 11836170001), 5uL RNAsin (Promega N2611), 5uL cycloheximide (100mg/mL stock in DMSO), 10uL phosphatase inhibitor cocktail (ThermoScientific 78440), and 2uL of Calyculin A (1mg/mL in ethanol stock] per 2mL added 1 hour prior]. The lysate was then centrifuged at 2000xg for 10 min at 4C. The supernatant from each tube was transferred to new tubes and 140uL of 10% NP40 and 140uL DHPC (300 mM stock in chloroform). The tubes were mixed briefly and then incubated for 2 min on ice. The tubes were then spun at Rmax for 10 min at 4C and the supernatant was collected. For the input RNA sample, 50uL of this supernatant was added to 350uL of buffer RLT (Qiagen RNeasy Micro Kit) and stored on ice until purification. For the IP samples, immunoprecipitation was performed using Protein A Dynabeads (Life Technologies 10001D) loaded with pS6 antibody (Cell Signal 2215S). Briefly, we rinsed the pS6-loaded magnetic beads 2x in 0.15M KCl buffer and distributed the beads into two microcentrifuge tubes for each IP. After the second wash, the 0.15M KCl buffer was removed and then ~1mL of clarified supernatant was added to each tube and mixed to resuspend the beads. The tubes were incubated with end-over-end mixing for 10 min at 4C, which allows for antibody binding. After a brief spin, the tubes were placed on the magnet, and the supernatant was removed. The beads were then rinsed 4x in 0.9mL of cold 0.35M KCl buffer (10mM HEPES, 350mM KCl, 5mM MgCl2, 1% NP40, plus the following supplements added per 4mL: 5uL 1M DTT, 10uL RNAsin, 5uL cycloheximide, and 2uL Calyculin A). After the 3rd wash, the samples incubated at room temperature for 5 min, which allows for the dissociation of some of the non-specific RNA. After the 4th wash, the supernatant was removed, and the beads were resuspended in 350uL of buffer RLT and incubated on ice for 5 min. RNA from both the input and IP samples was purified using the Qiagen RNeasy Micro Kit (Qiagen 74004). RNA from both the input and IP samples was purified using the Qiagen RNeasy Micro Kit (Qiagen 74004). cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio 634888). We used 2uL of input RNA and the 10.5uL of the remaining IP RNA for cDNA synthesis and the maximum number of PCR cycles (18) during the cDNA amplification step. Library preparation was performed using NEBNext Ultra II FS DNA library Prep Kit for Illumina (NEB E7805S).
Library preparation was performed at the Molecular Evolution core facility at GT using NEBNext Ultra II FS DNA library Prep Kit for Illumina (NEB E7805S). Either 1ng (IP samples), or 5ng (Input samples) of cDNA were used as a starting material for the library preparation. The samples were pooled by equimolar normalization and sequenced on together in a single run on an Illumina NextSeq 500 instrument with 76 cycles (single-end).

tag: batch

value: a

value: brain

tag: antibody

value: IP - pS6 antibody

tag: condition

value: MT


title: Naive Control 3

description: Gene expression data from SP19-naive animal subsequently treated with saline.

value: whole lung homogenate

value: alveolar macrophage


title: 607: control 4 (saline at pnd 7)


title: Naive SP3 2


title: 231.TA1del.capMNase.rep3

value: MDA-MB-231 with TA1del mutant


title: MC9 Input

value: Input


title: Naive Control 4


title: Naive Control 2


title: MC22 IP

value: b

value: Control


title: SP3

city: Inglewood

first: Helen

middle: E

last: Vuong

state: CA

address: 10953 Penney Ave

institute: UCLA

data_processing:
Illumina HiSeq4000 software used for real-time basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTQC, then mapped to mm10 whole genome using HISAT 2.1.0 with parameters -q -t -p 4 --no-unal
Fragments Per Kilobase of transcript per million mapped reads (FPKM) were calculated as the total reads in a sample and divide that number by 1,000,000. By dividing the read counts by the "per million" scaling factor this normalizes for sequencing depth.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: E14.5 fetal brain

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: embryo day 14.5

value: C57 Bl/6J

tag: group

value: consortium of spore-former microbiome


title: 329: control 1 (saline at pnd 7)


title: 845: kainate 7 (KA-ELS at pnd 7)


title: SP2


title: 231.TA1del.capMNase.rep1

tag: cell line


title: 231.TA1del.capMNase.rep2


title: SP1

tag: tissue


title: MC22 Input


title: Naive Control 1

tag: cell type

value: naive

value: saline control


title: 231.ctrl.capMNase.MNaseFragment

value: MDA-MB-231 with empty vector


title: MC21 Input


title: 231.wtGATA3.capMNase.rep3

value: MDA-MB-231 with wild-type GATA3


title: ABX3

value: antibiotic treated microbiome


title: 362: kainate 3 (KA-ELS at pnd 7)

value: sprague dawley

value: dorsal CA1 hippocampus

value: postnatal day 14


title: 231.wtGATA3.capMNase.rep2


title: MC10 IP

value: a

value: brain

value: IP - pS6 antibody


title: 269: kainate 2 (KA-ELS at pnd 7)


title: MC10 Input

value: Input


title: ABX2


title: ABX1


title: 231.wtGATA3.capMNase.rep1


title: 22: kainate 1 (KA-ELS at pnd 7)


title: MC21 IP

value: b

value: MT


title: ATRA+bFGF 3

city: fujisawa

first: rei

last: nakano

address: 1866 Kameino

country: Japan

institute: Nihon University

data_processing:
Base Quality and Phred score relationship with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads.  The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.  RNA-seq Adapter sequences (Oligonucleotide sequences of adapters from TruSeqTM RNA and DNA Sample Prep Kits):  RNA 5' Adapter (RA5), part # 15013205:   5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'  RNA 3' Adapter (RA3), part # 15013207:   5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(6-nucleotide index)ATCTCGTATGCCGTCTTCTGCTTG-3'
Algorithm for mapping sequences: appropriate software is chosen according to the characteristics of the reference genome. In general, TopHat2 is chosen for animal and plant genomes, and Bowtie2 is chosen for the genomes of bacteria and other species with a high gene density. The mismatch parameter is set to two, and other parameters are set to default. Appropriate parameters are also set, such as the longest intron length. Only filtered reads are used to analyze the mapping status of RNA-seq data to the reference genome.
 In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used. In RNA-seq, FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, is the most commonest method of estimating gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments(Trapnell, Cole, et al., 2010). "HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode. The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not. HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode. The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: FPKM

organism: Canis lupus familiaris

source_name: primary cell culture

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA from eukaryotic organisms is enriched using oligo(dT) beads. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. 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?RNase H -?. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. 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, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: canine DFAT were treated with ATRA (10 ?M) and bFGF (100 ng/ml) for 28 days

value: ATRA + bFGF


title: 231.ctrl.capMNase.rep3


title: Petro24 Input

organism: Petrotilapia sp. 'chitimba'

value: Control

tag: name

value: Petrotilapia chitimba


title: 771: kainate 5 (KA-ELS at pnd 7)

tag: strain


title: ATRA+bFGF 2

tag: treatment


title: ATRA+bFGF 1


title: 231.ctrl.capMNase.rep2


title: SPF2

value: embryo day 14.5

value: C57 Bl/6J

value: specific pathogen free microbiome


title: Petro23 IP


title: SPF1


title: control 3

value: control


title: REXO2_rescued_B

city: Warsaw

first: Sylwia

last: Czarnomska

state: Mazowieckie

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description: cervix carcinoma; HeLa (DSMZ ACC57) modified by introduction of an FRT sequence and tetracycline repressor (see PMID: 22658674)

data_processing:
RNAseq raw data were preprocessed with FastQC (version 0.11.3) and trimmed of adapters using cutadapt (version 1.9.2.dev0). Low-quality bases and not properly paired reads were removed prior to mapping using Trimmomatic (version 0.32).
Trimmed reads were mapped to the human genome (GRCh38) using STAR aligner (version 2.5.2b) and the basic GENECODE v26 annotation with introduced features that allowed for quantification of all reads mapped in the D-loop region.
Mapped reads were counted using htseq-count (version 0.9.1) with settings -f bam -r pos -s reverse -t exon -i gene_id -m union and additionally re-counted with the option --nonunique all to collect data for 7SRNA and whole D-loop region separately.
Differential gene expression analysis was performed in edgeR package (version 3.18.1). Wiggle files of uniquely mapped reads were converted to BigWig format with the use of wigToBigWig package.
Genome_build: GRCh38

source_name: transgenic Flp-In T-REx-HeLa cell line

extract_protocol:
Total RNA was isolated with the use of TRI Reagent (T9424, Sigma) according to the manufacturer’s instructions. RNA was subjected to TURBO DNase (AM2238, Ambion) treatment and depletion of nuclear-encoded rRNAs (RiboZero Kit, Epicenter).
Libraries were constructed as previously described in Sultan et al., 2012 (PMID: 22609201) with minor modifications. Fragmentation and first strand cDNA synthesis were performed as in TruSeq RNA Library Prep kit v2 protocol (Illumina, RS-122-2001, instruction number 15026495 Rev. D), using SuperScript III reverse transcriptase (18080-085, Thermo Fisher Scientific). CutSmart buffer (NEB) was used for digestion with the USER Enzyme (NEB).  Enriched library quality was verified using 2100 Bioanalyzer and High Sensitivity DNA kit (5067-4626, Agilent). The libraries’ concentration was estimated by qPCR means with KAPA Universal Library Quantification Kit (KK4824, Kapa Biosystems), according to the supplied protocol. Sequencing was carried out on an Illumina NextSeq 500 sequencing platform, using NextSeq 500 High Output Kit (150 cycles) (FC-404-1002, Illumina) and pair-end sequencing procedures of 2x75 cycles (Instructions: 15048776 Rev. D, 15046563 Rev. F).

tag: experimental set

value: transcriptome (REXO2)

tag: parental cells

value: HeLa (DSMZ ACC57)

tag: sequenced rna species

value: > ~100 nucleotides

tag: is it control sample?

value: yes (rescue of REXO2 silencing)

value: transgenic HeLa cells expressing in the tet-inducible manner  miRNAs silencing endogenous copy of REXO2 gene and miRNA-insensitive form of REXO2


title: REXO2_rescued_C


title: Petro12IP

value: a

value: brain


title: control 2


title: REXO2_silenced_B

value: no

value: transgenic HeLa cells expressing in the tet-inducible manner  miRNAs silencing endogenous copy of REXO2 gene


title: control 1


title: Petro23Input

value: b

value: Input

value: MT


title: Petro11 IP

value: IP - pS6 antibody

value: Control

value: Petrotilapia chitimba


title: REXO2_silenced_A


title: CLIB214 CSE4-3HA R4 input DNA

city: Dublin

first: Geraldine

last: Butler

address: Belfield, Dublin 4

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute

data_processing:
Raw reads were provided by BGI (http://www.genomics.cn/en/index)
ChIP-seq reads were mapped to the genome of C. parapsilosis CDC317 (Butler et al. 2009) using the aln/samse algorithm from BWA v0.7.17-r1188 (Li and Durbin 2009), with default parameters.
Mapped reads were sorted and indexed with Samtools v 1.9 (Li et al., 2009).
Read coverage across the genome was computed using Bedtools v2.27.1 (Quinlan and Hall, 2010).
Genome coverage files were changed into bigwig format using bedGraphToBigWig v4 (Kent et al., 2010).
Genome_build: Candida parapsilosis CDC317
Supplementary_files_format_and_content: BigWig files represent read coverage information across the genome. Increased coverage is expected in regions where Cse4 binds.

organism: Candida parapsilosis

source_name: yeast cells

growth_protocol: Yeast cells were cultured to log phase in 200 ml YPD.

extract_protocol:
Immunoprecipitation was performed with EZview Red Anti-HA Affinity Gel (Sigma–Aldrich) or mouse IgG1 (Cell Signaling Technology) as isotype control. After overnight incubation with the selected antibody, bound DNA was washed with FA lysis buffer containing 1mM PMSF and eluted with HA peptide (Sigma–Aldrich) by incubation for 30 minutes at 30C. Following addition of Pronase (Sigma–Aldrich) and ChIP elution buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% w/v SDS) to the HA peptide elution supernatant, crosslinks were reversed, and the samples were purified by phenol–chloroform extraction.
BGISEQ500 ChIP-seq library construction carried by Beijing Genomics Institute (http://www.genomics.cn/en/index).

treatment_protocol: Cells were crosslinked for 20 minutes, at room temperature, using 37% formaldehyde to a final concentration of 1%. The reaction was followed by addition of 2.5 M glycine to stop crosslinking and cells were washed with ice-cold TBS (100 mM Tris–HCl, pH 7.5, 150 mM NaCl) and resuspended in FA lysis buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 0.1% w/v SDS) containing 1 mM PMSF. Cells were lysed for a total breakage time of 18 minutes using glass beads and chromatin fragmentation was obtained by sonication with a Bioruptor Standard (Diagenode) in 30s pulse - 30s rest cycles for a total of 30 minutes.

value: CLIB214 R4

tag: chip antibody


title: CLIB214 control IP

value: EZview Red Anti-HA Affinity Gel (Sigma–Aldrich)


title: parental_C

source_name: Flp-In T-REx-HeLa cell line

value: transcriptome (REXO2)

value: yes

value: parental Flp-In T-REx-HeLa cells


title: Petro24 IP


title: parental_B

value: HeLa (DSMZ ACC57)

value: > ~100 nucleotides


title: CLIB214 CSE4-3HA R1 input DNA

value: CLIB214 R1


title: CLIB214 CSE4-3HA R4 IP


title: parental_A


title: CLIB214 CSE4-3HA R1 IP


title: 90-137 CSE4-3HA N2 input DNA


title: Petro12 Input

value: a

value: brain


title: REXO2_rescued_A

value: yes (rescue of REXO2 silencing)

value: transgenic HeLa cells expressing in the tet-inducible manner  miRNAs silencing endogenous copy of REXO2 gene and miRNA-insensitive form of REXO2


title: U251 sh-ZEB2 Clone3

city: Shenyang

first: Wei

last: Wang

state: Liaoning

address: 155 Nanjing North Street

department: Department of Neurosurgery

institute: the First Affiliated Hospital of China Medical University

description:
Test
miRNAs
SAMPLE 6

data_processing:
Gene globe data analysis center was employed to analyze the data from three independent experiments according to the miRCURY LNA miRNA miRNome PCR Panels. All kits and analysis tools in the present arrays were provided by Qiagen (Hilden, Germany).
For the normalization it uses the average of four housekeeping genes: miR-191-5p, miR-103a-3p, let-7a-5p, miR-16-5p, and U6 snRNA.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control (U251 sh-ZEB2/U251 sh-NC) ratios.

label: SYBR Green

source_name: U251TR Clone3

label_protocol: miRCURY LNA miRNA custom probe PCR assays (QIAGEN, Hilden, Germany) were recuited to perform the miRNA microarray analysis following the Manufacturer’s instructions. Total RNA was extracted by miRNeasy mini kit (Qiagen) per the manufacturer's protocol. Then 500 ng RNA was reverse transcribed to cDNA by QuantiTect reverse transcription kit (Qiagen). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was conducted as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s, and 72 °C for 20s. All experiments were performed three times independently.

growth_protocol: U251 obtained from from Cell Bank of Chinese Academy of Sciences (Shanghai, China). Cells were grown in DMEM, supplemented with 10% FBS. All cell lines were maintained in a humidified incubator with 5% of CO2 and 95% air at 37°C.

extract_protocol: MicroRNA and total RNA in the U251 cells were extracted by miRNeasy mini kit(Qiagen, Hilden, Germany) per the manufacturer’s protocol.

treatment_protocol: U251 cells were introduced into short hairpin RNA targeting ZEB2 or the scambled negative control RNA (pGFP-V-RS_sh-ZEB2 and  pGFP-V-RS_sh-NC). The stable sub-clones were selected subsequently following by the manufacturer's protocol (OriGene, Rockville, MD, U.S.).

value: glioma cell

tag: genotype

value: ZEB2-knockdown subline (passage 5)


title: 90-137 CSE4-3HA N1 input DNA


title: 90-137 CSE4-3HA N2 IP


title: U251 sh-ZEB2 Clone2

description:
Test
miRNAs
SAMPLE 5

source_name: U251TR Clone2


title: U251 sh-NC Clone3

description:
Control
miRNAs
SAMPLE 3

source_name: U251 Clone3

value: parental cell line (passage 3)


title: Petro11 Input

tag: batch

value: Input

value: Control


title: U251 sh-NC Clone2

description:
Control
miRNAs
SAMPLE 2

source_name: U251 Clone2


title: 90-137 CSE4-3HA N1 IP


title: U251 sh-NC Clone1

description:
Control
miRNAs
SAMPLE 1

source_name: U251 Clone1


title: DC2 cells treated with SAG, rep1

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (Irizarry et al, 2003), as impelemented by TAC 4.0 software..

label: Biotin

source_name: DC2 immortalized epididymal principal murine cell line cultured in free serum

label_protocol: Total RNA (100 ng per sample) was labeled using the GeneChip® WT Plus Reagent Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Thermofisher).

growth_protocol: DC2 is a conditionally immortalized mouse epididymal epithelial cell line isolated from the distal caput of the mouse harbouring a temperature-sensitive simian virus 40 large T antigen. The functional expression of the SV40 large T antigen is induced by culturing the cells in vitro at permissive temperature (33°C). At a non-permissive temperature (37°C-39°C), the cells cease to proliferate.

extract_protocol: Total RNA was isolated from DC2 cells. Total RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, and potential genomic DNA contamination was eliminated with the RNase-free DNase set (Qiagen). Total RNA was eluted in RNAse-free water and its concentration was quantified with a NanoDrop 1000 microvolume spectrophotometer (Thermo Scientific). Ribonucleic acid quality was assessed with the Eukaryote Total RNA Pico Series II kit (Agilent) on a 2100 Bioanalyzer by the transcriptomic core facility of the CHUQ. The minimal accepted number for RNA integrity was 7.

treatment_protocol: Immortalized DC2 cells were treated for 24 hrs with 250 nM of Smoothened agonist (SAG, n=3, SAG 1, SAG 2 and SAG 3), 20 mM of Cyclopamine (Cyclo, n=3, Cyclo 1, Cyclo 2 and Cyclo 3) and control medium condition (Ctrl, n=3, Ctrl 1, Ctrl 2 and Ctrl 3).

value: 250 nM of SAG


title: DC2 cells treated with SAG, rep2


title: DC2 cells treated with Ciclopamine, rep3

value: 20 mM of Cyclopamine


title: DC2 cells treated with SAG, rep3


title: spt8-ko,WT--16C-IP rep1

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
ChIP-seq reads were aligned to S. cerevisiae genome using bwa version 0.7.17-r1188 with the following configurations…
reads that were marked as duplicates and mapped to multiple locations were removed by samtools version 1.9
read counts per bin were normalized to one million mapped reads (RPM) by deeptools version 3.2.1
Calling peak used MACS2 version 2.1.2
Genome_build: R64-1-1

organism: Saccharomyces cerevisiae

source_name: spt8-ko,WT--16C-IP rep1

extract_protocol:
Lysates were clarified from sonicated yeast cells and Rbp1-DNA complexes were isolated with antibody.Associated DNAs were purified by PCR clean-up kit (Axygen)
Libraries were prepared according to Illumina's instructions by Novogene.

value: WT

tag: culture temperature

value: 8WG16; Covance MMS-126R


title: spt8-ko,WT--30C-input


title: spt8-ko,WT--16C-IP rep2

source_name: spt8-ko,WT--16C-IP rep2


title: spt8-ko,WT--30C-IP rep2

source_name: spt8-ko,WT--30C-IP rep2


title: spt8-ko,WT--30C-IP rep1

source_name: spt8-ko,WT--30C-IP rep1


title: spt8-ko,WT--16C-input


title: spt8-ko,GAR--30C-IP rep2

source_name: spt8-ko,GAR--30C-IP rep2

value: GAR


title: DC2 cells treated with Ciclopamine, rep2


title: spt8-ko,GAR--30C-input


title: control-PDB-2

city: Tsukuba

first: Myco

last: Umemura

state: Ibaraki

address: Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology (AIST)

hyb_protocol: The labeled-cDNA was re-suspended in a 60 uL of hybridization solution (10.2 uL of 20x SSC, 21 uL of formamide, 0.6 uL of salmon testes, 1.8 uL of 10% SDS, and 26.4 uL of distilled water). After heat denaturation at 95C for 5 min and incubation at room temperature for 30 min, the labeled-cDNA mixture was applied onto the custom array slide for A. flavus (ID: 052932) designed on Agilent eArray for hybridization at 42C for 15 h.

scan_protocol: Scanned on a GenePix 4200A scanner (Axon Instruments at Molecular Devices, USA).

data_processing: Set measurements less than 0.01 to 0.01, normalize to 50 percentile per chip, and normalize to median per gene.

organism: Aspergillus flavus

source_name: control, PDB, rep 2

label_protocol: Extracted mRNA was labeled with Cy3 using CyScribe cDNA Post Labeling Kit (GE Healthcare, UK) according to the manufacturer's protocol.

growth_protocol: 1E5 spores of a strain were inoculated to 30 mL of V8 and PDB media in a 100-mL flask with buffle and cultured for 2 days at 30C, 160 rpm.

extract_protocol: Hyphae was collected through Miracloth (Merck Millipore) and mRNA was extracted using ISOGEN (Nippon Gene, Japan) according to the manufacturer's protocol.

tag: genotype/variation

value: control

tag: media

value: PDB


title: DC2 cells treated with Ciclopamine, rep1


title: ustRoe-PDB-1

source_name: ustRoe, PDB, rep 1

value: ustRoe


title: ustRoe-PDB-2

source_name: ustRoe, PDB, rep 2


title: DC2 cells treated with vehicle, rep3

value: vehicle


title: DC2 cells treated with vehicle, rep2


title: DC2 cells treated with vehicle, rep1


title: control-V8-2

source_name: control, V8, rep 2


title: spt8-ko,GAR--16C-IP rep2

source_name: spt8-ko,GAR--16C-IP rep2


title: HUDEP2_BCL11A+55KO_ATF4-r1

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome hg38 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: hg38;
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks

value: Immortalized Human Erythroid Progenitor

value: Erythroid cells

tag: differentiation

value: Undifferentiated

value: ATF4 (Cell Signaling Technology, 11815S, lot 4)


title: spt8-ko,GAR--30C-IP rep1

source_name: spt8-ko,GAR--30C-IP rep1


title: control-PDB-1

source_name: control, PDB, rep 1


title: Experienced SP3 3

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: whole lung homogenate

value: whole lung homogenate

value: alveolar macrophage

tag: sp19 exposure

value: experienced


title: spt8-ko,GAR--16C-input


title: control-V8-1

source_name: control, V8, rep 1


title: WT,WT--30C-IP rep2

source_name: WT,WT--30C-IP rep2


title: WT,WT--30C-IP rep1

source_name: WT,WT--30C-IP rep1


title: WT,WT--30C-input


title: WT,WT--16C-IP rep1

source_name: WT,WT--16C-IP rep1


title: spt8-ko,GAR--16C-IP rep1

source_name: spt8-ko,GAR--16C-IP rep1


title: WT,WT--16C-input


title: WT,GAR--30C-IP rep1

source_name: WT,GAR--30C-IP rep1


title: WT,GAR--30C-input


title: ustRoe-V8-2

source_name: ustRoe, V8, rep 2


title: WT,GAR--16C-IP rep1

source_name: WT,GAR--16C-IP rep1


title: WT,GAR--30C-IP rep2

source_name: WT,GAR--30C-IP rep2


title: 889: control 8 (saline at pnd 7)

source_name: dorsal CA1 hippocampus

value: sprague dawley

tag: tissue

value: dorsal CA1 hippocampus

tag: age

value: postnatal day 14


title: ZZ3: PBMC_BCG_wk3_ZZ

city: Seattle

first: Matthew

middle: Price

last: Wood

state: WA

address: 307 Westlake Ave North

department: Global Infectious Diseases

institute: Seattle Children's Research Institute

hyb_protocol: 100 nanograms of RNA was directly hybridized for 18 hours using the Non-human Primate Immunology v2.0 chipset.

scan_protocol: Images were acquired from 280 fields for each sample

data_processing: Raw data were processed in nSolver 4.0 using Advanced Analysis with R version 3.3.2 by running Normalization with the default settings of a threshold count value of 20 and an observation frequency of 1 with automatic selection of optimal house keeping genes.

organism: Macaca mulatta

source_name: Peripheral Blood, 3 weeks post-BCG

extract_protocol: Ficoll-paque gradient centrifugation was used to isolate 3.0EE6 macaque peripheral bllood mononuclear cells (PBMC) from EDTA-treated whole blood. Cellular RNA was extracted using the Macherey Nagel Nucleospin column purification system following the manufactureres instructions. PBMC were lysed by resuspending the 3.0EE6-cell pellat in 300µL of buffer RA1 with 1% beta-mercaptoethanol and storing long term at -80˚C. Lysed cells were thawed and RNA was purified prior to nanostring analysis.

tag: gender

value: F

tag: infant id

tag: week post-bcg timepoint

tag: bcg status

value: unvaccinated


title: ZZ0: PBMC_BCG_wk0_ZZ

source_name: Peripheral Blood, pre-BCG


title: WT,GAR--16C-IP rep2

source_name: WT,GAR--16C-IP rep2

tag: strain

value: GAR

value: 8WG16; Covance MMS-126R


title: WT,GAR--16C-input


title: FW3: PBMC_BCG_wk3_FW


title: 875: control 7 (saline at pnd 7)


title: WT,WT--16C-IP rep2

source_name: WT,WT--16C-IP rep2

value: WT


title: FV3: PBMC_BCG_wk3_FV


title: HEK293T_Tg-3

city: La Jolla

first: R. Luke

last: Wiseman

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

data_processing:
Basescaling was performed by BGI
Single end, 100 bp-long reads from RNA Seq experiments were aligned to the GRCh37.p13 human genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Counts Data were analyzed using DESeq
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: XLSX files contain counts data for each sample and DESeq differential expression analysis of test conditions vs. DMSO

source_name: human embryonic kidney cells

growth_protocol: HEK293T cells were maintained in standard DMEM supplemented with 10%FBS and 1%PSQ at 37C and 5% CO2

extract_protocol:
Three independent experiments were performed. Cells were lysed and total RNA was collected (RNeasy mini kit, Qiagen)
Libraries were constructed using standard protocols at BGI

treatment_protocol: Cells were treated with DMSO or compound for 4 hours

tag: cell line

value: human embryonic kidney

tag: treatment

value: 4 hours at 37C-UPR Activator


title: 785: control 5 (saline at pnd 7)


title: HEK293T_Tg-2


title: 522: control 3 (saline at pnd 7)


title: HEK293T_Tg-1


title: 519: control 2 (saline at pnd 7)


title: ustRoe-V8-1

source_name: ustRoe, V8, rep 1

value: ustRoe


title: 880: kainate 8 (KA-ELS at pnd 7)


title: HEK293T_IXA6-3

value: 4 hours at 37C-IRE1/XBP1s Activator


title: FU3: PBMC_BCG_wk3_FU


title: AB3: PBMC_BCG_wk3_AB


title: HEK293T_IXA6-2


title: HEK293T_IXA6-1


title: 788: kainate 6 (KA-ELS at pnd 7)


title: 231.ctrl.capMNase.rep1

value: MDA-MB-231 with empty vector

tag: passages


title: FW0: PBMC_BCG_wk0_FW


title: HEK293T_IXA4-3


title: 587: kainate 4 (KA-ELS at pnd 7)


title: FU0: PBMC_BCG_wk0_FU


title: AB0: PBMC_BCG_wk0_AB


title: U251 sh-ZEB2 Clone1

description:
Test
miRNAs
SAMPLE 4

source_name: U251TR Clone1

tag: cell type

value: glioma cell

tag: genotype

value: ZEB2-knockdown subline (passage 5)


title: AA3: PBMC_BCG_wk3_AA


title: FV0: PBMC_BCG_wk0_FV


title: HEK293T_IXA4-2


title: HEK293T_IXA4-1


title: AA0: PBMC_BCG_wk0_AA


title: HEK293T_IXA1-3


title: FD0: PBMC_BCG_wk0_FD

value: M

value: BCG-vaccinated


title: FD3: PBMC_BCG_wk3_FD


title: SmallRNA_Seq_NRPD1-3xMYC#2

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: small RNA

data_processing:
For BS-seq, adapter,and low-quality sequences (q < 20) were trimmed and clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP allowing two mismatches. Only cytosines with a depth of at least four in all libraries were retained for further analysis.
For SRNA-seq, after trimming off adapter sequences, clean reads with size ranging from 18-30 nt were mapped to the TAIR 10 genome using Bowtie (Langmead et al., 2009). Only reads that had at least one perfect match to the genome and cannot be mapped to annotated structural RNAs (rRNAs, tRNAs, snRNAs and snoRNAs) were retained for downstream analysis. 24-nt reads counts of regions were normalized to reads per 10 million (RPTM) based on total mapped clean reads (excluding structural sRNAs) in the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq WIG files give methylation level for Cs with depth >= 4; SRNA-seq TDF files represent normalized RPTM (reads per ten million) counts of 24-nt RNAs that are uniquely mapped to the TAIR10 genome.

organism: Arabidopsis thaliana

source_name: flower tissue

growth_protocol: flower tissue were havested from plants in soil under long-day conditions (22°C, 16-h light, 8-h dark)

extract_protocol:
Total RNA was extracted using Trizol. Standard small RNA library preparation and high throughput sequencing were performed at the Beijing Genomics Institute (Wuhan, China).
Libraries were prepared for sequencing according to the manufacturer's (Illumina, Inc) instructions.

value: flower


title: SmallRNA_Seq_NRPD1-3xMYC#1

description: small RNA


title: HEK293T_IXA1-2


title: SmallRNA_Seq_nrpd1-3

description: small RNA


title: HEK293T_DMSO-3

value: 4 hours at 37C


title: SmallRNA_Seq_Col-0

description: small RNA


title: BS_Seq_RDR2-3xMYC#2

description: treated with bisulfite

source_name: 14-day old seedling

growth_protocol: 14-day-old seedlings were grown on 1/2 MS plates supplemented with 0.6% agarose and 1% sucrose under long-day conditions(22°C, 16-h light, 8-h dark)

extract_protocol:
Genomic DNA was extracted from 14-day-old seedlings and sent to BGI (Wuhan, China) for bisulfite treatment, library construction, and sequencing.
Libraries were prepared for sequencing according to the manufacturer's (Illumina, Inc) instructions.

value: seedling


title: AW3: PBMC_BCG_wk3_AW


title: FA0: PBMC_BCG_wk0_FA

value: F


title: BS_Seq_rdr2-2

description: treated with bisulfite


title: FA3: PBMC_BCG_wk3_FA


title: AV3: PBMC_BCG_wk3_AV


title: AW0: PBMC_BCG_wk0_AW


title: AV0: PBMC_BCG_wk0_AV


title: BS_Seq_NRPE1-3xFLAG#1

description: treated with bisulfite


title: TAMs 5

city: Houston

first: Pan

last: Su

state: TX

address: 6550 FANNIN STREET

institute: Houston Methodist Research Institute

data_processing:
BasecallVersion 0.5.6.153 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome.
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: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: tumor-associated macrophages (TAMs)

growth_protocol: Human PBMC-derived MΦs were cultured in RPMI 1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MΦs were cocultured with human multiple myeloma cell lines U266 and ARP1 for 72 hours to generate tumor-associated macrophages in vitro.

value: PBMC-derived tumor-associated macrophages (TAMs)

tag: cell source

value: generated in vitro and cocultured with human myeloma cell lines U266 or ARP1


title: TAMs 4


title: FB3: PBMC_BCG_wk3_FB


title: BS_Seq_nrpe1-11

description: treated with bisulfite


title: TAMs 6


title: TAMs 3


title: BS_Seq_Col-0 x nrpd1-3_F1

description: treated with bisulfite


title: HEK293T_IXA1-1


title: FB0: PBMC_BCG_wk0_FB


title: AT3: PBMC_BCG_wk3_AT


title: HEK293T_DMSO-2


title: TAMs 2


title: AT0: PBMC_BCG_wk0_AT


title: SPF3

source_name: E14.5 fetal brain

tag: developmental stage

value: embryo day 14.5

value: brain

value: C57 Bl/6J

tag: group

value: specific pathogen free microbiome


title: 90-137 control IP

source_name: yeast cells

tag: chip antibody

value: EZview Red Anti-HA Affinity Gel (Sigma–Aldrich)


title: BS_Seq_nrpd1-3 x Col-0_F1

description: treated with bisulfite


title: BS_Seq_RDR2-3xMYC#1

description: treated with bisulfite


title: AFDN-DT_OV_rep2

first: Ping

last: Xu

address: Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
All sequenced reads were mapped to the hg38 genome using HISAT2
The sam files were sorted with the samtools
The expression of each gene was quantified using the DEseq2

source_name: HGC27 cell

growth_protocol: HGC27 cell line was purchased from the Shanghai Cell Bank of the Chinese Academy of Sciences and cultured in RPMI 1640 (Hyclone, UT, USA) supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies, CA, USA) according to manufactures’ instructions
The RNA-seq library were constructed using the VAHTS mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, China) according to manufactures’ instruction.

treatment_protocol: The AFDN-DT overexpression lentivirus were transfected into the HGC27 cells, and positively transduced cells were selected by puromycin.

tag: genotype/variation

value: AFDN-DT overexpression

value: gastric cancer


title: HEK293T_DMSO-1

tag: tissue

value: human embryonic kidney


title: BS_Seq_NRPD1-3xMYC#2

description: treated with bisulfite


title: TAMs 1


title: AFDN-DT_OV_rep1

institute: Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine


title: MΦs 3

source_name: Human PBMC-derived MΦs

value: PBMC-derived macrophages

value: generated in vitro


title: Control_rep1

value: Vector transduced


title: MΦs 2


title: BS_Seq_Col-0_replicate2

description: treated with bisulfite


title: Control_rep2


title: MΦs 1


title: NPC70A_91739

status: Public on Apr 16 2020

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify quality problems before and after alignment.
We used the Tuxedo Suite software package for alignment
Reads were aligned to the reference genome (UCSC mm10)  using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: ACVR1 WT_neurospheres

growth_protocol: Mouse neurospheres are cultured in DMEM/F12 with N2 and B27 supplements, and EGF and FGF growth factors at final concentration of 20 ng/ul.

extract_protocol:
RNA was extracted using the Qiagen RNeasy mini kit (cat# 74104)
RiboGone and the TruSeq stranded Library prep kit with 100ng input and 13 cycles of PCR
HiSeq4000, Ribodepleted, stranded TruSeq. H4K PE50 Cycle, Pico kit

tag: strain background

value: ACVR1 WT

value: neurospheres


title: NPC3_91738


title: NPC1_91737


title: NPAC C3_91736

source_name: ACVR1 G328V_neurospheres

value: ACVR1 G328V


title: NPAC C1_91734


title: NPAC C2_91735


title: BS_Seq_nrpd1-3_replicate2

description: treated with bisulfite

value: seedling


title: Sample-3_control3

city: London

first: Noreen

last: Eder

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Adapter trim with cutadapt 1.5
Align with Star 2.2.2a
Merge lane level bam files with samtools 1.8
Assess expected counts per feature with RSEM 1.3.0
Normalise and call differentially expressed genes with DESeq2
Genome_build: GRCm38-r86
Supplementary_files_format_and_content: Merged RSEM Counts in a tab delimited text file

extract_protocol:
Brains were harvested and RNA of right hemisphere was stabilised in RNAlater and extracted using the RNeasy Mini Kit (Qiagen) according to manufactures protocol.
The libraries were prepared with the KAPA mRNA HyperPrep kit (Roche), normalising samples to 500 ng RNA input and prepared these into Illumina compatible libraries according to the kit manufacturer’s instructions.

value: NexCre -/- YAP5SAnls +/-

tag: age

value: post natal day 11

value: brain right hemisphere


title: Sample-12_background2

value: WT


title: Sample-4_control4


title: Sample-8_mutant3

value: NexCre +/- YAP5SAnls +/-


title: Sample-6_mutant1


title: Sample-9_mutant4


title: Sample-7_mutant2


title: Sample-1_control1


title: Sample-10_mutant5


title: Sample-13_background3


title: Sample-5_control5


title: Sample-11_background1


title: R8208

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to  GRCm38 genome build
Gene counts were obtained using featureCounts on GENCODE vM16 annotations
Genome_build: GRCm38

source_name: embryo - Brain - Microglia

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Applied Biosystems™ Thermo Fisher Scientific) according to manufacturer's protocol. All mouse RNAs were analyzed on Agilent Bioanalyser for quality assessment with median RNA Integrity Number of RIN 7.7.
cDNA libraries were prepared using 2 ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific) using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina) (31 samples/lane).

value: Brain - Microglia

tag: development stage


title: R8204

source_name: embryo - Brain - BAM

value: Brain - border-associated macrophages


title: R8207


title: R8210


title: R8206


title: R8209


title: R8203


title: HUDEP2_BCL11A+58KO_r1

city: Guangzhou

first: Peng

last: Huang

address: Xinzao, Panyu District

institute: Guangzhou Medical University

description: processed data file: 2340_2345_nor.bigwig

data_processing:
library strategy: Capture-C
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with the normalized Capture-C interaction signals

growth_protocol: HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.

extract_protocol: Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).

treatment_protocol:
The GATA binding motif at the BCL11A +58 enhancer was disrupted using a CRISPR-Cas9-mediated approach in pooled HUDEP2 cells.
HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.

value: Immortalized Human Erythroid Progenitor

value: Erythroid cells

tag: differentiation

value: Differentiated for 5 days


title: R8201


title: R8196


title: R8205


title: R8199


title: R8200


title: Sample-2_control2


title: R8194


title: R8193


title: R8202


title: R8191


title: R8190


title: R10356


title: R8186


title: R10357


title: R8185


title: R8189


title: R10351


title: R10345


title: R8192


title: R10344


title: R10339


title: R10321


title: R10327


title: R10333


title: R8195


title: R10326


title: R10320


title: R8172


title: R10338_R


title: ATlo rep3 [0326R8]

city: New York

first: Keisuke

last: Yamamoto

state: NY

address: 550 First Avenue

department: Radiation Oncology

institute: NYU School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Heatmaps and other statistics was performed using R3.2
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts of sequencing reads (used for GSEA); Normalized abundance measurements

source_name: autophagy-low (ATlo)

growth_protocol: Murine pancreatic cancer cells were embedded in Matrigel and grown as organoids in DMEM supplemented with 10 % FBS.

extract_protocol:
Total RNA was extracted from sorted cells using PureLink RNA Mini Kit (ThermoFisher Scientific).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA library preparation kit according to manufacturer’s instructions by the NYU Genome Technology Center.

treatment_protocol: Organoids were dissociated into single cells and sorted into autophagy-high (AThi) and autophagy-low (ATlo) populations according to GFP/RFP signal ratio.

tag: cell line background

value: mouse pancreatic cancer cells

value: GFP-LC3-RFP autophagy flux reporter

tag: sorted population

value: autophagy-low (ATlo)


title: ATlo rep1 [0226R8]


title: AThi rep2 [0319R5]

source_name: autophagy-high (AThi)

value: autophagy-high (AThi)


title: ATlo rep2 [0319R8]


title: AThi rep1 [0226R4]


title: R10350

tag: strain


title: R10332


title: R10315


title: Midbrain Astrocyte_shPTB_4w-2

city: Shenzhen

first: Zhengyu

last: LIANG

state: Guangzhou

address: 1088 Xueyuan Avenue

department: Department of Biology

institute: Southern University of Science and Technology

data_processing:
RNA-seq reads were trimmed for adaptor sequence and filtered with low-complexity or low-quality sequence using cutadapt 2.3 with parameters -a A{10} -m 22.
Then the reads were mapped to the pre-indexed mm10 transcriptome using salmon v0.14.1 with parameters: quant -l A --validateMappings --seqBias
R package DEseq2 were applied for the downstream DEGs analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and reads number for each samples

source_name: Mouse astrocyte

extract_protocol:
The total RNA was purified by a Direct-zol RNA MiniPrep kit (Zymo Research)
Total 2ug of total RNA was first converted to cDNA by superscript III first strand synthesis kit with primer Biotin-B-T. The cDNA was purified by PCR Clean-Up Kit column to remove free primers and enzyme. Then terminal transferase was applied to block the terminal of a cDNA 3′ end. Streptavidin-coaged magnetic beads were further applied to isolate cDNAs. After RNA degradation by sodium hydroxide, second-strand cDNA was synthesized by random primer. The second strand cDNA was eluted from beads by heat denaturing. The cDNA was then used as template to construct libraries.

value: Midbrain

value: astrocyte

tag: genetic manipulation

value: shRNA against PTB

tag: culture conditions

value: neuronal differentiation medium; 4 weeks


title: R10314

tag: cell type


title: Midbrain Astrocyte_shPTB_4w-1


title: Midbrain Astrocyte_shPTB_2w-2

value: neuronal differentiation medium; 2 weeks


title: Midbrain Astrocyte_shPTB_2w-1


title: Cortical Astrocyte_shPTB_2w-2

value: Cortex


title: Midbrain Astrocyte-2

value: Mock

value: growth medium


title: Cortical Astrocyte_shPTB_4w-2


title: Cortical Astrocyte_shPTB_4w-1


title: IP_HFD2

city: Cologne

first: Alexander

last: Jais

address: Gleueler Str. 50

department: Neuronal Control of Metabolism

country: Germany

institute: Max Planck Institute for Metabolism Research

data_processing:
Illumina HiSeq 4000
Sequenced reads were aligned to the reference genome using hisat 2.1.0.
Transcript abundance was derived using stringtie 1.3.4d.
Differential gene expression analysis was carried out uing cuffdiff (cufflinks suite 2.2.1)
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel speadsheet containing mean expression levels per group, fold change and significance level for each annotated gene.

source_name: IP_HFD2 (HFD 3 days)

extract_protocol:
10-week-old male C57/BL6N mice were put either on a control diet or a high fat diet for 3 days. Afterwards, mice were sacrificed by cervical dislocation. The hypothalamus was rapidly dissected using a stainless steel brain matrix (World Precision Instruments) and immediately frozen in liquid nitrogen. Hypothalamic tissues were pooled (8 per IP, 4 IPs per condition)
Due to low amount of input material, pre-amplification using the Ovation RNASeq System V2 was performed. Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input.

value: immunoprecipitation of phosphorylated S6 ribosomal protein-tagged ribosomes

tag: diet

value: high fat diet

value: Hypothalamus

value: 10 weeks

tag: genotype


title: Input_HFD4

source_name: Input_HFD4 (HFD 3 days)

value: Input


title: IP_HFD3

source_name: IP_HFD3 (HFD 3 days)


title: IP_HFD1

source_name: IP_HFD1 (HFD 3 days)


title: Cortical Astrocyte-2


title: Cortical Astrocyte-1


title: Input_HFD3

source_name: Input_HFD3 (HFD 3 days)


title: IP_HFD4

source_name: IP_HFD4 (HFD 3 days)


title: Input_HFD2

source_name: Input_HFD2 (HFD 3 days)


title: Midbrain Astrocyte-1


title: Input_NCD2

source_name: Input_NCD2 (CD 3 days)

value: control diet


title: Input_NCD4

source_name: Input_NCD4  (CD 3 days)


title: Input_HFD1

source_name: Input_HFD1 (HFD 3 days)


title: IP_NCD2

source_name: IP_NCD2  (CD 3 days)


title: IP_NCD4

source_name: IP_NCD4  (CD 3 days)


title: IP_NCD3

source_name: IP_NCD3  (CD 3 days)


title: Input_NCD3

source_name: Input_NCD3  (CD 3 days)


title: HFD4_IP-GFP

description:
IP HFD4
K002000202_83194

data_processing:
library strategy: BacTRAP-based ribosome profiling
Sequenced reads were aligned to the reference genome using hisat 2.1.0.
Transcript abundance was derived using stringtie 1.3.4d.
Differential gene expression analysis was carried out uing cuffdiff (cufflinks suite 2.2.1)
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel speadsheet containing mean expression levels per group, fold change and significance level for each annotated gene.

extract_protocol:
The hypothalamus was rapidly dissected using a stainless steel brain matrixand immediately frozen in liquid nitrogen. RNA was purified after ribosomal immunoprecipitation using the RNeasy Micro Kit (QIAGEN). RNA integrity was assessed using an Agilent 2100 bioanalyzer.
Due to low amount of input material, pre-amplification using the Ovation RNASeq System V2 was performed. Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input.

value: 10-12 weeks

value: high-fat diet (HFD) for 3 days


title: HFD4_Input

description:
Input HFD4
K002000202_83192


title: HFD3_Input

description:
Input HFD3
K002000202_83188


title: HFD3_IP-GFP

description:
IP HFD3
K002000202_83190


title: HFD2_Input

description:
Input HFD2
K002000202_83184


title: HFD1_Input

description:
Input HFD1
K002000202_83180


title: HFD1_IP-GFP

description:
IP HFD1
K002000202_83182


title: CD4_IP-GFP

description:
IP CD4
K002000202_83178

value: control diet (CD) for 3 days


title: CD3_Input

description:
Input CD3
K002000202_83172


title: HFD2_IP-GFP

description:
IP HFD2
K002000202_83186


title: Single Cell P20 IFE Basal GC050905_H10

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

institute: Université Libre de Bruxelles (ULB)

description: SmartSEQ2 scRNAseq

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated matrix containing raw transcript counts

source_name: Lrig1-CreERT2/RosaYFP IFE basal epidermal cells FACS sorted for Cd34-/Itga6+/YFP-

growth_protocol: The dermis and epidermis were removed from the tail bone using forceps. The samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 4°C overnight. The next day, the epidermis was separated from the dermis. Epidermis was then incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Tissues were then cut in small pieces with a scalpel and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (cFCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in PBS 2% cFCS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Basal IFE and infundibulum cells were stained using PE-conjugated anti-a6-integrin (clone GoH3; 1/200, ebioscience) and bulge cells were stained with biotinylated CD34 (clone RAM34; 1:50, BD Biosciences). Primary antibodies were washed with PBS 2% cFCS and cells incubated for 30 min in APC-conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Secondary antibody was washed with PBS 2% FCS and cells were incubated in Hoechst solution (1:4000 in PBS 2%cFCS) prior FACS analysis. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. For H2BGFP proliferation experiments, K5tTA/TRE-mCMV-H2B-GFP mice chased with doxycycline were used. basal cells were targeted using CD34 negative and α6 integrin positive gating. For P20 basal epidermal cells sorting, Lrig1-CreERT2/RosaYFP mice were used and basal cells from the interfollicular epidermis were targeted using CD34 negative, α6 integrin positive and YFP negative gating. Analysis were perfomed on a FACS Fortessa (BD Bioscience). Cell sorting was performed using a FACS Aria at high pressure (70 psi) and FACS Diva software (BD Biosciences).

extract_protocol:
Single-cell transcriptomes were generated using a modified Smartseq-2 protocol. Lysis buffer (2 µl) in 96-well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer, 2.5 mM dNTPs, 2.5 µM oligo-dT30-VN and ERCC controls at a final dilution of 1:400 million. Reverse transcription and PCR were performed according to the Smartseq-2 protocol: 5,7 µl reverse transcription mix and 15 µl PCR Master mix. cDNA was amplified for 23 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8 × ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 25 µl buffer EB (Qiagen) and transferred to 96_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermo Fisher Scientific) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit.
Next-generation sequencing library preparation was performed using the Illumina Nextera DNA library preparation kit with volumes reduced by one-tenth (Illumina). In brief, 100 pg cDNA in a volume of 500 nl was tagmented by adding 1.5 µl Tn5-buffer mix and incubating for 10 min at 55 °C. Tagmented samples were barcoded with Nextera indexes A-D and amplified with 11 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6 × ratio. Library pools were eluted in buffer EB and quality controlled using an Agilent 2100 BioAnalyser and High Sensitivity DNA kits before adjusting to a concentration of 4 nM. The diluted pools were quantified using the KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before final dilution to 2 nM. Sequencing was performed on a HiSeq4000 on two lanes in high output mode.
scRNAseq

tag: library type

value: Nextera XT


title: Single Cell P20 IFE Basal GC050905_H07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_H09

description: SmartSEQ2 scRNAseq


title: CD2_Input

description:
Input CD2
K002000202_83168


title: CD4_Input

description:
Input CD4
K002000202_83176


title: CD2_IP-GFP

description:
IP CD2
K002000202_83170


title: Single Cell P20 IFE Basal GC050905_H01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_H06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_H08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_H05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_H04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_H02

description: SmartSEQ2 scRNAseq


title: CD1_IP-GFP

description:
IP CD1
K002000202_83166


title: Single Cell P20 IFE Basal GC050905_G09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G07

description: SmartSEQ2 scRNAseq


title: Cortical Astrocyte_shPTB_2w-1

value: astrocyte


title: Single Cell P20 IFE Basal GC050905_G05

description: SmartSEQ2 scRNAseq


title: CD1_Input

description:
Input CD1
K002000202_83164


title: CD3_IP-GFP

description:
IP CD3
K002000202_83174


title: Single Cell P20 IFE Basal GC050905_G03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_H03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_G10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_F03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_E02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_B01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_A05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_D04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050905_C07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_H03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_G01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_E04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D04

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C07

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_D11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_F10

description: SmartSEQ2 scRNAseq


title: ATAC-seq distal radius E59

city: Cambridge

first: Terence

middle: D

last: Capellini

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

data_processing:
Alignment to hg19. Bowtie2 version 2.3.2. Default parameters for hg19 alignment.
Filter for duplicates. MACS2 version 2.1.1.2. macs2 filterdup -i file -g hs --keep-dup 1 -o outfile
Peak calling. MACS2 version 2.1.1.2. macs2 callpeak -B -t rep1file -n name --nomodel --shift -100 --extsize 200
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: E59_proximal_femur_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the proximal femur ATAC-seq experiment.
Supplementary_files_format_and_content: E59_distal_femur_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the distal femur ATAC-seq experiment.
Supplementary_files_format_and_content: E59_proximal_tibia_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the proximal tibia ATAC-seq experiment.
Supplementary_files_format_and_content: E59_distal_tibia_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the distal tibia ATAC-seq experiment.
Supplementary_files_format_and_content: E59_proximal_humerus_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the proximal humerus ATAC-seq experiment.
Supplementary_files_format_and_content: E59_distal_humerus_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the distal humerus ATAC-seq experiment.
Supplementary_files_format_and_content: E59_proximal_radius_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the proximal radius ATAC-seq experiment.
Supplementary_files_format_and_content: E59_distal_radius_peaks_hg19.bed: bed format; contains the coordinates of the peaks called and filtered as described for the distal radius ATAC-seq experiment.

source_name: Distal radial growth plates E59

growth_protocol: in vivo collected embryonic day 59 (E59) growth plate chondrocytes.

extract_protocol:
Upon arrival the sample was dissected under a light dissection microscope in identical fashion to all mouse samples reported. ll forelimb and hindlimb long bone elements were complete but then manually separated from one another, and each proximal or distal cartilaginous end was then micro-dissected from the bony diaphysis. Proximal and distal bone end samples for each long bone (i.e., femur, tibia, humerus, radius) were then sent out for sequencing running a pooled library for 3 rounds of sequencing on the Illumina NextSeq 500 in order to obtain approximately 50 million reads per sample.
Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturer's protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500, for three rounds, after which raw reads for each sample were pooled.

treatment_protocol: Human products of conception were collected from late first-trimester and early second-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

value: Distal radial growth plates

value: chondrocytes

tag: reagent

value: tn5 transposase

tag: developmental stage


title: Single Cell P20 IFE Basal GC050904_D10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C03

description: SmartSEQ2 scRNAseq


title: ATAC-seq distal humerus E59

source_name: Distal humeral growth plates E59

value: Distal humeral growth plates


title: ATAC-seq proximal humerus E59

source_name: Proximal humeral growth plates E59

value: Proximal humeral growth plates


title: ATAC-seq distal tibia E59

source_name: Distal tibial growth plates E59

value: Distal tibial growth plates


title: ATAC-seq proximal radius E59

source_name: Proximal radial growth plates E59

value: Proximal radial growth plates


title: Single Cell P20 IFE Basal GC050904_C01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C02

description: SmartSEQ2 scRNAseq


title: ATAC-seq proximal tibia E59

source_name: Proximal tibial growth plates E59

value: Proximal tibial growth plates


title: ATAC-seq distal femur E59

source_name: Distal femoral growth plates E59

value: Distal femoral growth plates


title: Single Cell P20 IFE Basal GC050904_B11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_B12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_B10

description: SmartSEQ2 scRNAseq


title: ATAC-seq proximal femur E59

source_name: Proximal femoral growth plates E59

value: Proximal femoral growth plates


title: Single Cell P20 IFE Basal GC050904_B09

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_C04

description: SmartSEQ2 scRNAseq