title: Human_Placenta_ChIP-Seq_H3K4me3

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
ChIP-Seq reads were trimmed with TrimGalore v0.6.4 and then aligned to the corresponding reference genome using Bowtie v2.3.5 with default settings. PCR duplicates were removed using the rmdup function of samtools v1.10. The data reproducibility between biological replicates was confirmed, then reads from replicates were pooled together for further analysis.
The bam files were converted to tdf format using igvtools, which can then be visualized using IGV.
Genome_build: GRCh38
Supplementary_files_format_and_content: tdf files generated with igvtools

source_name: Human placenta

extract_protocol:
Placenta samples for human were collected following previous study (Dunn-Fletcher, et al. 2018), and frozen at -80 degree for use.
ChIP-Seq for placenta samples was performed using the MAGnifyTM Chromatin Immunoprecipitation System (ThermoFisher, 492024). Chromatin fragmentation was performed using Diagenode Bioruptor Plus Sonicator. The antibodies used include H3K4me1 (Abcam, ab8895), H3K4me3 (Abcam, ab8580), H3K27ac (Abcam, ab4729).
ChIP-Seq libraries were constructed using Takara SMARTer ThruPLEX DNA-Seq Kit (Takara, R400674), and then sequenced as 50 bp single-end reads with HiSeq2500 (Illumina).

value: Placenta

value: H3K4me3 (Abcam, ab8580)


title: ES-F12_S72_001

status: Public on Dec 31 2021

type: SRA

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
Base calling was performed using Off-line Basecaller (OLB) v1.9.4 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: plain text

molecule: total RNA

organism: Mus musculus

source_name: ES

growth_protocol: C57B6N × 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 3μM CHIR99021, 1μM PD0325901, 103U/ml ESGRO LIF on a gelatin-coated dish or in serum ESM (2iL): Knockout DMEM (Thermo Fisher Scientific) , 20% FBS, 1xNEAA, 0.1mM β-mercaptoethanol, 1 × penicillin-streptomycin, 3μM CHIR99021, 1μM PD0325901, and 103U/ml ESGRO LIF on mouse embryonic fibroblasts (MEF) feeder dish. CD1 TSCs (#1-4M, #2-2M, #8M, #1F, #2-3F, #2-4F) were derived in serum-free TS medium: Neurobasal: DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 50ng/ml human FGF4, 10μg/ml heparin, 20ng/ml human Activin A, 10μM XAV939, 10μM Y27632 on MEF feeder dish. CD1 (Clea) or PWK (BRC, RIKEN) × C57BL6N (Charles River) F1 blastocysts were collected at E3.5. CD1-Tg(CAG-EGFP) mice were kindly gifted from Prof. T. Wakayama (Yamanashi university). Culture conditions used in this study is summarized in Supplementary Table 1. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in +C10F4HPDGF medium (Suppl table 1): StemFit® Basic02, 1xpenicillin-streptomycin (Thermo Fisher Scientific), 10μM CHIR99021 (Reprocell), 50ng/ml human FGF4 (Sigma), 1ng/ml heparin (Sigma), 25ng/ml human PDGF-AA (R&D). Embryos were cultured in +C10F4HPDGF medium for at least 5 days until they formed outgrowths. The outgrowth was dissociated with 1xTrypLE™ Select (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate. After 5-7 days, PrES cell colonies reached 50-80% confluence and the cells were passaged into a 12-well MEF feeder plate. PrES cells were frozen in Cellbanker® 1plus (Zenoaq). XEN cells were derived according to a standard protocol (1) with minor modifications. CD1 blastocysts were collected at E3.5. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in serum-containing ES medium: RPMI1640 (Thermo Fisher Scientific), 20% fetal bovine serum (FBS, Biosera), 1 × penicillin-streptomycin (Thermo Fisher Scientific), 1 × non-essential amino acids (NEAA, Thermo Fisher Scientific), 0.1mM β-mercaptoethanol (β-ME, Sigma), 103U/ml ESGRO LIF on a MEF feeder plate. Embryos were cultured for at least 7 days until they formed outgrowths. The outgrowth was removed by pipetting and the remaining adherent cells were continuously cultured for another 7 days. The proliferated cells were dissociated with 0.05% trypsin-EDTA (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate, then expanded into a 6-well plate. XEN cells were frozen in Cellbanker® 1plus (Zenoaq) and stored in a -150°C freezer (Panasonic). Removal of the primary outgrowth was not necessary when CHIR99021 (3μM) was added.

extract_protocol:
mRNA were extracted following Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combi

tag: strain

tag: treatment

value: not treated

tag: cell type

value: single cell ES


title: Human_Placenta_ChIP-Seq_H3K4me1

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: OP50:BT247_12h_rep1

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

country: Germany

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include Raw reads counts for each Sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole body

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

treatment_protocol: Worms were exposed to OP50, MYb11, MYb115 and BT at the stage L4. The experiments with BT were performed at 20°C.

value: Wild type (N2)

tag: developmental stage

tag: pathogen

tag: timepoint

value: 12 hrs

tag: medium

value: mNGM

tag: temperature


title: ES-F11_S71_002


title: Human_Placenta_ChIP-Seq_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: Human_Placenta_ChIP-Seq_Input


title: MYb115:none_12h_rep1


title: MYb11:BT407_24h_rep1

value: 24 hrs


title: MYb11:BT407_12h_rep1


title: ES-F11_S71_001


title: MDA-MB-231_siNUP933_S6_L005

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

institute: UCSF

description: processed data file: MDA-MB-231_data.xlsx

data_processing:
RNA-seq reads were mapped to the human genome (hg19 assembly) with STAR (Dobin et al., 2013) and gene expression levels were quantified using RSEM (Li and Dewey, 2011) and Bowtie2.
GENCODE v26 annotations were used for further analysis. Differential expression in WCE samples was computed using DESeq2 (Love et al., 2014) with default parameters. Subcellular localization was quantified similarly using DESeq2, using gene-level RSEM output.
Genome_build: hg19
Supplementary_files_format_and_content: gene-level RSEM output

growth_protocol: Human mammary MDA-MB-231 and MCF7 cells were grown in RPMI-1640 (Gibco BRL) supplemented with 10% heat inactivated fetal calf serum (Gibco), 1mM sodium pyruvate, and a penicillin streptomycin mixture (100 U/ml; 0.1 mg/ml).

extract_protocol:
TRIREAGENT
SENSE mRNA-Seq Library prep kit (Lexogen)

treatment_protocol: cells were seeded in 6-well plates at 50% confluence, and 24 h later, they were transfected with siRNA control and siRNA NUP93 SMART pool using the Lipofectamine 2000 transfection reagent

tag: cell line

tag: molecule subtype

value: WCE PolyA RNA


title: ES-F10_S70_002


title: MYb11:BT247_12h_rep1


title: ES-F10_S70_001


title: MYb11:none_12h_rep1


title: OP50:BT247_24h_rep1


title: NS_29

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the human reference genome (b37) using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: b37
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: skin

extract_protocol:
Total RNA was isolated with RNeasy Kit (Qiagen) from 5mm skin biopsy that was previously powderized in liquid nitrogen.
Complemetary DNA (cDNA) was prepared using the NuGEN Ovation RNA-Seq System to obtain the strand-specific RNA-seq libraries from 100 ng of total RNA.Ribosomal RNA transcripts were depleted using the Insert Dependent Adaptor Cleavage (InDA-C) technology.. Equimolar pool of the final indexed RNA-Seq libraries were sequenced on an Illumina HiSeq 2500 (paired-end reads 130 bases + 130 bases) to obtain about 50 million paired-end reads per library.

value: skin

tag: disease state

value: lesional

tag: patient name

tag: clinical manifestation

value: NS-ILC


title: MDA-MB-231_siNUP932_S5_L005


title: OP50:BT407_12h_rep1


title: MDA-MB-231_sictrl3_S3_L005

value: siCtrl


title: SF268_NER1500_D21_R1

city: New York

first: Colin

last: Tang

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the TKOv3 library sequences with bowtie.
Sequenced reads aligned to GRCh38 with salmon. Differential expression analysis was performed with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited .txt file

source_name: Glioblastoma

growth_protocol: Cells were cultured in DMEM + 10% FBS

extract_protocol: CRISPR screen sequencing libraries were made with nested PCRs of the sgRNA region.

treatment_protocol: Inhibitors or DMSO were added to the cultured cells and treated for indicated times.

value: neratinib 1.5uM

value: 21 days


title: MYb11:BT247_24h_rep1


title: MYb115:BT247_24h_rep1


title: ES-E9_S57_001


title: OP50:BT407_12h_rep2


title: 13M

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine

description: vst.csv

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using bowtie2  with parameters –local, keeping only alignments with MAPQ>=10
Reads Per Gene were calculated using FeatureCount of subread package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene expression values normalized with DESeq2 variance stabilizing transformation (VST) for each Sample

source_name: breast metastasis from esophagus

extract_protocol:
RNA was extracted from FFPE samples with Qiagen AllPrep DNA/RNA FFPE kit.
1 µg of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using TruSeq RNA Access Library Prep protocols

value: esophagus

tag: tumor type

value: Distal metastsis


title: MDA-MB-231_sictrl2_S2_L005


title: ES-E8_S56_002

value: not treated


title: HBV6-Ncl

city: Emeryville

first: Tobias

last: Flecken

state: CA

address: 5300 Chiron Way

department: Infectious Diseases

institute: Novartis Institutes for Biomedical Research

description: ChIP anti-Ncl (cl 4E2, abcam ab13541)

data_processing:
base calling: RTA 1.18.54 (from Illumina MCS 2.6.2)
alignment: bowtie2 2.3.0 was used for alignment to 1.1mer viral genomes (with -t -no-unal -no-discordant -no-mixed -I 120 -X 200 option) and all sequences (combined hg38/HBV/phiX; only -t option)
paired read merging: custom script was used to merge paired reads in the output SAM file based on viral genome coordinates. Unsequenced insert was represented as N with low quality score.
BAM conversion: SAM file was converted to BAM, sorted, and indexed using samtools 0.1.19
BEDGRAPH conversion: BAM file was converted to BEDGRAPH using bedtools 2.18.1 (-bg -trackline options)
1mer conversion: custom script was used to wrap around reads that aligned in the overhang of the 1.1mer to the start of the sequence
scaling and wig conversion: custom script was used to convert BEDGRAPH to WIG files while simultaneously scaling it per 106 total reads in the library (hg38+HBV+phiX)
Genome_build: GenBank V01460.1 was used as HBV reference genome (genotype D). GRCh38.p10 was used for the human genome, NC_001422.1 for phiX
Supplementary_files_format_and_content: WIG files contain the number of HBV reads per million total reads for each position of the respective HBV reference genome. Sequences are shifted by -500 nt compared to EcoRI site.

growth_protocol: HepG2-hNTCP cells (Tropberger et al., PNAS 2015) were grown to confluency in collagen-coated tissue culture flasks (Corning) using DMEM/F12 with 10% FBS and Pen/Strep (all ThermoFisher). Cells were transferred to Williams E medium with Supplement B (CM4000), 0.1 µM Dexamethason (all ThermoFisher) and 2% DMSO (Sigma-Aldrich) two days before infection. Cells were infected with cell culture-derived HBV (Tropberger et al., PNAS 2015) at a multiplicity of infection (MOI) of 1000:1 in the presence of 4% polyethylenglycol (PEG8000; Sigma-Aldrich). Excess virus was washed away 1 day post infection (dpi) with 0.1% Trypsin/EDTA (ThermoFisher) and medium. Cells were maintained with 3 media exchanges per week until 12 dpi to allow establishment of infection.

extract_protocol:
Cells were fixed in freshly prepared 1% formaldehyde in PBS (both ThermoFisher Scientific) for 5 min prior to quenching with 125 mM glycine in PBS. Pelleted cells were either used directly for analysis (HBV1-3) or snap-frozen and stored at -80°C until use (HBV4-5). Next, cells were washed with cold lysis buffer [PBS with 0.1% Triton X-100, 0.1% NP-40, 1 mM dithiothreitol (DTT), 50 ng/ml trichostatin A (TSA) and 1x EDTA-free protease inhibitor (Roche, Basel, Switzerland)] and lysed in the same buffer for 10 min on ice. Nuclei were pelleted, resuspended in digestion buffer [H2O with 50 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 10% glycerol, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)] and digested with 600 IU/ml micrococcal nuclease (MNase; ThermoFisher Scientific) for 12 min at 37°C. Digestion was stopped by addition of 10 mM EDTA. Nuclei were pelleted at 6500 x g and supernatants collected. The pellet was resuspended in digestion buffer with 10 mM EDTA and 300 mM NaCl and mildly sonicated using a W 375 sonicator (Qsonica, Newtown, CT) at 50% duty cycle and power setting 3. Nuclei were again pelleted, supernatants combined and mixed with an equal amount of sucrose buffer [H2O with 50 mM Tris-HCl pH 7.5, 50 mM NaCl, 5 mM EDTA, 0.01% NP-40, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)]. Samples were concentrated using Amicon Ultra-4 100 kDa centrifugal filter units (Millipore-Sigma; Merck KGaA, Darmstadt, Germany) and spun on a 5-30% continuous sucrose gradient in sucrose buffer for 4 h at 40,000 x g and 4°C using a SW41Ti rotor (Beckman Coulter Inc., Brea, CA). Chemicals were obtained from Millipore-Sigma unless noted otherwise. Mononucleosome containing fractions were pooled and concentrated to ~500 µl prior to addition of 100 ng/µl bovine serum albumin (ThermoFisher Scientific). Mononucleosomes were either stored at -20°C or used immediately for ChIP. Antibodies were bound to 20 µl/ChIP Dynabeads Protein G (ThermoFisher) in ChIP buffer [H2O with 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 200 µg/ml BSA] at 4°C and added to 2 µg of chromatin in ChIP buffer and allowed to bind overnight. Samples were washed six times in LiCl wash buffer [H2O with 150 mM LiCl, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, and 0.7% sodium deoxycholate] and eluted in 100 µl elution buffer [H2O with 1% SDS and 100 mM NaHCO3]. Crosslinks were reversed by digestion with Proteinase K (ThermoFisher) for 5 h at 65°C and then digested for another 30 min with DNase-free RNase A (ThermoFisher) at 37°C. DNA was purified using the QIAquick PCR purification kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
1 ng of DNA was used for sequencing library construction with the KAPA Hyper Prep Kit (Roche) according to the manufacturer’s instructions. For barcoding, 2 µl of TruSeq RNA adapters stocks were used (Illumina, Inc., San Diego, CA). Up to 6 libraries were pooled per sequencing run and 500 ng pooled library subject to HBV-specific target enrichment using the xGen Lockdown Reagents Hybridization and Wash Kit (Integrated DNA technologies, Skokie, IL) according to the manufacturer’s instructions. A custom set of xGen lockdown probes of 60 bp length tiling the entire HBV genome of genotypes A-D was used for target enrichment (Integrated DNA technologies) together with Dynabeads MyOne T-270 Streptavidin (ThermoFisher). The pull-down was amplified for 8 PCR cycles (KAPA HiFi HotStart ReadyMix, Roche) and the product cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Inc.). The product was used to dilute the original library to 20 nM. Sequencing was performed using an Illumina MiSeq sequencer with a MiSeq v3 reagent kit for 2x76 bp paired-end reads (Illumina, Inc.).

tag: hbv genotype

value: D

tag: agent

value: Hepatitis B virus

tag: antibody

value: ChIP anti-Ncl (cl 4E2, abcam ab13541)


title: ES-E8_S56_001

tag: strain

tag: treatment

tag: cell type

value: single cell ES


title: HBV5-Ncl

description: ChIP anti-Ncl (cl 4E2, abcam ab13541)


title: ES-E7_S55_002


title: 13P

description: vst.csv

source_name: breast tumor

tag: tissue

value: breast

value: Primary


title: HBV5-H3K4me3

description: ChIP anti-H3K4me3 (abcam ab8580)

value: ChIP anti-H3K4me3 (abcam ab8580)


title: HBV5-HBcAg

description: ChIP anti-HBcAg (DAKO B0586)

value: ChIP anti-HBcAg (DAKO B0586)


title: 12M

description: vst.csv

source_name: breast metastasis from fallopian tube

value: fallopian tube


title: HBV4-Ncl

description: ChIP anti-Ncl (cl 4E2, abcam ab13541)


title: ES-E9_S57_002


title: ES-E6_S54_002


title: HBV4-HBcAg

description: ChIP anti-HBcAg (DAKO B0586)


title: 11M

description: vst.csv

source_name: breast metastasis from stomach

value: stomach


title: SF268_DMSO_D21_R1

value: vehicle


title: HBV4-H3K4me3

description: ChIP anti-H3K4me3 (abcam ab8580)


title: 12P

description: vst.csv


title: HBV4-input

description: input


title: ES-E6_S54_001


title: 11P

description: vst.csv


title: ES-E5_S53_002


title: HBV3-Ncl

description: ChIP anti-Ncl (cl 4E2, abcam ab13541)


title: HBV6-input

description: input


title: HBV6-H3K4me3

description: ChIP anti-H3K4me3 (abcam ab8580)


title: 10M

description: vst.csv

source_name: breast metastasis from lung

value: lung


title: HBV3-input

description: input


title: ES-E5_S53_001


title: HBV2-Ncl

description: ChIP anti-Ncl (cl 4E2, abcam ab13541)


title: ES-E7_S55_001


title: HBV5-input

description: input


title: HBV3-HBcAg

description: ChIP anti-HBcAg (DAKO B0586)


title: HBV1-HBcAg

description: ChIP anti-HBcAg (DAKO B0586)


title: ES-E4_S52_002


title: HBV2-input

description: input


title: HBV2-HBcAg

description: ChIP anti-HBcAg (DAKO B0586)


title: L1701728: kd_4-3_dark_4d

city: Würzburg

first: Markus

last: Henninger

address: Julius-von-Sachs Platz 2

institute: University of Würzburg

data_processing:
Sequenced reads were mapped to TAIR10 by STAR for the whole genome using featurecount.
Analysis were performed with DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: Seedling

extract_protocol:
Seedlings were harvested, frozen in liquid nitrogen and RNA was harvested using QIAGEN RNEasy Micro-Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 4 days after germination

tag: genotype

tag: light

value: dark

value: seedling


title: ES-E3_S51_002


title: HBV1-Ncl

description: ChIP anti-Ncl (cl 4E2, abcam ab13541)


title: 10P

description: vst.csv


title: HBV1-input

description: input


title: ES-E4_S52_001


title: 9P

description: vst.csv


title: 8P

description: vst.csv


title: ES-E2_S50_002


title: ES-E3_S51_001


title: 7M

description: vst.csv

source_name: breast metastasis from liver

value: liver

value: Distal metastsis


title: 9M

description: vst.csv

source_name: breast metastasis from skin(chest)

value: skin(chest)


title: B6 Diabetic

type: RNA

city: Perth

first: Lois

last: Balmer

state: Western Australia

address: 6 Verdun Street, Nedlands

department: Centre for Medical Research

country: Australia

institute: UWA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normalized using Illuminaio in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: 8 weeks

value: Diabetic 21 days

value: Kidneys


title: ES-E1_S49_002

value: not treated

value: single cell ES


title: ES-E2_S50_001


title: 6M

description: vst.csv

source_name: breast metastasis from ovary

value: ovary


title: 6P

description: vst.csv

value: breast

value: Primary


title: 5M

description: vst.csv

source_name: breast metastasis from brain

value: brain


title: ES-E1_S49_001


title: 7P

description: vst.csv


title: ES-E12_S60_002


title: FVB Control

value: FVB/N

value: Control 21 days


title: ES-E12_S60_001


title: 5P

description: vst.csv


title: 4M

description: vst.csv

value: lung


title: B6 Control


title: ES-E11_S59_002


title: ES-E11_S59_001


title: 6 h stress Pokkali 7-day-old seedling, Biological replicate 3

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of 6 h stressed 7-day-old Pokkali seedling

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using ArrayAssist ver 5.5  (Stratagene, CA, USA).

label: Biotin

organism: Oryza sativa Indica Group

source_name: 7-day-old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each variety were surface sterilized with 70% ethanol followed by 0.1 % HgCl2 with repeated rinses with Mili-Q water, and were allowed to imbibe in water for 16 h. The seedlings were grown hydroponically for seven days on rice growth medium (RGM), pH 4.8.

extract_protocol: Trizol extraction of total RNA of whole seedlings was performed according to the manufacturer's instructions.

treatment_protocol: The seven-day-old seedings of each variety were subjected to salinity stress by placing them in 200 mM NaCl solution for 3 h and 6 h at 28±1oC, respectively. Control tissues were maintained on RGM for 6 h at 28±1oC.

tag: cultivar

value: Pokkali

tag: stress

value: salinity stress

tag: time


title: 8M

description: vst.csv

value: liver


title: 6 h stress IR29 7-day-old seedling, Biological replicate 3

description: Gene expression data of 6 h stressed 7-day-old IR29 seedling

value: seedling


title: 6 h stress IR29 7-day-old seedling, Biological replicate 2


title: 4P

description: vst.csv


title: FVB Diabetic


title: 6 h stress IR29 7-day-old seedling, Biological replicate 1


title: 6 h stress Pokkali 7-day-old seedling, Biological replicate 1


title: ES-E10_S58_002


title: 3M

description: vst.csv

value: Distal metastsis


title: 6 h stress Nonabokra 7-day-old seedling, Biological replicate 2

description: Gene expression data of 6 h stressed 7-day-old Nonabokra seedling

value: Nonabokra


title: 3 h stress IR29 7-day-old seedling, Biological replicate 1

description: Gene expression data of 3 h drought stressed 7-day-old IR29 seedling


title: 3 h stress Pokkali 7-day-old seedling, Biological replicate 2

description: Gene expression data of 3 h drought stressed 7-day-old Pokkali seedling


title: 6 h stress Nonabokra 7-day-old seedling, Biological replicate 3


title: 3P

description: vst.csv


title: 3 h stress Pokkali 7-day-old seedling, Biological replicate 3


title: ES-D9_S45_002


title: 6 h stress Pokkali 7-day-old seedling, Biological replicate 2


title: 6 h stress Nonabokra 7-day-old seedling, Biological replicate 1


title: 3 h stress IR29 7-day-old seedling, Biological replicate 3


title: 3 h stress Pokkali 7-day-old seedling, Biological replicate 1


title: 3 h stress Nonabokra 7-day-old seedling, Biological replicate 2

description: Gene expression data of 3 h drought stressed 7-day-old Nonabokra seedling


title: ES-D9_S45_001


title: ES-E10_S58_001


title: 2M

description: vst.csv

source_name: breast metastasis from back

value: back


title: 2P

description: vst.csv


title: 1M

description: vst.csv


title: 3 h stress Nonabokra 7-day-old seedling, Biological replicate 3


title: 3 h stress Nonabokra 7-day-old seedling, Biological replicate 1


title: ES-D8_S44_001


title: 1P

description: vst.csv


title: Control IR29 7-day-old seedling, Biological replicate 2

description: Gene expression data of control unstressed 7-day-old IR29 seedling

value: control unstressed

value: control


title: Control IR29 7-day-old seedling, Biological replicate 1


title: Control IR29 7-day-old seedling, Biological replicate 3


title: D425_shCTD_3

city: Cincinnati

first: Zaili

last: Luo

state: OH

address: 3333 Burnet Ave.

institute: CCHMC

description:
shCTDNEP1
D425_shCTDNEP1.txt

data_processing:
Illumina Casava software used for basecalling.
WGS: each sample underwent paired-end (2 x 150bp) sequencing on Illumina HiSeq X Ten instrument generating around 1x coverage per sample.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Tophat using default options
Whole Genome Sequencing; Nextera TruSeq
WGS: Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 (mouse) or hg19 (human) whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm10/hg19

growth_protocol: NPC cells was firstly isolated from postnatal day4 cerebellum and culture in the neural stem cell medium with EGF, FGF, LIF, B27 and heparin; For medulloblastoma cell lines, cell were cultured in the DMEM with Glutamine and FBS.

extract_protocol:
RNA seq: Samples were flash frozen on dry ice, and total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001).

value: medulloblastoma cells

tag: cell line

tag: genotype/variation


title: ES-D7_S43_001

value: not treated

value: single cell ES


title: Control Pokkali 7-day-old seedling, Biological replicate 3

description: Gene expression data of control unstressed 7-day-old Pokkali seedling


title: D425_shCTD_2

description:
shCTDNEP1
D425_shCTDNEP1.txt


title: Control Pokkali 7-day-old seedling, Biological replicate 1


title: ES-D6_S42_002


title: D425_shCTD_1

description:
shCTDNEP1
D425_shCTDNEP1.txt


title: ES-D7_S43_002


title: Control Nonabokra 7-day-old seedling, Biological replicate 3

description: Gene expression data of control unstressed 7-day-old Nonabokra seedling


title: Control Nonabokra 7-day-old seedling, Biological replicate 2


title: Control mouse thalamic regions

city: Anyang

first: Yeong-Gon

last: Choi

state: Kyeonggi-do

address: Kwanpyeongro 170 beongil 15, Dongan-gu

department: Ilsong Institute of Life Science

country: South Korea

institute: Hallym University

description:
Gene expression data from normal thalamic regions
Control mouse 1 thalamic regions
Control mouse 2 thalamic regions
CTL Thl_Duplicate Mean

hyb_protocol: Following labeling, each cDNA was hybridized for 17 hr at 45℃ at 60 rpm on Affymetrix MouseGene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0007.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The quality control was estimated by confirming the order of the signal intensities of the Poly-A controls and Hybridization controls using Expression Console Software (Affymetrix, USA). The microarray data was analyzed using a GenPlex V3.0 (ISTECH, Korea). The data were analyzed with Robust Multiarray Average (RMA) quantification method as a probe set summarization algorithm for log transformation with base 2 (log2) and Quantile normalization method as a normalization method in the Preprocessing module of GenPlex V3.0. The mean signal intensities of all genes (35,557 probes (28,853 genes) in a platform) were obtained from 2 chips of each experimental group.

label: biotin

source_name: Control C57BL/6 mouse thalamic regions

label_protocol: Fragmented and biotinylated cDNA were prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual from 300 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual, Affymetrix).

growth_protocol: Six-week old male inbred C57BL/6 mice (20-22 g) were grown up.

extract_protocol: The total RNA in the spleen, cervical spinal cord and, thalamic tissues of each group (n=2 per each group) was extracted using an RNeasy Plus Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

treatment_protocol: Six-week old male inbred C57BL/6 mice (20-22 g, n=7) were intraperitoneally inoculated with 1% (w/v) brain homogenates (100 µl) of C57BL mouse-adapted ME7 scrapie strain dissolved in saline 0.9%, while mice in the control group (n=7) were injected with 1% (w/v) brain homogenates (100 µl) of control mouse.

tag: gender

value: Male

tag: developmental stage

value: Adult

value: Control

value: thalamus tissues


title: Control Nonabokra 7-day-old seedling, Biological replicate 1


title: ME7 mouse cervical spinal cord

description:
Gene expression data from cervical spinal cord of ME7-inoculated mouse
ME7 mouse 1 cervical spinal cord
ME7 mouse 2 cervical spinal cord
ME7 Csc_Duplicate Mean

source_name: ME7 C57BL/6 mouse cervical spinal cord

value: Cervical spinal cord tissues


title: ES-D6_S42_001

source_name: ES


title: ME7 mouse spleen

description:
Gene expression data from spleen of ME7-inoculated mouse
ME7 mouse 1 spleen
ME7 mouse 2 spleen
ME7 Sp_Duplicate Mean

source_name: ME7 C57BL/6 mouse spleen

value: Spleen tissues


title: Control Pokkali 7-day-old seedling, Biological replicate 2

value: Pokkali


title: D425_GFP_3

description:
shGFP
D425_shCTDNEP1.txt

value: shGFP


title: Control mouse spleen

description:
Gene expression data from normal spleen
Control mouse 1 spleen
Control mouse 2 spleen
CTL Sp_Duplicate Mean

source_name: Control C57BL/6 mouse spleen


title: ES-D8_S44_002


title: ES-D5_S41_002


title: ME7 mouse thalamic regions

description:
Gene expression data from thalamic regions of ME7-inoculated mouse
ME7 mouse 1 thalamic regions
ME7 mouse 2 thalamic regions
ME7 Thl_Duplicate Mean

source_name: ME7 C57BL/6 mouse thalamic regions


title: Control mouse cervical spinal cord

description:
Gene expression data from normal cervical spinal cord
Control mouse 1 cervical spinal cord
Control mouse 2 cervical spinal cord
CTL Csc_Duplicate Mean

source_name: Control C57BL/6 mouse cervical spinal cord


title: D425_GFP_2

description:
shGFP
D425_shCTDNEP1.txt


title: ES-D5_S41_001


title: ES-D4_S40_002


title: 3 h stress IR29 7-day-old seedling, Biological replicate 2

value: salinity stress

value: seedling


title: D425_GFP_1

description:
shGFP
D425_shCTDNEP1.txt


title: Empty vector 4

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

data_processing:
Used HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data
Reads were trimmed for quality using a minimum phred value of 20 and minimum length of 20 using Fastx-Trimmer
Reads were mapped with STAR (Dobin et al, 2013) to the mouse genome downloaded from Ensembl (GRCm38).
FeatureCounts (Liao et al, 2014) was used to count reads mapped to gene bodies on the correct strand with a minimum mapping quality of 10 using Ensembl genome annotation (Mus musculus.GRCm38.85.gtf).
Genome_build: GRCh38
Supplementary_files_format_and_content: DUX4_mx.tsv expression count matrix

source_name: Skeletal muscle organoids

growth_protocol: Generation of human skeletal micro-muscles expressing inducible DUX4. Human skeletal micromuscles (hµMs) were generated as per Mills et al. 2018 (doi:10.1016/j.biomaterials.2018.11.030. PubMed PMID: 30527761). Briefly, human skeletal muscle myoblasts (Lonza, Victoria, Australia) were mixed in a hydrogel containing 3.3 mg/ml collagen I and 22% (v/v) Matrigel (In Vitro Technologies, Victoria, Australia) . The bovine acid-solubilized collagen I (Devro, Australia) was first salt balanced and pH neutralized using 10X DMEM (ThermoFisher Scientific) and 0.1 M NaOH, respectively, prior to mixing with Matrigel and then combined with the myoblasts. The mixture was prepared on ice and pipetted into the micro-muscle cell-culture inserts [Mills et al, 2017; doi:10.1073/pnas.1707316114. PubMed PMID: 28916735]. The mixture was left to gel for 1 hr at 37°C, prior to addition of growth medium (1:1 mixture of DMEM:MCDB (ThermoFisher Scientific)  supplemented with 20% fetal bovine serum (FBS, ThermoFisher Scientific), 1% insulin-transferrin-selenium (ITS, Invitrogen), 1% penicillin-streptomycin (P/S, ThermoFisher Scientific)). After 2 days, growth medium was switched to differentiation media containing MEMα (ThermoFisher Scientific) with 1% P/S (ThermoFisher Scientific), 0.5% ITS (ITS, ThermoFisher Scientific) and 2% B-27 supplement (ThermoFisher Scientific), with 10 μM DAPT (Stem Cell Technologies)  and 1 μM Dabrafenib (Stem Cell Technologies) to induce myoblast differentiation [Mills et al. 2018]. After 7 days of differentiation, hµMs were cultured in a maintenance media consisting of MEM α (ThermoFisher Scientific) with 1% P/S (ThermoFisher Scientific), 0.5% ITS (ITS, ThermoFisher Scientific) and 2% B-27 supplement (ThermoFisher Scientific).

extract_protocol:
Total RNA was extracted from harvested mouse muscles or 5-6 pooled human micromuscles using TRIzol (Life Technologies, Victoria, Australia) as per manufacturer’s protocol.
200 ng of total RNA was subject to poly-A enrichment and library preparation using Illumina TruSeq reagents.

treatment_protocol: On day 12, hµMs were treated with AAV:TET and AAV:MCS vectors, or the AAV:TET and AAV:Dux. Vectors were administered at 5x109 vg/tissue for AAV:TET and 1x109 vg/tissue for AAV:MCS and AAV:Dux and cultured in  media containing Doxycycline at 0.5µg.ml-1. After 48 hrs hµMs were taken for RNA-sequencing and other analysis.

value: Empty vector


title: ES-D4_S40_001


title: Empty vector 3


title: ES-D3_S39_002


title: Empty vector 2


title: ES-D3_S39_001


title: S72h_Cont_1

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

country: France

institute: INRAE - University PARIS SACLAY

description: Gene expression data

hyb_protocol: Hybridization cocktail and post-hybridization processing was performed according to the “Target Preparation for Affymetrix GeneChip® Eukaryotic Array Analysis” protocol found in the appendix of the Nugen protocol of the fragmentation kit.

scan_protocol: scanned with an Affymetrix Genechip Scanner 3000, generating CEL files for each array.

data_processing: data were normalized with RMA

label_protocol: RNA was amplified with Ovation Pico WTA System v2  (Nugen Technologies, Inc.  #3302-12),  fragmented and biotin labeled using the Encore Biotin Module, (Nugen Technologies, Inc. #4200-12), according to the manufacturer's

growth_protocol: GFP-expressing Listeria monocytogenes EGDe strain  was grown in brain-heart infusion (BHI) at 37°C. Human HepG2 hepatocytes (ATCC HB-8065) were grown as recommanded by ATCC.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), from three biological replicates, according to the manufacturer's instructions.  RNA was treated with DNase I to remove residual DNA and then cleaned with DNase Inactivation Reagent (Ambion® Inc.) RNA was quality checked an then store at -80°C.

treatment_protocol: Cells were uninfected or infected with GFP-Listeria at multiplicity of infection of 1. After 1h infection, extracellular bacteria were killed by adding gentamicin and cells were incubated for 3 days with 25 μg/ml gentamicin containing media.

value: 72h and FACS


title: Empty vector 1


title: S72h_Inf_3

description: Gene expression data

value: GFP-expressing Listeria monocytogenes EGDe


title: S72h_Cont_2

description: Gene expression data

value: control


title: S72h_Cont_3

description: Gene expression data


title: ES-D2_S38_002


title: S72h_Inf_1

description: Gene expression data


title: S72h_Inf_2

description: Gene expression data


title: Patient_8_post_G207

city: Columbus

first: Katherine

middle: E

last: Miller

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
mRNA
Paired-end 2 x 50bp reads, Illumina GAIIx

data_processing:
bcl to fastq was performed using Illumina bcl2fastq conversion software version 2.20.0.422.
Paired-end FASTQ files were used as input for Salmon version 0.9.1 (https://combine-lab.github.io/salmon/getting_started/).
The Salmon transcriptome index was prepared using the following command: "salmon index -t GRCh38_latest_rna.fna -i GRCh38_latest_rna.fna_transcripts_index -k 31"; the GRCh38_latest_rna.fna was obtained from NCBI via ftp.ncbi.nlm.nih.gov.
The following parameters were used with Salmon processing:
libType: A
numBootstraps: 100
index: GRCh38_latest_rna.fna_transcripts_index
Genome_build: GRCh38
Supplementary_files_format_and_content: *.quant.sf: Salmon output; tab-delimited text files including transcript per million (TPM) values; each sample has a separate file labeled "Sample_name.quant.sf".

source_name: glioblastoma

extract_protocol:
Covaris truXTRAC® FFPE Kit.
Illumina TruSeq stranded mRNA kit.

value: brain tumor

tag: diagnosis

value: glioblastoma

tag: glioblastoma subtype

value: Proneural/Neural

tag: brain location

value: right frontal

tag: g207 treatment

value: post-G207 inoculation

tag: age (years)

tag: Sex

value: male

tag: survival post g207 (days)


title: a72h_Inf_2

description: Gene expression data

tag: treatment


title: Patient_7_post_G207

tag: tissue

value: Mesenchymal

value: female


title: a72h_Cont_3

description: Gene expression data


title: a72h_Inf_3

description: Gene expression data


title: Patient_5_post_G207


title: a72h_Cont_2

description: Gene expression data


title: Patient_6_post_G207

value: right frontoparietal


title: ES-D2_S38_001

tag: strain

value: not treated

tag: cell type

value: single cell ES


title: DUX4 over-expression 3

value: DUX4 over-expression


title: a24h_Inf_2

description: Gene expression data


title: a24h_Cont_3

description: Gene expression data


title: a24h_Inf_1

description: Gene expression data


title: Patient_3_post_G207

value: Classical/Proneural

value: left frontoparietal


title: ES-D1_S37_002


title: ES-D1_S37_001


title: DUX4 over-expression 2


title: Patient_1_post_G207

value: left frontal


title: DUX4 over-expression 4


title: DUX4 over-expression 1


title: a24h_Cont_2

description: Gene expression data


title: ES-D11_S47_002


title: ES-D12_S48_002


title: ES-D12_S48_001


title: anti-H3K9/14Ac RA

city: Suita

first: Fumihiro

last: Fujiki

address: Yamada-oka, 1-7

institute: Osaka University Graduate School of Medicine

data_processing:
Reads were aligned to the hg19 human genome using bowtie2 version 2.2.5.
Duplicate reads were removed before peak calling using MACS version 1.4.2.
Peaks were assigned to genomic regions using BEDTools.
According to RefSeq, genes located within 10 kb upstream or downstream of peaks were identified and extracted.
After annotation, enriched regions in each sample were filterd as follows; p < 1e-5, Fold Enrichment ≥ 5, and Peak Tag count ≥ 5.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files show annotated and enriched regions.

source_name: CD4+CD45RO+ T cell

growth_protocol: All cells were cultured in 10% AB serum/X-VIVO 15 medium supplemented with 40 IU/ml rhIL-2.

extract_protocol:
Chromatin precipitation was peformed using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, Danvers, MA, USA) according to the manufacturer’ s instructions.
Libraries were prepared by using TruSeq ChIP Sample Prep Kit (Illumina) according to TruSeq ChIP Sample Preparation Guide Rev.B.

treatment_protocol: T cells were stimulated with anti-CD3 and anti-CD28 mAbs in the presence of DMSO, RA ( 1μM）, or LE540 (10 μM） and were cultured for 1 week.

value: CD4+CD45RO+ T cell

tag: differentiation stage

value: effector

tag: chip antibody

value: anti-H3K9/14Ac #9677 (Cell Signaling Technology)

tag: sample name in data anaysis

value: RA


title: anti-H3K27me3 RA

value: anti-H3K27me3 #9733 (Cell Signaling Technology)


title: anti-H3K27me3 LE540

value: memory


title: a24h_Inf_3

description: Gene expression data

tag: cell line

value: GFP-expressing Listeria monocytogenes EGDe

tag: time


title: ES-D10_S46_002


title: anti-H3K9/14Ac LE540


title: ES-D10_S46_001


title: ES-C9_S33_002


title: anti-H3K9/14Ac DMSO

value: intermediate

value: DMSO


title: ES-C9_S33_001


title: ES-C7_S31_002


title: ES-C8_S32_002


title: ES-C8_S32_001


title: ES-C7_S31_001


title: ES-C6_S30_002


title: s_F1A_Acs_3

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F1A_Acs_3

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hybrid of both hg19 and mm10. The FASTA of the combined genome is available on the series record.  Mouse reads were discarded in downstream analysis.
Supplementary_files_format_and_content: tab-delimited file containing normalized counts for human genes.

source_name: human iPSCs-derived macrophages

growth_protocol: iPSCs-derived macrophages were cultured in RPMI1640/GlutaMax medium supplemented with 10% fetal bovine serum, and 100 ng/ml human M-CSF.

extract_protocol:
RNA from cells suspended in Trizol was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated wih 75% ethonol. Sample were resuspended in RNAase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 70 000 iPSCs-derived macrophages (WT, ACK1 deficient and BRK deficient) per well in 12 well plates were washed once with PBS and incubated or not with 450 000 mouse apoptotic thymocytes in RPMI for 90 minutes. WT iPScs-derived macrophages were also pretreated for 30 minutes with AIM100 (ACK1 inhibitor; 2uM) or cpd4f (BRK inhibitor; 0.5 uM) in RPMI and then incubated or not with mouse apoptotic thymocytes. After 90 minutes incubation media was removed and macrophages were washed once with PBS. Then 1 ml trizol (15596018, Life Technology ) was added per well and cells were harvested and stored at -80C.

value: human iPSCs-derived macrophages

tag: condition

value: apop cells

value: no inhibitor

tag: genotype

value: ACK1 deficient


title: s_F9A_ACs_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F9A_ACs_1

value: BRK deficient


title: s_F9A_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F9A_1

value: cell alone


title: s_F9A_3

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F9A_3


title: s_F9A_ACs_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F9A_ACs_2


title: s_F9A_ACs_3

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F9A_ACs_3


title: ES-C6_S30_001

first: Takaho

last: Endo

data_processing:
Base calling was performed using Off-line Basecaller (OLB) v1.9.4 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: plain text

extract_protocol:
mRNA were extracted following Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combi

value: not treated

value: single cell ES


title: s_F1A_Acs_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F1A_Acs_2


title: ES-D11_S47_001


title: anti-H3K27me3 DMSO

value: CD4+CD45RO+ T cell


title: ES-C5_S29_002


title: s_F1A_3

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F1A_3


title: s_F1A_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F1A_2


title: s_F1A_Acs_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F1A_Acs_1


title: s_C12_Cpd4f_Acs_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_Cpd4f_Acs_2

value: BRK inhibitor

value: WT


title: s_F1A_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F1A_1


title: ES-C4_S28_001


title: ES-C3_S27_002


title: D3BKO

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

institute: Georgia State University

description: 170413_I283_FCHHW2KBBXX_L1_FLGRMsP326G6AAAPEI-25

data_processing:
raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Brown adipose tissue

extract_protocol:
Brown adipose tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeq 2000 or other sequencer when necessary

tag: strain background

tag: age

value: 45 week

value: Chow diet feeding for 45 weeks

value: Brown adipose tissue


title: ES-C3_S27_001

city: Yokohama

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN


title: ES-C4_S28_002


title: D3BWT

description: 170413_I283_FCHHW2KBBXX_L2_FLGRMsP326F6AAAPEI-23


title: s_F9A_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_F9A_2


title: ES-C2_S26_002


title: Old Exercise 4

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Genome_build: A custom genome assembly to interrogate both nuclear and rDNA methylation was generated by adding the consensus rDNA repeat sequences, BK000964.3, as a separate chromosome to the GRCm39 (GCA_000001635.9) mouse reference genome assembly.
Supplementary_files_format_and_content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome

source_name: tibialis anterior

extract_protocol:
DNA was isolated from the TA muscle using the Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) as specified in the protocol.
“Classic” RRBS library preparation was performed by digesting genomic DNA with 30 units of MspI enzyme (New England BioLabs, R0106), and fragments were ligated to pre-annealed adapters containing 5’-methyl-cyotosine. Adapter-ligated fragments ≥50 base pairs were recovered using the DNA Clean & Concentrator Kit (Zymo Research, D4003) and bisulfite-converted using the EZ DNA Methylation-Lightning KitTM (Zymo Research, D5030) following the standard protocol. Preparative-scale PCR was performed, and the products were purified again using the Clean and Concentrator kit.

treatment_protocol: Young mice (4 month), aged mice (24 month), and mice subjected to progressive weighted wheel running (PoWeR) from 22-24 months were euthanized, and DNA from TA muscles were subject to reduced representation bisulfite sequencing (RRBS), ribosomal DNA-specific analysis, and Zymo Research's DNAge analysis.

value: Skeletal Muscle

tag: group

value: Exercise


title: Old Exercise 5


title: ES-C2_S26_001


title: Old Exercise 2


title: ES-C1_S25_002


title: s_C12_AIM100_Acs_3

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_AIM100_Acs_3

value: ACK1 inhibitor


title: s_C12_Cpd4f_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_Cpd4f_1

value: human iPSCs-derived macrophages


title: ES-C5_S29_001


title: Old Exercise 3


title: Old Exercise 1


title: Old Sedentary 5

value: Sedentary


title: Old Sedentary 4


title: s_C12_AIM100_Acs_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_AIM100_Acs_2

value: apop cells


title: Liver_3

city: Beijing

first: Shengli

last: Zhang

address: 2rd, Yuanmingyuan West Road

department: Colledge of Animal Science and Techonology

country: China

institute: China Agricultural University

description: WGBS; 150bp paired-end

data_processing:
Programs FastQC (0.11.5) and Trim Galore (0.4.5) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus ARS-UCD1.2) using bowtie2 under the Bismark software (0.19.0)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position,strand, coverage for methylated cytosine, coverage for unmethylated cytosine, CG type, three bases near the cytosine.

organism: Bos taurus

source_name: Liver

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

tag: breed

value: Holstein

value: Liver


title: ES-C12_S36_002


title: Liver_2

description: WGBS; 150bp paired-end


title: ES-C12_S36_001


title: Old Sedentary 3


title: s_C12_Cpd4f_Acs_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_Cpd4f_Acs_1


title: Liver_1

description: WGBS; 150bp paired-end


title: s_C12_AIM100_Acs_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_AIM100_Acs_1


title: ES-C11_S35_002


title: Muscle_3

description: WGBS; 150bp paired-end

source_name: Longissimus dorsi muscle

value: Longissimus dorsi muscle


title: s_C12_AIM100_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_AIM100_1

value: cell alone


title: s_C12_Cpd4f_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_Cpd4f_2


title: Old Sedentary 1


title: s_C12_Acs_3

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_Acs_3

value: no inhibitor


title: Muscle_2

description: WGBS; 150bp paired-end


title: ES-C1_S25_001

value: not treated

value: single cell ES


title: ES-C10_S34_001


title: Muscle_1

description: WGBS; 150bp paired-end


title: s_C12_Acs_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_Acs_2

value: WT


title: Brain_3

description: WGBS; 150bp paired-end

source_name: Cerebral Cortex

value: Cerebral Cortex


title: s_C12_Acs_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_Acs_1


title: Young Sedentary 3


title: ES-B9_S21_002


title: Brain_2

description: WGBS; 150bp paired-end


title: s_C12_AIM100_2

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_AIM100_2


title: s_C12_3

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_3


title: Old Sedentary 2


title: Brain_1

description: WGBS; 150bp paired-end


title: ES-B9_S21_001


title: Young Sedentary 2


title: ES-B8_S20_002


title: Young Sedentary 1


title: s_C12_1

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_C12_1


title: ES-B8_S20_001


title: exoASO-STAT6_3

city: Cambridge

first: Kelvin

state: Massachusetts

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

data_processing:
10x Genomics Cell Ranger pipeline (v.1.2) was utilized to perform de-multiplexing raw base call (BCL) files, alignment (mapped to the 10X reference for mm10), filtering, barcode counting, and UMI counting with the default parameters.
In addition, the cellranger aggr pipeline was employed to combine data from multiple samples into an experiment-wide feature-barcode matrix for further data analysis.
Data analysis and visualization were performed with the Seurat package (v.3.1.5) in R (v.4.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: raw read count matrix text file

source_name: Tumor

growth_protocol: To establish syngeneic tumor models, CT26 (5×105 cells to BALB/c) were injected subcutaneously to the right flank of mice.

extract_protocol:
Tumors were digested with mouse tumor dissociation kit from Miltenyi Biotec and CD45 positive cells were enriched with EasySep™ Mouse CD45 Positive Selection Kit from StemCell Technologies.
Library was constructed by following a protocol from 10X Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics).

treatment_protocol: exoASO-Scramble, and exoASO-STAT6 were injected intratumorally into CT26 tumors every other day, 3 injection total. Tumors were collected 24 h after last dose.

value: BALB/c

value: CT26 tumors

value: CD45 positive cells


title: Young Sedentary 5

value: Skeletal Muscle


title: ES-C10_S34_002


title: ES-C11_S35_001


title: exoASO-STAT6_2


title: Young Sedentary 4


title: 4E2

city: Gyeonggi-do

first: Jisoo

last: Kim

address: 22, Giheungdanji-ro 24beon-gil, Giheung-gu, Yongin-si

department: New growth team

institute: hy R&BD center

data_processing:
Processing raw reads started with quality check and filtering of low quality (<Q25) reads by Trimmomatic ver. 0.32
After QC pass, paired-end sequence data were merged together using fastq_mergepairs command of VSEARCH version 2.13.4 with default parameters. Primers were then trimmed with the alignment algorithm of Myers & Miller(1988) at a similarity cut off of 0.8.
Chimeric reads were filtered on reads with <97% similarity by reference based chimeric detection using UCHIME algorithm (Edgar RC et al.,2011)
After chimeric filtering, reads that are not identified to the species level (with <97% similarity) in the EzBioCloud database (Yoon SH et al., 2017) were compiled and cluster_fast command (Rognes T et al., 2016) was used to perform de-novo clustering to generate additional OTUs.
Genome_build: the EzBioCloud database (Yoon SH et al., 2017)
Supplementary_files_format_and_content: tab-delimited text file includes OTU relative abundance of each sample

organism: feces metagenome

source_name: Human stool

extract_protocol:
Total stool DNA samples were extracted using the QIAamp DNA Stool Mini Kit (Qiagen, USA).
Libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: Stool slurry sample from 3 adults

tag: disease state

value: Healthy


title: ES-B7_S19_002

tag: treatment


title: 4D2


title: ES-B7_S19_001


title: exoASO-Scramble_3

tag: tissue


title: exoASO-STAT6_1

tag: strain


title: 4C2


title: ES-B6_S18_002

tag: cell type


title: 4B2


title: ES-B6_S18_001


title: exoASO-Scramble_1


title: exoASO-Scramble_2


title: 4A2


title: 4F2


title: 3F2


title: ES-B5_S17_002


title: ES-B5_S17_001


title: Candida albicans orf19.3120 KO_6hr_biological rep 1

first: Nitesh

middle: Kumar

last: Khandelwal

state: Delhi

address: Near Munirka

department: School of Life Sciences

institute: Jawaharlal Nehru University

description: Gene expression after 6hr in orf19.3120 KO Candida albicans cells

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Agilent Candida albicans 8x15k Microarray Gene expression  (AMADID: 026377) designed by Genotypic Technology Private Limited. 600ng of cy3 labeled samples were  fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift ( Gene based Analysis was performed)

organism: Candida albicans

source_name: Candida albicans cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: C.albicans strains were grown over night in YEPD in biological duplicates. From primary cultures, cells of  0.2 OD600 were inoculated in 15 ml YEPD and allowed to grow for  6 hrs to reach log phase

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit following the manufacturer's recommendations.


title: ES-B4_S16_002

source_name: ES


title: WT iTreg

city: Shanghai

first: Ying

last: Lu

address: 280 S. Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adaptors, short-fragment reads and other low-quality reads. The raw reads were aligned to the mouse genome with Bowtie2 and HISAT.
Genome_build: mm9
Supplementary_files_format_and_content: Tables with  for FPKM values for each sample

source_name: Treg cells

growth_protocol: We purified CD4+CD25hiYFP+ nTreg cells from spleens and LNs. CD4+YFP-CD441oCD62Lhi Naïve CD4+ T cells were sorted from 8-week-old MondoA+/+Foxp3Cre mice and MondoAfl/flFoxp3Cre mice and cultured in iTreg polarization condition for 4 days.

extract_protocol:
Total RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tregs were sorted from 8-week-old MondoA+/+Foxp3Cre mice and MondoAfl/flFoxp3Cre mice and activated on a 24-well plate pre-coated with 5 μg/ml anti-CD3 in T cell culture medium supplemented with 2 μg/ml anti-CD28 and 100 U/ml IL-2 for 48 hours.

value: 8 weeks


title: 3D2


title: KO iTreg


title: Candida albicans orf19.3120 KO_6hr_biological rep 2


title: KO nTreg-CD3/28


title: ES-B4_S16_001


title: 3B2


title: 3C2


title: WT nTreg-CD3/28


title: ES-B3_S15_002


title: ES-B3_S15_001


title: ES-B2_S14_002


title: 2F2


title: 3A2


title: KO nTreg


title: ES-B1_S13_002


title: 2F1


title: NCD-IAT_Stromal vascular cells 3

city: Seoul

first: Jae Bum

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: Biological Sciences

institute: Seoul National University

data_processing:
Illumina 1.9 was used for base calling.
Read pairs were aligned using Tophat to the Mus musculus genome (GRCm38/mm10).
Each transcript and gene were estimated with Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Stromal vascular cells

growth_protocol: 18 week old C57BL/6J male mice

extract_protocol:
EAT and IAT were isolated from mice. Each adipose tissues were incubated with collagenase I buffer to separate adipocyte and SVCs.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: inguinal adipose tissue

value: Stromal vascular cells

tag: gender

value: male

value: 18 week-old


title: NCD-IAT_Stromal vascular cells 1


title: NCD-IAT_Stromal vascular cells 2


title: 2E2


title: NCD-EAT_Stromal vascular cells 2

value: epdidiymal adipose tissue


title: 2D2


title: 3E2


title: 2D1


title: ES-B1_S13_001


title: 2E1


title: ES-B2_S14_001


title: NCD-IAT_Adipocyte 2

source_name: Adipocyte

value: Primary adipocyte


title: 2C1


title: ES-B12_S24_002

value: not treated


title: NCD-EAT_Stromal vascular cells 3


title: 2B2


title: NCD-EAT_Stromal vascular cells 1


title: ES-A9_S9_002

value: single cell ES


title: 2B1


title: ES-B12_S24_001


title: 1F2


title: 2C2


title: WT nTreg


title: NCD-IAT_Adipocyte 3


title: ES-B11_S23_001


title: ES-B10_S22_002


title: NCD-IAT_Adipocyte 1


title: ES-B10_S22_001


title: 1E2


title: ES-A7_S7_001


title: 1D2


title: NCD-EAT_Adipocyte 3


title: 1D1


title: Subject ID: C8; Tissue: saliva

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

department: Pediatrics

country: Spain

institute: GENVIP research group

hyb_protocol: We used the standard gene expression protocol for 12x RNA hybridization with 5ul of RNA as input, a hybridization time of 18h for all samples and mixing control and COVID-19 samples to avoid technical sample bias.

scan_protocol: SPRINT nCounter machine

data_processing: Normalization of the gene expression data was carried out for each tissue separately by selecting the optimal number and best reference candidate from the set of housekeeping (HK) genes included in the panel, as well as other endogenous genes that showed high levels of stability between samples. We excluded HK candidate genes with less than 50 raw counts in any of the samples compared from the reference selection analysis. Data normalization was performed through a combined approach using both DESeq2 and RUVSeq as described in Bhattacharya et al. (2021) (https://academic.oup.com/bib/article-abstract/22/3/bbaa163/5891144). Genes with counts below the background (mean + 2 standard deviations (SD) of the negative control spikes in the code set) were not included in the differential expression (DE) analysis. After data normalization and background thresholding, we eliminated lower expressed genes from the list.

source_name: saliva

extract_protocol: RNA was isolated using PAXgene blood miRNA extraction kit (Qiagen) following manufacturer recommendations and carrying out the on-column DNase I treatment during the extraction process. RNA from saliva and nasal epithelium specimens was isolated using 500ul of sample and the RNeasy microkit (Qiagen). We used Oragene RNA neutralizer solution (DNA Genotek) to precipitate impurities and inhibitors and slightly modified the protocol provided by the extraction kit as recommended by the Oragene tubes supplier

tag: subject id

value: saliva

value: Male

value: Control


title: 2A2


title: ES-A5_S5_002


title: ES-B11_S23_002


title: 1C2


title: ES-A9_S9_001


title: 2A1


title: ES-A4_S4_002


title: Subject ID: C8; Tissue: nasal

source_name: nasal

value: nasal


title: Subject ID: C6; Tissue: saliva

value: Female


title: Subject ID: C9; Tissue: saliva


title: ES-A8_S8_001


title: 1F1


title: NCD-EAT_Adipocyte 2


title: 1B1


title: Subject ID: C9; Tissue: nasal


title: ES-A5_S5_001


title: ES-A3_S3_002


title: ES-A7_S7_002


title: NCD-EAT_Adipocyte 1


title: ES-A8_S8_002


title: 1E1


title: ES-A6_S6_002


title: ES-A2_S2_002


title: Hybrid_Carrot_Orange

city: Kolkata

first: Saikat

last: Chakrabarti

state: West Bengal

address: CN-6, Sector V

institute: CSIR-IICB

data_processing:
Quality of the raw data  was checked  using FastQC.
Pre-processing of the data is done with Cutadapt.
HISAT was used to align the high quality data to the reference with the default parameters
HTSeq  was used to estimate and calculate transcript abundance.
DESeq was used to calculate the differentially expressed transcripts.
Supplementary_files_format_and_content: raw and normalized counts

organism: Daucus carota subsp. sativus

source_name: Hybrid (Orange) Carrot

extract_protocol:
Whole RNA was extracted from red and orange carrot roots using NEBNext® Poly(A) mRNA Magnetic Isolation Module
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment was done

value: sativus

value: Orange variety of Daucus carota root


title: ES-A6_S6_001


title: Subject ID: C7; Tissue: saliva


title: 1B2

value: Stool slurry sample from 3 adults

value: Healthy


title: ES-A2_S2_001


title: Delhi_Carrot_Red

source_name: Delhi (Red) Carrot

value: Red variety of Daucus carota root


title: Subject ID: C4; Tissue: nasal


title: Subject ID: C6; Tissue: nasal


title: Subject ID: C5; Tissue: nasal


title: ATAC_5FU_2hr

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
Sequence reads were aligned to the hg38 genome assembly using bowtie2
Bigwig file were created by bamCoverage with Effective genome size 2.7e9
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: Cell line

growth_protocol: Cells were cultured in DMEM with 10% fetal calf serum.

extract_protocol:
ATACseq or Cut-tag experiments were performed using standard protocols.
Library construction was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme, Nanjing, China) according to the manufacturer’s guide.

treatment_protocol: Cells were treated with 100uM 5FU for 2h or 4h.

tag: agent

value: 100uM 5FU

tag: time point


title: 5Fu 100uM 2hr rep2

data_processing:
Sequencing reads from RNA-seq were aligned to the mouse reference genome (Version mm10 from UCSC) using Tophat (2.1.0) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: Hg38
Supplementary_files_format_and_content: FPKM

source_name: Cell lines

growth_protocol: DMEM with 10% fetal calf serum.

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standart protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5FU 100uM for 2h.

tag: cell line

value: Human CRC cell line

value: 100uM 5FU for 2h


title: ES-A1_S1_002

growth_protocol: C57B6N × 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 3μM CHIR99021, 1μM PD0325901, 103U/ml ESGRO LIF on a gelatin-coated dish or in serum ESM (2iL): Knockout DMEM (Thermo Fisher Scientific) , 20% FBS, 1xNEAA, 0.1mM β-mercaptoethanol, 1 × penicillin-streptomycin, 3μM CHIR99021, 1μM PD0325901, and 103U/ml ESGRO LIF on mouse embryonic fibroblasts (MEF) feeder dish. CD1 TSCs (#1-4M, #2-2M, #8M, #1F, #2-3F, #2-4F) were derived in serum-free TS medium: Neurobasal: DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 50ng/ml human FGF4, 10μg/ml heparin, 20ng/ml human Activin A, 10μM XAV939, 10μM Y27632 on MEF feeder dish. CD1 (Clea) or PWK (BRC, RIKEN) × C57BL6N (Charles River) F1 blastocysts were collected at E3.5. CD1-Tg(CAG-EGFP) mice were kindly gifted from Prof. T. Wakayama (Yamanashi university). Culture conditions used in this study is summarized in Supplementary Table 1. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in +C10F4HPDGF medium (Suppl table 1): StemFit® Basic02, 1xpenicillin-streptomycin (Thermo Fisher Scientific), 10μM CHIR99021 (Reprocell), 50ng/ml human FGF4 (Sigma), 1ng/ml heparin (Sigma), 25ng/ml human PDGF-AA (R&D). Embryos were cultured in +C10F4HPDGF medium for at least 5 days until they formed outgrowths. The outgrowth was dissociated with 1xTrypLE™ Select (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate. After 5-7 days, PrES cell colonies reached 50-80% confluence and the cells were passaged into a 12-well MEF feeder plate. PrES cells were frozen in Cellbanker® 1plus (Zenoaq). XEN cells were derived according to a standard protocol (1) with minor modifications. CD1 blastocysts were collected at E3.5. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in serum-containing ES medium: RPMI1640 (Thermo Fisher Scientific), 20% fetal bovine serum (FBS, Biosera), 1 × penicillin-streptomycin (Thermo Fisher Scientific), 1 × non-essential amino acids (NEAA, Thermo Fisher Scientific), 0.1mM β-mercaptoethanol (β-ME, Sigma), 103U/ml ESGRO LIF on a MEF feeder plate. Embryos were cultured for at least 7 days until they formed outgrowths. The outgrowth was removed by pipetting and the remaining adherent cells were continuously cultured for another 7 days. The proliferated cells were dissociated with 0.05% trypsin-EDTA (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate, then expanded into a 6-well plate. XEN cells were frozen in Cellbanker® 1plus (Zenoaq) and stored in a -150°C freezer (Panasonic). Removal of the primary outgrowth was not necessary when CHIR99021 (3μM) was added.


title: Subject ID: C5; Tissue: saliva


title: Ribotag3_WT_M480

city: Mannheim

first: Carmen

last: Ruiz de Almodóvar

address: Ludolf-Krehl-Straße 13-17

institute: ECAS

description:
ribosome bound RNA
WT

data_processing:
Raw reads were mapped to the Mm genome (ensembl) with STAR.
Duplicate reads were removed with custom bash script.
Read conting was done using Htseq-count.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Text format read counts over ensembl genes from Htseq-count.

source_name: cerebellum

growth_protocol: Cerebellum was collected at P56.

extract_protocol:
The pull-down of Rpl22HA/HA was performed as described before (Sanz, E., Yang, L., Su, T., Morris, D.R., McKnight, G.S., and Amieux, P.S. (2009). Cell-type-specific isolation of ribosome-associated mRNA from complex tissues. Proc Natl Acad Sci U S A 106, 13939-13944.) using the Pcp2Cre:Rpl22HA/HA and Pcp2Cre:Tie2flox/flox:Rpl22HA/HA mouse lines. In short, cerebellar tissue samples were homogenized on ice in 10% w/v polysome buffer. Samples were centrifuged for 10min at 12.000rpm at 4°C, supernatant was collected and 10µl were kept as input. Remaining sample was incubated o/n at 4°C with anti-HA antibody-coated magnetic beats. Magnetic beads were washed with ice-cold HS-buffer and finally re-suspended in RLT buffer from RNeasy® Mini Kit (Qiagen; 74104).
Library preparation and sequencing were performed by BGI Genomics, China.

treatment_protocol: constitutive Cre line; require no special inductive treatment

value: whole cerebellum

tag: batch


title: ES-A4_S4_001


title: 5Fu 100uM 2hr rep1


title: 1A2


title: Subject ID: C7; Tissue: nasal


title: 1C1


title: Subject ID: C3; Tissue: nasal


title: Ctrl_rep2

value: none; control


title: Subject ID: C2; Tissue: saliva


title: ES-A3_S3_001

value: not treated


title: JUND_treat

data_processing:
Library strategy: Cut & Tag
Sequence reads were aligned to the hg38 genome assembly using bowtie2
Bigwig file were created by bamCoverage with Effective genome size 2.7e9
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

tag: antibody

value: JUND


title: 1A1


title: Subject ID: C4; Tissue: saliva

value: saliva


title: Subject ID: C2; Tissue: nasal

value: Male


title: Ctrl_rep1


title: ATAC_5FU_4hr


title: Ribotag3_WT_M476

description:
ribosome bound RNA
WT

tag: genotype


title: ES-A12_S12_001

value: single cell ES


title: Subject ID: C3; Tissue: saliva

tag: age

value: Control


title: Ribotag3_WT_M479

description:
ribosome bound RNA
WT


title: ATAC_ctrl_rep1


title: ES-A1_S1_001


title: JUND_ctrl


title: ES-A12_S12_002


title: Subject ID: C12; Tissue: saliva

value: Female


title: JUN_treat

value: JUN


title: Ribotag3_WT_F473

description:
ribosome bound RNA
WT


title: Ribotag3_WT_M477

description:
ribosome bound RNA
WT


title: ES-A11_S11_002


title: ES-A11_S11_001


title: Subject ID: C12; Tissue: nasal

value: nasal


title: JUN_ctrl


title: ATAC_ctrl_rep2


title: Ribotag3_KO_M456

description:
ribosome bound RNA
KO


title: ES-A10_S10_002


title: Subject ID: C11; Tissue: nasal


title: Subject ID: C11; Tissue: saliva


title: Ribotag2_KO_M390

description:
ribosome bound RNA
KO


title: FOS_ctrl

value: FOS


title: EGR1_treat


title: Cnr1-/- microglia, 3

city: Bonn

first: Eva

middle: Carolina

last: Beins

address: Venusberg-Campus 1

institute: University of Bonn

description: Sample 6

data_processing:
Lexogen QuantSeq pipeline implemented in Partek® Flow® Genomic Analysis Software
Sequenced reads were trimmed and then mapped to mm10 whole genome using STAR- 2.6.1d
Aligned reads were quantified using Partek E/M against mm10 - Ensembl Transcript release 99
Gene counts were normalised using TMM
Differential gene expression analysis was performed with TMM normalised counts using one-factorial ANOVA. A low-expression filter was applied to exclude genes with an average coverage of less than 10 and Limma-voom shrinkage of error term variance was applied. Multiple test correction was performed using FDR step-up.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TMM normalised gene counts for every gene and every sample

source_name: Enriched microglia (CD11b magnetic beads)

extract_protocol:
Mice were perfused with PBS, brain mechanically dissociated, myelin removall with 40% Percoll, magnetic cell separation using CD11b MicroBeads (MACS®, Miltenyi Biotec), RNA isolation with Qiagen RNeasy Mini Kit
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: Cnr1 tm1Zim

value: d/d

tag: Sex

value: male

value: 3 months


title: Ribotag2_WT_M386

description:
ribosome bound RNA
WT


title: ES-A10_S10_001


title: FOS_treat

value: 100uM 5FU


title: Cnr1+/+ microglia, 3

description: Sample 5

value: wt/wt


title: Kank4#6

city: shanghai

first: junhao

last: hu

address: HaiKe

institute: interdisciplinary research center on biology and chemistry

data_processing:
Reads cleaning: raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files by both read quality and length (Q30 > 20, length > 36).
Alignment: clean reads were processed to pseudo-align to human transcriptome GRCh38 using salmon.
Quantification: transcriptional level expression was aggregated to gene level expression using tximport. Ensembl release 95 was used to annotate genes.
Quality check: sample clustering was performed with principle component analysis analysis and sample to sample distance correlation analysis.
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 1.5 and adjusted p-value < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression raw counts

source_name: HUVEC

growth_protocol: HUVECs were allowed to grow in 3D fibrin gel and can absorb growth factor from HPF in chip .

extract_protocol:
standard smartSeq2 protocol
TruSeq RNA Library Prep Kit v2

treatment_protocol: HUVECs were infected by empty vector ctrl and KANK4 followed by extracted from microfluidic chips.

value: HUVEC

value: overexpressing KANK4

tag: culture method

value: 3D fibrin gel


title: Subject ID: C10; Tissue: nasal


title: Cnr1+/+ microglia, 2

description: Sample 4


title: Ribotag1_WT_M379

description:
ribosome bound RNA
WT

value: whole cerebellum


title: RNA-seq_cKO-rep3_E16.5

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

description:
E16.5_RNA-seq_ReadCount.txt
E16.5_RNA-seq_cKO-WT_DEG.txt

data_processing:
Genome_build: GRCm38
High-quality reads of RNA-seq were quantified using Salmon (v.1.0.0) and differential gene expression analysis was conducted using DESeq2(v1.26.0).

source_name: Hippocampus

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard MGI protocols.

value: Embryonic day 16.5

value: Arid1a conditional knock out

value: Hippocampus


title: Kank4#5


title: Cnr1-/- microglia, 2

description: Sample 3


title: RNA-seq_cKO-rep2_E16.5


title: Subject ID: C1; Tissue: saliva

value: saliva

value: Female

value: Control


title: EGR1_ctrl


title: Kank4#3


title: Cnr1-/- microglia, 1

description: Sample 1


title: RNA-seq_cKO-rep1_E16.5


title: Ribotag1_KO_M374

description:
ribosome bound RNA
KO


title: Cnr1+/+ microglia, 1

description: Sample 2


title: Subject ID: B1985; Tissue: Blood

source_name: Blood

value: Blood

value: Male

value: COVID

value: Mild


title: Subject ID: B1983; Tissue: Blood


title: ckoNPC_2_LWGS

city: Cincinnati

first: Zaili

last: Luo

address: 3333 Burnet Ave.

institute: CCHMC

description: Low coverage of WGS

data_processing:
Illumina Casava software used for basecalling.
WGS: each sample underwent paired-end (2 x 150bp) sequencing on Illumina HiSeq X Ten instrument generating around 1x coverage per sample.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Tophat using default options
Whole Genome Sequencing; Nextera TruSeq
WGS: Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 (mouse) or hg19 (human) whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm10/hg19

source_name: Cerebellum of postnatal day4

extract_protocol:
WGS: Samples were flash frozen on dry ice and extract the genome DNA by extraction kit.
Genome DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neural progenitor cells

tag: passages

value: passage 20


title: Vector#6

value: vector


title: RNA-seq_WT-rep3_E16.5

value: Wild type


title: Subject ID: B1937; Tissue: saliva


title: Subject ID: B1981; Tissue: Blood


title: Vector#3

value: HUVEC


title: Subject ID: B1989; Tissue: Blood


title: Vector#2

value: 3D fibrin gel


title: RNA-seq_WT-rep2_E16.5


title: wtNPC_LWGS

description: Low coverage of WGS


title: ckoNPC_1_LWGS

description: Low coverage of WGS


title: Subject ID: C10; Tissue: saliva


title: Ribotag1_KO_F371

description:
ribosome bound RNA
KO

value: whole cerebellum


title: RNA-seq_cKO-rep2_P21

description:
P21_RNA-seq_ReadCount.txt
P21_RNA-seq_cKO-WT_DEG.txt

value: Three weeks


title: RNA-seq_WT-rep1_E16.5

value: Embryonic day 16.5


title: wtNPC

description: ATAC-seq wtNPC at passage 15

extract_protocol:
ATAC-seq: cells (50,000 cells) were spun down at 500 x g for 5 min at 4C, lysed in cold Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Afterspinning down at 500 x g for 10 min at 4C, nuclei were resuspended in transposition mix containing 25 μl TD (2x reaction buffer) 2.5 μl TDE1 (Nextera Tn5 Transposase), 22.5 μl Nuclease Free H2O, at 37°C for 30 min. Immediately following transposition, DNA were purified using a Qiagen MinElute PCR Purification Kit. Transposed DNA fragments were subsequently amplified and the amplified library was purified using Qiagen MinElute PCR Purification Kit. Libraries were generated using the Ad1_noMX and Ad2.1–2.4 barcoded primers and were amplified for 7–9 total cycles.
Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500.

value: passage 15

tag: genotype/variation

value: wtNPC


title: Subject ID: B1935; Tissue: saliva

value: saliva


title: NPCT_2

description:
ckoNPC tumor from NSG mice after 3 months
P4_P20_Tumor_NPC.txt

extract_protocol:
RNA seq: Samples were flash frozen on dry ice, and total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001).

value: Cerebellum tumor

value: ckoNPC tumor


title: Subject ID: B1935; Tissue: nasal

value: nasal

value: Male


title: RNA-seq_WT-rep2_P21

value: Hippocampus


title: RNA-seq_WT-rep1_P21


title: NPCT_1

value: Neural progenitor cells


title: ckoNPC

description: ATAC-seq ckoNPC at passage 15

value: ckoNPC


title: Subject ID: B1933; Tissue: nasal

value: Female

value: COVID

value: Mild


title: ckoNPC_2

description:
ckoNPC_2 at p20
P4_P20_Tumor_NPC.txt

value: passage 20


title: Subject ID: B1937; Tissue: nasal


title: ChIP-seq_cKO_input

data_processing:
Genome_build: GRCm38
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.3.5.1) with default parameters. MACS (v.2.2.5) was used to call peaks (-q 0.01) relative to the input sample.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

value: Arid1a conditional knock out

tag: chip antibody


title: RNA-seq_cKO-rep1_P21

value: Three weeks

tag: tissue


title: Subject ID: B1913; Tissue: saliva


title: wtNPC_2

description:
wtNPC_2 at p20
P4_P20_Tumor_NPC.txt

tag: strain


title: ChIP-seq_cKO_H3K27me3

value: H3K27me3, Millipore, 07-449


title: ckoNPC_1

description:
ckoNPC_1 at p20
P4_P20_Tumor_NPC.txt

tag: cell type


title: ChIP-seq_cKO_H3K27ac

value: H3K27ac, Abcam, ab4729


title: Subject ID: B1912; Tissue: nasal

tag: gender


title: Subject ID: B1913; Tissue: Blood

tag: subject id

value: Blood


title: Subject ID: B1913; Tissue: nasal


title: Subject ID: B0719; Tissue: saliva

value: saliva


title: 6NPC

description:
Nes: CTD f/+-NPCs-2
P4_P20_Tumor_NPC.txt

value: passage 4

value: Nes:CTD f/+-NPCs-2


title: wtNPC_1

description:
wtNPC_1 at p20
P4_P20_Tumor_NPC.txt

value: wtNPC


title: ChIP-seq_WT_input

value: Wild type


title: 5NPC

description:
WT-NPCs-2
P4_P20_Tumor_NPC.txt


title: ChIP-seq_WT_H3K27me3

value: Hippocampus


title: ChIP-seq_cKO_H3K4me3

value: H3K4me3, Abcam, ab8580


title: Subject ID: B0719; Tissue: nasal

value: nasal


title: Subject ID: B0660; Tissue: saliva

value: Male


title: 4NPC

description:
Nes: CTD f/f NPCs-2
P4_P20_Tumor_NPC.txt

value: Neural progenitor cells

value: Nes:CTD f/f NPCs-2


title: Subject ID: B0660; Tissue: nasal

value: COVID

value: Mild


title: Subject ID: B0528; Tissue: Blood

value: Female

value: Control


title: 1NPC

description:
WT-NPCs-1
P4_P20_Tumor_NPC.txt


title: FADMR(female AD mice + methionine restricted feed) H8

city: Shenzhen

first: Jin

last: Xin

state: Guangdong

address: Beishan road

institute: BGI

data_processing:
Filtering and trimming the reads using Trimmomatic v0.38 with parameters “HEADCROP:9 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:20”.
Clean reads were mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6 ) using Hisat2 v2-2.1.0 with default parameters.
The reads of each sample were then assembled into transcripts and compared with reference gene models using StringTie v1.3.4d.
Merging the all transcripts to obtain a consensus transcript using StringTie-Merge program.
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
DEG analysis was performed using Ballgown v2.12.0.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .

source_name: hippocampus

extract_protocol:
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard BGI-500 protocols

tag: treatment


title: ChIP-seq_WT_H3K4me3

value: Three weeks


title: ChIP-seq_WT_H3K27ac

value: H3K27ac, Abcam, ab4729


title: Subject ID: B0660; Tissue: Blood

value: Blood


title: Subject ID: B0525; Tissue: Blood


title: FADMR(female AD mice + methionine restricted feed) H7


title: Eµ-MycT/+WT , replicate 3

city: Barcelona

first: José

last: Yélamos

address: Dr. Aiguader, 88

department: Cancer Research Program

institute: Hospital del Mar Medical Research Institute (IMIM)

data_processing:
Illumina bcl2fastq version 2.17.1.14: basecalling
STAR v2.5.3a mapping to Mus musculus Ensembl release 87 (mm10) with geneCounts option to get raw counts per gene and per sample
Differential expression analysis is performed with the DESeq2 R/Bioconductor package
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text files: raw counts per gene and per sample

source_name: Purified bone marrow pre-B cells from tumor-free, 4-week-old mice

growth_protocol: Bone marrow cell suspensions were washed in PBS, resuspended in PBS containing 0.5% BSA and incubated with antibodies on ice for 30 min. Red Blood Cells were lysed using ACK lysis buffer. Pre-B cells (B220+CD19+c-kit-IgM-IgD-) were purified by Fluorescence-activated cell sorting, performed in a FACS AriaIISORP (BD Biosciences)

extract_protocol:
Total RNA was isolated from sorted bone marrow pre-B cells by using the Rneasy Total RNA Isolation kit (Qiagen), with on-column DNase I (Qiagen) digestion
Single-end Illumina RNA Truseq stranded protocol (polyA selected).

treatment_protocol: Bone marrow pre-B cells purified by cell sorting

value: Bone marrow pre-B cells

value: WT


title: Subject ID: B0524; Tissue: Blood


title: Eµ-MycT/+WT, replicate 2


title: 2NPC

description:
Nes: CTD f/+-NPCs-1
P4_P20_Tumor_NPC.txt

value: passage 4

value: Nes:CTD f/+-NPCs-1


title: FADMR(female AD mice + methionine restricted feed) H6


title: PN81.UM

city: Stanford

first: Minyoung

last: Youn

address: 269 Campus Drive, CCSR 1210

institute: Stanford University

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence using Trimmomatic 0.38, then mapped to hg38 STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf provided from genecode
Sequences were imported into R , scaled, filter for low counts ( < 1 cpm) and TMM normalized using the edgeR package.
Genome_build: hg38
Supplementary_files_format_and_content: adult samples.xlsx - Matrix table with log2 counts per million reads for each adult sample
pediatric samples.xlsx - Matrix table with log2 counts per million reads for each pediatric sample.
CML.xlsx - Matrix table with log2 counts per million reads for each CML sample and log-fold changes (pediatric CML vs adult CML).

source_name: CD34+ cells

extract_protocol:
CD34+ bone marrow cells were isolated. RNAs were prepared using the RNeasy Micro Kit (Qiagen).
cDNA libraries were generated using KAPA-stranded mRNA-Seq kit (Roche), and then size selected.
Prepared libraries will be sequenced on the Illumina HiSeq 4000 (Illumina), with a minimum 30 million paired-end 75 bp reads per sample.

tag: developmental stage

value: pediatric

tag: disease

value: Normal

value: CD34+ hematopoietic stem/progenitor cells


title: Subject ID: B0518; Tissue: Blood


title: Eµ-MycT/+WT, replicate 1


title: Eµ-MycT/+Parp-2-/- , replicate 3

value: Knock-Out Parp2


title: 3NPC

description:
Nes: CTD f/f NPCs-1
P4_P20_Tumor_NPC.txt

value: Neural progenitor cells

value: Nes:CTD f/f NPCs-1


title: PN71.UM


title: FADMR(female AD mice + methionine restricted feed) H4


title: Subject ID: B0517; Tissue: Blood


title: FADMR(female AD mice + methionine restricted feed) H9


title: Subject ID: B0516; Tissue: Blood

value: Male


title: Subject ID: B0527; Tissue: Blood


title: FADMR(female AD mice + methionine restricted feed) H5


title: Subject ID: B0515; Tissue: Blood


title: Eµ-MycT/+Parp-2-/- , replicate 2


title: FADMR(female AD mice + methionine restricted feed) H3


title: PN74


title: FADMR(female AD mice + methionine restricted feed) H2


title: Subject ID: B0514; Tissue: Blood


title: PN18


title: Subject ID: B0513; Tissue: Blood


title: PN85


title: Eµ-MycT/+Parp-1-/- , replicate 3

value: Knock-Out Parp1


title: PN06


title: Eµ-MycT/+Parp-1-/-, replicate 2


title: FADMR(female AD mice + methionine restricted feed) H10


title: FADMR(female AD mice + methionine restricted feed) H11


title: Subject ID: B0512; Tissue: Blood

value: Female


title: FWTMR(female control mice + methionine restricted feed) G9


title: PN46


title: RNA-Seq.MN_WT_2

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
ChIP-Seq data were first processed using Trim Galore, then aligned to reference genome (mm10) using Bowtie2 with default settings. The PCR duplicates for each dataset were removed using the rmdup function of samtools. The reads from biological replicates were pooled together for further analysis.
The raw data for RNA-Seq were first processed with Trim Galore. TPM values for each gene were calculated using RSEM. To perform differential expression analysis, reads were aligned to reference genome using STAR, then read numbers for each gene were counted using the featureCount function from Subread, finally differential expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: BED files for ChIP-Seq peaks called by macs2. Tab-delimited text files contain TPM values for each gene calculated using RSEM.

source_name: Induced motor neuron

growth_protocol: Mouse ESCs were grown in ES medium [DMEM (Gibco, 11965092) supplied with 15% FBS (HyClone, SH3007103), 1× HEPES (Gibco, 15630080), 1× NEAA (Gibco, 11140050), 1× Glutamax-I (Gibco, 35050061), 1× Anti-Anti (Gibco, 15240062), 0.1% 2-Mercaptoethanol (Gibco, 21985023) and 1 ng/μL LIF (Gibco, A35933)]. The MN induction procedure takes 6 days: 1) Trypsin treatment of mESCs to single cells, and seed ~5M cells to 15-cm Petri dish with 30 mL ADFNK medium [44% Advanced DMEM, 44% Neurobasal, 10% Knockout serum, 1× Glutamax-I (Gibco, 35050061), 1× Anti-Anti (Gibco, 15240062) and 0.1% 2-Mercaptoethanol (Gibco, 21985023)](day 0); 2) Culture with shaking in  37OC  with 5% CO2  for two days to get embryoid body (day 2); 3) Change ADFNK medium [1 μM RA, 1 μM SAG], further culture for 2 days to neuron progenitor cells (day 4); 4) change ADFNK medium [1 μM RA (), 1 μM SAG (), 1 μM DOX (), 5 μM DAPT (Sigma, D5942-5MG)], further culture for 2 days to get mature motor neurons (day 6).

extract_protocol:
Total RNA is isolated using RNeasy Mini Kit (Qiagen) followed by PolyA extraction.
RNA-Seq libraries are constructed using Illumina TruSeq Stranded mRNA Library Prep Kit.

value: Motor neuron


title: FADMR(female AD mice + methionine restricted feed) H1


title: Eµ-MycT/+Parp-1-/-, replicate 1


title: PN12


title: PC4008.SF

value: CML


title: Subject ID: B0510; Tissue: Blood

value: Control


title: PN14


title: Eµ-MycT/+Parp-2-/- , replicate 1


title: PN31


title: RNA-Seq.MN_WT_1


title: FWTMR(female control mice + methionine restricted feed) G4


title: Subject ID: B0507; Tissue: saliva

value: saliva

value: COVID

value: Mild


title: Subject ID: B0507; Tissue: Blood

value: Blood


title: PC3010.SF


title: FWTMR(female control mice + methionine restricted feed) G7