title: RNASeq - UNC0638 Control Rep1

value: Control


title: Lenti/βAS3-FB-2

status: Public on Sep 21 2020

type: SRA

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
After sequencing, the reads were demultiplexted using bcl2fastq.
The fastq reads were aligned to the virus genome using bwa mem command.
bigWig files were generated using the bamCoverage command.
Genome_build: Lenti/βAS3-FB is an 8.9-kb LV carrying a complex anti-sickling β-globin gene cassette, as previously described by Romero et al. The β-globin gene is driven by FASTA files on series record. the endogenous β-globin promoter and enhancers in the anti-sense (reverse) orientation, with the expression regulated by a “mini” locus control region (LCR) comprised of portions of the β-globin locus DNAse hypersensitive sites (HS) HS2, HS3 and HS4. In addition, Lenti/βAS3-FB contains the Woodchuck Hepatitis Virus post-transcriptional regulatory element (wPRE) and a 77-bp insulator in the U3 region of the 3’ LTR, termed as FB (FII-BEAD). GlobeFB is a 6.5-kb LV carrying an anti-sickling β-globin gene cassette. The expression is regulated by a shortened LCR comprised of HS2 and HS3 and a shortened 3'UTR of the β-globin locus. EFS-ADA is a 4-kb LV for treating adenosine deaminase severe combined immunodeficiency (ADA-SCID) that is capable of high-level and consistent ADA gene transfer and expression.  The EFS-ADA vector consists of the human elongation factor-α gene “short” promoter (EFS) driving the expression of a codon-optimized human ADA gene cassette followed by the wPRE, all in the sense (forward) orientation. All vectors consist of a pCCL backbone and differ only by the internal promoters and transgene cassettes.
Supplementary_files_format_and_content: bigWig file

molecule: total RNA

organism: synthetic construct

growth_protocol: 293T cells were cultured in Dulbecco's modified Eagle's mediun, 10% Fetal Bovine Serum, and 1% Penicillin, Streptomycin, and Glutamine

extract_protocol:
Total RNA was extracted from raw viral supernatant using the QIAmp Viral RNA Mini Kit (Qiagen). Viral RNA was treated with TurboDNAse (Invitrogen) and sent to the UCLA Technology Center for Genomics and Bioinformatics Core for downstream library preparation.
cDNA library was prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche Sequencing, Pleasanton, CA) following the manufacturer’s manual without rRNA depletion to avoid bias. Briefly, RNA was fragmented into ~400 bp fragments; 1st strand cDNA was synthesized with random priming followed by 2nd strand synthesis.

treatment_protocol: LVs were packaged by transient transfection of 293T cells with fixed amounts of HIV Gag/Pol, Rev and VSV-G expression plasmids and equimolar amounts of each of the different vector transfer plasmids using TransIT-293 (Mirus Bio, Madison, WI) as described in the supplemental method and Cooper et al. Virus was collected 3 days post transfection.

tag: lentiviral vector

tag: vector length


title: Lenti/βAS3-FB-1

source_name: Lenti/βAS3-FB is an 8.9-kb LV carrying a complex anti-sickling β-globin gene cassette


title: RNASeq - Pom HRI Rep1

city: Philadelphia

first: Gerd

last: Blobel

state: Pennsylvania

address: 3615 Civic Center Blvd., Abramson Research Center 316H

department: Hematology

institute: Children's Hospital of Philadelphia

data_processing:
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/).
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR, followed by RSEM for gene quantifications.
Genome_build: hg38 assembly
Supplementary_files_format_and_content: TSV Files

organism: Homo sapiens

source_name: Primary CD34+ cell culture

growth_protocol: For in vitro cell culture, peripheral blood mononuclear cells were obtained from the University of Pennsylvania Human Immunology Core (Philadelphia, PA). CD34+ cells were purified using MACS MicroBead kit (Miltenyi) and cultured in three-phase in vitro culture. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 1 ng/mL IL-3, 3 units/mL erythropoietin, 2% penicillin/streptomycin, 200 μg/mL holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 10 μg/mL heparin. For Phase II medium, the IL-3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/mL erythropoietin, 2% penicillin/streptomycin, 1 mg/mL holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 10 μg/mL heparin. Cells were maintained in Phase I from the day of collection until day 8, at which time cells were spin-infected and transitioned to Phase II media. On day 13 of culture, cells were transitioned to Phase III media

extract_protocol:
RNA samples were harvested in TRIzol (ThermoFisher Scientific) and purified with the RNeasy Mini kit (Qiagen). For RNA-Seq, approximately 200 ng of RNA was then depleted for rRNA and globins using the Ribo-Zero removal reagents and protocol from the ScriptSeq Complete kit (Illumina Cat # BHMR1224), followed by purification using the RNeasy MinElute Clean Up kit (Qiagen Cat # 74202).
Sequencing libraries were then constructed from depleted RNA using the TruSeq Stranded Total RNA kit (Illumina Cat # 20020598) and PCR-amplified for 13 cycles. The size and quality of each library were then evaluated by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and quantified using qPCR. Libraries were sequenced in paired-end mode on the NextSeq 500 to generate 2 x 76 bp reads using Illumina-supplied kits as appropriate.

treatment_protocol: For pharmacologic treatments, cells were treated starting on day 6 of culture with DMSO (vehicle control) 1 uM or 0.1 uM of pomalidomide (Sigma-Aldrich), or 0.125 μM of UNC0638 (Tocris Biosciences) Drugs were replenished every 2-3 days. RNA samples for RT-qPCR were harvested on day 13 of culture for optimal RNA yield. For shRNA treatments, two independent shRNAs targeting HRI were utilized for each sample, while scrambled non-targeting shRNA was used as control. Lentivirus for the above shRNA were produced in HEK293T and concentrated using Lenti-X Concentrator (Takara Bio) as per manufacturer’s specifications. Spin-infection were performed on day 8 of culture at 2250 RPM for 90 minutes.

tag: cell type

value: Three-phase in vitro culture of CD34+ primay human cells

tag: day of isolation

value: Day 13 of culture

tag: data file subset

value: RNASeq

tag: shRNA depletion type

value: HRI

tag: pharmacologic treatment type

value: Pomalidomide


title: RNASeq - Pom Control Rep2


title: RS4;11_parental

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample.

source_name: pro-B MLL leukemia cell line RS4;11

growth_protocol: Cells were cultured in Gibco RPMI 1640 containing 10% FBS at 37°C with 5% CO2 and were maintained between a density of 5 × 10^5 cells/ml and 2 × 10^6 cells/ml.

extract_protocol:
Tissue blocks were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

treatment_protocol: Induced drug-resistant cells were generated by treating parental MLL leukemia cell lines SEM and RS4;11 with gradually increasing concentration of bortezomib for at least 4 weeks. Bortezomib treatment was started with a concentration of 1 nM and the concentration of bortezomib was increased by 1 nM every 3 days. The remaining cells after the treatment were considered as bortezomib-resistant cells and were collected for analysis. SEM resistant cells were treated with DMSO, LBH589 (5 nM), or SAHA (2 uM) for 20 hours. RS4;11 resistant cells were treated with DMSO, LBH589 (50 nM), or SAHA (2 uM) for 20 hours.

tag: tissue

value: pro-B mix linage leukemia (MLL) cell line

tag: cell line

value: parental RS4;11

tag: drug treatment


title: IAPP-100A

city: Cambridge

first: Can

last: Kayatekin

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description: Induced 1

data_processing:
Reads were mapped with TopHat v2.0.13 (Trapnell, Pachter, & Salzberg, 2009) against the sacCer3 version of the yeast genome using the following parameters:  “-I  2500,  --solexa1.3-quals,  --segment-length 20, --no-novel-juncs , --no-coverage-search,  --b2-very-sensitive, -g 1, and  -G gtf file”
We used the annotation file “Saccharomyces_cerevisiae.R64-1-1.80.gtf.gz” downloaded from ENSEMBL.
We assigned reads to genes with htseq-count (Anders, Pyl, & Huber, 2015) using the options “--mode=intersection-strict, --stranded=reverse”, and the same gtf file used in the mapping.
We ran edgeR (Robinson, McCarthy, & Smyth, 2010) to assay differential gene expression
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts per million (cpm) and differential expression analysis performed with edgeR

organism: Saccharomyces cerevisiae

source_name: IAPP-100 nM Estradiol

growth_protocol: Cells were grown in log phase throughout

extract_protocol:
RNA was extracted from yeast pellets using a hot acid phenol protocol
RNA-seq libraries from yeast total RNA were prepared for sequencing with the TruSeq Stranded mRNA Library Prep Kit and sequenced on a HiSeq 2500.

treatment_protocol: 6 hour induction with 100 nM estradiol

tag: strain background

tag: genotype/variation

value: 6xIAPP integrated in single copy at LEU2, under the control of an estradiol-inducible promoter

tag: treatment

value: induced with 100 nM Estradiol


title: RNASeq - Pom Control Rep1


title: Prdm16 Knockout_12m_rep2

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

description:
RMH1579
processed data file: fpkm_nooutliers_prdm16_12month_forgeo_061520.txt

data_processing:
The quality of RNA-seq reads was ascertained via FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). The average sequencing depth was 39 million reads per sample, with a median per-base quality >30 for all samples. No further trimming of the bases was performed prior to read mapping.
Sequencing reads were mapped to the mouse reference genome (mm10) using TopHat-2.1.0 (PMID 19289445) or STAR (2.5.1b) (PMID 23104886) aligners, with an average mapping rate of 72%.
Transcript/gene assembly and abundance estimation were performed using Cufflinks-2.1.1 (PMID 20436464), resulting in the generation of gene expression counts normalized for library size and transcript length (FPKM).
CyberT has been implemented for differential gene expression analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited files with FPKM for all the samples.

organism: Mus musculus

source_name: Prdm16 knockout heart

extract_protocol:
Hearts were dissected from Control and Prdm16 knockout mice at 3 and 12 months of age.
RNA from collected hearts was extracted using FavorPrep™ RNA isolation kit (Catalog no. FATRK001). For 3-month-old hearts, strand-specific poly(A) RNAseq libraries were generated using NEBNext Ultra™ II Directional RNA Library Prep Kit with sample purification beads from Illumina (NEB, Catalog no. E7795S). For 12-month-old hearts, RNAseq libraries were prepared and sequenced at Genome Institute of Singapore (GIS), ASTAR, Singapore using their platform technologies.

value: Prdm16 knockout

value: Heart

tag: age

value: 12 months


title: RS4;11_resistant_SAHA

description: RS4;11_resistant_DMSO_LBH589_SAHA.fpkm.txt

value: bortezomib-derived pro-B MLL leukemia cell line RS4;11

value: SAHA


title: Control_12m_rep2

description:
RMH1576
processed data file: fpkm_nooutliers_prdm16_12month_forgeo_061520.txt

source_name: Control heart


title: RS4;11_resistant_LBH589


title: IAPP-0B

description: uninduced 2

treatment_protocol: 6 hour incubation with DMSO

value: uninduced (DMSO)


title: RS4;11_resistant_DMSO

value: DMSO


title: IAPP-0A

description: uninduced 1


title: Lenti/βAS3-FB-3


title: SEM_resistant_DMSO

source_name: pro-B MLL leukemia cell line SEM

value: bortezomib-derived pro-B MLL leukemia cell line SEM


title: RNASeq - DMSO HRI Rep2

value: Three-phase in vitro culture of CD34+ primay human cells


title: RNASeq - DMSO HRI Rep1

value: Day 13 of culture


title: Prdm16 Knockout_3m_rep3

description:
CbMu3
processed data file: fpkm_allsamples_prdm16_3month_forgeo_061520.txt

value: 3 months


title: SEM_parental_rep2


title: Prdm16 Knockout_3m_rep2

description:
CbMu2
processed data file: fpkm_allsamples_prdm16_3month_forgeo_061520.txt


title: RNASeq - DMSO Control Rep2

value: RNASeq

value: Control


title: Prdm16 Knockout_12m_rep1

description:
RMH1578
processed data file: fpkm_nooutliers_prdm16_12month_forgeo_061520.txt


title: Prdm16 Knockout_3m_rep1

description:
CbMu1
processed data file: fpkm_allsamples_prdm16_3month_forgeo_061520.txt


title: SEM_resistant_rep2

value: pro-B mix linage leukemia (MLL) cell line


title: Control_3m_rep3

description:
CbCntr3
processed data file: fpkm_allsamples_prdm16_3month_forgeo_061520.txt


title: IAPP-100B

description: Induced 2


title: Control_3m_rep2

description:
CbCntr2
processed data file: fpkm_allsamples_prdm16_3month_forgeo_061520.txt


title: RS4;11_parental_rep2


title: Neo1

first: Todd

last: Gierahn

address: 500 Main St

institute: MIT

data_processing:
Extract cell barcode and UMI from read 1
Filter polyA and library primer sequences from read 2
Align read 2 to human genome using STAR
Identify reads mapped to exon sequences
Use UMI to count number of molecules of each gene captured for each cell
Genome_build: hg19
Supplementary_files_format_and_content: DGE files containing transcript counts for each cell

source_name: tracheal aspirate

extract_protocol:
Seq-Well protocol - Gierahn (2017) Nature Methods 14 395
3'-barcoded RNA-seq

value: tracheal aspirate

tag: disease state

value: severe bronchopulmonary dysplasia

tag: gestational age at birth

value: 25 weeks 0 days

value: mixed cell types

tag: gender

value: female

value: collected on postnatal day 8


title: Control_3m_rep1

description:
CbCntr1
processed data file: fpkm_allsamples_prdm16_3month_forgeo_061520.txt

value: Heart


title: SEM_resistant_rep1


title: Control_12m_rep1

description:
RMH1575
processed data file: fpkm_nooutliers_prdm16_12month_forgeo_061520.txt

value: 12 months


title: RS4;11_parental_rep1

value: bortezomib-derived pro-B MLL leukemia cell line RS4;11


title: Lung Tumor-34

type: RNA

city: Lucknow

first: Neetu

address: Chowk

department: Center for Advance Research

country: India

institute: King George's Medical University

description:
Well differentiated-Histopathological Inference
m RNA expression

hyb_protocol: Following fragmentation,  5.5 ug of  fragmented biotin labeled ss cDNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 7G, Affymetrix.

data_processing: The CEL files were generated after scanning the array-chips through GeneChip Scanner-7G (Affymetrix, CA). Further, the generated CEL files were converted into .rma-gene-ful.chp and .rma-alt-splice-dabg.chp files through Affymetrix Expression Console™ Software (version 1.3). Further, the data was analyzed through Transcriptome Analysis Console v3.0. After running ANOVA, a multi-testing correction has been performed using the Benjamini-Hochberg Step-Up FDR-controlling procedure for all the expressed genes and expressed PSRs/Junctions (i.e. expressed in at least one condition). (By default, the Alpha level has been set as 0.05 in False Discovery Rate field) 15.

label: Biotin

source_name: Squamous cell Carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug of  fragmented ss cDNA (Gene chip Whole Transcriptome (WT) Expression array;P.No. 703147, Affymetrix).

growth_protocol: 10 Lung tumor and 5 Lung control samples were included in the study from Homo sapiens.

extract_protocol: Total RNA was extracted from 50 to 100 mg of both control and tumor specimens following the Guanidium Thiocyanate method 27 using the Trizol-reagent (Invitrogen, Carlsbad, CA) according to manufacturer's instructions.

tag: disease

value: Non-Small Cell Lung Cancer Stage IIIA


title: monocyte-derived macrophage, vehicle trained, 4h after P3C restimulation, donor B.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.44.0).

label: biotin

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Buffy coats were obtained from healthy donors after written consent (Sanquin Blood Bank, Nijmegen, the Netherlands). Peripheral blood mononuclear cells (PBMCs) were isolated using  Ficoll-Paque PLUS (GE Healthcare Biosciences). After Ficoll isolation the monocyte fraction of the PBMCs was increased by hyperosmotic Percoll gradient isolation (Sigma). Percoll monocytes were cultured in RPMI 1640 (Dutch modification) culture medium (Invitrogen) supplemented with 10 μg/mL gentamicin (Centraform), 10 mmol/L Glutamax (Invitrogen), 10 mmol/L pyruvate (Invitrogen), and 10% human pooled serum, without addition of extra growth hormones.

extract_protocol: Total RNA was isolated from the cells using TRIzol reagent, which was further purified using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Adherent monocytes were stimulated (trained) with aldosterone (10nM; Sigma) or its vehicle control ethanol for 24h, followed by a resting period of 5 days in RPMI with 10% serum at 2,5×106  cells per well in 6 well plates. On day 6, before or after 4h of Pam3Cys restimulation (10ug/ml (EMC Microcollections)), RNA was extracted.

tag: donorid

value: B

tag: training condition

value: vehicle (control; ethanol with final concentration 0.001%)

tag: restimulated at day6 with p3c for 4hrs

value: yes


title: RS4;11_resistant_rep2


title: monocyte-derived macrophage, aldosterone trained, 4h after P3C restimulation, donor B.

value: aldosterone (10nM; dissolved in ethanol)


title: RS4;11_resistant_rep1


title: dim10_N6492_H3K9me3_ChIPseq

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: genomic DNA ChIPseq libraries

library_source: genomic

data_processing:
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed.  The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 25bp windows.  Output file was a .tdf file, displayable on IGV.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 25bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).

molecule: genomic DNA

organism: Neurospora crassa

source_name: germinated condia

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were washed in PBS prior to crosslinking.

extract_protocol:
Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit  and eluted in 30 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 8 cycles (or 12 cycles for WT H3K27me2me3) at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP.

tag: antibody used


title: Neo3

value: moderate bronchopulmonary dysplasia

value: 24 weeks 3 days

tag: cell type

value: male

value: collected on postnatal day 6


title: RNASeq - DMSO Control Rep1

value: Three-phase in vitro culture of CD34+ primay human cells

tag: day of isolation

value: Day 13 of culture

tag: data file subset

value: RNASeq

tag: shRNA depletion type

value: Control

tag: pharmacologic treatment type

value: DMSO


title: monocyte-derived macrophage, aldosterone trained, 4h after P3C restimulation, donor C.

value: C


title: Lung Tumor-8

treatment_protocol: 10 Lung tumor and 5 Lung control samples were included in the study from Homo sapiens.


title: Lung Tumor-33

source_name: Primary Sarcomatoid Carcinoma after metastasis Adenocarcinoma


title: Lung Tumor-13

source_name: Adenocarcinoma


title: Lung Tumor-11


title: AML63

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

country: United Kingdom

institute: Nottingham Trent University

description: IO 360 panel

hyb_protocol: Hybridisation was performed in a PCR for 20 hours at 65°C.

scan_protocol: Scanned with NanoString Digital analyser with 555 FOV

data_processing: Data was normalised using the nSolver software, version 4.0.

label: Nanostring bar coding

source_name: Bone Marrow

label_protocol: RNA ispecies were identified and counted using the NanoString IO 360 Panel.

growth_protocol: Human Samples

extract_protocol: RNA extraction was carried out using Qiagen RNeasy RNA isolation kits. Quantitation of RNA was performed using Nanodrop and Qubit RNA high sensitivity assay.

treatment_protocol: At time of initial diagnosis.

tag: tp53 status

value: Wild type/NA/ND

tag: disease state at sampling

value: Diagnosis


title: monocyte-derived macrophage, vehicle trained, 4h after P3C restimulation, donor C.


title: AML64

description: IO 360 panel


title: Lung Tumor-12

value: Non-Small Cell Lung Cancer Stage IIIA


title: monocyte-derived macrophage, aldosterone trained, not restimulated, donor C.

value: no


title: monocyte-derived macrophage, vehicle trained, not restimulated, donor B.

value: B

value: vehicle (control; ethanol with final concentration 0.001%)


title: monocyte-derived macrophage, aldosterone trained, 4h after P3C restimulation, donor A.

value: A

value: aldosterone (10nM; dissolved in ethanol)

value: yes


title: monocyte-derived macrophage, aldosterone trained, not restimulated, donor B.


title: s20_V4_T_A

city: LONGJUMEAU

first: Angela

last: PATATIAN

address: 1CHEMIN DE SAULXIER

department: ESSONNE

country: France

institute: GENEX

hyb_protocol: All cRNAs were hybridized to human whole genome oligo microarrays (Agilent Technologies V3  AMADID 072363) which contains 60.000 probes, derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner G2505C (Agilent Technologies)

data_processing:
Microarray data were quantified (GeneExtraction Feature V12) and normalized with R (Bioconductor) by qunatile methode ( normalization between arrays using Limma Package) and intensities values are in log2.
Fold-changes (FC) were deduced from multy-Anova test (Mkmisc Package with R). Modulated genes were selected for a FC≥+/-2 Pval ≤0.05

source_name: no treated skin explant

label_protocol: RNAs of each sample were used for reverse transcription, amplification and Cy3 labeling, using the Low Input Labeling kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The study was approved by an ethics committee and performed in accordance with the Declaration of Helsinki after the patient had given informed consent.Full-thickness human skin biopsies were obtained from abdomen of healthy female donors who had undergone plastic surgery. The hypodermis was removed from the skin and circular explants were excised using a sample punch. The samples were placed immediately in BIO-EC’s Explant Medium (BEM) for 5 days and were cultured under classical cell culture conditions (37°C in 5% CO2).

extract_protocol: Total RNAs were extracted from skin explants fixed in RNA-Later® (Qiagen, REF76106) using the ReliaPrep Tissue Miniprep kit (Promega Z6111) after mechanical disruption and homogenization by TissueLyser (Qiagen).

treatment_protocol: On day 5 (D5), the explants of the concerned batches were placed in the exposure system Pollubox® and treated with 2 cigarettes smoke.

value: keratinocytes/fibroblastes

tag: tissue

value: skin  abdominoplasty


title: s22_V4_T_C

tag: age


title: Lung Tumor-5


title: s21_V4_T_B


title: Lung Tumor-7


title: AML60

description: IO 360 panel


title: s18_V4_CS2_B

source_name: Skin explant treated by cigarette smoke from 2 cigarettes


title: s17_V4_CS2_A


title: AML62

description: IO 360 panel


title: AML61

description: IO 360 panel


title: Lung Tumor-3

source_name: Advanced Adenocarcinoma


title: ci-Ins2_2

city: Lausanne

first: Adriana

last: Rodriguez Trejo

state: Vaud

address: Rue du Bugnon 9

department: DNF

country: Switzerland

institute: UNIL

description: ci-Ins2 gapmeR transfected cells

data_processing:
To determine transcript expression levels, reads were mapped to the rat transcriptome (ENSEMBL 92, rn6) using STAR (2.5.3a) and quantified with RSEM (1.3.0).
To identify differentially expressed genes, reads were mapped to the rat genome (rn6) using HISAT (2.1.0) and gene counts for rat genes (ENSEMBL 92, rn6) estimated using HTseq.
Normalization and differential gene expression (FDR<0.05) were performed using DESeq2 (v.1.12.4).
Gene enrichment analysis for significantly up or downregulated genes relative to all islet expressed genes was carried out using the DAVID webserver.
Genome_build: rn6
Supplementary_files_format_and_content: The Gene_expression_ci-Ins2_knockdown.xlsx file includes the RSEM read quantification of annotated genes for each sample, as well as the downregulated and upregulated genes and KEGG pathways in the ci-Ins2 knockdown samples.

organism: Rattus norvegicus

source_name: Pancreatic islet cells

growth_protocol: Pancreatic islets were isolated by collagenase digestion (Gotoh M et al., Transplantation, 1987) and Histopaque density gradient. Thereafter, islets were dissociated into single cells with trypsin-EDTA (Gibco) and cultured in RPMI 1640 GlutaMAX medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco), 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma).

extract_protocol:
Total RNA was extracted with the miRNeasy micro kit (Qiagen).
Libraries were prepared and sequenced by the Lausanne Genomic Technologies Facility with the TruSeq Stranded mRNA Library Prep kit and a HiSeq 2500 instrument for a single end run of 125 cycles using the SBS chemistry v4 (Illumina).

treatment_protocol: Dissociated islet cells were transfected using Lipofectamine RNAiMAX (Thermo Fisher) with either control or rat ci-Ins2 antisense LNA oligonucleotides (gapmeRs, Qiagen) with the following sequences: control gapmeR: 5’-AACACGTCTATACGC-3’; rat ci-Ins2 gapmeR: 5’-GCTTACAGACACATAG-3’. Cells were then cultured for 48 h before total RNA extraction.

tag: strain

value: Wistar

value: Pancreatic islet cells

tag: transfected with

value: ci-Ins2 gapmeR


title: ci-Ins2_3

description: ci-Ins2 gapmeR transfected cells


title: AML59

description: IO 360 panel


title: ci-Ins2_1

description: ci-Ins2 gapmeR transfected cells


title: AML58

description: IO 360 panel


title: monocyte-derived macrophage, vehicle trained, 4h after P3C restimulation, donor A.


title: monocyte-derived macrophage, aldosterone trained, not restimulated, donor A.


title: Lung Tumor-1


title: monocyte-derived macrophage, vehicle trained, not restimulated, donor C.


title: s16_V3_T_C


title: monocyte-derived macrophage, vehicle trained, not restimulated, donor A.


title: Lung Control-22

description:
Lung Control
m RNA expression

source_name: Right Uper Lung, Aspergilloma

value: control


title: s15_V3_T_B


title: control_2

description: Control gapmeR transfected cells

value: Control gapmeR


title: s19_V4_CS2_C


title: AML57

description: IO 360 panel


title: control_3

description: Control gapmeR transfected cells


title: Lung Control-3

description:
Lung Control
m RNA expression

source_name: Right Destroyed Lung


title: Lung Control-1

description:
Lung Control
m RNA expression

source_name: Left Side Collapse And Consolidated Lung


title: AML55

description: IO 360 panel


title: AML56

description: IO 360 panel


title: AML54

description: IO 360 panel


title: control_1

description: Control gapmeR transfected cells


title: AML53

description: IO 360 panel


title: SLX18986_DKO_mouse

first: Sam

last: Watcham

address: Jeffery Cheah Biomedical Centre

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
Reads aligned to mm10 and processed using Cell Ranger v1.3.
Counts extracted using Scanpy in python
Each sample was filtered for potential doublets by simulating synthetic doublets from pairs of scRNAseq profiles and assigning scores based on a k nearest-neighbor classifier on principal component analysis (PCA) transformed data. The top 4.5% of cells with the highest doublet scores from each sample were removed from further analysis. Cells with >10% of unique molecular identifier (UMI) counts mapping to mitochondrial genes, expressing fewer than 1200 genes, or with the total number of UMI counts further than 3 standard deviations from the mean for all cells were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: Counts: Normalized UMI counts per gene, per cell

source_name: Blood progenitors from Aldh2-/-Adh5-/- mouse

extract_protocol:
The femurs, tibiae, iliac crest, humeri, and vertebrae of 6-16 weeks old mice were crushed, washed with 10 ml of PBS supplemented with 2 % heat-inactivated FBS, and strained through 70-μm meshes. Cell suspension was depleted of red blood cells by ammonium chloride lysis (STEMCELL Technologies), and stained with the lineage depletion kit (19816A, STEMCELL Technologies) following the manufacturer’s instructions.
Cells were washed in PBS with 0.04% BSA and re-suspended before loading 10,000 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584). Quantification of library construction was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584).

value: Blood (Lin-c-Kit+)

tag: genotype


title: SLX18986_Adh5_mouse

source_name: Blood progenitors from Adh5-/- mouse


title: Lung Control-2

description:
Lung Control
m RNA expression

source_name: Left Lung Apical Lobe Cavitary Leison

tag: disease


title: Lung Control-6

description:
Lung Control
m RNA expression

source_name: Right Lung Lower Lobe Cyst


title: AML51

description: IO 360 panel

value: Wild type/NA/ND


title: SLX18986_Aldh2_mouse

source_name: Blood progenitors from Aldh2-/- mouse


title: s14_V3_T_A


title: s13_V3_CS2_C


title: AML50

description: IO 360 panel

value: Diagnosis


title: SLX18986_WT_mouse

source_name: Blood progenitors from WT mouse

value: WT


title: AML49

description: IO 360 panel


title: AML52

description: IO 360 panel


title: AML48

description: IO 360 panel


title: Mouse CD19+/CD13+/CD19+ population

city: Stanford

first: Ansuman

middle: T

last: Satpathy

address: BMI1 4600, 240 Pasteur Drive

institute: Stanford University

description: single-cell RNA-sequencing

data_processing:
Data was processed using CellRanger v3.0.2 with prebuilt mm10 index v3.0.0
Cells were processed using Scrublet to remove suspected doublets
Data was subsequently processed using Scanpy, excluding suspected doublets, cells with fewer than 250 genes detected, or greater than 10% mitochondrial reads
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is provided as a tab-delimited UMI counts table, from the original CellRanger filtered feature barcode output.  No above filtering (e.g. Scrublet) was performed on this table.

molecule: polyA RNA

source_name: Brain

extract_protocol:
Adapted from Lin et al., protocols.io, 2018; the removal of vessels prior to digestion, as written in the protocol, was not performed
10x Genomics 5' single-cell RNA-sequencing

value: brain

tag: cell population

value: CD19+/CD13+/CD19+ cells

tag: developmental stage

value: adult


title: s11_V3_CS2_A


title: s12_V3_CS2_B


title: s8_V1_CS2_C


title: s10_V1_T_B


title: AML46

description: IO 360 panel


title: s5_V2_T_C


title: s6_V1_CS2_A


title: SEM_parental_rep1

source_name: pro-B MLL leukemia cell line SEM

value: pro-B mix linage leukemia (MLL) cell line

tag: cell line

value: bortezomib-derived pro-B MLL leukemia cell line SEM

tag: drug treatment


title: AML45

description: IO 360 panel


title: AML47

description: IO 360 panel


title: SOD1-ALS iPSC-derived MN_3

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

country: Germany

institute: University Medical Center Rostock

description:
SOD1 R115G_D8.9
SOD1-ALS-2_3

hyb_protocol: 5.5 ug of biotinylated and fragmented single-stranded cDNA were hybridized for 17 hr at 45C on Affymetrix Human Gene ST 2.0 Arrays according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 4). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Partek Genomics Suite version 7.0 (PGS 7.0) using default analysis settings to obtain background corrected and summarized probe sets.

source_name: SOD1-ALS_iPSC-derived spinal motor neurons

label_protocol: Biotinylated, fragmented single-stranded cDNA samples were prepared according to the Ambion WT Expression Kit (AM4411973) protocol and the GeneChip WT Terminal Labeling Kit (900671) protocol from 300 ng total RNA.

growth_protocol: Neurons were cultured in N2B27 medium with 10 ng/µl BDNF, 500 µM dbcAMP and 10 ng/µl GDNF.

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

treatment_protocol: Not applicable

tag: disease status

value: Familial ALS (fALS)

tag: donor id/status

value: fALS patient2 carrying SOD1 mutation

tag: cell type

value: Spinal motor neurons

tag: iPSc source

value: Fibroblast


title: s9_V1_T_A

value: keratinocytes/fibroblastes

value: skin  abdominoplasty


title: AML44

description: IO 360 panel

source_name: Bone Marrow


title: s3_V2_CS2_C


title: s2_V2_CS2_B


title: s4_V2_T_A

source_name: no treated skin explant


title: SOD1-ALS iPSC-derived MN_2

description:
SOD1 D90A_ MM9
SOD1-ALS-1_2

value: fALS patient1 carrying SOD1 mutation


title: AML43

description: IO 360 panel


title: NSCs SB rep2

city: shanghai

first: wang

last: ying

address: 320 yueyang road

country: China

institute: shanghai instiutes for biological science chinese acadeema of science

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Index of the reference genome (GRCh38 (hg38)) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. The feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor.
Genome_build: Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

source_name: Neural stem cell

growth_protocol: The  Human iPSCs-derived NSCs cells were maintained as adherent culture in 50% DMEM-F12 and 50% Neurobasal®-A, containing 1x N2 supplement, 1x B27 supplement (Minus Vitamin A), 1x NEAA, 1x Glutamax, 10 ng/ml FGF-Basic (AA10-155) Recombinant Human Protein (bFGF, Gibco), 10 ng/ml LIF Recombinant Human Protein (hlif, Gibco), 3 µМ CHIR99021 (Selleckchem), 5 µМ SB431542 (Selleckchem), and 200 µМ L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma).

extract_protocol:
Total RNA of indicated samples was isolated with Trizol Reagent (Sigma).RNA quantification and qualification were performed with Agilgent 2000 Bioanalyzer.
The mRNA was enriched by oligo (dT) magnetic beads with polyA structure.

treatment_protocol: In a 2D adherent culture system, cells were cultured in either the presence or absence of respective ligands for 24 h.

value: iPS-derived neural stem cells

tag: passages

tag: primary source

value: human fibroblast cells


title: NSCs SB rep1


title: AML42

description: IO 360 panel

tag: tp53 status

value: Mutated

tag: disease state at sampling


title: s1_V2_CS2_A

source_name: Skin explant treated by cigarette smoke from 2 cigarettes

tag: tissue

tag: age


title: SOD1-ALS iPSC-derived MN_1

description:
SOD1 D90A_MM4
SOD1-ALS-1_1


title: NSCs ST rep2


title: FUS-ALS iPSC-derived MN_4

description:
FUS R521C_KG2
FUS-ALS-2_4

source_name: FUS-ALS_iPSC-derived spinal motor neurons

value: fALS patient2 carrying FUS mutation


title: NSCs ST rep1


title: FUS-ALS iPSC-derived MN_3

description:
FUS R521C_KGF
FUS-ALS-2_3


title: Scgb1a1 WT, 12 wk, replicate 3

city: Phoenix

first: Deepak

middle: K

last: Nayak

state: Arizona

address: 475 N. 5th Street

institute: University of Arizona College of Medicine

description:
R-3-WT-12
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

data_processing:
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Gene counts were  imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal features as well as any feature not expressed in at least the smallest condition size minus one sample were excluded from further analysis and TMM size factors were recalculated to created effective TMM size factors.
The TMM size factors and the matrix of counts were imported into R/Bioconductor package Limma and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript and sample were then calculated for all samples with the voomWithQualityWeights function.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include voom normalized log CPM values for each sample

source_name: Alveolar macrophage

growth_protocol: Primary cells were freshly isolated from mice housed in a specific pathogen-free environment.

extract_protocol:
Alveolar macrophages were purified from bronchoalveolar lavage cells after staining with antibodies and sorting by flow-cytometry. Purified alveolar macrophages were immediately lysed in RNA Lysis buffer and total RNA was extracted.
Libraries were prepared according to Illumina's sequencing workflow. Briefly, the total RNA was treated with DNase I and poly-A library was prepared following Cofactor Genomics' picoRNA workflow (CFG003-60).

treatment_protocol: C57BL/6 mice having wildtype expression  (WT)  or germ-line deletion (KO) of the Scgb1a1 gene

tag: strain

tag: genotype/variation

value: Scgb1a1+/+, WT

value: Lung

value: 12 wk


title: AML39

description: IO 360 panel

value: Diagnosis


title: AML40

description: IO 360 panel


title: FUS-ALS iPSC-derived MN_1

description:
FUS R521L_ B1
FUS-ALS-1_1

value: fALS patient1 carrying FUS mutation


title: NSCs V rep2


title: s7_V1_CS2_B


title: FUS-ALS iPSC-derived MN_2

description:
FUS R521L_C10
FUS-ALS-1_2


title: AML41

description: IO 360 panel


title: NSCs V rep1


title: Scgb1a1 WT, 40 wk, replicate 2

description:
S-2-WT-40
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: 40 wk


title: AML38

description: IO 360 panel


title: Healthy control iPSC-derived MN_3

description:
C3_424.9.1V1303
Control 3

source_name: healthy control_iPSC-derived spinal motor neurons

value: Healthy

value: Healthy donor3-clone 1


title: Scgb1a1 WT, 12 wk, replicate 2

description:
R-2-WT-12
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: Healthy control iPSC-derived MN_4

description:
C4_T12.9V0908-1
Control 4

value: Healthy donor2-clone 2

value: Spinal motor neurons


title: Scgb1a1 WT, 40 wk, replicate 1

description:
S-1-WT-40
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: Day 30 CM+aCF

city: San Francisco

last: McDevitt

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

data_processing:
Demultiplex with CellRanger 2.0.2
Align with CellRanger 2.0.2
Generate counts with CellRanger 2.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix Market Format Counts Matrices

source_name: engineered cardiac microtissues

extract_protocol:
Day 0 samples were collected immediately after mixing of dissociated cell types. Day 7 & day 30 samples were collected immediately after dissociating microtissues to single cells after 45 minute treatment with 0.25% Trysin
10x Genomics Chromium Single Cell 3’ v2 Library and Gel Bead Kit
single-cell RNA-sequencing

tag: sample type

value: mixture of hiPSC-cardiomyocytes and adult cardiac fibroblasts dissociated from day 30 microtissues


title: AML37

description: IO 360 panel


title: Healthy control iPSC-derived MN_1

description:
C1_301V1303
Control 1

value: Healthy donor1-clone 1

value: Fibroblast


title: AML CD34+/CD38+ donor 3

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: cell sorting performed on FACS Aria

hyb_protocol: Affymetrix GeneChip®Human Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip WT Pico Reagent Kit User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1

source_name: AML bone marrow

label_protocol: 500pg of total RNA were amplified and labeled using the GeneChip WT Pico Reagent Kit (Catalog Number 902622,Affymetrix, Santa Clara, CA)

growth_protocol: Cells were thawed in RPMI 1640 medium supplemented with 10% FCS and antibiotics at 37°C using DNase I. Cells were immediately sorted without previous culturing.

extract_protocol: Total RNA was extracted from primary cells using RNeasy Micro-Kit (Qiagen) and used for Gene Chip analyses.

treatment_protocol: Cells were sorted for CD34+/CD38+ and CD34+/CD38- fractions using a BD FACS Aria. Thereafter, sorted cells were resuspended in RLT buffer and frozen at -80°C.

tag: time of sampling

value: diagnosis

tag: immune phenotype

tag: diagnosis

value: AML

value: bone marrow


title: DMSO-vehicle control SGBS cells C

type: genomic

city: Lille

first: Mickaël

last: Canouil

address: 1, Place de Verdun

institute: CNRS UMR1283/8199 - EGID

description: Differentiated pre-adipocyte SGBS cell line

hyb_protocol: Bisulfite-converted DNA was subjected to genome-wide DNA methylation analysis using Illumina’s Infinium ‘850K’ Methylation EPIC array, according to Illumina protocols

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina protocols

data_processing:
Proccessing performed using minfi and Enmix R packages. Background correction with 'oob'; Dye Bias Correction with 'RELIC'; Normalisation with 'quantile1'
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Experiment C

label_protocol: Standard Illumina Protocol

growth_protocol: SGBS cells were and maintained in DMEM/F12 supplemented with 10 % foetal bovine serum and 0.01 % penicillin/streptomycin (15140-122 - Life Technologies), as previously de-scribed (Wabitsch et al., 2001). Confluent preadipocytes were differentiated under serum-free culture conditions by washing twice with phosphate buffered saline (PBS) and then exposing to DMEM/F12 supplemented with 2 µmol/l rosiglitazone, 25 nmol/l dexamethasone, 0.5 mmol/l methylisobuthylxantine, 0.1 µmol/l cortisol, 0.01 mg/ml transferrin, 0.2 nmol/l triiodotyronin, and 20 nmol/l human insulin for 4 days. The cells were then cultured for a further 8 days in fresh DMEM/F12 supple-mented with 0.1 µmol/l cortisol, 0.01 mg/ml transferrin, 0.2 nmol/l triiodotyronin, and 20 nmol/l human insulin.

extract_protocol: DNA was extracted from SGBS cells treated with atorvastatin and mevastatin at day 6 for 6 days and collected the cells at day 12. DNA was extracted using the Nucleo-Spin Tissue kit (Takara Bio). Bisulfite conversion of 500 ng genomic DNA was per-formed using the EZ-96 DNA Methylation kit (Zymo Research) following the manu-facturer’s protocol.

treatment_protocol: At 6 days of differentiation, SGBS cells were treated with 10 µM mevastatin (M2537, Sigma Aldrich) or atorvastatin (PZ0001, Sigma Alrich) and compared to a Dimethyl sulfoxide (DMSO)-vehicle control (D2650, Sigma Aldrich). The cells were then incu-bated for a further 6 days.

tag: treatment

value: DMSO

tag: plate


title: Day 30 CM+fCF

value: mixture of hiPSC-cardiomyocytes and fetal cardiac fibroblasts dissociated from day 30 microtissues


title: Scgb1a1 WT, 8 wk, replicate 3

description:
Q-3-WT-8
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: Scgb1a1+/+, WT

value: Lung

value: 8 wk


title: Scgb1a1 WT, 12 wk, replicate 1

description:
R-1-WT-12
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: 12 wk


title: AML36

description: IO 360 panel

value: Mutated

value: Diagnosis


title: Day 30 CM+EC

value: mixture of hiPSC-cardiomyocytes and hiPSC-endothelial cells dissociated from day 30 microtissues


title: AML CD34+/CD38- donor 3

description: cell sorting performed on FACS Aria


title: Healthy control iPSC-derived MN_2

description:
C2_T12.2V1104
Control 2

tag: disease status

value: Healthy

tag: donor id/status

value: Healthy donor2-clone 1


title: Scgb1a1 WT, 8 wk, replicate 2

description:
Q-2-WT-8
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: AML35

description: IO 360 panel


title: Scgb1a1 WT, 40 wk, replicate 3

description:
S-3-WT-40
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: 40 wk


title: Atorvastatin-treated SGBS cells B

source_name: Experiment B

value: Atorvastatin


title: Scgb1a1 WT, 8 wk, replicate 1

description:
Q-1-WT-8
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: Mevastatin-treated SGBS cells C

value: Mevastatin


title: Day 30 CM

value: hiPSC-cardiomyocytes dissociated from day 30 microtissues


title: AML CD34+/CD38- donor 2

description: cell sorting performed on FACS Aria

value: diagnosis

value: AML


title: DMSO-vehicle control SGBS cells B

value: DMSO


title: Scgb1a1 WT, 4 wk, replicate 3

description:
P-3-WT-4
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: 4 wk


title: Atorvastatin-treated SGBS cells A

source_name: Experiment A


title: Day 7 CM+EC

value: mixture of hiPSC-cardiomyocytes and hiPSC-endothelial cells dissociated from day 7 microtissues


title: AML CD34+/CD38+ donor 2

description: cell sorting performed on FACS Aria

value: bone marrow


title: Scgb1a1 WT, 4 wk, replicate 1

description:
P-1-WT-4
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: Scgb1a1+/+, WT

value: Lung


title: AML34

description: IO 360 panel

value: Mutated


title: Day 7 CM+fCF

value: mixture of hiPSC-cardiomyocytes and fetal cardiac fibroblasts dissociated from day 7 microtissues


title: AML33

description: IO 360 panel

value: Diagnosis


title: AML31

description: IO 360 panel


title: AML32

description: IO 360 panel


title: AML CD34+/CD38+ donor 1

description: cell sorting performed on FACS Aria


title: Day 7 CM

value: hiPSC-cardiomyocytes dissociated from day 7 microtissues


title: Mevastatin-treated SGBS cells A


title: Scgb1a1 KO, 40 wk, replicate 3

description:
D-3-KO-40
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: Scgb1a1-/-, KO


title: Scgb1a1 KO, 40 wk, replicate 1

description:
D-1-KO-40
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: 40 wk


title: Scgb1a1 KO, 12 wk, replicate 3

description:
C-3-KO-12
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: 12 wk


title: Atorvastatin-treated SGBS cells D

source_name: Experiment D

value: Atorvastatin


title: rep6_control

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description:
paired end 75 bases each direction
R6C_S36

data_processing:
The sequencing data were first assessed for quality control using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK).
Then all sequenced libraries were mapped to the human genome (GRCh38/hg38) using the STAR RNA-seq aligner (v.2.5) (Dobin et al., 2013) with the following parameter: “--outSAMmapqUnique 60”. The reads distribution across the genome was assessed using bamutils (from ngsutils v.0.5.9) (Breese & Liu, 2013). Uniquely mapped sequencing reads were assigned to GRCh38/hg38 refGene genes using featureCounts (subread v.1.5.1) (Liao, Smyth, Shi, 2014) with the following parameters: “-s 2 –p –Q 10”.
counts per million (CPM) from EdgeR
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: CPM (count per million reads) for each gene

growth_protocol: SH-SY5Y cells (CRL-2266, ATCC, Manassas, VA) were cultured in a 1:1 mixture of EMEM (ATCC) and F12K medium (10025-CV, Thermo Fisher Scientific) with 10% (vol/vol) fetal bovine serum (ATCC) and 1% penicillin and streptomycin. The cells used in this experiment were from passages 6 to 14. We did 6 independent replicates with each pair of replicates started in a new week (one on Monday, one on Tuesday. Cells were plated at a density of 1.5 x 106 in 25 cm2 canted neck flasks (Corning, Corning, NY).

extract_protocol:
RNA was extracted using a Direct-zol DNA/RNA miniprep kit (R2080, Zymo Research, www.zymoresearch.com) per manufacturer’s instructions
Fifty nanograms of total RNA was used for each sequencing library. cDNA library preparation was carried out at the Center for Medical Genomics, and included mRNA enrichment using oligo dT-beads to capture polyA RNA, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and all libraries were pooled at equal molarity. Five microliter aliquots of 2 nM pooled libraries per lane were denatured, neutralized and applied to flow cell deposition on both surfaces of the flow cell; library cluster amplification was performed on a cBot 2 System (Illumina, Inc.). The resulting flow cell was sequenced on an Illumina HiSeq 4000, 75 base paired-end sequencing (Illumina, Inc.).

treatment_protocol: We modeled chronic intermittent exposure to ethanol (CIE) by using a pattern of 4 h exposure to 40 mM ethanol on 4 successive days, followed by 3 days without, repeated for 3 weeks (see Supplementary Figure 1). One hour after seeding, the cells were treated for 4 h with a “binge level” concentration of ethanol (40 mM) or left untreated, after which both sets of cells were washed with 4 mL 1X phosphate-buffered saline (PBS), and medium without ethanol was added. The 4 h ethanol exposure, wash and fresh medium was repeated Monday through Thursday. After washing the cells on Thursday afternoon, all dishes were split and plated in medium without ethanol until the following Monday. This pattern was repeated in week 2. In week 3, the treated group was split into two flasks on Monday and both were treated with ethanol as above for 3 days but on Thursday, one group was treated with 40 mM ethanol for 4 h, the other received medium without ethanol. The experimental procedures meant that primarily adherent cells remained. Cells were collected after 4 h.

value: control

tag: replicate


title: AML30

description: IO 360 panel


title: Day 0 CM+aCF

value: mixture of hiPSC-cardiomyocytes and adult cardiac fibroblasts at time of tissue formation


title: Scgb1a1 KO, 40 wk, replicate 2

description:
D-2-KO-40
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: AML CD34+/CD38- donor 1

description: cell sorting performed on FACS Aria

value: diagnosis

value: AML


title: DMSO-vehicle control SGBS cells A

value: DMSO


title: Scgb1a1 KO, 12 wk, replicate 2

description:
C-2-KO-12
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: AML26

description: IO 360 panel


title: DMSO-vehicle control SGBS cells D


title: AML29

description: IO 360 panel


title: rep6_ethanol+withdrawal

description:
paired end 75 bases each direction
R6EN_S35

value: ethanol+24h withdrawal


title: AML28

description: IO 360 panel


title: Mevastatin-treated SGBS cells D

value: Mevastatin


title: normal CD34+/CD38- donor 2

description: cell sorting performed on FACS Aria

source_name: normal bone marrow

value: purchased from Lonza

value: normal healthy donor

value: bone marrow


title: Atorvastatin-treated SGBS cells C


title: normal CD34+/CD38- donor 3

description: cell sorting performed on FACS Aria


title: normal CD34+/CD38+ donor 3

description: cell sorting performed on FACS Aria


title: Day 0 CM+EC

value: mixture of hiPSC-cardiomyocytes and hiPSC-endothelial cells at time of tissue formation


title: Scgb1a1 KO, 12 wk, replicate 1

description:
C-1-KO-12
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: Lung


title: Mevastatin-treated SGBS cells B


title: Scgb1a1 WT, 4 wk, replicate 2

description:
P-2-WT-4
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: Scgb1a1+/+, WT

value: 4 wk


title: Day 7 CM+aCF

value: mixture of hiPSC-cardiomyocytes and adult cardiac fibroblasts dissociated from day 7 microtissues


title: Scgb1a1 KO, 8 wk, replicate 3

description:
B-3-KO-8
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz

value: Scgb1a1-/-, KO

value: 8 wk


title: normal CD34+/CD38+ donor 2

description: cell sorting performed on FACS Aria


title: AML24

description: IO 360 panel

value: Mutated

value: Diagnosis


title: Scgb1a1 KO, 8 wk, replicate 2

description:
B-2-KO-8
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: rep5_control

description:
paired end 75 bases each direction
R5C_S33

value: control


title: AML27

description: IO 360 panel


title: AML25

description: IO 360 panel


title: Scgb1a1 KO, 8 wk, replicate 1

description:
B-1-KO-8
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: rep5_ethanol

description:
paired end 75 bases each direction
R5E_S31

value: ethanol


title: rep5_ethanol+withdrawal

description:
paired end 75 bases each direction
R5EN_S32


title: AML23

description: IO 360 panel


title: CML CD34+/CD38+ donor 1

description: cell sorting performed on FACS Aria

source_name: CML leukaphersis sample

value: diagnosis

value: CML

value: leukapheresis sample


title: CML CD34+/CD38+ donor 2

description: cell sorting performed on FACS Aria


title: CML CD34+/CD38+ donor 3

description: cell sorting performed on FACS Aria


title: AML21

description: IO 360 panel


title: rep6_ethanol

description:
paired end 75 bases each direction
R6E_S34


title: Scgb1a1 KO, 4 wk, replicate 2

description:
A-2-KO-4
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: rep4_control

description:
paired end 75 bases each direction
R4C_S30


title: Scgb1a1 KO, 4 wk, replicate 3

description:
A-3-KO-4
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: CML CD34+/CD38- donor 3

description: cell sorting performed on FACS Aria


title: rep4_ethanol+withdrawal

description:
paired end 75 bases each direction
R4EN_S29

value: ethanol+24h withdrawal


title: rep4_ethanol

description:
paired end 75 bases each direction
R4E_S28


title: Scgb1a1 KO, 4 wk, replicate 1

description:
A-1-KO-4
CD45+, CD11chi, and Siglec-Fhi bronchoalveolar lavage cell
voom_normalized_logCPM_per_gene.txt.gz


title: CML CD34+/CD38- donor 1

description: cell sorting performed on FACS Aria


title: AML19

description: IO 360 panel


title: Ectoderm sample 7 from pooled stage HH18 chick

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
2 individual chicks
st18_7
miRNA

data_processing:
bcl2fastq v.
RNA-seq reads were trimmed with Cutadapt v1.8.1 with parameters -m 5 -a NNNNTGGAATTCTCGGGTG  (discard reads smaller than 5 bases, trim 3' side with adapter)
Trimmed reads were aligned to the mature and precursor miRNA separately using Kallisto v0.44.0 with 15 bp kmer index of each reference, and parameters  -l 23 -s 5
Genome_build: Gallus gallus 5.0 miRBase mature miRNA & Gallus gallus 5.0 miRBase hairpin miRNA
Supplementary_files_format_and_content: Transcript abundances were generated by Kallisto, and estimated counts were extracted from each file to make a tab-delimited counts matrix for all samples.

organism: Gallus gallus

source_name: Frontonasal ectodermal zone ectoderm

growth_protocol: Fertilized chicken eggs (Gallus gallus, Rhode Island Red, Petaluma Farms, CA) were incubated at 39° C in humidified conditions and prepared for surgical manipulation.

extract_protocol:
The frontonasal ectodermal zone was dissected from untreated chick embryos from stages HH18 or HH22 stages. RNA was isolated using an miRNeasy mini kit (Qiagen cat#217004).
Ilumina TruSeq small RNA-Seq library kit

treatment_protocol: No treatment was performed. Tissue was collected from normal chicken embryos at two different developmental stages (HH18 and HH22).

value: Frontonasal ectodermal zone ectoderm

tag: Stage

value: Normal stage HH18 (48hr)


title: AML18

description: IO 360 panel


title: rep2_ethanol+withdrawal

description:
paired end 75 bases each direction
R2EN_S23


title: CML CD34+/CD38- donor 2

description: cell sorting performed on FACS Aria


title: rep2_control

description:
paired end 75 bases each direction
R2C_S24


title: AML20

description: IO 360 panel


title: Ectoderm sample 8 from pooled stage HH18 chick

description:
2 individual chicks
st18_8
miRNA


title: AML17

description: IO 360 panel


title: rep2_ethanol

description:
paired end 75 bases each direction
R2E_S22


title: rep1_control

description:
paired end 75 bases each direction
R1C_S21


title: Ectoderm sample 6 from pooled stage HH18 chick

description:
2 individual chicks
st18_6
miRNA


title: AML15

description: IO 360 panel


title: Ectoderm sample 4 from pooled stage HH22 chick

description:
2 individual chicks
st22_4
miRNA

value: Normal stage HH22 (72hr)


title: Ectoderm sample 5 from pooled stage HH18 chick

description:
2 individual chicks
st18_5
miRNA


title: normal CD34+/CD38+ donor 1

description: cell sorting performed on FACS Aria

value: purchased from Lonza

value: normal healthy donor

value: bone marrow


title: rep1_ethanol+withdrawal

description:
paired end 75 bases each direction
R1EN_S20


title: AML14

description: IO 360 panel


title: Ectoderm sample 3 from pooled stage HH22 chick

description:
2 individual chicks
st22_3
miRNA


title: rep1_ethanol

description:
paired end 75 bases each direction
R1E_S19


title: WAT hypoxia replicate 10

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox10

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. Based on visual inspection two arrays were excluded; there was no homogenous hybridization on these arrays. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7).

growth_protocol: Male C57BL/6JOlaHsd mice arrived at 10 weeks of age and were individually housed and maintained under environmentally controlled conditions (21 ± 1ºC, 12 h/12 h light–dark cycle, 50 ± 10% humidity) and had ad-libitum access to feed and water. During the first three weeks of the study, mice could adapt to the new environment and received a purified low-fat diet that contained 10% energy from fat (Hoevenaars et al., Genes & Nutr 2012). Thereafter, mice received a purified high-fat diet that contained 40% energy from fat for the remaining 6 weeks of the study.

extract_protocol: Total RNA was isolated from WAT using TRIzol reagent, chloroform, and isoamyl alcohol (PCI) (Invitrogen, Breda, The Netherlands) followed by purification with RNeasy columns (Qiagen, Venlo, The Netherlands) using the instructions of the manufacturer.

treatment_protocol: After the 6 weeks of high- versus low-fat feeding, mice were fasted and were either set under hypoxia (12% oxygen) or remained under normoxia (20.9% oxygen) for exposure for 6 hours within the indirect calorimetry system (Duivenvoorde et al., J Gerontol A Biol Sci Med Sci. 2014). Mice were decapitated directly after the exposure and epididymal WAT was removed and snap-frozen in liquid nitrogen.

tag: gender

value: male

value: epididymal white adipose tissue

source_name: WAT_reference pool of all samples


title: Ectoderm sample 2 from pooled stage HH22 chick

description:
2 individual chicks
st22_2
miRNA


title: normal CD34+/CD38- donor 1

description: cell sorting performed on FACS Aria


title: AML16

description: IO 360 panel

source_name: Bone Marrow

tag: tp53 status


title: WAT hypoxia replicate 09

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox09


title: 42-cnd1-rep3

city: Kennesaw

first: Martin

middle: Lyn

last: Hudson

state: GA

address: 370 Paulding Avenue, Suite SC507, MD1201

department: Molecular and Cellular Biology

institute: Kennesaw State University

data_processing:
Read quality was determined using FastQC 0.11.5
Reads were aligned back to the C. elegans reference genome (wbcel235) using Hisat2-2.1.0
Samtools 1.5 (htslib 1.4.1) was used for file conversion and sorting
Stringtie 1.3.3.b was used to assemble and quantify transcripts
The script prepDE.py was used to generate gene and transcript count matrix files that were compatible with DESeq2 1.16.1 (R3.4.1), which was used to identify differentially expressed genes
Genome_build: wbcel235
Supplementary_files_format_and_content: tab-delimited text files in .tsv and gtf formats

organism: Caenorhabditis elegans

source_name: embryo

growth_protocol: Embryos were isolated by alkaline lysis from gravid worms grown in liquid culture.

extract_protocol:
Total RNA was extracted using RiboZol (AMRESCO) and followed the vendor’s protocol. Embryonic tissue was added to 1 mL of RiboZol and 500 uL aliquoted into two 5 PRIME Phase Lock Gel Tubes. At the isopropanol stage, 3uL of 20ng/ml glycogen was added to improve RNA pellet visualization.
Illumina TruSeq RNA v2 kit, according to manufacturer's protocol

treatment_protocol: Embryos were snap frozen in liquid nitrogen, ground to a fine powder and transferred to an RNase-free microfuge tube

value: embryonic total RNA

tag: genotype


title: Ectoderm sample 1 from pooled stage HH22 chick

description:
2 individual chicks
st22_1
miRNA

tag: tissue


title: 36_N2_rep3

value: wild type


title: WAT hypoxia replicate 08

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox08


title: AML11

description: IO 360 panel

value: Mutated

tag: disease state at sampling

value: Diagnosis


title: 34_cnd1-rep2

tag: strain


title: AML10

description: IO 360 panel


title: 28_N2_rep2


title: AML13

description: IO 360 panel


title: AML9

description: IO 360 panel


title: AML12

description: IO 360 panel


title: AML8

description: IO 360 panel


title: Ectoderm sample 3 from chick treated with PBS ctrl bead

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

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters)

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

extract_protocol: Agilent manufacturer's instruction.

treatment_protocol: Inhibition of neural SHH signaling was achieved by injecting hybridoma cells expressing either immuno‐neutralizing anti‐SHH antibody (5E1) or anti‐β‐galactosidase antibody control cells (40-1A) into the neural tube at Stage 10 (HH10). SHH-N treatment was performed using affi-Gel Blue beads (50 – 100 mesh, 200 – 250 diameter) soaked in recombinant SHH-N protein (400 ng/ml in PBS with 0.1% bovine serum albumin (BSA)) or 0.1% BSA (control) at 37° C for one hour. Forty-eight hours after SHH signal inhibition, SHH-soaked beads were placed between the facial ectoderm and the forebrain neuroectoderm. Embryos were collected at HH22 for genomic analysis.

value: PBS control bead


title: 27_N2_rep1


title: Ectoderm sample 2 from chick treated with PBS ctrl bead


title: Ectoderm sample 4 from chick treated with PBS ctrl bead


title: WAT hypoxia replicate 06

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox06


title: WAT hypoxia replicate 07

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox07


title: 6_cnd1-rep1


title: WAT hypoxia replicate 02

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox02


title: WAT hypoxia replicate 03

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox03


title: WAT hypoxia replicate 05

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox05


title: Day 0 CM+fCF

first: Todd

value: mixture of hiPSC-cardiomyocytes and fetal cardiac fibroblasts at time of tissue formation


title: WAT hypoxia replicate 04

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox04


title: AML6

description: IO 360 panel


title: AML7

description: IO 360 panel


title: WAT hypoxia replicate 01

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Whypox01


title: AML5

description: IO 360 panel


title: WAT normoxia replicate 12

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm12


title: AML3

description: IO 360 panel


title: Ectoderm sample 1 from chick treated with PBS ctrl bead


title: WAT normoxia replicate 11

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm11


title: AML4

description: IO 360 panel


title: smallRNA_mta_rep3

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

data_processing:
The adapter sequence was removed from the obtained raw reads with FASTX-Toolkit
Clean reads were mapped to all mature A. thaliana miRNAs from miRBase (release 22) using script countreads_mirna.pl (Eminaga et al., 2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: count reads, txt

organism: Arabidopsis thaliana

source_name: aerial tussue

growth_protocol: Plants were grown in soil under 16 hour light/8 hour dark cycle at 22°C

extract_protocol:
Aerial parts of 4 weeks plants were collected and immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Direct-zol kit (Zymo Research) according to manufacturers instructions. Total RNA integrity was analyzed on Agilent 2100 Bioanalyzer. 10ug of RNA was resolved on denaturing 15%PAA gel and small RNA fraction was cout out from the gel
Libraries were constructed using the TruSeq SmallRNA Library Preparation Kit (Illumina) as described in the manual.

tag: ecotype background

tag: genotype/variation

value: ABI3:MTA (mta)


title: AML1

description: IO 360 panel

data_processing: Data was normalised using the nSolver software, version 4.0.

extract_protocol: RNA extraction was carried out using Qiagen RNeasy RNA isolation kits. Quantitation of RNA was performed using Nanodrop and Qubit RNA high sensitivity assay.


title: AML2

description: IO 360 panel


title: Ectoderm sample 4 from chick treated with Shh-N bead

value: SHH-N protein bead


title: siAS1 TNFa 4 h Rep2

city: REGENSBURG

first: Claudia

last: GEBHARD

address: FRANZ-JOSEF-STRAUSS ALLEE 11

institute: UNIVERSITY HOSPITAL REGENSBURG

description: replicate 2

data_processing:
1. Alignment of PE fastq files using STAR (2.05b) using GRCh38  and the following options: STAR --runThreadN 10  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outReadsUnmapped Fastq --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000 --alignIntronMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outWigType bedGraph --outWigStrand Stranded
2. EdgeR analysis of combined STAR-derived read count tables, including batch effects.
Genome_build: GRCh38

source_name: PANC-1 (Pancreatic ductal adenocarcinoma cell line)

growth_protocol: DMEM 10%FCS 1% P/S

extract_protocol:
Rneasy Mini Kit (Qiagen) was used according to manufacturer´s instructions, including DNase I digestion.
Library was generated using the ScriptSeq Complete Kit (Illumina)

treatment_protocol: Cells were transfected with RNAimay for 72h afterwards, rHuTNF-alpha was added

tag: cell line

value: TNF treatment 4h

tag: transfection

value: SIK3 siRNA


title: siCtrl1 TNFa 4 h Rep2

description: replicate 2

value: control siRNA


title: siAS1 TNFa 4 h Rep1

description: replicate 1


title: Ectoderm sample 2 from chick treated with Shh-N bead

value: Frontonasal ectodermal zone ectoderm


title: Ectoderm sample 3 from chick treated with Shh-N bead


title: Ectoderm sample 2 from stage HH22 chick

value: Normal stage HH22 (72hr)


title: Ectoderm sample 1 from stage HH22 chick


title: Ectoderm sample 1 from chick treated with Shh-N bead


title: Ectoderm sample 3 from stage HH22 chick


title: WAT normoxia replicate 10

institute: Wageningen University

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm10


title: Ectoderm sample 4 from stage HH22 chick


title: Ectoderm sample 4 from stage HH18 chick

value: Normal stage HH18 (48hr)


title: WAT normoxia replicate 08

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm08


title: smallRNA_mta_rep1


title: siCtrl1 TNFa 4 h Rep1

description: replicate 1


title: WAT normoxia replicate 03

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm03


title: WAT normoxia replicate 09

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm09


title: WAT normoxia replicate 06

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm06


title: WAT normoxia replicate 04

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm04


title: WAT normoxia replicate 07

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm07


title: smallRNA_mta_rep2


title: WAT normoxia replicate 02

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm02


title: Day 0

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

description: Cultured hADSC

data_processing:
The small RNA sequencing data was first cleaned by executing our small RNA sequencing data cleaning pipeline. Next, the clean sequence data was aligned to miRBase to detect and estimate the expression of microRNAs. And then, the remaining read sequences were aligned to the fRNAdb to get the expression of various non-coding RNAs
Data cleaning: We first executed our data cleaning pipeline to get clean read sequence data. The pipeline include three processes: trimming the adapters, deleting too-short reads (at least 17bp) and deleting poly-N reads.
Effective sequence length distribution: After data cleaning, we analyzed the length distribution of the effective sequence to examine the composition of the sequence library. The majority of clean sequence reads in the normal samples are between 20 and 24 in length.
MicroRNA detection and abundance estimation: We aligned the clean sequence data to the miRBase using the bowtie algorithm.
Differentially expressed microRNA detection: Using the R package DESeq, we figured out the differentially expressed microRNAs for each sample pair. The criteria of the detection in this study are fold change > 2 and p-value < 0.1. In order to give an overview of the differential status of microRNA expression, we used volcano plots to present the microRNA with differential expression between the paired samples.
Other non-coding RNA detection and abundance estimation: The remaining read sequences except those mapped to the known microRNAs were aligned to the fRNAdb, a comprehensive non-coding RNA (ncRNA) sequence database, to detect other ncRNAs, including piwi-interacting RNA (piRNA), small nulear RNA (snRNA), small nucleolar RNA (snoRNA) and so on, and to estimate their expression levels.
Genome_build: miRBase 20
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample,Differentially expressed miRNA

source_name: Human adipose-derived mesenchymal stem cells

extract_protocol:
MiRNA was extracted using the mirVana™ miRNA Isolation Kit (Ambion, Waltham, USA) following the manufacturer's instructions.
Small RNA libraries were prepared using the Small RNA Sample Preparation kit (Illumina, SanDiego, USA) according to the manufacturer's protocols. The quality of the purified small RNA sequencing libraries was confirmed on an Agilent 2100 Bioanalyzer.

tag: country

value: China

tag: cell type

tag: age

value: adult

value: adipogenic differentiation 0 day


title: siAS1 TNFa 30 min Rep1

description: replicate 1

tag: treatment

value: TNF treatment 30min


title: siAS1 TNFa 30 min Rep2

description: replicate 2


title: siCtrl1 TNFa 30 min Rep2

description: replicate 2


title: Ectoderm sample 3 from stage HH18 chick


title: Day 14

description: Cultured hADSC

value: Human adipose-derived mesenchymal stem cells

value: adipogenic differentiation 14 days


title: smallRNA_Col0_rep2

value: wild-type (WT)


title: polyA_m6A_IP_mta

data_processing:
Raw reads where trimmed (first 30 nucleotides) with FASTX-Toolki
Adapters were removed using Trimmomatic
rRNA sequences where removed with Bowtie
Clean reads were aligned to the Arabidopis TAIR10 reference genome using HISAT2
Transcript-level abundance for RNA clean reads where estimated using Salmon. Multifasta file with Arabidopsis thaliana reference transcripts (cdna and ncrna) for quasi-mapping was additionally supplemented with pri-miRNA transcirpts described in mirEX2 database and with m6A controls spike-ins sequences.
genome build: TAIR10
processed data files format and content: transcript abundance matrix, combined output format from Salmon software .txt extension

extract_protocol:
Aerial parts of 4 weeks plants were collected and immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Direct-zol kit (Zymo Research) followed by polyA enrichment protocol. Immunoprecipitation was performed with EpiMark N6-Methyladenosine Enrichment Kit (NEB). Two RNA controls from the kit were spike into RNA samples before immunoprecipitation.
Libraries from input and immunopreciptated RNA were prepared with SENSE Total RNA-Seq Library Prep Kit (Lexogen).

tag: fraction

value: m6A-IP fraction


title: WAT normoxia replicate 05

city: Wageningen

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm05

value: male

value: epididymal white adipose tissue


title: smallRNA_Col0_rep3


title: smallRNA_Col0_rep1


title: Ectoderm sample 2 from stage HH18 chick


title: WAT normoxia replicate 01

description:
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Wnorm01


title: 824 TPC1_LPS

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava v1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with HiSat2 (v2.0.11) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.3.1) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
hg38
Processed DeSeq2 normalized RNA-seq tag counts annotated to the hg38 reference genome and batch corrected with SV1 and SV2
Genome_build: hg38
Supplementary_files_format_and_content: norm_data_SVA2.csv

source_name: TPC-1 cell line

growth_protocol: TPC-1 cells were grown in RPMI 1640 Dutch modification (Life Technologies, Carlsbad, CA, USA) supplemented with gentamycin 50 μg/ml, pyruvate 1 mM, glutamax 2 mM and 10% Fetal Calf Serum (FCS, Gibco, Life Technologies).

extract_protocol:
Cells were lysed in Trizol reagent; RNA was extracted according TriZol manufacturer protocol.
mRNA converting into cDNA with Transcriptor High Fidelity cDNA synthesis Kit, libraray preperation with TruSeq RNA Sample Preparation 2 Kit

treatment_protocol: For co-culture, TPC-1 cells were seeded in the upper transwell and maintained in RPMI with glucose 5 mM, pyruvate 1 mM, gentamicin 50 μg/mL and HEPES 10 mM (Life Technologies, Carlsbad, California, USA); after 24 h of co-culture with TC-induced macrophages, TC-induced macrophages were restimulated with RPMI ("none) or LPS (TLR4 ligand) for 24h.

tag: donor

value: G

tag: stimuli

value: LPS


title: polyA_RNA_mta

value: ABI3:MTA (mta)

value: polyA RNA


title: siCtrl1 TNFa 30 min Rep1

description: replicate 1

value: control siRNA


title: AML22

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

institute: Nottingham Trent University

description: IO 360 panel

value: Mutated

value: Diagnosis


title: Ectoderm sample 1 from stage HH18 chick

value: Frontonasal ectodermal zone ectoderm

value: Normal stage HH18 (48hr)


title: 823 TPC1_none


title: siAS1 Unst. Rep1

description: replicate 1

value: TNF treatment 0h

value: SIK3 siRNA


title: siCtrl1 Unst. Rep2

description: replicate 2


title: 806 TPC1_none

value: F


title: siAS1 Unst. Rep2

description: replicate 2


title: 807 TPC1_LPS


title: Ectoderm sample 4 from chick treated with 40-1A ctrl cells

value: Injected with 40-1A control cells


title: polyA_RNA_wt

value: wild-type (WT)


title: polyA_m6A_IP_wt

value: m6A-IP fraction


title: 790 TPC1_LPS

value: E


title: siCtrl1 Unst. Rep1

description: replicate 1


title: 789 TPC1_none


title: dim7-triple_N7096_H3K27me2me3_ChIPseq

city: Colorado Springs

first: Andrew

last: Klocko

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

institute: University of Colorado Colorado Springs

description: genomic DNA ChIPseq libraries

data_processing:
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed.  The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 25bp windows.  Output file was a .tdf file, displayable on IGV.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 25bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).

source_name: germinated conidia

extract_protocol:
Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit  and eluted in 30 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 8 cycles (or 12 cycles for WT H3K27me2me3) at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP.

tag: antibody used


title: Ectoderm sample 2 from chick treated with 40-1A ctrl cells


title: PigGeCKOv1.0_screenJEV4th

city: Wuhan

first: Shengsong

last: Xie

state: Hubei

address: 1st Shizishan Street, Hongshan

institute: Huazhong Agricultural University

description: sequencing result of the fourth challenge round of JEV screening

data_processing:
Mapped read counts were subsequently used as input for the MAGeCK analysis software package (version 0.5)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sgRNAs ...

organism: Sus scrofa

source_name: PK-15-Cas9 cells

growth_protocol: Construction of a genome-wide sgRNA library plasmid.Generation of mutant cell libraries and screening.

extract_protocol:
The genomic DNA of each sample was extracted using a Blood & Cell Culture DNA Midi Kit (QIAGEN).
The sgRNA-coding region was amplified by PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB) in a reaction volume of 50 µL. PCR products were mixed and purified with a MinElute PCR purification Kit (QIAGEN). The purified PCR products were amplified by PCR using different barcoded primers. All PCR products were pooled and purified with a MinElute PCR purification Kit (QIAGEN), followed by Illumina Next-generation sequencing.

treatment_protocol: A total of ~2 × 108 PK-15-Cas9 cells were seeded into T225 flasks and infected with the library lentiviruses at an MOI of 0.3. Three days post-infection, GFP-positive cells were collected by Fluorescence-Activated Cell Sorting and reseeded into 100 mm dishes. Six days post-infection, DNA from ~7 × 106 cells was extracted using a Blood & Cell Culture DNA Midi Kit (QIAGEN) and amplified to examine the coverage of mutant cell libraries. For the CRISPR screening, ~6 × 107 mutant cells were infected with JEV-RP9 at an MOI of 0.03 in DMEM without FBS and incubated at 37 oC and 5% CO2. After 1.5 hrs incubation, the inoculum was removed and replaced with fresh DMEM supplementing with 2% FBS and 1% penicillin-streptomycin. At the eleventh day after post-infection, viable cells were collected and expanded for the deep sequencing analysis and the next round of infection.

value: porcine kidney-15 (PK-15) cells

tag: knock-in

value: Cas9 puro


title: Ectoderm sample 1 from chick treated with 40-1A ctrl cells


title: PigGeCKOv1.0_plasimd

description: sequencing result of sgRNA library from plasmid pools

source_name: plasmid


title: PigGeCKOv1.0_screenJEV3rd

description: sequencing result of  the third challenge round of JEV screening


title: PigGeCKOv1.0_cellpool

description: sequencing result of sgRNA library from sorted mutant cell populations


title: WT_N3752_H3K27me2me3_ChIPseq

description: genomic DNA ChIPseq libraries

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were washed in PBS prior to crosslinking.


title: Ectoderm sample 4 from chick treated with 5E1

value: Injected with 5E1 cells


title: Ectoderm sample 3 from chick treated with 5E1


title: 773 TPC1_LPS

value: C

value: LPS


title: 772 TPC1_none


title: colon_Fe800_rep5

status: Public on Sep 20 2020

city: Changsha

first: Shuai

last: CHEN

state: Hunan

address: Yuandaer Road 644

institute: Institute of Subtropical Agriculture, Chinese Academy of Sciences

data_processing:
The index-coded samples were clustered using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) on a cBot Cluster Generation System following the manufacturer's recommendation and then sequenced on an Illumina Novaseq platform. One hundred fifty bp paired-end reads were generated for the following data analysis
Hisat2 (v2.0.5) was used for reads mapping to the reference genome. FPKM of each gene was calculated after counting the reads numbers of each mapped gene using featureCounts (v1.5.0-p3).
After gene expression level quantification,  differential expression gene (DEG) analysis was performed by the DESeq2 R package (1.16.1), and P-value <0.05 were assigned as differential expression. The clusterProfiler R package was used to implement Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs. Protein-Protein Interactions (PPI) analysis of DEGs was based on the STRING database and further analyzed and visualized by Cytoscape (v3.8.0).
Genome_build: Sus_scrofa_Ensemble_90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and gene annotation information for each sample

source_name: intestine

extract_protocol:
colon was colltected and total RNA was isolated using Trizol reagent.
the RNA  was used to generated sequencing libraries by NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's protocol

value: Duroc x Landrace x Landrace

value: colon


title: colon_Fe50_rep4


title: colon_Fe800_rep4


title: Ectoderm sample 2 from chick treated with 5E1


title: colon_Fe50_rep1


title: colon_Fe800_rep3


title: colon_Fe800_rep2


title: colon_Fe50_rep3


title: colon_Fe50_rep5


title: Ectoderm sample 1 from chick treated with 5E1


title: colon_Fe50_rep2


title: Ectoderm sample 3 from chick treated with 40-1A ctrl cells


title: colon_Fe800_rep1


title: CM28_8 week neuron_Bonobo

city: La Jolla

first: Fred

middle: H

last: Gage

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

description:
processed data file:
Linker_Marchetto_Gage_count.txt
Linker_Marchetto_Gage_tpm.txt
CM28_R2

data_processing:
RNA and ChIP-Seq: trim raw FASTQ files, SolexaQA++
RNA: alignment to hg19, STAR
RNA: alignment to panTro4, STAR
RNA: alignment to gorgor3, STAR
RNA: alignment to rhemac2, STAR
RNA: join all alignments for each sample and sort by read id
RNA: select reads mapped uniquely to each genome (3mm same species, 5 mm different species)
RNA: Count reads in genes corresponding to the hg19 transcriptome reference, HT-Seq
RNA: Transform counts to TPM
ChIP-Seq: Alignment to hg19, bowtie
ChIP-Seq: Peak Calling, HOMER
Genome_build: hg19 (grch37), pantro4 (CSAC 2.1.4), gorgor3 (gorGor3.1), and rhemac2(MGSC Merged 1.0)
Supplementary_files_format_and_content: tab-delimited text file

organism: Pan paniscus

source_name: 8 week neuron

growth_protocol: Established iPSC colonies were kept in feeder-free conditions indefinitely and passed using mechanical dissociation. To obtain NPCs from iPSCs, embryoid bodies (EBs) were formed by mechanical dissociation of iPSC clusters and plated into low-adherence dishes in DMEM/F12 plus N2 and B27 (Invitrogen) medium in the presence of Noggin (R&D) for forebrain induction for approximately 7 days. Then, floating EBs were plated onto poly-ornithine/laminin (Sigma)-coated dishes in DMEM/F12 plus N2 and B27 (Invitrogen) with the addition of Noggin. Rosettes were collected after 7 days. Rosettes were then dissociated with accutase (Chemicon) and plated again onto coated dishes in DMEM/F12 plus N2 and B27 and 10 ng/ml of FGF2 (R&D). Homogeneous populations of NPCs were obtained after 1-2 passages with accutase under the same conditions. To obtain neurons, NPCs were cultured in DMEM/F12 plus N2 and B27 with the addition of laminin (1 µg/ml), BDNF (20 ng/ml), GDNF (20 ng/ml) and cyclic AMP (500 µg/ml) for up to 8 weeks.

extract_protocol:
Total cellular RNA was extracted from ~5x106 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit.

treatment_protocol: No additional treatment was performed

tag: individual

tag: Sex

value: M

tag: sh