title: Gamma_S67_1st

city: Bethesda

first: Hye Kyung

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

source_name: PBMCs

growth_protocol: Blood samples were collected from the COVID-19 patients infected by Alpha varient with or without the escape mutation.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

value: Male

tag: diseas state

value: COVID-19_Gamma varient

tag: geographical location

value: Ischgl, Austria

value: PBMC


title: NCI-H1963, DMSO, rep1

status: Public on Feb 23 2022

type: SRA

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 or STAR 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with different concentrations of iBAP for 24 hours, with DMSO as negative control

tag: cell line

tag: cell type

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

tag: treatment

value: treated with DMSO

tag: phenotype

value: normal cells


title: org2019_3391B_CNT1_MixN2018_Chronic50days

city: Milano

first: Nicolò

last: Caporale

state: MI

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncolology

data_processing:
RNA-seq quantification was performed directly from the reads using Salmon 6.1, using the hg38 Refseq annotation.
Only genes with at least 20 reads in at least 2 samples were included; small (<200 nt) genes, ribosomal RNA genes, and fusion genes were excluded.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: TotalSumExp.RData: SummarisedExperiment (https://bioconductor.org/packages/SummarizedExperiment) including count matrix and metadata for all the samples.
Supplementary_files_format_and_content: counts.csv: Count matrix for all the samples. Names of the columns are matched to the Sample titles.

source_name: Cortical brain organoids

growth_protocol: For the differentiation of cortical brain organoids, we used the protocol described by (Paşca et al., PMID: 26005811), with minor modifications to improve its efficiency, as we previously showed (PMID: 31607568). Human fetal primary neural stem cells (HFPNSC) were provided by Dr. Steve Pollard’s laboratory and cultured according to the published protocols (PMID: 23934830).

extract_protocol:
Total RNA was isolated with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA was quantified with Nanodrop and then the integrity was evaluated with Agilent 2100 Bioanalyzer (only if the quality ratios were not optimal after Nanodrop analysis). TruSeq Stranded Total RNA LT Sample Prep Kit, Illumina was used to run the library for each sample. Sequencing is performed with the Illumina HiSeq 2000 platform, sequencing on average 10 million 50bp paired-end reads per sample.

treatment_protocol:
For EDC chemical exposure of HFPNSC, cells were seeded in 6-well plates. When 70-80% confluency was reached, 0.1% DMSO or the other compounds diluted in DMSO, namely the 5 different concentrations of MIX N (from 0.1X to 1000X), 0.04 nM BPA, 10 μM T3 were added to the culture medium and used to culture cells for 48 hours or for 15 days (in the chronic setting), adding the chemical every time media change was performed (every other day). After the exposure cells were collected for RNA extraction.
For EDC chemical exposure of organoids, 0.1% DMSO, or the other compounds diluted in DMSO, MIX N in the 2 different concentrations used (1X and 1000X), 0.04 nM BPA or 10 uM T3 was added to the culture media and used to culture cells from day 0 to day 50.

value: hiPSC-derived cortical brain organoids

tag: Stage

value: Day 50

tag: passage

value: CNT

tag: Sex

value: Female

value: Chronic 50 days


title: Gamma_S65_1st

last: Lee

state: MD

molecule: polyA RNA

tag: gender


title: SLE, 227

type: RNA

city: Stanford

first: Gloria

last: Yiu

state: CA

address: CCSR Building Room 2215

institute: Stanford University

description: SLE

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their software package: https://www.fluidigm.com/products-services/instruments/biomark-hd
For the normalization, the average geomean of three housekeeping genes: B2M, GAPDH, and ACTB was subtracted from the average of each sample duplicate
Fold change was not utilized in the calculation of determining the interferon signature

label: FAM

source_name: SLE, PBMCs

label_protocol: For 10-50 ng total RNA of each sample, reverse transcription of the RNA to cDNA was performed at 50°C for 15 minutes using the High-Capacity Reverse Transcription kit (ABI). RT was performed directly on a 96-well PCR plate (ABI). PreAmp was performed on a thermocycler using the TaqMan PreAmp Master Mix Kit (Invitrogen) added to cDNA and pooled Taqman assays. RT enzyme was inactivated and the Taq polymerase reaction was started by bringing the sample to 95°C for 2 minutes. The cDNA was preamplified by denaturing for 10 cycles at 95°C for 15 seconds, annealing at 60°C for 4 minutes. The resulting cDNA product was diluted 1:2 with 1X TE buffer (Invitrogen). 2X Applied Biosystems Taqman Master Mix, Fluidigm Sample Loading Reagent, and preamplified cDNA were mixed and loaded into the 48.48 Dynamic Array (Fluidigm) sample inlets, followed by loading 10X assays into the assay inlets. Manufacturer’s instructions for chip priming, pipetting, mixing, and loading onto the BioMark system were followed. Real-time PCR was carried out with the following conditions: 10 min at 95°C, followed by 50 cycles of 15 sec at 95°C and 1 min at 60°C.

extract_protocol: 3ml of whole blood was collected into a Tempus Blood RNA Tube (Life Technologies #4342792) and frozen at -20°C for a minimum of 30 days. Batched samples were thawed and processed for RNA extraction using a Tempus RNA Isolation Kit (Life Technologies #4380204). All RNA samples were stored at -80°C prior to use. Samples were analyzed 3 using a Bioanalyzer (Agilent Technologies) to confirm RNA quality prior to assay. All samples had RNA Integrity Numbers (RIN) > 7.9.

tag: disease state

value: SLE

value: PBMCs

tag: tissue

value: whole blood

value: F

tag: age

tag: ifn score

tag: ifn classification

value: intermediate


title: org2019_3391B_VitC4_MixN2018_Chronic50days

value: VITC


title: Gamma_S64_1st

value: Male

value: COVID-19_Gamma varient

value: Ischgl, Austria


title: SLE, 223

description: SLE


title: SLE, 226

description: SLE

value: IFN-H


title: SLE, 200

description: SLE

value: IFN-L


title: SLE, 194

description: SLE

value: M


title: RHE DMSO 6h #1

city: Issy-les-Moulineaux

first: Georgios

last: Stamatas

address: 1, rue Camille Desmoulins

department: Consumer Health R&D

country: France

institute: Johnson & Johnson Santé Beauté France

hyb_protocol: washed and scanned according to the manufacturer’s instructions

scan_protocol: Scanner G2505C (Agilent Technologies)

data_processing: Proprietary R algorism

source_name: RHE DMSO 6h

growth_protocol: RHE from Episkin growth with EGF and albumine, experimets (treatments were performed without EGF and Alb)

extract_protocol: RHE extracted in RLT buffer + B mercaptoethanol 1%

treatment_protocol: Afatinib 100 nM

tag: tissue source

value: reconstructed Human Epidermis (RHE)

value: Keratinocytes

value: DMSO


title: RHE AFA 6h #4

source_name: RHE AFA 6h

value: AFA


title: RHE DMSO 6h #2


title: RHE AFA 6h #3


title: org2019_3391B_VitC3_MixN2018_Chronic50days

value: hiPSC-derived cortical brain organoids

value: Day 50

value: Female

value: Chronic 50 days


title: RHE AFA 6h #2


title: Alpha_S72_2nd

tag: diseas state

value: COVID-19_Alpha varient

value: PBMC


title: RHE AFA 72h #1

source_name: RHE AFA 72h


title: Alpha_S71_2nd

tag: geographical location


title: Alpha_S72_1st


title: SLE, 193

description: SLE

value: SLE

value: PBMCs

value: whole blood

value: F

value: intermediate


title: org2019_3391B_VitC1_MixN2018_Chronic50days

value: VITC


title: Alpha_S70_1st

value: Male

value: Ischgl, Austria


title: org2019_3391B_1000X4_MixN2018_Chronic50days


title: org2019_3391B_1000X3_MixN2018_Chronic50days


title: RHE AFA 6h #1

value: reconstructed Human Epidermis (RHE)

value: Keratinocytes


title: SLE, 164

description: SLE

value: M


title: Alpha_S71_1st


title: org2019_3391B_1000X2_MixN2018_Chronic50days

value: hiPSC-derived cortical brain organoids


title: RHE DMSO 24h #4

source_name: RHE DMSO 24h

value: DMSO


title: RHE DMSO 24h #3


title: SLE, 182

description: SLE

value: IFN-L


title: org2019_3391B_1000X1_MixN2018_Chronic50days

value: Day 50

value: Female

value: Chronic 50 days


title: SLE, 153

description: SLE

value: SLE


title: Alpha_S69_2nd

value: COVID-19_Alpha varient

value: PBMC


title: SLE, 141

description: SLE

value: PBMCs

value: whole blood

value: F

value: IFN-H


title: SLE, 127

description: SLE

value: intermediate


title: org2019_3391B_1X4_MixN2018_Chronic50days


title: RHE DMSO 24h #1

value: reconstructed Human Epidermis (RHE)


title: RHE AFA 24h #3

source_name: RHE AFA 24h

value: Keratinocytes

value: AFA


title: RHE AFA 24h #2


title: org2019_3391B_1X3_MixN2018_Chronic50days

value: hiPSC-derived cortical brain organoids


title: SLE, 174

description: SLE


title: SLE, 125

description: SLE


title: Alpha_S69_1st

value: Male

value: Ischgl, Austria


title: Alpha_S68_1st


title: RHE DMSO 24h #2

value: DMSO


title: org2019_3391B_1X1_MixN2018_Chronic50days

value: Day 50

value: Female


title: Alpha_S66_1st


title: org2019_3391B_1X2_MixN2018_Chronic50days

value: Chronic 50 days


title: RHE AFA 24h #1


title: org2019_3391B_1000X4_MixN2017_Chronic50days


title: SLE, 117

description: SLE

value: SLE


title: SLE, 79

description: SLE


title: Alpha_S63_2nd

value: COVID-19_Alpha varient

value: PBMC


title: BT-549-2

city: Guangzhou

first: Yingying

last: Ye

state: Guangdong

address: Guangdong Provincial Key Lab，Chinaoratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou

country: China

institute: Sun Yat-sen University

description: Gene expression of cell lines resistant to anti-CD47

hyb_protocol: Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 L hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13 (Agilent).

source_name: cell line

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

growth_protocol: Cells were cultured according to standard protocols.

extract_protocol: Total RNA was extracted by using the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol.

value: Breast cancer

tag: cell line


title: RHE AFA 24h #4

tag: cell type


title: MCF-7-2

description: Gene expression of cell lines sensitive to anti-CD47


title: T47D-2


title: SLE, 57

description: SLE

value: PBMCs

value: whole blood

value: F


title: org2019_3391B_1000X3_MixN2017_Chronic50days


title: Alpha_S66_2nd


title: Alpha_S63_1st


title: org2019_3391B_1000X1_MixN2017_Chronic50days


title: SLE, 119

description: SLE

value: IFN-H


title: SLE, 54

description: SLE


title: Alpha_S61_2nd


title: MB-231-2


title: Alpha_S70_2nd


title: org2019_3391B_1X4_MixN2017_Chronic50days


title: Alpha_S56_2nd


title: org2019_3391B_1X3_MixN2017_Chronic50days


title: Alpha_S56_3rd


title: SLE, 60

description: SLE


title: org2019_3391B_1000X2_MixN2017_Chronic50days


title: org2019_3391B_1X2_MixN2017_Chronic50days


title: Alpha_S50_2nd


title: BT474-2


title: BT-549-1


title: SLE, 17

description: SLE


title: MCF-7-1


title: MB-468-2


title: SLE, 37

description: SLE

value: intermediate


title: Alpha_S50_1st


title: org2019_3391B_1X1_MixN2017_Chronic50days


title: Alpha_S49_2nd


title: org2019_3391B_1000X4_MixN2015_Chronic50days


title: Alpha_S55_1st


title: T47D-1


title: healthy control, HC7

description: healthy control

source_name: healthy control, PBMCs

value: healthy control

value: Anonymized


title: org2019_3391B_1000X3_MixN2015_Chronic50days

value: hiPSC-derived cortical brain organoids


title: healthy control, HC9

description: healthy control


title: MB-468-1


title: SLE, 9

description: SLE


title: Alpha_S48_2nd

value: Ischgl, Austria


title: MB-231-1


title: healthy control, HC45

description: healthy control


title: Alpha_S48_1st


title: CD90-EPCR- MPP 12

city: Frankfurt

first: Florian

last: Buettner

state: Germany

address: Theodor-Stern-Kai 7

department: DKTK Frankfurt

country: Germany

institute: DKFZ

description:
AFO296A32
mRNA

data_processing:
Raw sequencing reads were mapped with STAR.
Expression counts estimates and transcripts per million (TPM) were generated using RSEM.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts_bulk_MPP_ENS.csv: Raw counts in comma-separated matrix format.

source_name: cord blood

extract_protocol:
Total RNA using RNeasy Plus Micro Kit (Qiagen) and quality was verified in an Agilent 2100 Bioanalyzer (Agilent).
KAPA Stranded with RiboErase RNA-seq kit (Kapa Biosystems).
RNA-seq 30 million single-end 100 bp reads/sample.

value: cord blood CD34+CD38-CD45RA-CD90-EPCR- cells

value: post-natal


title: CD90-EPCR- MPP 14

description:
AFO296A40
mRNA


title: CD90-EPCR- MPP 13

description:
AFO296A36
mRNA


title: org2019_3391B_1X4_MixN2015_Chronic50days

value: Day 50

value: Female


title: BT474-1


title: Alpha_S46_3rd

value: Male


title: org2019_3391B_1000X1_MixN2015_Chronic50days

value: Chronic 50 days


title: healthy control, HC40

description: healthy control


title: healthy control, HC4

description: healthy control


title: healthy control, HC39

description: healthy control


title: org2019_3391B_1X3_MixN2015_Chronic50days


title: org2019_3391B_1X2_MixN2015_Chronic50days


title: CD90-EPCR- MPP 10

description:
AFO296A16
mRNA


title: Alpha_S49_1st

value: COVID-19_Alpha varient

value: PBMC


title: org2019_3391B_1000X2_MixN2015_Chronic50days


title: Alpha_S46_2nd


title: Alpha_S46_1st


title: Alpha_S44_3rd


title: healthy control, HC31

description: healthy control

value: PBMCs


title: CD90-EPCR- MPP 11

description:
AFO296A20
mRNA


title: healthy control, HC23

description: healthy control

value: whole blood


title: healthy control, HC28

description: healthy control


title: fetalC2019_E3381-1_1000X4_MixN2018_Chronic 15 days

source_name: Fetal brain

value: Fetal brain cortical progenitors

value: Chronic 15 days


title: zr1900_1

city: Pieve Emanuele

first: Giampaolo

last: Trivellin

state: Lombardy

address: Via Rita Levi Montalcini 4

institute: Humanitas University

data_processing:
Libraries were sequenced on an Illumina HiSeq with a 50bp single- or paired-end protocol and demultiplexed. Quality of raw data files (fastq) were evaluated using the fastqc, and trimmed with Trimmomatic. Then, only high-quality reads were aligned to the human reference genome hg19 using Star in a two-pass approach. A first STAR pass allowed us to obtain a database of splice junctions, from which we filtered out any non-canonical junctions. A new genome was generated with the splice junctions and a second STAR pass was run. Coverage per sample was computed in 1 kb bins and a per sample upper quartile normalization was performed. The normalized average coverage was then computed for all X-LAG samples in the one hand and for the normal samples on the other. Raw count of reads per gene per sample was obtained using the feature Counts.
Genome_build: human genome GRCh37/hg19
Supplementary_files_format_and_content: counts

source_name: Pituitary

extract_protocol: total RNA was extracted from pituitary tumor samples of four individuals with X-LAG (3 females, 1 male) and from three samples of normal adult pituitaries (2 males, 1 female) obtained at autopsy.

value: Pituitary

tag: clinical phenotype


title: Alpha_S44_2nd


title: healthy control, HC22

description: healthy control

value: healthy control


title: fetalC2019_E3381-1_1000X2_MixN2018_Chronic 15 days

tag: treatment


title: healthy control, HC18

description: healthy control

value: Anonymized


title: Alpha_S44_1st


title: fetalC2019_E3381-1_1000X1_MixN2018_Chronic 15 days


title: zr1179_1

value: X-linked acrogigantism


title: zr1143_4


title: fetalC2019_E3381-1_1X4_MixN2018_Chronic 15 days


title: Alpha_S43_1st

value: Ischgl, Austria


title: zr1035_1


title: Alpha_S42_2nd


title: healthy control, HC16

description: healthy control


title: zr873_1


title: fetalC2019_E3381-1_1X3_MixN2018_Chronic 15 days


title: zr1139_1


title: healthy control, HC12

description: healthy control


title: Alpha_S42_1st


title: zr1900_2


title: fetalC2019_E3381-1_1X2_MixN2018_Chronic 15 days


title: healthy control, HC1

description: healthy control


title: healthy control, BB3

description: healthy control


title: Alpha_S38_3rd


title: Alpha_S38_2nd


title: fetalC2019_E3381-1_VITC4_MixN2018_Chronic 15 days

value: VITC


title: A1ATD1 192

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: raw.csv

data_processing:
The quality of the data was assessed using FastQC, MultiQC
Reads were aligned using STAR v2.7.3a (parameters --outSAMtype BAM SortedByCoordinate)
Protein-coding gene quantification was performed using Subread featureCounts v2.0.0 (default parameters)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: csv file of raw expression levels

source_name: Forward programmed megakaryocytes

growth_protocol: The hiPSC line A1ATD1c was forward programmed towards the megakarycoyte lineage using method describes in Moreau et al. 2016 (PMID: 27052461) and cell material collected after 40 days of standard culture. Rainbow vectors allowing fluorescence reporting of transcription factor expression (as described in Dalby et al. 2018) have been used to programme the cells.

extract_protocol:
The single cells were sorted in 96-well plates containing cell lysis buffer (2.3mL of 0.2% Triton X-100 with RNase inhibitor) and frozen to -80°C before library preparation.
The method for single cell cDNA library making has been adapted from Smartseq2 for full-length RNAseq from single cells and Fluidigm (PMID: 24385147). Briefly, the reverse transcription was initiated with oligo-dT primers using SuperScript-II reverse transcriptase (Thermo Scientific) and supplemented with ERCC RNA Spike-In. The cDNA was then PCR amplified for 21 cycles using the KAPA HiFi Hotstart ReadyMix and IS primers (Kappa biosystems). After purification of the amplified cDNA, the indexed library was made using the Illumina Nextera XT DNA kit, 96 cells eventually pooled and library quality checked on an Agilent high sensitivity DNA chip before sequencing on one lane of an HiSeq-4000 (Illumina).

treatment_protocol: The megakaryocytes have been sorted by FACS at day40 and 24 single cells of each rainbow transgene pattern (GFT, GF, GT, FT, G, F, T, Neg; G:GATA1, F:FLI1, T:TAL1) directly lysed in 0.2% Triton-X before NGS library preparation (see detailed methods in Dalby et al. 2018)

tag: hipsc line

tag: differentiation day

value: Day 40

tag: transgene pattern

value: FT


title: 10X scRNA-seq HNES1 naive hPSC

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: Single-cell RNA seq, 10X Chromium

data_processing:
The Cell Ranger count pipeline (v.3.1.0) was used to align raw sequencing reads to the GRCh38 human genome (Single Cell 3' v3 chemistry).
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X barcode file: Tsv files contain barcodes of detected cells.
Supplementary_files_format_and_content: 10X feature file: Tsv files contain IDs of detected genes.
Supplementary_files_format_and_content: 10X matrix file: Mtx files contain matrix of raw count values.
Supplementary_files_format_and_content: 10X cloupe file: The Cell Ranger cloupe file.

source_name: embryo

growth_protocol: Naïve HNES1 hPSCs were cultured in a humidified incubator at 5% O2, 5% CO2 and 37°C, on irradiated mouse embryonic fibroblast (MEFs DR4) and were passaged every 2-3 days using TrypLE, and plated into PXGL medium with ROCK inhibitor (10μM) and Geltrex  (0.5μl per cm2 surface are). HNES1 were cultured in PXGL culture conditions: N2B27 (1:1 DMEM/F12:Neurobasal, 0.5x N2 supplement, 0.5x B27 supplement, 1x nonessential amino acids, 2mM l-Glutamine, 1x Penicillin/Streptomycin, 0.1mM β-mercaptoethanol, supplemented with 1μM PD0325901, 2μM Gö6983, 10ng/ mL human LIF

extract_protocol:
Chromium Single Cell 3′ Library & Gel Bead Kit v3
Single-cell RNA was isolated from individual cells, harvested and dissociated with 0.25% trypsin (10min at 37°C) resuspended in 0.1% BSA in DMEM/F12, and processed with a Chromium Single Cell 3′ Library & Gel Bead Kit v3 and Chromium Chip B Kit
Single-cell RNA-seq libraries were prepared using the following: Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics, PN-1000075), Chromium Chip B Kit (10x Genomics, PN-1000073) and Chromium Single Cell 3' Reagent Kits v3 User Guide (Manual Part CG000183 Rev C, 10X Genomics). Cell suspensions were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing single cells. RNA from the barcoded cells for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to the manufacturer’s protocol with no modifications. cDNA quality and quantity were measured with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape) after which 25% of material was used for gene expression library preparation. Library quality was confirmed with Agilent TapeStation 4200 (High Sensitivity D1000 ScreenTape to evaluate library sizes) and Qubit 4.0 Flourometer (ThermoFisher Qubit™ dsDNA HS Assay Kit to evaluate dsDNA quantity). Each sample was normalized and pooled in equal molar concentration. To confirm concentration, pool was qPCRed using KAPA Library Quantification Kit on QuantStudio 6 Flex before sequencing. Pool was sequenced on S2 flowcell on Illumina NovaSeq6000 sequencer with following parameters: 28 bp, read 1; 8 bp, i7 index; and 91 bp, read 2.

treatment_protocol: HNES1 hPSCs were plated into PXGL with ROCK inhibitor (10μM), onto Geltrex (1μl per cm2 surface are)

tag: developmental stage

value: ICM of blastocysts (day 6) of supernumerary frozen human embryos

tag: background

value: Human naive pluripotent stem cells (HNES1)


title: org2019_3391B_VitC2_MixN2018_Chronic50days

value: hiPSC-derived cortical brain organoids

tag: Stage

value: Day 50

tag: passage

tag: Sex

value: Female

value: Chronic 50 days


title: healthy control, BB2

description: healthy control

tag: disease state

value: PBMCs

tag: tissue

value: whole blood

tag: gender

tag: age

tag: ifn score


title: healthy control, BB1

description: healthy control

tag: ifn classification


title: fetalC2019_E3381-1_VITC2_MixN2018_Chronic 15 days

value: Fetal brain cortical progenitors

value: Male

value: Chronic 15 days


title: fetalC2019_E3381-1_VITC3_MixN2018_Chronic 15 days


title: A1ATD1 190

description: raw.csv


title: Alpha_S35_1st

tag: diseas state

value: COVID-19_Alpha varient

tag: geographical location

tag: cell type

value: PBMC


title: healthy control, 80-0008-01

description: healthy control

value: healthy control

value: Anonymized


title: healthy control, 80-0009-01

description: healthy control


title: fetalC2019_E3381-1_VITC1_MixN2018_Chronic 15 days

tag: treatment

value: VITC


title: Alpha_S35_2nd

value: Ischgl, Austria


title: healthy control, 80-0007-01

description: healthy control


title: A1ATD1 188

description: raw.csv

tag: hipsc line

tag: differentiation day

value: Day 40

value: FT


title: A1ATD1 187

description: raw.csv

tag: transgene pattern


title: fetalC2019_E3381-1_CNT4_MixN2018_Chronic 15 days

value: CNT


title: Alpha_S34_1st


title: fetalC2019_E3381-1_1X1_MixN2018_Chronic 15 days


title: healthy control, 80-0006-01

description: healthy control


title: fetalC2019_E3381-1_CNT3_MixN2018_Chronic 15 days


title: Alpha_S33_2nd


title: Alpha_S34_2nd


title: healthy control, 80-0005-01

description: healthy control


title: healthy control, 80-0004-01

description: healthy control


title: A1ATD1 186

description: raw.csv


title: A1ATD1 191

description: raw.csv


title: fetalC2019_E3381-1_CNT2_MixN2018_Chronic 15 days


title: A1ATD1 185

description: raw.csv


title: org2019_3391B_1X1_MixN2015_Chronic50days

value: hiPSC-derived cortical brain organoids

value: Day 50


title: Alpha_S33_1st

value: Female


title: fetalC2019_E3381-1_CNT1_MixN2018_Chronic 15 days


title: Alpha_S38_1st


title: fetalC2019_E3381-1_DMSO4_MixN2018_Chronic 15 days

value: DMSO


title: A1ATD1 189

description: raw.csv


title: Alpha_S31_1st


title: Alpha_S32_1st


title: fetalC2019_E3381-1_DMSO3_MixN2018_Chronic 15 days


title: A1ATD1 183

description: raw.csv

value: T


title: Alpha_S30_2nd


title: fetalC2019_E3381-1_DMSO2_MixN2018_Chronic 15 days

value: Fetal brain cortical progenitors


title: A1ATD1 181

description: raw.csv


title: Alpha_S30_1st


title: fetalC2019_E3381-1_DMSO1_MixN2018_Chronic 15 days

value: Male


title: Alpha_S29_2nd


title: SLE, 1129

description: SLE

value: SLE

value: PBMCs

value: whole blood

value: F

value: intermediate


title: healthy control, 80-0001-01

description: healthy control

value: healthy control

value: Anonymized


title: healthy control, 80-0002-01

description: healthy control


title: SLE, 1114

description: SLE


title: A1ATD1 180

description: raw.csv

value: Day 40


title: fetalC2019_E3381-1_T34_MixN2018_Chronic 15 days

value: Chronic 15 days


title: healthy control, 80-0003-01

description: healthy control


title: fetalC2019_E3381-1_T33_MixN2018_Chronic 15 days


title: A1ATD1 184

description: raw.csv


title: A1ATD1 179

description: raw.csv


title: SLE, 1105

description: SLE

value: IFN-L


title: Alpha_S28_2nd

value: COVID-19_Alpha varient

value: Ischgl, Austria

value: PBMC


title: fetalC2019_E3381-1_T32_MixN2018_Chronic 15 days


title: Alpha_S28_1st


title: A1ATD1 177

description: raw.csv


title: SLE, 1104

description: SLE


title: A1ATD1 182

description: raw.csv


title: Alpha_S29_1st

value: Female


title: SLE, 1102

description: SLE

value: IFN-H


title: Alpha_S27_2nd


title: A1ATD1 176

description: raw.csv

value: T


title: fetalC2019_E3381-1_BPA0.04X4_MixN2018_Chronic 15 days

value: Fetal brain cortical progenitors

value: Male


title: fetalC2019_E3381-1_T31_MixN2018_Chronic 15 days


title: A1ATD1 175

description: raw.csv


title: SLE, 1044

description: SLE

value: SLE

value: PBMCs


title: Alpha_S27_1st


title: A1ATD1 178

description: raw.csv


title: A1ATD1 174

description: raw.csv


title: fetalC2019_E3381-1_BPA0.04X2_MixN2018_Chronic 15 days


title: SLE, 1018

description: SLE

value: whole blood

value: F


title: SLE, 1043

description: SLE


title: Alpha_S23_2nd


title: A1ATD1 173

description: raw.csv


title: SLE, 1014

description: SLE


title: fetalC2019_E3381-1_BPA0.04X3_MixN2018_Chronic 15 days


title: Alpha_S22_2nd


title: fetalC2019_E3381-1_BPA0.04X1_MixN2018_Chronic 15 days


title: A1ATD1 172

description: raw.csv


title: fetalC2019_E3381-1_1000X4_MixN2017_Chronic 15 days


title: SLE, 986

description: SLE


title: fetalC2019_E3381-1_1000X3_MixN2017_Chronic 15 days


title: Alpha_S21_1st


title: A1ATD1 170

description: raw.csv


title: SLE, 981

description: SLE


title: fetalC2019_E3381-1_1000X2_MixN2017_Chronic 15 days


title: Alpha_S21_2nd


title: SLE, 967

description: SLE


title: A1ATD1 169

description: raw.csv


title: SLE, 971

description: SLE

value: intermediate


title: fetalC2019_E3381-1_1X4_MixN2017_Chronic 15 days


title: Alpha_S20_2nd


title: Alpha_S20_1st


title: A1ATD1 168

description: raw.csv


title: Alpha_S26_1st


title: fetalC2019_E3381-1_1X3_MixN2017_Chronic 15 days


title: Alpha_S19_2nd


title: A1ATD1 167

description: raw.csv


title: fetalC2019_E3381-1_1X2_MixN2017_Chronic 15 days


title: A1ATD1 166

description: raw.csv


title: fetalC2019_E3381-1_1X1_MixN2017_Chronic 15 days


title: A1ATD1 171

description: raw.csv


title: SLE, 938

description: SLE


title: Alpha_S11_3rd


title: Alpha_S19_1st


title: fetalC2019_E3381-1_1000X4_MixN2015_Chronic 15 days


title: SLE, 931

description: SLE


title: Alpha_S11_2nd


title: fetalC2019_E3381-1_1000X3_MixN2015_Chronic 15 days


title: A1ATD1 164

description: raw.csv


title: Alpha_S10_2nd


title: Alpha_S11_1st


title: SLE, 889

description: SLE


title: A1ATD1 163

description: raw.csv


title: A1ATD1 162

description: raw.csv


title: Alpha_S10_1st


title: fetalC2019_E3381-1_1000X2_MixN2015_Chronic 15 days


title: fetalC2019_E3381-1_1000X1_MixN2015_Chronic 15 days


title: SLE, 950

description: SLE

value: M


title: SLE, 871

description: SLE


title: A1ATD1 161

description: raw.csv

value: Day 40


title: SLE, 859

description: SLE


title: SLE, 858

description: SLE


title: SLE, 847

description: SLE


title: fetalC2019_E3381-1_1X4_MixN2015_Chronic 15 days

value: Chronic 15 days


title: A1ATD1 160

description: raw.csv


title: fetalC2019_E3381-1_1X3_MixN2015_Chronic 15 days


title: Alpha_S08_1st


title: SLE, 932

description: SLE


title: A1ATD1 158

description: raw.csv

value: neg


title: fetalC2019_E3381-1_1X1_MixN2015_Chronic 15 days


title: SLE, 811

description: SLE


title: Alpha_E484K_S62_3rd

value: COVID-19_Alpha_E484K varient


title: SLE, 809

description: SLE

value: IFN-L


title: A1ATD1 159

description: raw.csv


title: Alpha_E484K_S62_2nd

value: Ischgl, Austria

value: PBMC


title: A1ATD1 157

description: raw.csv


title: fetalC2019_E3381-1_1000X3_MixN2018_Acute 48 hours

value: Acute 48 hours


title: SLE, 804

description: SLE


title: fetalC2019_E3381-1_1000X4_MixN2018_Acute 48 hours


title: Alpha_S08_2nd

value: COVID-19_Alpha varient


title: A1ATD1 155

description: raw.csv


title: Alpha_E484K_S62_1st

value: Female


title: A1ATD1 165

description: raw.csv


title: fetalC2019_E3381-1_1000X1_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors

value: Male


title: A1ATD1 156

description: raw.csv


title: fetalC2019_E3381-1_1000X2_MixN2018_Acute 48 hours


title: SLE, 797

description: SLE

value: SLE

value: PBMCs


title: fetalC2019_E3381-1_1000X4_MixN2017_Acute 48 hours


title: A1ATD1 154

description: raw.csv


title: Alpha_E484K_S59_3rd


title: SLE, 818

description: SLE

value: whole blood


title: fetalC2019_E3381-1_1000X3_MixN2017_Acute 48 hours


title: A1ATD1 153

description: raw.csv


title: SLE, 785

description: SLE

value: F

value: IFN-H


title: A1ATD1 152

description: raw.csv

value: Day 40


title: Alpha_E484K_S59_2nd


title: fetalC2019_E3381-1_1000X2_MixN2017_Acute 48 hours


title: Alpha_E484K_S60_2nd


title: SLE, 769

description: SLE


title: SLE, 723

description: SLE


title: Alpha_E484K_S59_1st


title: fetalC2019_E3381-1_1000X1_MixN2017_Acute 48 hours


title: A1ATD1 151

description: raw.csv


title: SLE, 755

description: SLE

value: intermediate


title: SLE, 706

description: SLE


title: Alpha_E484K_S60_1st


title: Alpha_E484K_S58_1st


title: fetalC2019_E3381-1_1000X4_MixN2015_Acute 48 hours


title: SLE, 684

description: SLE


title: A1ATD1 149

description: raw.csv

value: neg


title: Alpha_E484K_S57_1st

value: COVID-19_Alpha_E484K varient


title: Alpha_E484K_S54_2nd


title: fetalC2019_E3381-1_1000X3_MixN2015_Acute 48 hours


title: SLE, 673

description: SLE


title: SLE, 669

description: SLE


title: A1ATD1 148

description: raw.csv


title: Alpha_E484K_S54_3rd


title: fetalC2019_E3381-1_1000X2_MixN2015_Acute 48 hours


title: A1ATD1 146

description: raw.csv


title: A1ATD1 147

description: raw.csv


title: fetalC2019_E3381-1_1000X1_MixN2015_Acute 48 hours


title: SLE, 663

description: SLE


title: Alpha_E484K_S54_1st


title: Alpha_E484K_S53_3rd


title: A1ATD1 150

description: raw.csv


title: fetalC2019_E3381-1_DMSO3_MixN2018_Acute 48 hours

value: DMSO


title: fetalC2019_E3381-1_DMSO4_MixN2018_Acute 48 hours


title: A1ATD1 144

description: raw.csv


title: A1ATD1 145

description: raw.csv


title: fetalC2019_E3381-1_DMSO2_MixN2018_Acute 48 hours


title: SLE, 627

description: SLE


title: SLE, 552

description: SLE


title: fetalC2019_E3381-1_DMSO1_MixN2018_Acute 48 hours


title: Alpha_E484K_S52_1st

value: Ischgl, Austria


title: A1ATD1 143

description: raw.csv


title: A1ATD1 142

description: raw.csv


title: A1ATD1 141

description: raw.csv

value: GFT


title: Alpha_E484K_S51_2nd

value: PBMC


title: fetalC2016_E3361-1_1000X1_MixN2015_Acute 48 hours

value: Acute 48 hours


title: fetalC2016_E3361-1_10X1_MixN2015_Acute 48 hours


title: SLE, 543

description: SLE

value: IFN-L


title: SLE, 662

description: SLE


title: A1ATD1 140

description: raw.csv


title: fetalC2016_E3361-1_100X1_MixN2015_Acute 48 hours

value: Fetal brain cortical progenitors


title: Alpha_E484K_S51_1st

value: Male


title: SLE, 521

description: SLE

value: SLE


title: Alpha_E484K_S45_2nd


title: Alpha_E484K_S53_2nd

value: Female


title: Alpha_E484K_S45_1st


title: A1ATD1 138

description: raw.csv


title: SLE, 444

description: SLE

value: PBMCs

value: whole blood


title: A1ATD1 139

description: raw.csv


title: SLE, 445

description: SLE

value: F


title: Alpha_E484K_S53_1st


title: Alpha_E484K_S41_3rd


title: fetalC2016_E3361-1_DMSO1_MixN2015_Acute 48 hours


title: A1ATD1 137

description: raw.csv

value: Day 40


title: SLE, 546

description: SLE

value: M


title: LUAD cell lines_KT_2_mTet2HD_TAPS

city: Shanghai

first: Chao

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

description: LUAD cell lines_TAPS.csv

library_source: genomic

data_processing:
For RNA data, the raw data were trimmed by Trim Galore (v0.5.0) with default settings. Then, the clean RNA-seq FASTQ data were mapped to mm10 using Hisat2 (v2.1.0) with default parameters. DEG analysis was performed by using DESeq2 package with the raw count. Only genes with padj less than 0.05 and at least 2-fold-change were considered to be differentially expressed.
For PBAT data, by using Trim Galore (v0.5.0) to remove low quality bases and adaptor sequences. The remaining clean reads were mapped to mm10 with single-end and non-directional mapping parameters by using BS-Seeker2 (v2.1.8). Duplicated reads were removed using SAMtools (v1.4) for the subsequent analysis. CGmap Tools (v0.1.2) was used for DNA methylation downstream analysis.
For TAPS data, the raw data were trimmed by Trim Galore (v0.5.0) with default settings. Then, the clean data were mapped to mm10 using bwa (0.7.15). Duplicated reads were removed using Picard (2.21.2). Call methylation uses astair call (3.2.6). CGmap Tools (v0.1.2) was used for DNA methylation downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA data, we provide a processed data files consisting of gene fpkm, log2FoldChange, padj. For DNA methylation data, we provide a processed data files consisting of DMR location, DMR methylation.

molecule: genomic DNA

organism: Mus musculus

source_name: lung adenocarcinoma tumor cells

growth_protocol: KT LUAD cell lines used in this study were established from mouse LUAD over the course of the study. KT tumors generated from individual KTR mice were dissected, and digested in protease and DNase solution. Dissociated cells were further processed for FACS sorting. All KT LUAD cell lines were grown in DMEM supplemented with 10% FBS and 1% pen-strep, and tested negative for mycoplasma contamination.

extract_protocol:
Pre-malignant lung epithelial cells were sorted by FACS, and part of them were then lysed dicrectly to release total RNA and genomic DNA. The remaining cells were collected and used to extract RNA and DNA by AllPrep DNA/RNA Micro Kit (Qiagen, 80284). Parental KT LUAD cells and KT LUAD cells complemented with Tet2CD or Tet2HD were harvested and then used to extract RNA and DNA by AllPrep DNA/RNA Mini Kit (Qiagen, 0204)
RNA libraries of pre-malignant cells were constructed by Smart-seq2 protocol.PBAT libraries of pre-malignant cells were constructed by PBAT protocol (Dai et al., 2016, Nature). RNA libraries of LUAD cell lines were constructed by kit (Vazyme, NR611). TAPS libraries of LUAD cell lines were constructed as described in the paper of Liu et al., 2019, Nature Biotechnology.
RNA-seq, WGBS (whole-genome bisulfite sequencing), TAPS (TET-assisted pyridine borane sequencing)

tag: strain

value: lung primary tumors


title: fetalC2016_E3361-1_0.1X1_MixN2015_Acute 48 hours

tag: Stage


title: fetalC2016_E3361-1_1X1_MixN2015_Acute 48 hours

tag: passage


title: Alpha_E484K_S41_2nd

value: COVID-19_Alpha_E484K varient


title: LUAD cell lines_KT_2_mTet2CD_TAPS

description: LUAD cell lines_TAPS.csv


title: fetalC2018_E3361-1_T3MixN3_MixN2018_Acute 48 hours

tag: Sex


title: A1ATD1 135

description: raw.csv


title: Alpha_E484K_S41_1st


title: fetalC2018_E3361-1_BPA1X3_MixN2018_Acute 48 hours


title: A1ATD1 134

description: raw.csv

value: GT


title: Alpha_E484K_S40_2nd

value: Ischgl, Austria


title: Alpha_E484K_S40_3rd


title: A1ATD1 133

description: raw.csv


title: SLE, 441

description: SLE

tag: disease state

value: IFN-H


title: Alpha_E484K_S40_1st

value: PBMC


title: fetalC2018_E3361-1_VITC3_MixN2018_Acute 48 hours

value: VITC

value: Acute 48 hours


title: A1ATD1 132

description: raw.csv


title: LUAD cell lines_KT_1_Vec_TAPS

description: LUAD cell lines_TAPS.csv

tag: tissue


title: A1ATD1 131

description: raw.csv


title: fetalC2018_E3361-1_CNT3_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors

value: CNT


title: LUAD cell lines_KT_2_mT2HD_RNA

description: LUAD cell lines_RNA.csv


title: A1ATD1 130

description: raw.csv


title: A1ATD1 136

description: raw.csv

value: GFT


title: Alpha_E484K_S39_2nd

tag: gender

value: Male


title: Alpha_E484K_S39_1st

tag: age


title: fetalC2018_E3361-1_1X3_MixN2018_Acute 48 hours


title: LUAD cell lines_KT_2_Vec_RNA

description: LUAD cell lines_RNA.csv


title: LUAD cell lines_KT_2_Vec_TAPS

description: LUAD cell lines_TAPS.csv


title: fetalC2018_E3361-1_10X3_MixN2018_Acute 48 hours


title: LUAD cell lines_KT_1_mTet2HD_TAPS

description: LUAD cell lines_TAPS.csv


title: 10X Multiome HNES1_DUX4_overexpression_ATAC

description:
Single-cell ATAC seq, 10X Multiome
Single Index Kit N Set A

data_processing:
The CellRanger-arc count pipeline (v.2.0.0) was used to align raw sequencing reads to the GRCh38 human genome (v2.0.0).
Genome_build: GRCh38
10X ATAC fragment file: Tsv files contain peaks of open chromatin
10X feature file: Tsv files contain IDs of detected genes
10X matrix file: Mtx files contain matrix of raw count values
10X web summary: The Cell Ranger-arc web summary file

extract_protocol:
Single-cell RNA and single-cell genomic DNA were isolated from individual nuclei, from TrypLE-dissociated (10min, 37°C), flow-sorted, lysed cells, and processed with a Chromium Single Cell Multiome ATAC + Gene Expression kit
Single Cell Multiome ATAC + Gene Expression kit

tag: developmental stage

value: ICM of blastocysts (day 6) of supernumerary frozen human embryos

tag: background

value: Human naive pluripotent stem cells (HNES1)

tag: molecule subtype

value: genomic DNA


title: LUAD cell lines_KT_1_mTet2CD_TAPS

description: LUAD cell lines_TAPS.csv


title: fetalC2018_E3361-1_100X3_MixN2018_Acute 48 hours


title: 10X Multiome HNES1_wildtype_ATAC


title: A1ATD1 127

description: raw.csv

value: Day 40


title: A1ATD1 128

description: raw.csv


title: LUAD cell lines_KT_1_mT2CD_RNA

description: LUAD cell lines_RNA.csv


title: Alpha_E484K_S39_3rd

tag: diseas state

tag: geographical location


title: fetalC2018_E3361-1_DMSO3_MixN2018_Acute 48 hours

tag: treatment

value: DMSO


title: 10X Multiome HNES1_DUX4_overexpression_RNA

description:
Single-cell RNA seq, 10X Multiome
Dual Index Kit TT, Set A

value: nuclear RNA


title: A1ATD1 126

description: raw.csv

tag: hipsc line

value: GF


title: LUAD cell lines_KT_2_mT2CD_RNA

description: LUAD cell lines_RNA.csv

value: lung primary tumors


title: Pre-malignant_KT_PBAT_4

source_name: Pre-malignant lung epithelial cells

value: lung


title: fetalC2018_E3361-1_T3MixN2_MixN2018_Acute 48 hours


title: 10X Multiome HNES1_wildtype_RNA


title: fetalC2018_E3361-1_T33_MixN2018_Acute 48 hours


title: fetalC2018_E3361-1_0.1X3_MixN2018_Acute 48 hours


title: A1ATD1 125

description: raw.csv

tag: differentiation day


title: fetalC2018_E3361-1_T32_MixN2018_Acute 48 hours


title: A1ATD1 124

description: raw.csv

tag: transgene pattern


title: Pre-malignant_KT_PBAT_3

tag: strain


title: A1ATD1 123

description: raw.csv


title: fetalC2018_E3361-1_BPA1X2_MixN2018_Acute 48 hours

tag: Stage


title: pNK-iNK3

city: Hefei

first: Xianghui

last: Du

state: Anhui

address: 443 Huangshan Road

department: Institute of Immunology

institute: Division of Life Sciences and Medicine

data_processing:
Filtering of Clean Reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low-quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Alignment with Ribosome RNA (rRNA). Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
Alignment with Reference Genome. An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
Quantification of Gene Abundance. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Genome_build: Ensembl_release100
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: natural killer cell

extract_protocol:
NK cells were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols:  After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-Zero TM  Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: source tissue

value: peripheral blood

tag: cultured

value: pNK-derived  induced NK cells


title: LUAD cell lines_KT_1_mT2HD_RNA

description: LUAD cell lines_RNA.csv


title: Pre-malignant_KT_PBAT_2


title: fetalC2018_E3361-1_1000X3_MixN2018_Acute 48 hours

tag: passage

tag: Sex


title: pNK-iNK2


title: A1ATD1 122

description: raw.csv


title: A1ATD1 121

description: raw.csv


title: pNK-iNK1


title: Pre-malignant_KT_PBAT_1

tag: tissue


title: LUAD cell lines_KT_1_Vec_RNA

description: LUAD cell lines_RNA.csv


title: fetalC2018_E3361-1_VITC2_MixN2018_Acute 48 hours

value: VITC


title: pNK-iNK4


title: fetalC2018_E3361-1_CNT2_MixN2018_Acute 48 hours

value: Acute 48 hours


title: Pre-malignant_K_PBAT_3


title: BM-iNK4

value: bone marrow

value: HSC-derived  induced NK cells


title: A1ATD1 120

description: raw.csv


title: A1ATD1 119

description: raw.csv

value: G


title: Pre-malignant_K_PBAT_2


title: A1ATD1 118

description: raw.csv


title: fetalC2018_E3361-1_1X2_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors

value: Male


title: A1ATD1 117

description: raw.csv


title: Pre-malignant_K_PBAT_1


title: fetalC2018_E3361-1_10X2_MixN2018_Acute 48 hours


title: fetalC2018_E3361-1_BPA0.04X2_MixN2018_Acute 48 hours


title: CB-iNK4

value: umbilical cord blood


title: Pre-malignant_KT_RNA_3


title: Pre-malignant_KT_RNA_4


title: BM-iNK1


title: A1ATD1 116

description: raw.csv


title: Pre-malignant_KT_RNA_2


title: CB-iNK3


title: Pre-malignant_K_PBAT_4


title: fetalC2018_E3361-1_1000X2_MixN2018_Acute 48 hours


title: A1ATD1 115

description: raw.csv


title: A1ATD1 114

description: raw.csv


title: Pre-malignant_KT_RNA_1


title: fetalC2018_E3361-1_0.1X2_MixN2018_Acute 48 hours


title: CB-iNK2


title: BM-iNK3


title: BM-iNK2


title: A1ATD1 113

description: raw.csv


title: A1ATD1 129

description: raw.csv

value: GT


title: fetalC2018_E3361-1_DMSO2_MixN2018_Acute 48 hours


title: CB-iNK1


title: pNK4

value: Freshly isolated primary NK cells


title: A1ATD1 112

description: raw.csv

value: Day 40


title: Pre-malignant_K_RNA_3


title: Pre-malignant_K_RNA_2


title: fetalC2018_E3361-1_T3MixN1_MixN2018_Acute 48 hours


title: fetalC2018_E3361-1_T31_MixN2018_Acute 48 hours


title: Pre-malignant_K_RNA_1


title: fetalC2018_E3361-1_BPA1X1_MixN2018_Acute 48 hours


title: A1ATD1 111

description: raw.csv

value: FT


title: pNK2


title: fetalC2018_E3361-1_100X2_MixN2018_Acute 48 hours


title: A1ATD1 110

description: raw.csv


title: pNK1


title: A1ATD1 109

description: raw.csv


title: fetalC2018_E3361-1_VITC1_MixN2018_Acute 48 hours


title: dNK4

value: decidua


title: dNK3


title: A1ATD1 108

description: raw.csv


title: fetalC2018_E3361-1_CNT1_MixN2018_Acute 48 hours

value: CNT


title: A1ATD1 107

description: raw.csv


title: RRS-NKp46- ILC3-RNAseq KO2

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: cells were isolated from small intestinal lamina propria

data_processing:
Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used for quantification and qualification of the sample library
Reads were mapped to Mouse Genome Assembly GRCm38.p5 by STAR v2.5. Gene and isoform expression quantification was called by RSEM v1.2 with default parameters on GENCODE mouse M16 gene annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: Excel, tracking ID，FPKM and gene name of different samples

source_name: lamina proprial lymphocytes

extract_protocol:
Cells were lysed in Trizol (Thermo Fisher Scientific) and total RNA was extracted.
Library construction and sequencing was performed by BGI Genomics, BGI-Wuhan. RNA were treated with DNase I and purified with magnetic beads with Oligo (dT). RNA were mixed with the fragmentation buffer and were fragmented into short fragments. Then cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments were connected with adapters. Suitable fragments were selected for the PCR amplification as templates. Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used for quantification and qualification of the sample library. 150bp paired sequencing was performed using Illumina.

tag: cell type

value: KO-NKp46- ILC3s

tag: gender

value: pooled male and female

tag: genotype

value: small intestinal lamina propria


title: RRS-NKp46- ILC3-RNAseq CTRL1

value: CTRL-NKp46- ILC3s


title: RRS-NKp46+ ILC3-RNAseq KO2

value: KO-NKp46+ ILC3s


title: RRS-NKp46- ILC3-RNAseq CTRL2


title: dNK2


title: dNK1


title: RRS-NKp46+ ILC3-RNAseq KO1


title: A1ATD1 105

description: raw.csv


title: fetalC2018_E3361-1_1X1_MixN2018_Acute 48 hours

value: Acute 48 hours


title: pNK3

value: peripheral blood


title: fetalC2018_E3361-1_BPA0.04X1_MixN2018_Acute 48 hours


title: A1ATD1 106

description: raw.csv


title: A1ATD1 104

description: raw.csv


title: fetalC2018_E3361-1_100X1_MixN2018_Acute 48 hours


title: NeuStino3218

city: Tokyo

first: Kohsuke

last: Shirakawa

address: 35 Shinanomachi, Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Samples were sequenced using Novaseq with paired-end 2 x 150-bp cycle
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.38 with LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36 as command option
Mapping of sequence reads using HISAT2 version 2.1.0
Raw read counts were determined using featureCounts version 1.6.3
Differentially expressed genes were identified using DESeq2 version 1.22.0
Genome_build: hg38
Supplementary_files_format_and_content: Fastq reads were generated using bcl2fastq Conversion Software version 1.8.4; First line begins with a '@' character and is followed by a sequence identifier. Second line represent raw nucleotide sequence letters. The last line encodes the quality values for the sequence.

source_name: human neutrophil

extract_protocol:
Human neutrophils were isolated from the peripheral blood of healthy volunteers, with written informed consent, using Lympholyte®-poly (CEDARLANE Laboratories, Burlington, Canada) according to the manufacturer’s instructions, after approval from the Ethics Review Committee of Keio University (#20200183). Polynuclear cells containing neutrophils were collected, washed, and resuspended in 5 mL of red blood cell (RBC) lysis buffer (BioLegend, San Diego, CA, USA), then washed twice in Hank’s buffered salt solution (HBSS) without Ca2+/Mg2+ (Wako Pure Chemicals, Osaka, Japan), and finally resuspended in the Roswell Park Memorial Institute (RPMI) 1640 medium (Wako). Cell cultures of neutrophils in RPMI 1640 medium (Wako) containing 15 mM HEPES were exposed to hydrogen gas using a hydrogen-filling device with a built-in hydrogen-absorbing alloy (Doctors Man Co, Ltd., Kanagawa, Japan). The control medium was left untreated. Aliquots containing 1×10^7 isolated human neutrophils were stimulated with 100 nM phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, St. Louis, MO, USA) in the control or hydrogen gas-exposed medium at 37 °C for 1 h in 15-mL Falcon tubes (Fisher Scientific, Waltham, MA, USA).
Libraries were prepared for sequencing using library creation kits (NEBNext Ultra Directional RNA Library Prep Kit, Illumina, San Diego, CA, USA)

value: circulating neutrophil

value: control medium


title: RRS-NKp46+ ILC3-RNAseq CTRL2

value: CTRL-NKp46+ ILC3s


title: NeuStino3225


title: fetalC2018_E3361-1_10X1_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors

value: Male


title: RRS-NKp46+ ILC3-RNAseq CTRL1


title: RRS-NKp46- ILC3-RNAseq KO1


title: A1ATD1 103

description: raw.csv


title: fetalC2018_E3361-1_1000X1_MixN2018_Acute 48 hours


title: NeuStino3187


title: A1ATD1 102

description: raw.csv


title: fetalC2018_E3361-1_0.1X1_MixN2018_Acute 48 hours


title: fetalC2018_E3361-1_DMSO1_MixN2018_Acute 48 hours

value: DMSO


title: A1ATD1 101

description: raw.csv

value: Day 40


title: NeuStiHydo3225

value: stimulated with 100 nM PMA in hydrogen gas-exposed medium


title: Cdh16Cre-ACSL4F-F-2

city: Nanjing

first: Xinghua

last: Gao

address: jiangning longmian avenue 639,nanjing

institute: china pharmaceutical university

description:
processed data file:
ACSL4F-F_vs_Cdh16Cre-ACSL4F-F_ kidney tissue_gene_expression_anno.xls

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm8
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Mouse renal tissue

extract_protocol:
renal tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AKI in age-mached male C57BL/6J mice with I/R treatment.

tag: strain background

tag: genotype/varaition

value: ACSL4 conditonal konckout

value: I/R opreation treatment

tag: time point

value: ischemic 30 min treatment and sacrifice after 24 hour

value: Mouse renal tissue


title: Cdh16Cre-ACSL4F-F-1

tag: treatment


title: fetalC2018_E3381-1_BPA1X3_MixN2018_Acute 48 hours


title: ACSL4F-F-3

description:
processed data file:
Control_vs_ACSL4F-F_ kidney tissue_gene_expression_anno.xls; ACSL4F-F_vs_Cdh16Cre-ACSL4F-F_ kidney tissue_gene_expression_anno.xls

value: wild type


title: NeuStiHydo3218


title: A1ATD1 99

description: raw.csv

tag: hipsc line

value: FT


title: A1ATD1 100

description: raw.csv

tag: differentiation day


title: NeuStiHydo3187


title: A1ATD1 98

description: raw.csv

tag: transgene pattern


title: ACSL4F-F-1


title: ACSL4F-F-2


title: A1ATD1 97

description: raw.csv


title: fetalC2018_E3381-1_0.1X3_MixN2018_Acute 48 hours


title: NeuStiCont3187

value: stimulated with 100 nM PMA in control medium


title: A1ATD1 96

description: raw.csv


title: Control-3

description:
processed data file:
Control_vs_ACSL4F-F_ kidney tissue_gene_expression_anno.xls

value: sham opreation treatment

value: ischemic 0 min treatment and sacrifice after 24 hour


title: NeuStiCont3218

value: circulating neutrophil


title: fetalC2018_E3381-1_10X3_MixN2018_Acute 48 hours

value: Acute 48 hours


title: Cdh16Cre-ACSL4F-F-3


title: NeuStiCont3225


title: A1ATD1 95

description: raw.csv

value: T


title: fetalC2018_E3381-1_1X3_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors


title: I-BET151-BRD4_rep2

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

data_processing:
Library strategy: CUT&Tag
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Paired-end reads were aligned using Bowtie2 (v2.2.5) with options: --local --very-sensitive-local --no-unal --no-mixed –nodiscordant --phred33 -I 10 -X 700.
For peak calling, parameters used were macs2 (v2.1.2) callpeak -p 1e-5 -f BAMPE -g hs -n sample-name -B --keep-dup all.
Motif enrichment was done using HOMER with options: -fdr 0.05 -len 8,10,12.
Bigwig files were generated with bamCoverage function in deepTools(v3.4.3) with default parameter settings.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamcoverage
Supplementary_files_format_and_content: peak text files

source_name: MEL1 hESC line

growth_protocol: PPs were cultured on feeder with basal medium (EF6): DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF and 10 μM 616452.

extract_protocol:
CUT&Tag assay was performed as follows. First, ConA Beads (CST, #93569) were pipetted into a new tube, 10 μl per sample, and washed by Activation Buffer. 1 × 10^5 cells on d7 were harvested and washed by Wash Buffer. The cells were mixed with ConA Beads and incubated with Anti-Brd4 antibody (Abcam) (1:100) overnight at 4°C. Donkey anti-rabbit lgG antibody (Invitrogen) was diluted at 1:100 and added into the samples. then, the samples were incubated for 1 h at RT. After washing away the unbounded secondary antibody, Hyperactive pG-Tn5 Transposase (Vazyme) was added and incubated with cells for 1 h at RT. The samples were washed by Dig-med Buffer and followed with tagmentation by Tagmentation Buffer. Next, DNA was isolated by phenol-chloroform and dissolved in TE-buffer.
The standard processing was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep Index Kit V2 for Illumina ® (Vazyme TD202). The library concentration was measured using Qubit dsDNA BR Assay Kit (Invitrogen) by Qubit (Invitrogen).

treatment_protocol: DMSO samples were treated with DMSO and I-BET151 samples were treated with 1 μM I-BET151 for 7 days.

tag: cell line

value: MEL1 hESC line

value: hPSC-derived pancreatic progenitor cells

tag: chip antibody

value: Anti-Brd4 antibody (Abcam, ab128874)


title: Control-2


title: A1ATD1 94

description: raw.csv

value: Day 40


title: I-BET151-BRD4_rep1


title: Control-1


title: fetalC2018_E3381-1_T3MixN3_MixN2018_Acute 48 hours

tag: Stage

value: Male


title: fetalC2018_E3381-1_100X3_MixN2018_Acute 48 hours


title: fetalC2018_E3381-1_1000X3_MixN2018_Acute 48 hours


title: fetalC2018_E3381-1_BPA0.04X3_MixN2018_Acute 48 hours


title: DMSO-BRD4_rep2

value: DMSO


title: A1ATD1 93

description: raw.csv


title: fetalC2018_E3381-1_DMSO3_MixN2018_Acute 48 hours


title: A1ATD1 92

description: raw.csv


title: fetalC2018_E3381-1_T3MixN2_MixN2018_Acute 48 hours


title: REP2

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description:
MCF7 Set 2 REST knockdown, estrogen + progesterone treated.
mRNA
Sample_REP2
Raw_Counts.RSEM.txt

data_processing:
Illumina bcl2fastq conversion software used for basecalling.
Reads were aligned using the STAR (2.5.2b) software.
Raw read counts were obtained using RSEM software.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Raw_Counts.RSEM.txt: Tab-delimited text file of raw count values for each Sample.

source_name: MCF7-breast cancer cell lines

growth_protocol: MCF-7 cells were obtained from ATCC (Manassas, VA). They were cultured in DMEM (Corning, Tewksbury, MA) containing 10% FBS (R&D Systems, Inc., Minneapolis, MN) and 1% penicillin/streptomycin (Gibco, Waltham, MA) in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was harvested using Trizol.
Sequencing libraries were prepared using the NuGEN Universal Plus Stranded (fr-secondstrand) mRNA Sample Preparation Kit.

treatment_protocol: Cultured MCF-7 cells were plated in 6-well plates at 300,000 cells per well in antibiotic free media. After 24 hours at 37oC, 5%CO2, cells were transfected with a 100pmol mixture of Silencer Select siRNAs (S11934, S11932, S119323) to REST from Ambion (Life Technologies, Carlsbad, CA) using Lipofectamine 2000 transfection reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s protocol. Control experiments included ON-TARGETplus nontargeting scrambled siRNA 2 (ThermoFisher Scientific, Waltham, MA). After 24 hours, transfected cells were treated with vehicle (PBS), estradiol (10nM), progesterone (1uM), or estradiol and progesterone in charcoal stripped serum, phenol red free medium (Lonza, Morristown, NJ).

tag: sirna

value: Set 2 REST knockdown

value: estrogen + progesterone


title: fetalC2018_E3381-1_T32_MixN2018_Acute 48 hours

tag: passage


title: REP1

description:
MCF7 Set 1 REST knockdown, estrogen + progesterone treated.
mRNA
Sample_REP1
Raw_Counts.RSEM.txt

value: Set 1 REST knockdown


title: fetalC2018_E3381-1_BPA1X2_MixN2018_Acute 48 hours

tag: Sex


title: A1ATD1 90

description: raw.csv


title: A1ATD1 89

description: raw.csv


title: A1ATD1 91

description: raw.csv


title: fetalC2018_E3381-1_BPA0.04X2_MixN2018_Acute 48 hours


title: CEP1

description:
MCF7 Set 1 control, estrogen + progesterone treated.
mRNA
Sample_CEP1
Raw_Counts.RSEM.txt

value: Set 1 control


title: Female Morphine Group (100)

city: Scarborough

first: Adriana

last: Lelis Carvalho

address: 81 Research Drive

institute: MMCRI

description: global circulating miRNA screen after 12 days of treatment

hyb_protocol: Samples were combined with a hybridization mix, injected into arrays, and placed in the Affymetrix® GeneChip® Hybridization Oven 645 at 48° C and 60 RPM for 42 hours.

scan_protocol: Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450 and scanned with the Affymetrix® GeneChip® Scanner 3000.

data_processing: Affymetrix Power Tools v2.10.2.2 (APT) software package (Thermo Fisher Scientific). Simplified Expression Analysis (SEA) algorithm was used to summarize probesets and the Detectable Above BackGround (DABG) algorithm was used to assign p-values to probeset intensities.

label: biotin

source_name: serum after 12 days of morphine solution (18 mg/kg) delivery

label_protocol: Exactly 8ul of RNA was tagged with a Poly-A tail, using an ATP driven reaction from the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit.  Samples were then labeled with a biotinylated molecule using a ligation reaction.  Efficiency of the biotin ligation reaction was verified using NeutrAvidin (10mg/mL) with a gel-shift assay.

growth_protocol: not applicable

extract_protocol: Total RNA was isolated from 200 µL mouse serum following a standardized protocol (PMID: 24357537) using the miRNeasy Serum Plasma kit with ce-miR-39 spike-in (QIAGEN), QIAcube (QIAGEN) automation, and eluted with 14 µL of nuclease-free water. Multiple serum aliquots from the same patient were processed simultaneously, RNA pooled, and stored in small aliquots to isolate sufficient RNA for downstream applications.

treatment_protocol: At the baseline (day 0), osmotic minipumps filled with either sterile vehicle solution (0.9% saline) or morphine solution (60mg/mL) were implanted in 8 week-old C57BL/6J mice, resulting in 0,36 mg morphine delivered per day for 25 days.

tag: tissue

value: serum

value: female

tag: strain

tag: age

value: 10 weeks of age


title: fetalC2018_E3381-1_VITC2_MixN2018_Acute 48 hours

data_processing:
RNA-seq quantification was performed directly from the reads using Salmon 6.1, using the hg38 Refseq annotation.
Only genes with at least 20 reads in at least 2 samples were included; small (<200 nt) genes, ribosomal RNA genes, and fusion genes were excluded.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: TotalSumExp.RData: SummarisedExperiment (https://bioconductor.org/packages/SummarizedExperiment) including count matrix and metadata for all the samples.
Supplementary_files_format_and_content: counts.csv: Count matrix for all the samples. Names of the columns are matched to the Sample titles.

extract_protocol:
Total RNA was isolated with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA was quantified with Nanodrop and then the integrity was evaluated with Agilent 2100 Bioanalyzer (only if the quality ratios were not optimal after Nanodrop analysis). TruSeq Stranded Total RNA LT Sample Prep Kit, Illumina was used to run the library for each sample. Sequencing is performed with the Illumina HiSeq 2000 platform, sequencing on average 10 million 50bp paired-end reads per sample.

value: VITC


title: A1ATD1 87

description: raw.csv


title: DMSO-BRD4_rep1

tag: cell type


title: RE2

description:
MCF7 Set 2 REST knockdown, estrogen treated.
mRNA
Sample_RE2
Raw_Counts.RSEM.txt

value: estrogen


title: Female Morphine Group (94)

tag: gender


title: A1ATD1 86

description: raw.csv

value: F


title: RE1

description:
MCF7 Set 1 REST knockdown, estrogen treated.
mRNA
Sample_RE1
Raw_Counts.RSEM.txt


title: fetalC2018_E3381-1_CNT2_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors

value: CNT

value: Acute 48 hours


title: fetalC2018_E3381-1_0.1X2_MixN2018_Acute 48 hours


title: Male Morphine Group (78)

value: male


title: CE2

description:
MCF7 Set 2 control, estrogen treated.
mRNA
Sample_CE2
Raw_Counts.RSEM.txt

value: Set 2 control


title: Female Morphine Group (93)


title: Female Vehicle Group (88)

source_name: serum after 12 days of vehicle solution (0.9% saline) delivery


title: CEP2

description:
MCF7 Set 2 control, estrogen + progesterone treated.
mRNA
Sample_CEP2
Raw_Counts.RSEM.txt


title: A1ATD1 85

description: raw.csv

value: Day 40


title: Female Vehicle Group (91)


title: Female Morphine Group (92)


title: A1ATD1 84

description: raw.csv


title: fetalC2018_E3381-1_10X2_MixN2018_Acute 48 hours

value: Male


title: RP2

description:
MCF7 Set 2 REST knockdown, progesterone treated.
mRNA
Sample_RP2
Raw_Counts.RSEM.txt

value: Set 2 REST knockdown

value: progesterone


title: A1ATD1 88

description: raw.csv

value: T


title: Female Vehicle Group (85)


title: CE1

description:
MCF7 Set 1 control, estrogen treated.
mRNA
Sample_CE1
Raw_Counts.RSEM.txt

value: Set 1 control


title: fetalC2018_E3381-1_1X2_MixN2018_Acute 48 hours


title: fetalC2018_E3381-1_1000X2_MixN2018_Acute 48 hours


title: A1ATD1 83

description: raw.csv


title: Male Morphine Group (79)

value: serum


title: fetalC2018_E3381-1_DMSO2_MixN2018_Acute 48 hours

value: DMSO


title: CP2

description:
MCF7 Set 2 control, progesterone treated.
mRNA
Sample_CP2
Raw_Counts.RSEM.txt


title: A1ATD1 82

description: raw.csv


title: RP1

description:
MCF7 Set 1 REST knockdown, progesterone treated.
mRNA
Sample_RP1
Raw_Counts.RSEM.txt

value: Set 1 REST knockdown


title: Male Morphine Group (76)

value: 10 weeks of age


title: Male Morphine Group (77)


title: A1ATD1 81

description: raw.csv


title: CP1

description:
MCF7 Set 1 control, progesterone treated.
mRNA
Sample_CP1
Raw_Counts.RSEM.txt


title: A1ATD1 80

description: raw.csv


title: fetalC2018_E3381-1_T31_MixN2018_Acute 48 hours


title: fetalC2018_E3381-1_T3MixN1_MixN2018_Acute 48 hours


title: RV2

description:
MCF7 Set 2 REST knockdown, vehicle treated.
mRNA
Sample_RV2
Raw_Counts.RSEM.txt

value: vehicle


title: fetalC2018_E3381-1_BPA1X1_MixN2018_Acute 48 hours


title: A1ATD1 79

description: raw.csv

value: F


title: RV1

description:
MCF7 Set 1 REST knockdown, vehicle treated.
mRNA
Sample_RV1
Raw_Counts.RSEM.txt


title: A1ATD1 78

description: raw.csv


title: fetalC2018_E3381-1_BPA0.04X1_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors


title: A1ATD1 77

description: raw.csv


title: CV2

description:
MCF7 Set 2 control, vehicle treated.
mRNA
Sample_CV2
Raw_Counts.RSEM.txt


title: fetalC2018_E3381-1_VITC1_MixN2018_Acute 48 hours

value: VITC


title: CV1

description:
MCF7 Set 1 control, vehicle treated.
mRNA
Sample_CV1
Raw_Counts.RSEM.txt


title: Male Morphine Group (75)


title: A1ATD1 76

description: raw.csv


title: A1ATD1 75

description: raw.csv


title: fetalC2018_E3381-1_CNT1_MixN2018_Acute 48 hours

value: CNT

value: Acute 48 hours


title: Male Vehicle Group (70)

value: male


title: I-BET151_ATAC-2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the human hg38 reference genome assembly using Bowtie2 (v2.2.5) (Langmead et al., 2012) with options: --no-discordant --no-unal --no-mixed -X 2000 --local.
The BAM files were removed the null and not unmapped reads using sambamba(v0.7.1)(Tarasov et al., 2015) view with the default parameter settings.
The BAM files were removed the duplicated reads using sambamba(v0.7.1)(Tarasov et al., 2015) markdup with the default parameter settings.
For peak calling, parameters used were macs2 (v2.1.2) (Zhang et al., 2008) callpeak with parameter settings: -q 0.05 --nomodel --shift -100 --extsize 200. The peaks visualization in genome was showed by IGV software (Robinson et al., 2011).
The peaks annotations were performed with R package ChIPseeker (Yu et al., 2015) from the bioconductor project. Motif enrichment was done using HOMER with options: -fdr 0.05 -len 8,10,12.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamcoverage
Supplementary_files_format_and_content: peak text files

growth_protocol: PP cells were cultured in  basal medium (EF6): DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF and 10 μM 616452.

extract_protocol:
5×10^4 cells were collected and lysed using lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to collect cell nuclei. Then, nuclei were resuspended in the mixture containing 10 μl 5× TTBL, 5 μl TTE Mix V50 and 35 μl ddH2O. The mixture were incubated at 37°C for 30 min. Then, the fragments were purified by the standard processing of TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and VAHTS DNA Clean Beads (Vazyme N411).
The standard processing was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep Index Kit V2 for Illumina ® (Vazyme TD202). The library concentration was measured using Qubit dsDNA BR Assay Kit (Invitrogen) by Qubit (Invitrogen).

tag: cell line background

tag: source cell type

value: human embryonic stem cell (hESC) line

value: hPSC-derived pancreatic progenitor cells

value: 1 μM I-BET151 for 7 days


title: Male Vehicle Group (71)


title: fetalC2018_E3381-1_0.1X1_MixN2018_Acute 48 hours

tag: treatment

value: Male


title: DMSO_ATAC-2


title: fetalC2018_E3381-1_1X1_MixN2018_Acute 48 hours


title: hPSC-CMs_15_Orf9c OE

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W Walnut Street, R4 272

department: Department of Pediatrics

institute: Indiana University School of Medicine

data_processing:
Quality control for raw mRNA-seq data was generated by FastQC v0.11.5
Illumina adapter sequences and low-quality bases were trimmed by Trim Galore v0.4.5
High-quality paired-end reads was mapped to human genome (hg38) with the aligner STAR v2.7.2b
bam-filter in ngsutilsj v0.4.8 (https://compgen.io/ngsutilsj) was used to keep only properly and uniquely mapped paired reads (MAPQ ≥ 10) for downstream analysis
FeatureCounts from package subread v1.6.5 was employed for quantification of gene expression by summarizing mapped reads to corresponding genes according to GENECODE v31 annotation.
Analysis of differential expression genes (DEGs) was performed by edgeR v3.32.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include with raw read counts for every gene and every sample by featureCounts

source_name: cardiomyocytes

growth_protocol: All purified hESCs derived-cardiomyocytes are cultured in DMEM (no glucose) with 10% FBS.

extract_protocol:
Total RNAs are extracted by Qiagen RNeasy Mini Kit (250).
Purified mRNA by enriching the polyA RNA.
mRNA-seq by using altra-low mRNA-seq protocol

value: human pluripotent stem cell-derived cardiomyocytes

tag: genotype

value: Orf9c OE


title: Male Vehicle Group (69)

value: serum


title: 5_OA chondrocytes_Ctrl

city: Wien

first: Katharina

middle: M.

last: Pichler

state: Wien

address: Odoakergasse

department: Department of Orthopedics and Trauma Surgery

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Plus Labeling Assay User Manual (Fluidics Protocol FS450_0002)

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 1.1

source_name: OA chondrocytes, isolated, 24 h

label_protocol: 100ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Plus Kit (Catalog Number 902415, Affymetrix, Santa Clara, CA)

growth_protocol: Chondrocytes were isolated from femoral condyles and tibial plateaus and cultured in growth medium [DMEM GlutaMAX (Gibco) supplemented with 10% fetal calf serum (Biochrom), 1% penicillin/streptomycin (Gibco), and 0.1% amphotericin B (Sigma)] in a humidified atmosphere of 5% CO2/95% air at 37 °C.

extract_protocol: Total RNA was extracted according to the manufacturer's instructions (innuPREP RNA Mini Kit).

treatment_protocol: For treatment, chondrocytes were serum-starved overnight and then treated with 100µg/ml Galectin-4 for 24 h.

value: articular cartilage

tag: disease state

value: osteoarthritis


title: fetalC2018_E3381-1_100X1_MixN2018_Acute 48 hours

first: Nicolò

last: Caporale

address: Via Adamello, 16

institute: European Institute of Oncolology


title: hPSC-CMs_11_control

value: control


title: A1ATD1 72

description: raw.csv

tag: hipsc line

tag: differentiation day

value: Day 40

tag: transgene pattern

value: neg


title: fetalC2018_E3381-1_DMSO1_MixN2018_Acute 48 hours

value: Fetal brain cortical progenitors

tag: Stage

value: DMSO


title: A1ATD1 73

description: raw.csv

value: F


title: Male Vehicle Group (72)

value: 10 weeks of age


title: 4_OA chondrocytes_Gal4


title: A1ATD1 71

description: raw.csv


title: hPSC-CMs_6_control


title: A1ATD1 70

description: raw.csv


title: tolDC_input_DNA

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

data_processing:
read maping with Bowtie2
read filter with SAMtools
Peak calling was performed using SPP (with parameters –npeak=300000 –savr –savp -rf)
Irreproducible discovery rate (IDR) was used to filter peaks (IDR < 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: Input-normalized replicate-combined fold enrichment scores computed by MACS2 in bigWig format.

source_name: tolerogenic monocyte-derivated Dendritic Cells (TL)

growth_protocol: PBMCs were isolated using Ficoll-Paque gradient centrifugation. MOs were isolated from PBMCs using positive selection with MACS CD14 microbeads (Miltenyi Biotec). Cells were resuspended in RPMI Medium 1640 + GlutaMAXTM-1 (Gibco, Life Technologies) containing 10% fetal bovine serum, 100 unit’s/mL penicillin, and 100 μg/mL streptomycin. For TolDC differentiation, the medium was supplemented with 10 ng/mL human IL-4, 10 ng/mL GM-CSF (PeproTech), and 10 nM of Vitamin D3 or calcitriol (Sigma Aldrich)

extract_protocol:
Chromatin immunoprecipitation was performed using iDeal ChIP-seq kit for Transcription Factors (Diagenode) according to the manufacturer's instructions. Briefly, cells at day 3 of differentiation were cross-linked with 1% formaldehyde for 15 min and glycine added to quench (final concentration 125 mM, incubated for 5 min at room temperature). Cells were washed once with cold PBS, scraped off the plates and pelleted. To obtain a soluble chromatin extract, cells were resuspended in 1 ml LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1× complete protease inhibitor) and incubated rotating at 4 °C for 10 min. Samples were centrifuged, resuspended in 1 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1× complete protease inhibitor) and incubated rotating at 4 °C for 10 min. Finally, samples were centrifuged, resuspended in 1 ml LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100 and 1× complete protease inhibitor). Chromatin extracts were sonicated for 12.5 min using a Covaris. The lysates were incubated with anti-VDR antibody (12550, Cell Signaling) bound to 30 μl protein A or protein G Dynabeads and incubated overnight at 4 °C with 5% kept as input DNA. Magnetic beads were sequentially washed with low-salt buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 1 mM EDTA and 50 mM Tris-HCl), high-salt buffer (500 mM NaCl, 0.1% SDS, 1% Triton X-100, 1 mM EDTA and 50 mM Tris-HCl), LiCl buffer (150 mM LiCl, 0.5% sodium deoxycholate, 0.1% SDS, 1% Nonidet P-40, 1 mM EDTA and 50 mM Tris-HCl) and TE buffer (1 mM EDTA and 10 mM Tris-HCl). For ChIP–seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA and 200 mM NaCl) and incubated for 30 min at 65 °C. After centrifugation, the eluate was reverse-cross-linked overnight at 65 °C. The eluate was then treated with RNaseA for 1 h at 37 °C and with Proteinase K (Roche) for 1 h at 55 °C and the DNA was recovered using a Qiagen PCR purification kit.
reverse-crosslinked DNA was used to construct high-throughput sequencing libraries using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370).

tag: culture time (days)

value: 1,25-dihydroxyvitamin D3

tag: chip antibody


title: hPSC-CMs_10_Orf9c OE


title: A1ATD1 74

description: raw.csv


title: 5_OA chondrocytess_Gal4


title: A1ATD1 69

description: raw.csv


title: hPSC-CMs_5_Orf9c OE


title: tolDC_VDR_ChIPSeq_rep2

value: VDR (Cell Signaling, D2K6W, lot 3)


title: A1ATD1 68

description: raw.csv


title: tolDC_VDR_ChIPSeq_rep1


title: A1ATD1 67

description: raw.csv


title: D27 megakaryocyte culture sorted for progenitor cells, TAL1.1

description:
SIGAD6
D27.TAL1.1
Single cell RNA Seq
cDNA
counts.mtx

data_processing:
Quality of fastq files was assessed with Fastqc v0.11.3 and summarised with MultiQC v1.8.
Alignment and protein-coding gene quantification was performed using 10x cellranger v3.1.0.
The processing was performed with regard to the regular gene expression library (GSE166726).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.mtx: MatrixMarket of raw expression levels for cells.
Supplementary_files_format_and_content: meta.csv: Comma-separated file of cell sample identities.

source_name: A1ATD induced pluripotent stem cells

growth_protocol: Moreau et al., 2016. Megakaryocyte forward programming.

extract_protocol:
10X library preparation.
10X VDJ protocol.

treatment_protocol: Cells were stained with antibodies against MICB, PVR and CD42 and sorted using FACS Aria III, selecting viable cells by DAPI staining. These were directly prepared for 10X sequencing.

tag: cell line

tag: day of differentiation

value: Induced pluripotent stem cell-derived megakaryocytes

tag: sorted for

value: MICBhi, PVRhii, CD42lo

tag: enriched transgene


title: D27 megakaryocyte culture sorted for progenitor cells, TAL1.2

description:
SIGAB6
D27.TAL1.2
Single cell RNA Seq
cDNA
counts.mtx

tag: cell type


title: D27 megakaryocyte culture sorted for progenitor cells, pWPRE.2

description:
SIGAA6
D27.pWPRE.2
Single cell RNA Seq
cDNA
counts.mtx

value: GATA1, FLI1


title: DC_VDR_ChIPSeq_rep2

source_name: monocyte-derivated Dendritic Cells (DC)


title: A1ATD1 66

description: raw.csv

data_processing:
The quality of the data was assessed using FastQC, MultiQC
Reads were aligned using STAR v2.7.3a (parameters --outSAMtype BAM SortedByCoordinate)
Protein-coding gene quantification was performed using Subread featureCounts v2.0.0 (default parameters)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: csv file of raw expression levels

source_name: Forward programmed megakaryocytes

extract_protocol:
The single cells were sorted in 96-well plates containing cell lysis buffer (2.3mL of 0.2% Triton X-100 with RNase inhibitor) and frozen to -80°C before library preparation.
The method for single cell cDNA library making has been adapted from Smartseq2 for full-length RNAseq from single cells and Fluidigm (PMID: 24385147). Briefly, the reverse transcription was initiated with oligo-dT primers using SuperScript-II reverse transcriptase (Thermo Scientific) and supplemented with ERCC RNA Spike-In. The cDNA was then PCR amplified for 21 cycles using the KAPA HiFi Hotstart ReadyMix and IS primers (Kappa biosystems). After purification of the amplified cDNA, the indexed library was made using the Illumina Nextera XT DNA kit, 96 cells eventually pooled and library quality checked on an Agilent high sensitivity DNA chip before sequencing on one lane of an HiSeq-4000 (Illumina).

value: GFT


title: DC_VDR_ChIPSeq_rep1


title: A1ATD1 65

description: raw.csv


title: A1ATD1 64

description: raw.csv


title: 2_OA chondrocytes_Ctrl

tag: tissue


title: 2_OA chondrocytes_Gal4


title: 3_OA chondrocytes_Gal4


title: 3_OA chondrocytes_Ctrl


title: Induced pluripotent stem cell derived megakaryocytes on D20, TAL1

description:
D20.TAL1
Single cell RNA-Seq
cDNA
counts.mtx

data_processing:
Quality of fastq files was assessed with Fastqc v0.11.3 and summarised with MultiQC v1.8.
Alignment and protein-coding gene quantification were performed using 10x cellranger v3.1.0.
To maintain consistency between sequencing runs, alignment was performed by using only R2 strands, trimmed to 91 nt.
Cells with fewer than 200 unique features and cells with more than 25% of counts from mitochondrial genes were discarded from count matrix.
The processing was performed with regard to the regular gene expression library (GSE160604).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.mtx: MatrixMarket of raw expression levels for cells.
Supplementary_files_format_and_content: meta.csv: Comma-separated metadata for cells.

source_name: A1ATD1 induced pluripotent stem cells

growth_protocol: Moreau et al., 2016. Megakaryocyte forward programming by lentiviral transduction with 3 transcription factors and two cytokine combinations.

treatment_protocol: Cells were methanol fixed, as per 10X protocol, and stored at -80 degrees C. They were then rehydrated as per 10X protocol and submitted for library preparation.

tag: transgene library

tag: library batch

value: Batch 1


title: 1_OA chondrocytes_Ctrl


title: 1_OA chondrocytes_Gal4


title: 4_OA chondrocytes_Ctrl


title: MO_input_DNA

source_name: monocytes (MO)

tag: treatment


title: MO_VDR_ChIPSeq_rep1


title: MO_VDR_ChIPSeq_rep2


title: A1ATD1 63

description: raw.csv


title: D27 megakaryocyte culture sorted for progenitor cells

description:
D27
Single cell RNA-Seq
cDNA

data_processing:
Quality of fastq files was assessed with Fastqc v0.11.3 and summarised with MultiQC v1.8.
Alignment and protein-coding gene quantification was performed using 10x cellranger v3.1.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.mtx: MatrixMarket of raw expression levels for cells.


title: Induced pluripotent stem cell derived megakaryocytes on D20, wPRE

description:
D20.wPRE
Single cell RNA-Seq
cDNA
counts.mtx

value: wPRE


title: A1ATD1 61

description: raw.csv


title: D27 megakaryocyte culture sorted for progenitor cells, pWPRE.1

description:
SIGAC6
D27.pWPRE.1
Single cell RNA Seq
cDNA
counts.mtx


title: Induced pluripotent stem cell derived megakaryocytes on D15, TAL1

description:
D15.TAL1
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 62

description: raw.csv


title: hPSC-CMs_1_control

value: human pluripotent stem cell-derived cardiomyocytes

tag: genotype


title: DC_input_DNA


title: Differentiating megakaryocytes on D10, wPRE

description:
D10.wPRE
Single cell RNA-Seq
cDNA
counts.mtx

value: Differentiating megakaryocytes


title: A1ATD1 60

description: raw.csv


title: A1ATD1 57

description: raw.csv


title: A1ATD1 58

description: raw.csv


title: Differentiating megakaryocytes on D9, batch 2, TAL1

description:
D9.TAL1.2
Single cell RNA-Seq
cDNA
counts.mtx

value: Batch 2


title: Differentiating megakaryocytes on D10, TAL1

description:
D10.TAL1
Single cell RNA-Seq
cDNA
counts.mtx


title: Induced pluripotent stem cell derived megakaryocytes on D15, wPRE

description:
D15.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 56

description: raw.csv

value: Day 40


title: Differentiating megakaryocytes on D9, batch 2, wPRE

description:
D9.wPRE.2
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 55

description: raw.csv


title: Differentiating megakaryocytes on D9, TAL1

description:
D9.TAL1
Single cell RNA-Seq
cDNA
counts.mtx


title: Differentiating megakaryocytes on D8, batch 2, wPRE

description:
D8.wPRE.2
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 52

description: raw.csv


title: Differentiating megakaryocytes on D8, batch 2, TAL1

description:
D8.TAL1.2
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 53

description: raw.csv


title: A1ATD1 54

description: raw.csv


title: A1ATD1 50

description: raw.csv


title: A1ATD1 51

description: raw.csv


title: A1ATD1 49

description: raw.csv

value: GT


title: Differentiating megakaryocytes on D7, TAL1

description:
D7.TAL1
Single cell RNA-Seq
cDNA
counts.mtx


title: Differentiating megakaryocytes on D6, TAL1

description:
D6.TAL1
Single cell RNA-Seq
cDNA
counts.mtx


title: Differentiating megakaryocytes on D5, batch 2, TAL1

description:
D5.TAL1.2
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 46

description: raw.csv


title: A1ATD1 48

description: raw.csv


title: A1ATD1 59

description: raw.csv


title: Differentiating megakaryocytes on D6, wPRE

description:
D6.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: Differentiating megakaryocytes on D5, batch 2, wPRE

description:
D5.wPRE.2
Single cell RNA-Seq
cDNA
counts.mtx


title: Differentiating megakaryocytes on D5, TAL1

description:
D5.TAL1
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 45

description: raw.csv


title: Mix_miRNA

city: Shenyang

first: Zhiyong

last: Liu

state: Liaoning Province

address: Dongling Road 120

institute: Shenyang Agriculral University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: BRAD：Brassica_rapa_v3.0
Supplementary_files_format_and_content: tab-delimited text files include sequence and expression of all miRNAs

organism: Brassica rapa subsp. pekinensis

source_name: root, stem and leaf

growth_protocol: The DH ‘FT’ seeds were seeded in the greenhouse of Shenyang Agricultural University after vernalization at 4 ℃ for 20 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA).

treatment_protocol: The seedlings with four true leaves included roots, stems, and leaves (Mix), and anthers at different developmental stages (Ant) were sampled

value: whole seedlings with four true leaves included roots, stems, and leaves

tag: molecule subtype

value: Small RNA


title: A1ATD1 44

description: raw.csv

tag: hipsc line


title: PM 3

city: Xi'an

first: Yuan

last: Zhang

address: No. 620, West Chang'an Avenue, Chang'an District

institute: Shaanxi Normal University

data_processing:
STAR is used to align clean reads to reference genome.
HTSeq v0.6.0 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.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: excel file of dif expression analysis result with read count and fpkm

source_name: microglia

extract_protocol:
RNA from microglia was extracted using RNA Easy Fast Tissue/Cell Kit (Cat.#DP451)
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

value: microglia


title: Differentiating megakaryocytes on D5, wPRE

description:
D5.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 43

description: raw.csv

tag: differentiation day

tag: transgene pattern


title: Differentiating megakaryocytes on D9, wPRE

description:
D9.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: PM 2


title: Differentiating megakaryocytes on D7, wPRE

description:
D7.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 42

description: raw.csv


title: PM 1


title: A1ATD1 41

description: raw.csv


title: A1ATD1 47

description: raw.csv


title: Differentiating megakaryocytes on D4, wPRE

description:
D4.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: Differentiating mesoderm on D3, TAL1

description:
D3.TAL1
Single cell RNA-Seq
cDNA
counts.mtx

value: Differentiating mesoderm


title: Ctrl 3


title: Ctrl 2


title: A1ATD1 40

description: raw.csv


title: Differentiating mesoderm on D3, wPRE

description:
D3.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: S51a-RCB

city: Faridabad

first: Prasenjit

last: Guchhait

state: Haryana

address: Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad-Gurgaon Expressway, 3rd Milestone,

country: India

institute: Prasenjit Guchhait

data_processing:
We have used FastQC and MultiQC for quality check
STAR was used for alignment
DESeq2 was used for normalization and quantification of reads
DAVID, METASCAPE was used for pathway enrichment analysis
Galaxy was also used for raw count calculation
Genome_build: Hg19
Supplementary_files_format_and_content: raw counts

source_name: whole blood

extract_protocol:
Platelet rich plasma was separated from whole blood by centrifugation. Platelet pellet in Trizol was then used for RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols (NEB, USA)

value: Platelets

tag: disease

tag: disease state

value: Asymptomatic

value: whole blood


title: A1ATD1 39

first: Irina

address: Puddicombe Way

institute: University of Cambridge

description: raw.csv


title: S55a-RCB


title: Differentiating mesoderm on D2, TAL1

description:
D2.TAL1
Single cell RNA-Seq
cDNA
counts.mtx

tag: cell line


title: A1ATD1 38

description: raw.csv


title: Ant_miRNA

source_name: anther

value: anther


title: S45-RCB

value: Symptomatic


title: Differentiating megakaryocytes on D4, TAL1

description:
D4.TAL1
Single cell RNA-Seq
cDNA
counts.mtx

tag: day of differentiation


title: Differentiating mesoderm on D2, wPRE

description:
D2.wPRE
Single cell RNA-Seq
cDNA
counts.mtx


title: A1ATD1 37

description: raw.csv