title: HEK293, PGC-1α ΔRS-res, Dox 6 days, cytoplasmic, rep3

first: Simeon

middle: R.

last: Mihaylov

address: 1 Midland Road

institute: The Francis Crick Institute

description: PGC-1a dRS-res_cytoplasmic_Rep3

data_processing:
For sequence analysis, the nf-core/rnaseq, written in the Nextflow domain-specific language (ver. 22.04.0), was used to perform the primary analysis of the samples in conjunction with Singularity (ver. 3.6.4). The command used was “nextflow run nf-core/rnaseq --input design.csv -profile crick --outdir ${PWD}/mouse --aligner star_rsem --fasta $GENOME_DIR/genome/Homo_sapiens.GRCh38.dna_sm.toplevel.fa --gtf Homo_sapiens.GRCh38.107.gtf.gz”. Briefly, adapter and quality trimming was performed using Trim Galore!. The RSEM package in conjunction with the STAR alignment algorithm was used for the mapping and subsequent transcript-level counting of the sequenced reads with respect to the human GRCh38/hg38 genome and annotation. Differential analysis was performed using DESeq2. A P-value of <0.05 and a fold change of 0.5 < log2 FC < -0.5 were used as the significance threshold for the identification of differentially expressed genes. One replicate from each group for cytoplasmic RNA (WT-res CyT Rep2, ΔRS-res CyT Rep3) had to be removed for inconsistencies during principle-component analysis. Nuclear export targets were defined as transcripts which are not differentially changed in whole-cell sequencing (transcripts with 0.5 < log2 FC < -0.5 with p-value < 0.05 were removed) and significantly down-regulated in cytoplasmic sequencing (log2 FC < -0.5 with p-value < 0.05). Alternative splicing analysis was performed using Whippet.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes counts for each Sample

molecule: cytoplasmic RNA

source_name: Flp-In T-REx 293

growth_protocol: Cells were maintained in DMEM supplemented with 10% tetracyclin-free FBS and 1% Pen/Strep antibiotics.

extract_protocol:
For total (whole-cell) RNA, a single well was used, while for cytoplasmic RNA – 6 wells were pooled together. Samples were collected from three consecutive passages for each group. Total (whole-cell) and fractionated extracts were added to PureZOL™ and RNA was extracted using Direct-zol RNA Miniprep Plus kit (Zymo Research).
Extracted RNA was quality-checked on an Agilent 4200 TapeStation to ensure RNA integrity number (RIN) above 9.5. Sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, kit code KK8561) according to manufacturer’s instructions. Briefly, samples were normalised to 600 ng of RNA in a final volume of 10 ml. Samples were specifically depleted for both cytoplasmic (5S, 5.8S, 18S, and 28S), and mitochondrial (12S and 16S) rRNA species, and eluted in 20 ml of Fragment, Prime and Elute Buffer. The fragmentation reaction was run for 6 min at 94°C for a library insert size of 200-300 bp. Fragmented RNA underwent first and second strand cDNA synthesis according to manufacturer’s instructions. The KAPA Unique Dual-Indexed Adapters Kit (15 μM) (Roche- KK8727) stock was diluted to 7 mM as recommended by the manufacturer for a total RNA input of 600 ng. The adaptor ligation was carried out by adding 5 ml of diluted adaptor and 45 ml of ligation mix (50 ml of ligation buffer + 10 ml of DNA ligase) to 60 ml of cDNA. The ligation reaction was run for 15 mins at 20°C. To remove short fragments such as adapter dimers, two SPRISelect bead clean-ups were done (0.63x SPRI and 0.7x SPRI). To amplify the library, 25 ml of Kapa HiFi HotStart PCR master mix plus 5 ml of Library Amplification Primer mix was added to 20 ml cDNA and 7 PCR cycles were performed as recommended by the manufacturer for a total RNA input of 600 ng. Amplified libraries were purified via a SPRISelect 1x bead clean-up. The quality and fragment size distributions of the purified libraries was assessed by a 4200 TapeStation Instrument (Agilent Technologies).

treatment_protocol: The expression of the GOIs (PGC-1α WT-res and PGC-1α ΔRS-res) was induced with 1µg/ml doxycycline for 6 days prior to RNA extraction.

value: Flp-In T-REx 293

value: human embryonic kidney cells

value: deltaRS-res

value: doxycycline


title: HEK293, PGC-1α WT-res, Dox 6 days, cytoplasmic, rep3

status: Public on Jul 19 2023

type: SRA

city: London

country: United Kingdom

description: PGC-1a WT-res_cytoplasmic_Rep3

library_source: transcriptomic

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT-res

tag: treatment


title: VAST6958885 ViPS_nTD_D0.12h

city: Oxford

first: Henderson

last: Zhu

address: Oxford Vaccine Group, Old Road, Headington, Old Road, Headington

department: Oxford Vaccine Group, Department of Paediatrics

institute: University of Oxford

data_processing:
Sequences assigned to be ribosomal RNA, sex chromosome genes, mitochondrial RNA or haemoglobin were excluded from downstream analysis.
Gene features were counted using HTSeq (version 0.9.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries (genes without an abundance greater than 1 count per million in 9 or more samples) were filtered out.
Assembly: Sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38, using STAR (version 2.6.1d).
Supplementary files format and content: R file containig normalized abundance measurements

molecule: total RNA

source_name: whole blood

extract_protocol:
Total RNA was extracted from all samples using the Tempus Spin RNA Isolation kit (Life Technologies).
Libraries were prepared using a poly-A selection step to exclude ribosomal RNA species (read length: 75bp paired-end, stranded).

tag: tissue

value: whole blood

value: WT

value: ViPS

tag: sequencing pool


title: 9C_M_1673

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 9C_M_1672


title: VAST6958871 ViPS_nTD_D7


title: VAST6958870 Control_nTD_D0.12h

value: Control


title: brain organoids, Vehicle; rep1

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
Alignment with STAR (v2.6.1b)
Assigned count estimates to genes with RSEM (v1.3.1)
Assembly: GRCh38
Supplementary files format and content: raw counts

molecule: polyA RNA

source_name: brain organoids (day 6)

extract_protocol:
Total RNA was isolated from cells using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain organoids (day 6)

value: iPSC (AICS-0023)

tag: Sex

value: male

value: vehicle control


title: VAST6958869 ViPS_nTD_D7


title: VAST6958873 Control_nTD_D7


title: VAST6958868 Control_TD_TD


title: 9C_M_1670


title: HEK293, PGC-1α WT-res, Dox 6 days, cytoplasmic, rep1

description: PGC-1a WT-res_cytoplasmic_Rep1


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, cytoplasmic, rep1

description: PGC-1a dRS-res_cytoplasmic_Rep1


title: VAST6958876 ViPS_TD_D0.12h


title: VAST6958865 Control_TD_TD


title: VAST6958867 Control_TD_TD


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, whole-cell, rep3

description: PGC-1a dRS-res_whole-cell_Rep3


title: VAST6958866 Control_TD_TD


title: HEK293, PGC-1α WT-res, Dox 6 days, whole-cell, rep3

description: PGC-1a WT-res_whole-cell_Rep3


title: VAST6958863 Control_TD_D0.12h


title: 9C_M_1669


title: VAST6958864 Control_TD_D0.12h


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, cytoplasmic, rep2

description: PGC-1a dRS-res_cytoplasmic_Rep2


title: 9C_M_1667


title: VAST6958872 ViPS_TD_D0.12h


title: 9C_M_1668


title: VAST6958862 ViPS_nTD_D0.12h


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, whole-cell, rep2

description: PGC-1a dRS-res_whole-cell_Rep2


title: HEK293, PGC-1α WT-res, Dox 6 days, whole-cell, rep2

description: PGC-1a WT-res_whole-cell_Rep2


title: VAST6958860 ViPS_nTD_D0.12h


title: VAST6958861 ViPS_TD_D0.12h


title: HEK293, PGC-1α WT-res, Dox 6 days, cytoplasmic, rep2

description: PGC-1a WT-res_cytoplasmic_Rep2


title: 9C_M_1671


title: VAST6958858 Control_TD_D0.12h


title: VAST6958859 ViPS_nTD_D0.12h


title: 9C_M_1666


title: VAST6958857 Control_TD_TD


title: VAST6958856 ViPS_nTD_D0.12h


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, whole-cell, rep1

description: PGC-1a dRS-res_whole-cell_Rep1


title: 9C_M_1665


title: VAST6958852 Control_nTD_D7


title: VAST6958853 ViPS_TD_TD


title: VAST6958854 Control_TD_TD


title: 9C_M_1664


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, ChIP, rep3

data_processing:
For sequence analysis, the nf-core/rnaseq, written in the Nextflow domain-specific language (ver. 22.04.0), was used to perform the primary analysis of the samples in conjunction with Singularity (ver. 3.6.4). The command used was “nextflow run nf-core/chipseq --narrow_peak --input design.csv -profile crick --genome GRCh38  --macs_fdr 0.05”. To summarize, the pipeline performs adapter trimming using TrimGalore!, read alignment using BWA, filtering using SAMtools, BEDTools, BamTools, pysam, and picard-tools, normalised coverage track generation using BEDTools and bedGraphToBig-Wig, peak calling using MACS, annotation relative to gene features using HOMER, consensus peak set creation using BEDTools, differential binding analysis using featureCounts and DESeq2, and extensive QC and version reporting using MultiQC, FastQC, prseq, deepTools, and phantompeakqualtools. All data were processed relative to the human GRCh38/hg38 genome and annotation. DNA binding was regarded as significant when PGC1α versus Sham was log2FC>0.5, P-value<0.05. Promoter was defined as the region 5,000 bp up- or downstream of a transcription start site (TSS).
bigwig files are scaled to 1 million mapped reads using BEDTools and bedGraphToBigWig
peaks called with MACS2 using "--narrow"
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Induced cells were crosslinked sequentially starting with 2mM DSG (disuccinimidyl glutarate) for 45 min at RT, followed by DPBS washes and incubation with 1% methanol-free formaldehyde for 10 min at RT. Formaldehyde was quenched with 1.25M glycine for 5 min at RT, followed by cell collection in the precence of 10% BSA in DPBS. Cell pellets were washed, lysed and sonicated for 60 cycles (30 sec ON, 30 sec OFF) using Diagenode Bioruptor Plus on a high power setting. Sonicated samples were mixed with Dynabeads Protein G pre-incubated with 10µg monoclonal anti-FLAG M2 antibody rotating overnight at 4 degrees. Beads were washed and protein:DNA eluted followed by sequential RNase A and proteinase K treatments. Genomic DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo Research).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina with 500pg DNA starting material for input and ChIP samples. Adaptor-ligated samples were cleaned up and size selected with SPRISelect beads (Beckman Coulter) for a final insert size of ~320bp. Libraries were amplified using NEB Q5 Master Mix and NEBNext Multiplex Oligos for Illumina for 11 cycles. The quality of the purified libraries was assessed using an Agilent D1000 ScreenTape Kit on an Agilent 4200 TapeStation.

value: doxycycline, ChIP

tag: chip antibody

value: monoclonal anti-FLAG M2 (Sigma-Aldrich F1804)


title: 9C_M_1663


title: VAST6958851 Control_TD_TD


title: HEK293, PGC-1α WT-res, Dox 6 days, ChIP, rep3


title: 9C_M_1662


title: VAST6958849 ViPS_TD_D0.12h


title: VAST6958850 ViPS_TD_TD


title: HEK293, Sham, Dox 6 days, ChIP, rep3

value: Sham


title: 9C_M_1661


title: VAST6958848 Control_TD_D0.12h


title: VAST6958847 ViPS_TD_TD


title: VAST6958846 ViPS_TD_D0.12h


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, ChIP, rep2


title: VAST6958844 Control_nTD_D0.12h


title: VAST6958845 Control_TD_D0.12h


title: HEK293, PGC-1α WT-res, Dox 6 days, whole-cell, rep1

description: PGC-1a WT-res_whole-cell_Rep1


title: HEK293, PGC-1α WT-res, Dox 6 days, ChIP, rep2


title: 9C_M_1659


title: VAST6958855 Control_nTD_D7


title: VAST6958841 Control_nTD_D0.12h


title: VAST6958843 Control_TD_D0.12h


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, ChIP, rep1


title: 9C_M_1657


title: VAST6958840 ViPS_nTD_D7


title: VAST6958842 ViPS_nTD_D7


title: VAST6958838 Control_nTD_D7


title: 9C_M_1658


title: VAST6958839 Control_TD_TD


title: HEK293, PGC-1α WT-res, Dox 6 days, ChIP, rep1


title: 9C_M_1656


title: HEK293, Sham, Dox 6 days, ChIP, rep2


title: VAST6958837 ViPS_TD_D0.12h


title: HEK293, Sham, Dox 6 days, ChIP, rep1


title: 9C_M_1654


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, input, rep3

value: doxycycline, INPUT


title: VAST6958835 Control_TD_TD


title: VAST6958834 Control_TD_TD


title: 9C_M_1660


title: HEK293, PGC-1α WT-res, Dox 6 days, input, rep3

value: Flp-In T-REx 293


title: 9C_M_1653


title: VAST6958833 ViTCV_nTD_D7

value: ViTCV


title: VAST6958832 Control_TD_D0.12h


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, input, rep2

value: human embryonic kidney cells

value: deltaRS-res


title: HEK293, Sham, Dox 6 days, input, rep3


title: VAST6958831 ViPS_nTD_D0.12h


title: VAST6958830 Control_TD_D0.12h


title: VAST6958829 Control_TD_D0.12h


title: VAST6958828 Control_nTD_D0.12h


title: 9C_M_1650


title: VAST6958827 ViTCV_nTD_D14


title: VAST6958826 ViTCV_TD_TD


title: 9C_M_1649


title: HEK293, Sham, Dox 6 days, input, rep2


title: VAST6958824 ViTCV_TD_TD


title: VAST6958836 ViPS_nTD_D0.12h


title: 9C_M_1648


title: VAST6958823 ViTCV_nTD_D7


title: 9C_M_1647


title: VAST6958825 ViTCV_nTD_D7


title: VAST6958822 ViTCV_nTD_D7


title: HEK293, PGC-1α WT-res, Dox 6 days, input, rep1

value: WT-res


title: HEK293, PGC-1α ΔRS-res, Dox 6 days, input, rep1


title: 9C_M_1646


title: VAST6958820 Control_TD_TD

value: whole blood


title: VAST6958821 ViTCV_nTD_D7

value: WT


title: 9C_M_1652


title: VAST6958819 ViPS_nTD_D7

value: ViPS


title: HEK293, Sham, Dox 6 days, input, rep1


title: 9C_M_1645


title: VAST6958817 Control_TD_D0

value: Control


title: HEK293, PGC-1α WT-res, Dox 6 days, input, rep2


title: VAST6958816 ViPS_TD_D0


title: VAST6958815 ViPS_nTD_D0


title: 9C_M_1644


title: VAST6958814 ViPS_nTD_D0


title: VAST6958813 Control_TD_D0


title: 9C_M_1643


title: P209L neurons 3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: P209L neurons replicate 3

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a)
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Assembly: hg38
Supplementary files format and content: gene-based TPM txt file for all samples

source_name: iPSC line AN1.1

extract_protocol:
Cultured cells were treated with RNAlater-ICE (Thermo Fisher Scientific, AM7030), and total RNA was extracted with Qiagen’s RNeasy Universal plus mini kit (73404, Qiagen).
A sequencing library was prepared with a TruSeq Stranded Total RNA Kit (Illumina).

value: iPSC line AN1.1

value: iPSC-derived neurons

value: hnRNPH2 P209L

tag: time

value: 3 weeks differentiated


title: P209L neurons 2

description: P209L neurons replicate 2


title: VAST6958812 ViTCV_nTD_D0.12h


title: VAST6958811 Control_TD_D0


title: P209L neurons 1

description: P209L neurons replicate 1


title: 9C_M_1651


title: VAST6958810 ViTCV_nTD_D0.12h


title: VAST6958809 ViTCV_nTD_D0.12h


title: R206Q neurons 3

description: R206Q neurons replicate 3

value: hnRNPH2 R206Q


title: R206Q neurons 2

description: R206Q neurons replicate 2


title: 9C_M_1641


title: VAST6958807 ViTCV_nTD_D0.12h


title: VAST6958806 ViPS_TD_V7


title: VAST6958805 ViPS_TD_V1


title: R206W neurons 3

description: R206W neurons replicate 3

value: hnRNPH2 R206W


title: R206Q neurons 1

description: R206Q neurons replicate 1


title: VAST6958804 ViPS_nTD_V7


title: 9C_M_1639


title: 9C_M_1638


title: R206W neurons 2

description: R206W neurons replicate 2


title: VAST6958802 ViTCV_TD_D0.12h


title: VAST6958801 ViPS_TD_D0


title: VAST6958803 ViPS_TD_V0


title: 9C_M_1637


title: R206W neurons 1

description: R206W neurons replicate 1


title: VAST6958800 ViTCV_nTD_D0.12h


title: VAST6958799 Control_TD_D0


title: 9C_M_1642


title: KO neurons 2

description: KO neurons replicate 2

value: hnRNPH2 KO


title: 9C_M_1636


title: VAST6958808 ViTCV_nTD_D0.12h


title: VAST6958798 ViPS_nTD_D0.12h


title: VAST6958797 ViPS_TD_D0


title: 9C_M_1640


title: VAST6958794 ViPS_nTD_D0


title: 9C_M_1635


title: VAST6958795 Control_TD_D0


title: 9C_M_1633


title: VAST6958796 ViTCV_TD_D0.12h


title: KO neurons 1

description: KO neurons replicate 1


title: WT neurons 3

description: WT neurons replicate 3

value: hnRNPH2 WT


title: VAST6958793 ViPS_TD_V7


title: WT neurons 1

description: WT neurons replicate 1


title: 9C_M_1632


title: VAST6958790 ViPS_nTD_V1


title: VAST6958791 ViPS_nTD_V7


title: WT neurons 2

description: WT neurons replicate 2


title: VAST6958792 ViTCV_TD_TD


title: 9C_M_1631


title: VAST6958789 ViPS_nTD_D7


title: P209L iPSC 3

description: P209L iPSC replicate 3

value: iPSCs


title: VAST6958788 Control_TD_D0.12h


title: 9C_M_1630


title: VAST6958786 ViTCV_nTD_D7

value: ViTCV


title: VAST6958787 ViPS_TD_D0


title: 9C_M_1634


title: 9C_M_1629


title: P209L iPSC 1

description: P209L iPSC replicate 1


title: VAST6958785 ViTCV_TD_TD


title: 9C_M_1627


title: R206Q iPSC 3

description: R206Q iPSC replicate 3


title: VAST6958782 ViPS_nTD_V0


title: R206Q iPSC 2

description: R206Q iPSC replicate 2


title: VAST6958779 ViTCV_nTD_D7


title: VAST6958780 ViPS_nTD_V0


title: VAST6958784 ViPS_nTD_V1


title: VAST6958781 ViTCV_nTD_D7


title: 9C_M_1626


title: VAST6958783 ViPS_TD_V1


title: R206Q iPSC 1

description: R206Q iPSC replicate 1


title: VAST6958778 ViTCV_nTD_D7


title: VAST6958777 ViPS_TD_V7


title: R206W iPSC 3

description: R206W iPSC replicate 3


title: VAST6958776 Control_nTD_D0


title: 9C_M_1624


title: VAST6958775 ViPS_nTD_D0


title: P209L iPSC 2

description: P209L iPSC replicate 2


title: R206W iPSC 2

description: R206W iPSC replicate 2


title: 9C_M_1628


title: VAST6958774 ViPS_TD_D0


title: VAST6958773 Control_TD_TD


title: 9C_M_1622


title: VAST6958771 ViPS_TD_V0


title: R206W iPSC 1

description: R206W iPSC replicate 1


title: VAST6958772 ViPS_TD_V1


title: VAST6958770 ViPS_nTD_V7


title: VAST6958769 ViPS_TD_V0


title: VAST6958768 ViPS_TD_V1


title: VAST6958765 ViPS_TD_V0


title: 9C_M_1625


title: 9C_M_1620


title: KO iPSC 1

description: KO iPSC replicate 1


title: WT iPSC 2

description: WT iPSC replicate 2


title: VAST6958766 ViPS_TD_V0


title: 9C_M_1619


title: VAST6958767 ViPS_nTD_V1


title: WT iPSC 3

description: WT iPSC replicate 3


title: VAST6958762 Control_TD_D0


title: VAST6958764 Control_TD_D0


title: WT iPSC 1

description: WT iPSC replicate 1


title: VAST6958760 ViPS_nTD_D0


title: hiNSC_MF_D24_R1

city: Hong Kong

first: Mingxi

last: WENG

state: Not Applicable

address: L408A, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

country: Hong Kong

institute: School of Biomedical Sciences, The University of Hong Kong

data_processing:
Raw reads in fastq format were aligned to the hg38 transcriptome using RSEM (Bo Li et al., 2011) and bowtie 2.0 (Langmead et al., 2012) (with options: rsem-calculate-expression --bowtie2 --bowtie2-sensitivity-level very_sensitive --no-bam-output --estimate-rspd --paired-end).
Gene level alignment results of samples were merged and annotated using glbase3 (Hutchins et al., 2014).
Read counts per genes were calculated using RSEM and normalized to GC content using EDAseq (Risso et al., 2011). GC-normalized read counts no less than 20 in at least two samples were kept, leading to a final read count table.
The table was used to inspect individual gene expression, generate correlation heatmaps, perform principal components analysis (PCA) and analyze differentially expressed genes (DEGs).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files. The first column is the ensemble gene ID(ensg). The second column contains the official gene names(name). The rest of the columns contain the normalized read counts for each sample.

growth_protocol: To initiate hiNSC reprogramming, at day -1, 10 μL of concentrated lentiviruses of C-MYC, eSOX17FNV and M2rtTA were added to 1 × 105 EPCs resuspended in 0.5 ml of EPC medium in a 24-well plates. Spin-infection was performed at 900g, 32℃ for 60 min using a Eppendorf 5910R centrifuge with swing-out buckets for plates. Cells were then re-suspended without medium change and cultured for another 1 day. At day 0, the medium was change to fresh EPC medium containing 1 μg/mL Dox and incubated for another 2 days. At day 2, the transduced cells were replated into Matrigel-coated 12-well plates in StemSpan SFEM containing Dox and cultured for another 2 days. After day 4, the medium was half changed to fresh hNSC medium (DMEM/F12:Neurobasal (Gibco, #21103049) (1:1), 1% N2, 2% B27 (minus vitamin-A, Gibco, #12587010), 1% GlutaMAX, 1% penicillin-streptomycin, 20 ng/ml bFGF, 20 ng/ml EGF, 3 μM CHIR99021 (SelleckChem, #S2924), 5 μM SB431542 (SelleckChem, #S1067), 64 μg/ml L-ascorbic-acid-2-phosphate (LAAP, Sigma, #49752)) supplemented with 0.5 μM purmorphamine (PMA, SelleckChem, #S3042), 100 μM Sodium butyrate (NaB, Sigma, #B5887), and 5 μM tranylcypromine (Sigma, # P8511) every 2 days. PMA, NaB and tranylcypromine were only present for 10 days, Dox was present from day 0 to passage 5. hiNSC colonies were picked at day 20 and further expanded in Matrigel-coated plates in hNSC medium.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, #15596018) following the user guide quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. ffective concentration of library was determined by Q-PCR. Finally, the qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

value: hiNSC


title: 9C_M_1617


title: VAST6958759 Control_TD_D0


title: 9C_M_1623


title: KO iPSC 2

description: KO iPSC replicate 2


title: 9C_M_1618


title: VAST6958761 ViPS_nTD_D0


title: 9C_M_1621


title: hiNSC_KMF_D24_R1


title: VAST6958756 ViPS_TD_V7


title: VAST6958758 ViPS_nTD_V0


title: 9C_M_1616


title: VAST6958757 ViPS_TD_D0


title: hiNSC_KMFT_D22_R2


title: 9C_M_1615


title: hiNSC_KMFT_D22_R1


title: VAST6958755 ViPS_nTD_V7


title: VAST6958754 ViPS_nTD_D0.12h


title: 9C_M_1613


title: VAST6958752 ViPS_TD_V1


title: VAST6958750 ViPS_nTD_D0


title: 9C_M_1612


title: hiNSC_275_P7_R2


title: 9C_M_1614


title: VAST6958751 ViPS_nTD_V1


title: VAST6958749 Control_TD_D0.12h


title: hiNSC_275_P7_R1


title: 9C_M_1611


title: VAST6958748 ViPS_nTD_V0


title: VAST6958747 ViTCV_nTD_D0.12h


title: hiNSC_014_P8_R2


title: VAST6958746 Control_nTD_D0


title: 9C_M_1610


title: hiNSC_014_P8_R1


title: VAST6958743 ViTCV_nTD_D0.12h


title: hiNSC_014_P11_R2


title: 9C_M_1609


title: VAST6958744 ViPS_TD_D0


title: VAST6958745 ViTCV_nTD_D0.12h


title: 9C_M_1608


title: hiNSC_014_P11_R1


title: VAST6958753 ViTCV_nTD_D0.12h


title: S2ThiPSC_hNPC_R2

value: NPC


title: VAST6958742 Control_TD_D0


title: VAST6958740 Control_TD_D0


title: VAST6958738 Control_TD_D0


title: VAST6958737 ViTCV_TD_TD


title: 9C_M_1605


title: VAST6958735 ViPS_nTD_V7


title: S2ThiPSC_NPC_R1


title: EPC_C275_5_D12_R1

value: EPC


title: EPC_C275_5_D12_R2


title: VAST6958734 ViPS_nTD_V7

value: whole blood


title: VAST6958733 ViPS_TD_V7

value: WT


title: 9C_M_1603


title: VAST6958732 Control_nTD_D0


title: sh_3A_R3

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

data_processing:
Raw data (raw reads) of fastq format were processed through in-house perl scripts to remove reads containing adapter and poly-N  sequences and reads with low quality.
Paired-end clean reads were aligned to the  Homo Sapiens reference genome hg38 using Hisat2 v2.0.5.
Feature Counts software (v1.5.0-p3) was used to count the number of reads mapped per gene. Then, FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including the read count values for all 18 samples
Supplementary files format and content: tab-delimited text file including the fpkm values for all 18 samples

source_name: LNCaP

growth_protocol: LNCaP cells with shHOXB13-mediated knockdown were rescued with either WT HOXB13, HOXB13 3A phospho mutant (T8, T41 and S31 mutations to alanine) or empty vector (EV) control using an inducible system. Cells were first androgen deprived by culturing them in RPMI medium containing 2% charcoal-stripped serum (CSS) for 48h. Then, cells were treated with vehicle (EtOH, 0.1% final) or 10nM R1881 (Steraloids, Cat#E3164-000) in freshly added CSS medium for another 24h.

extract_protocol:
Total RNA was extracted from cells using a RNeasy Mini Kit (Qiagen, Cat#74106) with DNAse I digestion (Qiagen, Cat#79254).
Libraries were prepared at Novogene Bioinformatics Technology Co., Ltd using the NEBNext Ultra II RNA Library Prep kit according to manufacturer's recommendations and sequenced as paired-end 150bp reads on an Illumina NovaSeq 6000 sequencer.

value: LNCaP

value: Human prostate cancer

value: shHOXB13 rescued with HOXB13 3A phospho mutant (T8, T41, S31 mutations to alanine) + 24h 10nM R1881 treatment


title: 9C_M_1607


title: 9C_M_1600


title: sh_3A_R2


title: VAST6958739 ViPS_TD_V0

value: ViPS


title: VAST6958731 ViTCV_nTD_D7


title: VAST6958741 ViTCV_TD_D0.12h


title: VAST6958729 ViTCV_nTD_D7


title: 9C_M_1599


title: VAST6958730 ViPS_nTD_V7


title: VAST6958728 ViPS_nTD_D0


title: sh_3A_R1


title: 9C_M_1606


title: VAST6958736 ViPS_TD_D0


title: VAST6958727 ViTCV_TD_TD


title: VAST6958725 ViPS_TD_D0


title: sh_WT_R3

value: shHOXB13 rescued with WT HOXB13 + 24h 10nM R1881 treatment


title: VAST6958726 ViPS_nTD_D7


title: 9C_M_1597


title: 9C_M_1604


title: VAST6958724 ViPS_nTD_V1


title: sh_WT_R2


title: VAST6958722 ViPS_nTD_V1


title: 9C_M_1596


title: VAST6958723 ViPS_nTD_V1


title: VAST6958721 ViPS_nTD_V1


title: 9C_M_1595


title: VAST6958720 ViPS_nTD_V0


title: VAST6958719 ViTCV_TD_TD


title: sh_EV_R3

value: shHOXB13 rescued with EV control + 24h 10nM R1881 treatment


title: VAST6958718 ViPS_nTD_V0


title: VAST6958717 ViPS_TD_V1


title: 9C_M_1593


title: VAST6958716 ViPS_nTD_V0


title: sh_EV_R2


title: 9C_M_1592


title: VAST6958714 ViPS_TD_V0


title: VAST6958713 Control_TD_D0

value: Control


title: VAST6958712 ViPS_nTD_D0


title: 9C_M_1591


title: VAST6958715 ViPS_nTD_V0


title: VAST6958711 Control_nTD_D0


title: sh_3A_V3

value: shHOXB13 rescued with HOXB13 3A phospho mutant (T8, T41, S31 mutations to alanine) + 24h EtOH (0.1percent final) treatment


title: sh_3A_V2


title: VAST6958710 Control_TD_D0


title: 9C_M_1598


title: sh_3A_V1


title: VAST6958707 ViTCV_nTD_D0.12h


title: VAST6958708 ViTCV_nTD_D0.12h


title: VAST6958706 ViPS_TD_V7


title: sh_WT_V3

value: shHOXB13 rescued with WT HOXB13 + 24h EtOH (0.1percent final) treatment


title: sh_EV_R1


title: sh_WT_R1


title: 9C_M_1594


title: VAST6958705 ViTCV_TD_D0.12h


title: VAST6958704 ViPS_TD_V7


title: sh_WT_V2


title: sh_WT_V1


title: sh_EV_V3

value: shHOXB13 rescued with EV control + 24h EtOH (0.1percent final) treatment


title: 9C_M_1585


title: VAST6958700 ViPS_TD_V0


title: 9C_M_1590


title: VAST6958703 ViPS_TD_V1


title: sh_EV_V2


title: 9C_M_1586


title: 9C_M_1589


title: VAST6958698 ViPS_TD_V1


title: VAST6958709 Control_TD_D0


title: sh_EV_V1


title: VAST6958699 ViTCV_TD_D0.12h


title: 9C_M_1588


title: 9C_M_1584


title: VAST6958701 ViPS_nTD_D0.12h


title: VAST6958697 ViTCV_nTD_D0


title: 9C_M_1583


title: VAST6958695 ViTCV_TD_TD


title: VAST6958694 ViTCV_nTD_D0


title: 9C_M_1582


title: 9C_M_1587


title: VAST6958693 ViTCV_nTD_D7


title: NLSKD_R3

data_processing:
Raw data (raw reads) of fastq format were processed through in-house perl scripts to remove reads containing adapter and poly-N  sequences and reads with low quality.
Paired-end clean reads were aligned to the  Homo Sapiens reference genome hg38 using Hisat2 v2.0.5.
Feature Counts software (v1.5.0-p3) was used to count the number of reads mapped per gene. Then, FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including the read count values for all 30 samples
Supplementary files format and content: tab-delimited text file including the fpkm values for all 30 samples

growth_protocol: LNCaP cells with shmTOR-mediated knockdown were rescued with either WT-mTOR, NES-mTOR (nuclear export signal tagged), NLS-mTOR (nuclear localization signal tagged), NLS-mTOR D2357E (NLS-mTOR with a kinase dead mutation; NLS-mTORKD) or empty vector (EV) control using an inducible system. Cells were first androgen deprived by culturing them in RPMI medium containing 2% charcoal-stripped serum (CSS) for 48h. Then, cells were treated with vehicle (EtOH, 0.1% final) or 10nM R1881 (Steraloids, Cat#E3164-000) in freshly added CSS medium for another 24h.

value: shmTOR rescued with NLS-mTOR (D2357E) + 24h 10nM R1881 treatment


title: NLSKD_R1


title: VAST6958702 ViTCV_TD_D0.12h

value: ViTCV


title: VAST6958696 ViTCV_TD_D0


title: NLSKD_R2


title: 9C_M_1581


title: 9C_M_1580


title: VAST6958692 ViTCV_nTD_D0


title: VAST6958691 ViTCV_nTD_D0


title: NLS_R3

value: shmTOR rescued with NLS-mTOR + 24h 10nM R1881 treatment


title: 9C_M_1579


title: VAST6958688 ViPS_TD_V7


title: VAST6958689 ViTCV_nTD_D7


title: VAST6958687 ViTCV_nTD_D7


title: 9C_M_1578


title: NLS_R1


title: NLS_R2


title: VAST6958684 ViPS_nTD_D0


title: VAST6958683 Control_TD_D0


title: 9C_M_1577


title: VAST6958686 ViTCV_nTD_D7


title: NES_R3

value: shmTOR rescued with NES-mTOR + 24h 10nM R1881 treatment


title: NES_R2


title: 9C_M_1576


title: NES_R1


title: VAST6958680 ViTCV_TD_D0


title: VAST6958690 ViPS_nTD_V7


title: VAST6958681 ViTCV_nTD_D0


title: 9C_M_1574


title: VAST6958682 ViTCV_nTD_D7


title: 9C_M_1575


title: VAST6958677 ViPS_nTD_V0


title: WT_R3

value: shmTOR rescued with WT-mTOR + 24h 10nM R1881 treatment


title: WT_R2


title: 9C_M_1573


title: VAST6958676 ViPS_nTD_V7

value: whole blood


title: VAST6958678 ViPS_TD_V1

value: WT


title: VAST6958685 ViPS_TD_V0


title: VAST6958674 NA_not_challenged_D0


title: VAST6958675 ViTCV_nTD_D0


title: WT_R1

value: LNCaP


title: 9C_M_1572


title: VAST6958673 ViTCV_nTD_D0


title: 9C_M_1571


title: VAST6958671 ViPS_nTD_D0


title: EV_R3

value: Human prostate cancer

value: shmTOR rescued with EV control + 24h 10nM R1881 treatment


title: 9C_M_1570


title: VAST6958679 ViPS_nTD_V1

value: ViPS


title: VAST6958672 ViTCV_TD_D0


title: EV_R1


title: EV_R2


title: 9C_M_1569


title: VAST6958670 ViTCV_nTD_D0.12h


title: VAST6958667 Control_TD_D0


title: 9C_M_1568


title: VAST6958665 ViTCV_nTD_D0


title: VAST6958664 ViTCV_nTD_D0


title: VAST6958666 ViTCV_TD_D0


title: NLSKD_V3

value: shmTOR rescued with NLS-mTOR (D2357E) + 24h EtOH (0.1percent final) treatment


title: VAST6958663 ViTCV_nTD_D0


title: 9C_M_1567


title: NLSKD_V2


title: 9C_M_1566


title: VAST6958662 ViTCV_nTD_D0.12h


title: VAST6958661 ViPS_nTD_V1


title: VAST6958660 ViTCV_nTD_D0.12h


title: 9C_M_1565


title: 9C_M_1564


title: VAST6958659 ViPS_nTD_V0


title: NLS_V3

value: shmTOR rescued with NLS-mTOR + 24h EtOH (0.1percent final) treatment


title: NLS_V2


title: VAST6958657 ViTCV_TD_V7


title: VAST6958658 ViTCV_nTD_D0.12h


title: VAST6958669 ViTCV_TD_D0.12h


title: 9C_M_1563


title: VAST6958668 ViTCV_nTD_D0.12h


title: VAST6958656 ViTCV_nTD_V7


title: NLS_V1


title: VAST6958655 ViPS_nTD_D7


title: NES_V3

value: shmTOR rescued with NES-mTOR + 24h EtOH (0.1percent final) treatment


title: 9C_M_1562


title: VAST6958653 ViTCV_TD_TD


title: VAST6958654 ViTCV_nTD_V7


title: VAST6958652 ViTCV_nTD_V7


title: VAST6958650 ViTCV_nTD_V7


title: VAST6958651 ViTCV_nTD_V7


title: 9C_M_1561


title: NES_V2


title: NLSKD_V1


title: NES_V1


title: VAST6958648 ViTCV_nTD_V7


title: 9C_M_1559


title: VAST6958647 Control_TD_TD

value: Control


title: VAST6958646 Control_TD_D0.12h


title: VAST6958645 ViPS_nTD_D0.12h


title: VAST6958644 ViTCV_nTD_V1


title: WT_V3

value: shmTOR rescued with WT-mTOR + 24h EtOH (0.1percent final) treatment


title: WT_V2


title: VAST6958643 ViTCV_TD_D0.12h


title: 9C_M_1554


title: 9C_M_1556


title: EV_V3

value: shmTOR rescued with EV control + 24h EtOH (0.1percent final) treatment


title: 9C_M_1555


title: VAST6958641 NA_not_challenged_D0


title: VAST6958642 ViTCV_TD_V1


title: EV_V2


title: VAST6958640 Control_TD_TD


title: WT_V1


title: VAST6958639 ViTCV_nTD_V1


title: 9C_M_1551


title: VAST6958638 ViTCV_nTD_V1


title: 9C_M_1553


title: VAST6958649 ViTCV_TD_V7


title: 9C_M_1550


title: VAST6958636 ViTCV_TD_D0


title: EV_V1


title: 9C_M_1557


title: VAST6958635 ViPS_TD_TD


title: 9C_M_1549


title: Y459673

city: Shanghai

first: Bozhong

last: Shi

address: 1678, Dongfang road, Pudong district

country: China

institute: Shanghai Children's Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: heart

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: heart

value: high Kyn


title: VAST6958634 ViTCV_nTD_D0

value: ViTCV


title: VAST6958632 ViTCV_nTD_V0


title: VAST6958633 ViTCV_nTD_D0


title: Z460578

description: 10x Genomics


title: VAST6958631 ViTCV_nTD_V1


title: 9C_M_1548


title: W456283

description: 10x Genomics

value: normal Kyn


title: 9C_M_1547


title: VAST6958628 ViTCV_nTD_V0


title: 9C_M_1546


title: VAST6958627 ViTCV_nTD_V1


title: VAST6958629 ViTCV_nTD_V0


title: 9C_M_1545


title: VAST6958626 ViTCV_nTD_V0


title: VAST6958625 ViTCV_nTD_V0


title: Drug Resistant Tuberculosis 4

type: RNA

city: Chennai

first: Ramalingam

last: Bethunaickan

state: Tamil Nadu

address: No.1.  Mayor Satya murthy Road, Chetpet

department: Immunology

country: India

institute: ICMR-National Institute for Research in Tuberculosis

hyb_protocol: Total RNA was processed using the Nanostring nCounter v3.0a array.

scan_protocol: Hybridized molecules are loaded to Nanostring sprint catridge and loaded onto nCounter SPRINT machine for scanning the barcodes. Raw counts data (.RCC) was retrieved from the machine after the scanning completes.

data_processing:
Raw data were normalized using nSolver 4.0 software. Normalization of the raw data was performed using the geometric mean of positive controls and top 100 highly expressed miRNAs (CV% < 50) as per the instructions in the manual (nCounter Data Analysis Guidelines for miRNA (LBL-C0046-01) and nSolverTM 4.0 Analysis Software User Manual (MAN-C0019-08)).
NSolver 4.0 software was used to compute Normalized counts.

label: not provided

source_name: Drug Resistant Tuberculosis

label_protocol: NanoString uses combination of oligonucleotide based barcodes. Each probe hybridising the miRNAs will be unique with combination of color dye combination which are barcoded barcodes.

extract_protocol: Total RNA including miRNA was isolated from the sorted monocytes (Range: 1 to 2.8 million cells) in RLT buffer using Phenol-Chloroform and Qiagen miRNAeasy mini kit (Cat#217004). Samples were extracted with standard Phenol-chloroform mixture. Aqueous phase obtained after centrifugation was mixed with 700 µl of QIAzol Lysis reagent and mixed well. Lysate was incubated at room temperature for 5 minutes and 140 µl of chloroform was added for phase separation. Rest of the protocol was followed as per manufacturer’s guidelines. RNA was eluted in 20µl of nuclease free water (Ambion, Cat # AM9932). Quantitation was performed using Qubit RNA HS assay (Invitrogen, Cat # Q32855) kit and also qualitatively analysed on Agilent 2100 bioanalyzer nano chip (Agilent, Cat # 5067-1511). 100ng of total RNA was used for miRNA assay.

value: blood

tag: gender

value: Female


title: Drug Resistant Tuberculosis 5

description: Poor ligation QC, Not used for normalization.

value: Male


title: VAST6958623 ViTCV_TD_V1

value: whole blood

value: WT


title: Drug Resistant Tuberculosis 3


title: VAST6958622 ViPS_nTD_D0


title: Drug Resistant Tuberculosis 6


title: 9C_M_1544


title: VAST6958637 ViTCV_nTD_V1


title: VAST6958621 ViTCV_TD_V0


title: Drug Resistant Tuberculosis 2


title: 9C_M_1542


title: VAST6958620 ViPS_nTD_V1


title: T485058

description: 10x Genomics


title: VAST6958630 Control_TD_TD


title: Drug Resistant Tuberculosis 1


title: 9C_M_1541


title: VAST6958619 ViPS_TD_TD


title: VAST6958618 ViPS_nTD_V0


title: 9C_M_1540


title: VAST6958616 Control_TD_TD


title: VAST6958624 ViTCV_TD_D0


title: VAST6958615 ViTCV_nTD_V0


title: Drug Sensitive Tuberculosis 6

source_name: Drug Sensitive Tuberculosis


title: 9C_M_1538


title: VAST6958612 ViTCV_TD_V7


title: 9C_M_1543


title: 9C_M_1539


title: VAST6958614 ViPS_nTD_V7


title: 9C_M_1537


title: VAST6958611 ViPS_nTD_D7


title: Drug Sensitive Tuberculosis 4


title: Drug Sensitive Tuberculosis 5


title: VAST6958608 ViTCV_nTD_V7


title: Drug Sensitive Tuberculosis 3


title: Drug Sensitive Tuberculosis 2


title: VAST6958610 ViTCV_nTD_V7


title: 9C_M_1535


title: 9C_M_1536


title: 9C_M_1534


title: VAST6958606 ViTCV_TD_V7


title: Latent Tuberculosis 6

source_name: Latent Tuberculosis


title: VAST6958603 ViTCV_TD_V0


title: VAST6958604 ViTCV_nTD_V1


title: 9C_M_1533


title: Latent Tuberculosis 5


title: VAST6958613 ViTCV_nTD_V7


title: VAST6958602 ViTCV_nTD_V0


title: VAST6958601 ViPS_nTD_V0


title: VAST6958609 ViTCV_TD_D0


title: 9C_M_1532


title: VAST6958607 Control_nTD_D7


title: VAST6958600 ViTCV_nTD_V1


title: 9C_M_1530


title: 9C_M_1531


title: VAST6958597 ViTCV_TD_V1


title: VAST6958598 ViPS_nTD_V1


title: Latent Tuberculosis 1


title: VAST6958595 ViTCV_nTD_V0


title: Latent Tuberculosis 3


title: VAST6958594 ViTCV_nTD_V0


title: VAST6958596 NA_not_challenged_V1


title: Latent Tuberculosis 2


title: Latent Tuberculosis 4


title: VAST6958599 ViTCV_nTD_V1


title: 9C_M_1529


title: VAST6958605 ViTCV_TD_V1


title: Drug Sensitive Tuberculosis 1


title: 9C_M_1528


title: VAST6958593 ViTCV_TD_V0


title: VAST6958591 ViTCV_nTD_V0


title: VAST6958617 ViTCV_TD_V0


title: VAST6958590 ViTCV_nTD_V7


title: 9C_M_1527


title: VAST6958589 ViTCV_nTD_V1


title: Healthy Control 5

source_name: Healthy Control


title: VAST6958588 Control_TD_D0.12h


title: Healthy Control 4


title: 9C_M_1525


title: VAST6958587 ViTCV_TD_V7


title: VAST6958586 ViPS_TD_D0.12h


title: Healthy Control 3


title: Healthy Control 6


title: VAST6958585 ViTCV_TD_V7


title: Healthy Control 2


title: Healthy Control 1


title: VAST6958582 ViTCV_nTD_D0


title: VAST6958584 ViPS_TD_D0.12h


title: 9C_M_1524


title: VAST6958592 NA_not_challenged_V0


title: 9C_M_1526


title: VAST6958581 ViPS_nTD_V7


title: 9C_M_1521


title: 9C_M_1522


title: VAST6958583 NA_not_challenged_V7


title: VAST6958579 ViTCV_nTD_D0


title: 9C_M_1520


title: VAST6958578 Control_nTD_D0.12h


title: VAST6958577 ViTCV_nTD_D0


title: VAST6958576 Control_TD_D0.12h


title: VAST6958574 Control_TD_D0.12h


title: VAST6958573 ViTCV_TD_V7


title: 9C_M_1518


title: 9C_M_1517


title: VAST6958580 ViTCV_TD_D0


title: VAST6958572 ViTCV_TD_D0.12h


title: 9C_M_1516


title: VAST6958571 ViTCV_nTD_D0


title: VAST6958569 ViTCV_nTD_V1


title: VAST6958575 ViTCV_nTD_D0


title: Lung_Mitsui_High_Day180_rep6

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description: Gene expression in lung of rat exposed to Mitsui (1.5 mg/m3) 180 days post exposure

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 6 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned within 3 hours after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 12.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)

organism: Rattus norvegicus

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 180, replicate 6

label_protocol: For each of the 72 samples (6 control, 6 exposed rats to low dose, 6 exposed rats to medium dose and 6 exposed rats to high dose per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction. Dye incorporation and cRNA yield and quality were checked by spectrophotometry.

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7 , Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to Mitsui (Low dose: 0.15 mg/m3, Medium dose: 0.5 mg/m3, High dose: 1.5 mg/m3).

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of instillation)


title: 9C_M_1515


title: VAST6958568 ViPS_nTD_D0.12h

value: ViPS


title: 9C_M_1514


title: VAST6958570 ViTCV_TD_V1


title: VAST6958567 ViTCV_nTD_V1


title: VAST6958565 ViTCV_nTD_D7


title: VAST6958566 ViTCV_TD_V1


title: VAST6958564 ViTCV_nTD_V0


title: 9C_M_1519


title: GFP+, tdTomato+ and GFP+tdTomato+ both eplithelial and mesenchymal cells in tooth bud

city: Houston

first: Mizuki

last: NAGATA

state: TX

address: 7500 Cambridge St

department: Orthodontics

institute: UTHealth

description: Postnatal day 6

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: mm10_trans_nono
Supplementary files format and content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Mandibular molars

extract_protocol:
Mandibular molars were extracted, tooth buds were enzymatically dissociated and GFP+, tdTomato+ and GFP+tdTomato+ cells were FACS-isolated. ~10,000 cells were loaded onto 10X Genomic Chromium platform
10X Genomic Chromium Single Cell 3' v3 Libraries

value: Mandibular molars

value: Gli1-GFP; PTHrP-creER; R26R(tdTomato/+)


title: Lung_Mitsui_High_Day180_rep3

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 180, replicate 3


title: Lung_Mitsui_High_Day180_rep5

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 180, replicate 5


title: Lung_Mitsui_High_Day180_rep2

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 180, replicate 2


title: Lung_Mitsui_High_Day180_rep4

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 180, replicate 4


title: VAST6958562 ViTCV_nTD_V0


title: VAST6958561 ViPS_nTD_D7


title: Lung_Mitsui_High_Day180_rep1

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 180, replicate 1


title: VAST6958560 ViTCV_TD_V0

source_name: whole blood


title: VAST6958558 ViPS_nTD_V1


title: Lung_Mitsui_Medium_Day180_rep5

description: Gene expression in lung of rat exposed to Mitsui (0.5 mg/m3) 180 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 180, replicate 5


title: VAST6958556 ViTCV_TD_V0


title: VAST6958557 ViPS_nTD_V0


title: VAST6958554 Control_TD_TD

value: Control


title: VAST6958563 ViTCV_nTD_D7


title: Lung_Mitsui_Medium_Day180_rep4

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 180, replicate 4


title: Tre2

city: Guang zhou

first: zhun

last: sun

address: Xinzao , Panyu District, Guangzhou

institute: Guang zhou medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm38.p5
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: lung

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: lung

value: IL-10 B-KO

value: LPS


title: Tre3


title: Tre4


title: VAST6958555 NA_not_challenged_V1


title: Tre5


title: Tre6


title: VAST6958553 NA_not_challenged_V0


title: Tre1


title: VAST6958552 ViTCV_TD_D0

value: ViTCV


title: Lung_Mitsui_Medium_Day180_rep6

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 180, replicate 6


title: con6

value: IL-10 B-WT


title: VAST6958551 ViPS_nTD_D0


title: Lung_Mitsui_Medium_Day180_rep2

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 180, replicate 2


title: Lung_Mitsui_Medium_Day180_rep1

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 180, replicate 1


title: VAST6958559 ViTCV_TD_V1


title: Lung_Mitsui_Low_Day180_rep4

description: Gene expression in lung of rat exposed to Mitsui (0.15 mg/m3) 180 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 180, replicate 4


title: con5


title: Lung_Mitsui_Low_Day180_rep6

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 180, replicate 6


title: Lung_Mitsui_Medium_Day180_rep3

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 180, replicate 3


title: VAST6958549 ViTCV_nTD_V7


title: VAST6958548 ViTCV_nTD_V7


title: con3


title: con4


title: VAST6958544 ViTCV_nTD_V7


title: VAST6958546 ViTCV_TD_V0


title: VAST6958542 ViPS_nTD_D0.12h


title: con2


title: VAST6958540 ViTCV_nTD_D0.12h


title: VAST6958543 ViTCV_nTD_D0.12h


title: VAST6958545 ViTCV_nTD_V7


title: VAST6958539 ViTCV_nTD_V7


title: VAST6958538 Control_TD_D0.12h


title: VAST6958541 ViTCV_nTD_V1


title: VAST6958547 ViTCV_TD_V7


title: VAST6958537 ViTCV_nTD_V1


title: Lung_Mitsui_Low_Day180_rep5

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 180, replicate 5


title: VAST6958536 ViTCV_nTD_V1


title: Lung_Mitsui_Low_Day180_rep1

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 180, replicate 1


title: Lung_Mitsui_Low_Day180_rep3

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 180, replicate 3


title: H3K27Ac ChIP, E15.5 BAT

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

data_processing:
Reads were aligned to the reference genome GRCm38 using Bowtie2 v.2.4.2 with parameters "-p 100 -N 1".
Mapped reads were extracted into BAM files using Samtools v.1.6 with parameters "view -bSF4". The BAM files are sorted with "samtools sort".
Duplicate reads are removed from each sample with "samtools rmdup". Reads that cannot be mapped uniquely are removed with "samtools view -bq 1".
From each sample Homer v.4.11.1 was used to make tag directories from BAM files with makeTagDirectory "-single". For Gata6, peaks were called with Homer's findPeaks with parameters "-size 200". The IgG sample was used as control. For H3K27ac, peaks were called with "findPeaks -style histone".
BED files are extracted from Homer's peak files using Homer's pos2bed.pl. Bigwig files were created from Homer's tag directories using Homer's makeUCSCfile with parameters "-o auto".
Assembly: CRCm38
Supplementary files format and content: bigWig, BED

source_name: Brown adipose tissue

extract_protocol:
Dissected whole embryonic interscapular BAT was pooled and approximately 65mg of tissue was fixed with 1% methanol-free formaldehyde for 10 minutes. After quenching, nuclei were isolated using a hypotonic buffer and Kimble dounce homogenizer. Nuclei were lysed in SDS buffer and chromatin was sonicated using an Active Motif EpiShear at 20% amplitude for 3 minutes with cycles of 15 sec ON 20 sec OFF to obtain fragments ranging from 200-600bp. Fragmented chromatin was incubated with 1 μg of antibody overnight at 4 C and bound to protein A/G magnetic beads for pull-down.
ChIP-seq libraries were prepared using the KAPA Hyperprep Kit and library barcodes were from the KAPA Unique Dual-Index kit. Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were cleaned up using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated by Azenta/Genewiz with Agilent Tapestation.

value: Brown adipose tissue

value: Active Motif #39133


title: Lung_Mitsui_Control_Day180_rep6

description: Gene expression in lung of control rat (filtered air) 180 days post exposure

source_name: Rat, Lung, Mitsui, Control, Day 180, replicate 6


title: Lung_Mitsui_Control_Day180_rep4

source_name: Rat, Lung, Mitsui, Control, Day 180, replicate 4


title: VAST6958534 ViTCV_TD_TD

value: whole blood


title: Lung_Mitsui_Control_Day180_rep3

source_name: Rat, Lung, Mitsui, Control, Day 180, replicate 3


title: IgG ChIP, E15.5 BAT

value: WT

value: Cell Signaling Technollgies #2729S


title: GATA6 ChIP, E15.5 BAT

value: Cell Signaling Technollgies #5851S


title: E14.5 embryo, Gata6-WT

data_processing:
Reads from sequencing runs corresponding to a given sample were pooled and aligned using Cell Ranger software (10x Genomics).
Assembly: mm10
Supplementary files format and content: HDF5 files containing count matrices

source_name: Dorsal upper back

extract_protocol:
Dorsal back tissue at the forelimb level was dissected and spinal cord and ribs were removed as much as possible. Tissue from each embryo was individually minced and digested with Type I Collagenase: 0.6mg ml-1 (Worthington Biochemical Corp) and Dispase II: 2.4mg ml-1 (Roche). Samples were placed at 37 °C for 45min, vortexed every 15 min and quenched with complete medium (DMEM/10% FBS). Dissociated cells were suspended using a P1000 pipette and filtered through a 100-μm filter. Cells were then pelleted at 400g for 4 min, and red blood cells were lysed in 155 mM NH4Cl, 12 mM NaHCO3 and 0.1 mM EDTA for 4 min. An equal volume of complete medium was added, and the cells were filtered through a 40-μm filter for downstream analyses. 5 control embryos and 6 mutant embryos were separately pooled in FACS buffer (HBSS, 3% 0.45 µM filtered FBS; Thermo Fisher) and sorted to select for live cells.
Single cell libraries were prepared using Chromium Next GEM Single Cell 3' v3.1 with Dual Index and sequenced on Illumina NovaSeq6000 by CHOP High Throughput Sequencing Core. Reads were aligned using Cell Ranger Count v7.0.1 through the 10x Genomics Cloud Analysis website with the following options: check_library_compatibility: true, chemistry: auto, include_introns: false, Reference: Mouse (mm10) 2020-A.

value: Dorsal upper back


title: Lung_Mitsui_Control_Day180_rep5

source_name: Rat, Lung, Mitsui, Control, Day 180, replicate 5

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of instillation)


title: VAST6958531 ViTCV_nTD_V0

source_name: whole blood


title: VAST6958532 ViTCV_nTD_V0


title: E14.5 embryo, Gata6-Myf5KO


title: Lung_Mitsui_Control_Day180_rep2

source_name: Rat, Lung, Mitsui, Control, Day 180, replicate 2


title: VAST6958533 ViTCV_nTD_V1


title: P209L 3

description: P209L replicate 3

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a)
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Assembly: mm10
Supplementary files format and content: gene-based TPM txt file for all samples

source_name: Cortex

extract_protocol:
Cortex was dissected, flash frozen and stored at - 80 degrees. Frozen samples were treated with RNAlater-ICE (Thermo Fisher Scientific, AM7030), and total RNA was extracted with Qiagen’s RNeasy Universal plus mini kit (73404, Qiagen).
A sequencing library was prepared with a TruSeq Stranded Total RNA Kit (Illumina).

value: Cortex

value: Bulk tissue

value: Hemizygous Hnrnph2 P209L

value: Male

value: 3 weeks


title: VAST6958530 ViTCV_TD_V0

value: ViTCV


title: VAST6958529 Control_nTD_D14

value: Control


title: VAST6958535 ViTCV_nTD_V0


title: VAST6958528 ViTCV_TD_V1


title: VAST6958527 ViPS_nTD_D7

value: ViPS


title: P209L 2

description: P209L replicate 2


title: Lung_Mitsui_Control_Day180_rep1

source_name: Rat, Lung, Mitsui, Control, Day 180, replicate 1


title: con1

source_name: lung

value: lung

value: IL-10 B-WT

value: LPS


title: P209L 1

description: P209L replicate 1


title: Lung_Mitsui_High_Day30_rep4

description: Gene expression in lung of rat exposed to Mitsui (1.5 mg/m3) 30 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 30, replicate 4


title: P209L Control 2

description: P209L Control replicate 2

value: Wild type


title: VAST6958526 ViTCV_nTD_V1

value: whole blood

value: WT


title: Lung_Mitsui_High_Day30_rep5

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 30, replicate 5

value: Sprague Dawley

value: accessory lobe of lung


title: Lung_Mitsui_High_Day30_rep6

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 30, replicate 6

value: female

value: 13 weeks-old (at the onset of instillation)


title: VAST6958521 ViPS_TD_D0


title: VAST6958523 ViPS_TD_D0


title: VAST6958522 Control_nTD_D7


title: VAST6958524 ViTCV_nTD_V0


title: P209L Control 1

description: P209L Control replicate 1

value: Cortex

value: Bulk tissue


title: VAST6958520 Control_TD_D0


title: R206W 3

description: R206W replicate 3

value: Hemizygous Hnrnph2 R206W

value: Male

value: 8 weeks


title: VAST6958517 Control_TD_D0

value: Control


title: VAST6958519 Control_TD_D0


title: VAST6958518 ViPS_nTD_D0

value: ViPS


title: R206W 2

description: R206W replicate 2


title: VAST6958516 ViTCV_TD_D0

value: ViTCV


title: VAST6958515 ViPS_nTD_D0


title: R206W 1

description: R206W replicate 1


title: VAST6958525 ViTCV_nTD_D7


title: Lung_Mitsui_High_Day30_rep3

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 30, replicate 3


title: Lung_Mitsui_High_Day30_rep1

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 30, replicate 1


title: Lung_Mitsui_Medium_Day30_rep6

description: Gene expression in lung of rat exposed to Mitsui (0.5 mg/m3) 30 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 30, replicate 6


title: Lung_Mitsui_High_Day30_rep2

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 30, replicate 2


title: VAST6958514 ViTCV_nTD_V0


title: VAST6958513 Control_nTD_D0


title: R206W Control 2

description: R206W Control replicate 2


title: R206W Control 3

description: R206W Control replicate 3


title: VAST6958511 ViPS_nTD_V7


title: R206W Control 1

description: R206W Control replicate 1


title: VAST6958508 ViTCV_TD_V0


title: VAST6958510 ViTCV_TD_V1


title: VAST6958507 Control_TD_D0


title: KO 3

description: KO replicate 3

value: Hemizygous Hnrnph2 KO


title: VAST6958506 ViTCV_nTD_D0


title: VAST6958505 ViPS_nTD_D0


title: VAST6958512 ViTCV_TD_V7


title: VAST6958509 ViPS_nTD_V1


title: Lung_Mitsui_Medium_Day30_rep4

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 30, replicate 4


title: VAST6958504 ViTCV_nTD_D0


title: Lung_Mitsui_Medium_Day30_rep5

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 30, replicate 5


title: Lung_Mitsui_Medium_Day30_rep1

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 30, replicate 1


title: Lung_Mitsui_Medium_Day30_rep3

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 30, replicate 3


title: VAST6958503 ViTCV_TD_D0.12h


title: VAST6958502 Control_nTD_D0.12h


title: Lung_Mitsui_Low_Day30_rep6

description: Gene expression in lung of rat exposed to Mitsui (0.15 mg/m3) 30 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 30, replicate 6


title: KO Control 3

description: KO Control replicate 3


title: VAST6958500 ViTCV_nTD_D0.12h

source_name: whole blood


title: VAST6958501 ViPS_TD_V7


title: Lung_Mitsui_Low_Day30_rep4

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 30, replicate 4


title: VAST6958498 ViPS_nTD_D0.12h


title: VAST6958497 ViPS_nTD_V7


title: Lung_Mitsui_Low_Day30_rep5

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 30, replicate 5


title: KO Control 1

description: KO Control replicate 1

source_name: Cortex


title: KO 2

description: KO replicate 2


title: KO Control 2

description: KO Control replicate 2


title: VAST6958499 ViPS_nTD_V0


title: VAST6958495 ViPS_TD_V7


title: VAST6958494 ViPS_TD_V1


title: VAST6958496 ViTCV_TD_V7


title: KO 1

description: KO replicate 1


title: VAST6958493 ViTCV_nTD_D7


title: Lung_Mitsui_Medium_Day30_rep2

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 30, replicate 2


title: S2G_oNSC2.5y_P2

data_processing:
Raw reads in fastq format were aligned to the mm10 transcriptome using RSEM (Bo Li et al., 2011) and bowtie 2.0 (Langmead et al., 2012) (with options: rsem-calculate-expression --bowtie2 --bowtie2-sensitivity-level very_sensitive --no-bam-output --estimate-rspd --paired-end).
Gene level alignment results of samples were merged and annotated using glbase3 (Hutchins et al., 2014).
Read counts per genes were calculated using RSEM and normalized to GC content using EDAseq (Risso et al., 2011). GC-normalized read counts no less than 20 in at least two samples were kept, leading to a final read count table.
The table was used to inspect individual gene expression, generate correlation heatmaps, perform principal components analysis (PCA) and analyze differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files. The first column is the ensemble gene ID(ensg). The second column contains the official gene names(name). The rest of the columns contain the normalized read counts for each sample.

source_name: NSC

growth_protocol: Mouse fibroblasts were transduced with M2rtTA lentivirus and Dox-inducible lentiviruses of transcription factors in MEF medium (DMEM high glucose supplemented with 10% FBS, 1x NEAA, 1x Glutamax and 1x P/S). 24 hours after transduction, the medium was switched to reprogramming medium. The medium switch day was defined as day 0 of reprogramming and cells were further cultured with media change every other day. For mouse iNSC reprogramming, cells were cultured in mNSC medium (DMEM/F-12 medium supplemented with 1x N2, 1x B27, 1x Glutamax, 10 ng/mL bFGF, 10 ng/mL EGF). 1 μg/mL Dox was added for 18 days. Mouse iNSC colonies were picked at day 20 and further expanded in Matrigel-coated plates in mNSC medium.

value: NSC


title: VAST6958492 ViTCV_TD_V1

data_processing:
Sequences assigned to be ribosomal RNA, sex chromosome genes, mitochondrial RNA or haemoglobin were excluded from downstream analysis.
Gene features were counted using HTSeq (version 0.9.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries (genes without an abundance greater than 1 count per million in 9 or more samples) were filtered out.
Assembly: Sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38, using STAR (version 2.6.1d).
Supplementary files format and content: R file containig normalized abundance measurements


title: S2G_oNSC2.5y_P5


title: Lung_Mitsui_Low_Day30_rep3

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 30, replicate 3


title: Lung_Mitsui_Low_Day30_rep2

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 30, replicate 2


title: VAST6958491 ViPS_nTD_D7


title: Lung_Mitsui_Low_Day30_rep1

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 30, replicate 1


title: VAST6958490 ViTCV_nTD_D7


title: S2G_TTF2.5y_R2

source_name: Tail-tip fibroblast

value: Tail-tip fibroblast

value: fibroblast


title: S2G_TTF2.5y_R1


title: VAST6958489 ViPS_nTD_V1

value: whole blood

value: WT


title: Lung_Mitsui_Control_Day30_rep6

description: Gene expression in lung of control rat (filtered air) 30 days post exposure

source_name: Rat, Lung, Mitsui, Control, Day 30, replicate 6

value: Sprague Dawley

value: accessory lobe of lung


title: VAST6958486 ViPS_nTD_V0


title: VAST6958485 ViTCV_TD_V0


title: VAST6958487 ViPS_TD_V0


title: S2G_TTF1.0y_miNSC_KMF_R2

value: miNSC


title: S2G_TTF1.0y_miNSC_KMF_R1


title: Lung_Mitsui_Control_Day30_rep4

source_name: Rat, Lung, Mitsui, Control, Day 30, replicate 4

value: female

value: 13 weeks-old (at the onset of instillation)


title: VAST6958484 ViPS_TD_V0


title: VAST6958483 ViTCV_nTD_D0.12h


title: VAST6958482 ViTCV_nTD_D0


title: S2G_TTF1.0y_miNSC_BKF_R2


title: VAST6958480 Control_nTD_D0


title: VAST6958481 ViTCV_TD_D0


title: Lung_Mitsui_Control_Day30_rep2

source_name: Rat, Lung, Mitsui, Control, Day 30, replicate 2


title: Lung_Mitsui_Control_Day30_rep3

source_name: Rat, Lung, Mitsui, Control, Day 30, replicate 3


title: S2G_TTF1.0y_miNSC_BKF_R1


title: Lung_Mitsui_Control_Day30_rep5

source_name: Rat, Lung, Mitsui, Control, Day 30, replicate 5


title: VAST6958479 ViPS_nTD_D0.12h


title: Lung_Mitsui_Control_Day30_rep1

source_name: Rat, Lung, Mitsui, Control, Day 30, replicate 1


title: Lung_Mitsui_High_Day3_rep6

description: Gene expression in lung of rat exposed to Mitsui (1.5 mg/m3) 3 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 3, replicate 6


title: VAST6958478 ViTCV_nTD_V7

source_name: whole blood


title: Lung_Mitsui_High_Day3_rep5

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 3, replicate 5


title: S2G_TTF1.0y_miNSC_4F1_P8_R2


title: VAST6958477 ViTCV_nTD_V7


title: VAST6958476 ViTCV_nTD_D0.12h


title: VAST6958475 ViPS_nTD_V7


title: Lung_Mitsui_High_Day3_rep4

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 3, replicate 4


title: S2G_TTF1.0y_miNSC_4F1_P18_R2


title: VAST6958488 ViPS_TD_V1


title: VAST6958474 ViTCV_nTD_V1


title: VAST6958473 ViTCV_nTD_V1


title: S2G_TTF1.0y_miNSC_4F1_P18_R1


title: VAST6958550 Control_TD_D0


title: VAST6958471 ViTCV_nTD_V0


title: VAST6958472 ViPS_nTD_V1


title: VAST6958470 ViTCV_nTD_D7


title: S2G_TTF1.0y_R2


title: S2G_TTF1.0y_R1


title: Lung_Mitsui_High_Day3_rep1

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 3, replicate 1


title: Lung_Mitsui_Low_Day180_rep2

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 180, replicate 2


title: Lung_Mitsui_High_Day3_rep2

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 3, replicate 2


title: VAST6958469 ViPS_nTD_V0


title: VAST6958468 ViPS_nTD_D7


title: VAST6958467 ViPS_nTD_D7


title: S2G_TTF1.0y_miNSC_4F1_P8_R1


title: S2G_MEF_miNSC_KMF_R2

source_name: MEF

value: MEF


title: VAST6958466 ViTCV_nTD_V0


title: VAST6958465 ViTCV_TD_TD


title: VAST6958463 ViPS_nTD_V7


title: S2G_MEF_miNSC_KMF_R1


title: Lung_Mitsui_Medium_Day3_rep5

description: Gene expression in lung of rat exposed to Mitsui (0.5 mg/m3) 3 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 3, replicate 5


title: Lung_Mitsui_High_Day3_rep3

source_name: Rat, Lung, Mitsui, Exposed to High dose, Day 3, replicate 3


title: S2G_MEF_miNSC_KF_R2


title: VAST6958461 ViPS_nTD_D0


title: VAST6958462 ViTCV_nTD_D0


title: VAST6958464 ViTCV_nTD_V7


title: S2G_MEF_miNSC_KF_R1


title: VAST6958459 ViTCV_TD_V7


title: S2G_MEF_miNSC_BKF_R2


title: VAST6958460 ViTCV_nTD_D0


title: VAST6958458 Control_TD_TD


title: Lung_Mitsui_Medium_Day3_rep3

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 3, replicate 3


title: VAST6958457 ViTCV_TD_V1


title: S2G_MEF_miNSC_BKF_R1


title: VAST6958456 ViPS_nTD_V1


title: S2G_EF1.0y_miNSC_4F_R2

source_name: Ear fibroblast

value: Ear fibroblast


title: S2G_EF1.0y_miNSC_4F_R1


title: VAST6958455 ViTCV_nTD_V1


title: VAST6958453 ViTCV_nTD_D0.12h


title: VAST6958454 ViTCV_TD_V0


title: Lung_Mitsui_Medium_Day3_rep4

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 3, replicate 4


title: VAST6958452 ViPS_nTD_V0


title: Lung_Mitsui_Low_Day3_rep6

description: Gene expression in lung of rat exposed to Mitsui (0.15 mg/m3) 3 days post exposure

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 3, replicate 6


title: Lung_Mitsui_Medium_Day3_rep1

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 3, replicate 1


title: S2G_DF2.5y_R2

source_name: Skin fibroblast

value: Skin fibroblast


title: VAST6958450 ViPS_nTD_D0


title: Lung_Mitsui_Low_Day3_rep4

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 3, replicate 4


title: S2G_DF2.5y_R1


title: VAST6958448 Control_TD_D0

value: Control


title: VAST6958447 ViTCV_TD_D0.12h


title: VAST6958449 ViPS_nTD_D0.12h

value: ViPS


title: VAST6958446 ViPS_nTD_D0


title: ICR_MEF_miNSC_KF_R2

value: ICR


title: VAST6958445 ViTCV_nTD_D0

value: ViTCV


title: VAST6958444 ViTCV_nTD_V0


title: Lung_Mitsui_Medium_Day3_rep2

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 3, replicate 2


title: Lung_Mitsui_Low_Day3_rep5

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 3, replicate 5


title: Lung_Mitsui_Low_Day3_rep2

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 3, replicate 2


title: Lung_Mitsui_Low_Day3_rep3

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 3, replicate 3


title: Lung_Mitsui_Low_Day3_rep1

source_name: Rat, Lung, Mitsui, Exposed to Low dose, Day 3, replicate 1


title: ICR_MEF_miNSC_BKF_R2


title: VAST6958443 ViTCV_TD_D0

source_name: whole blood


title: ICR_MEF_miNSC_BKF_R1


title: VAST6958441 ViTCV_nTD_V7


title: VAST6958440 ViPS_nTD_D0.12h


title: Lung_Mitsui_Control_Day3_rep6

description: Gene expression in lung of control rat (filtered air) 3 days post exposure

source_name: Rat, Lung, Mitsui, Control, Day 3, replicate 6


title: VAST6958442 ViTCV_nTD_V7


title: VAST6958438 ViPS_nTD_V7


title: pNSC

description: 10x Genomics

data_processing:
Raw sequencing reads were assigned into individual samples using bcl2fastq (Illumina) followed by alignment to mm10 mouse genome using Cell Ranger software v6.1.0 (10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mouse primary NSCs and iNSCs at passage 15 were dissociated into single cells using Accutase and resuspended in DPBS containing 0.04% BSA with more than 90% viability.
Single cell encapsulation and cDNA library was prepared from each sample using the 10X Genomic Chromium Single Cell Controller (10X Genomics) and Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit according to manufacturer’s instructions. In brief, single cells in suspension were counted and loaded into individual wells of 10X Chromium Single Cell chip. Single cells were encapsulated into Gel Beads-in-emulsion (GEM) by 10X Chromium Single Cell Controller. Single Cell 3’ Reagent Kit v3.1 was used to perform reverse transcription on GEMs, followed by cDNA purification and amplification. The double-stranded cDNA then went through enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection following manufacturer’s protocol. Library size and concentration were determined by Qubit, quantitative PCR and Bioanalyzer assays. Pooled libraries were then sequenced on Illumina NovaSeq 6000 platform using 151 bp paired-end sequencing.

value: NSC


title: VAST6958439 ViTCV_nTD_V0


title: VAST6958437 ViPS_TD_TD


title: VAST6958436 ViPS_nTD_V1


title: ICR_MEF_miNSC_KF_R1

source_name: MEF


title: VAST6958435 ViTCV_nTD_V1


title: miNSC_2F_KF

description: 10x Genomics


title: Lung_Mitsui_Control_Day3_rep3

source_name: Rat, Lung, Mitsui, Control, Day 3, replicate 3


title: Lung_Mitsui_Control_Day3_rep4

source_name: Rat, Lung, Mitsui, Control, Day 3, replicate 4


title: Lung_Mitsui_Control_Day3_rep5

source_name: Rat, Lung, Mitsui, Control, Day 3, replicate 5


title: VAST6958434 ViTCV_nTD_V1


title: VAST6958433 ViTCV_nTD_V0


title: OiNSCBKF

data_processing:
RRBS raw reads were trimmed with Trim Galore (version 0.6.6, -rrbs) followed by alignment to the mouse genome (GRCm38/mm10) using Bismark (version 0.23.1).
Then Bismark coverage files were generated from the deduplicated bam files using Bismark Methylation Extractor (–gzip –bedGraph).
Assembly: mm10
Supplementary files format and content: Bismark Coverage files in a GZIP compressed format (*.bismark.cov.gz).

source_name: OiNSCBKF

growth_protocol: MEFs isolated from E13.5 embryos and tail tip fibroblasts isolated from old mice we cultured in MEF medium (DMEM high glucose supplemented with 10% FBS, 1x NEAA, 1x Glutamax and 1x P/S). Mouse fibroblasts were transduced with M2rtTA lentivirus and Dox-inducible lentiviruses of transcription factors in MEF medium. 24 hours after transduction, the medium was switched to reprogramming medium. The medium switch day was defined as day 0 of reprogramming and cells were further cultured with media change every other day. For mouse iNSC reprogramming, cells were cultured in mNSC medium (DMEM/F-12 medium supplemented with 1x N2, 1x B27, 1x Glutamax, 10 ng/mL bFGF, 10 ng/mL EGF). 1 μg/mL Dox was added for 18 days. Mouse iNSC colonies were picked at day 20 and further expanded in Matrigel-coated plates in mNSC medium.

extract_protocol:
Genomic DNA (gDNA) of cells was isolated using Quick-DNA Microprep Kit (Zymo, #D3021) following the user guide and quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
The gDNA was digested using MspI, followed by end repair, and dA-tailing. The adapter ligation was performed by using adapters with all cytosines being methylated. After size selection, DNA fragments were bisulfite treated. After the bisulfite conversion, unmethylated cytosines were converted to U and further to T after PCR amplification, while methylated cytosines remained unchanged. After PCR amplification, the libraries were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 platform using 150 bp paired-end sequencing.

value: OiNSCBKF

value: old miNSC


title: VAST6958432 Control_TD_TD

extract_protocol:
Total RNA was extracted from all samples using the Tempus Spin RNA Isolation kit (Life Technologies).
Libraries were prepared using a poly-A selection step to exclude ribosomal RNA species (read length: 75bp paired-end, stranded).

value: whole blood


title: OiNSC3FR2


title: VAST6958431 ViTCV_nTD_V0

value: WT


title: Lung_Printex_High_Day180_rep6

description: Gene expression in lung of rat exposed to Printex (50 mg/m3) 180 days post exposure

source_name: Rat, Lung, Printex, Exposed to High dose, Day 180, replicate 6

label_protocol: For each of the 72 samples (6 control, 6 exposed rats to low dose, 6 exposed rats to medium dose and 6 exposed rats to high dose per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry.

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 6.7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to Printex (Low dose: 5 mg/m3, Medium dose: 15 mg/m3, High dose: 50 mg/m3).

value: Sprague Dawley


title: VAST6958430 ViPS_nTD_V0


title: VAST6958429 ViTCV_nTD_D14


title: Lung_Mitsui_Control_Day3_rep1

source_name: Rat, Lung, Mitsui, Control, Day 3, replicate 1

value: accessory lobe of lung


title: miNSC_3F_KMF

description: 10x Genomics

value: miNSC


title: VAST6958427 Control_TD_D0


title: OiNSC3FR1


title: OiNSC4FR2


title: VAST6958426 ViTCV_TD_V7


title: VAST6958425 ViTCV_nTD_V7


title: VAST6958424 ViPS_nTD_V7


title: OiNSC4FR1


title: Lung_Printex_High_Day180_rep5

source_name: Rat, Lung, Printex, Exposed to High dose, Day 180, replicate 5

value: female


title: VAST6958423 ViPS_nTD_V7


title: Lung_Printex_High_Day180_rep3

source_name: Rat, Lung, Printex, Exposed to High dose, Day 180, replicate 3

value: 13 weeks-old (at the onset of instillation)


title: Lung_Mitsui_Control_Day3_rep2

source_name: Rat, Lung, Mitsui, Control, Day 3, replicate 2


title: Lung_Printex_High_Day180_rep4

source_name: Rat, Lung, Printex, Exposed to High dose, Day 180, replicate 4


title: VAST6958422 ViTCV_nTD_D7


title: VAST6958421 ViTCV_nTD_D0


title: Lung_Printex_High_Day180_rep2

source_name: Rat, Lung, Printex, Exposed to High dose, Day 180, replicate 2


title: VAST6958428 ViPS_TD_D0


title: Lung_Printex_High_Day180_rep1

source_name: Rat, Lung, Printex, Exposed to High dose, Day 180, replicate 1


title: VAST6958420 ViTCV_nTD_V1


title: S2GOTTFR1

value: old fibroblasts


title: S2GOTTFR2


title: VAST6958418 Control_TD_D0.12h


title: OS2GNSCR2

value: old NSC


title: VAST6958417 ViTCV_TD_V1


title: VAST6958416 ViPS_TD_D0.12h


title: Lung_Mitsui_Medium_Day3_rep6

source_name: Rat, Lung, Mitsui, Exposed to Medium dose, Day 3, replicate 6


title: VAST6958415 ViPS_nTD_V1


title: OS2GNSCR1


title: ICRMEFR2

value: MEF


title: Lung_Printex_Medium_Day180_rep5

description: Gene expression in lung of rat exposed to Printex (15 mg/m3) 180 days post exposure

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 180, replicate 5


title: VAST6958413 ViPS_nTD_V0

source_name: whole blood


title: VAST6958412 ViTCV_TD_V0


title: Lung_Printex_Medium_Day180_rep6

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 180, replicate 6


title: Lung_Printex_Medium_Day180_rep4

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 180, replicate 4


title: Lung_Printex_Medium_Day180_rep3

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 180, replicate 3


title: VAST6958411 ViPS_nTD_V0


title: Lung_Printex_Medium_Day180_rep2

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 180, replicate 2


title: VAST6958410 Control_TD_TD

value: Control


title: FS2GNSCR2

value: fetal primary NSC


title: VAST6958419 ViPS_nTD_V1

value: ViPS


title: VAST6958409 ViPS_TD_V7


title: FS2GNSCR1


title: VAST6958407 ViPS_TD_TD


title: Lung_Printex_Medium_Day180_rep1

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 180, replicate 1


title: VAST6958406 ViTCV_TD_TD

value: ViTCV


title: VAST6958405 ViPS_TD_V1


title: VAST6958403 ViPS_TD_V0


title: Mouse_P0_D10_noFGF2-RNAseq_B1

city: Guangzhou

first: Zhonghui

last: Tang

state: Guangdong

address: No. 74 Zhongshan Second Road, Guangzhou

institute: Sun Yat-sen University

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using hisat2 version 2.1.0
Mapped reads were filtered for mapping quality (-q 20), and then calculated read counts using HTSeq version 0.11.2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: P0 prefrontal cortex tissue

growth_protocol: Prefrontal cortex (PFC) brain tissues were collected in ice-cold HBSS EB buffer: HBSS, no Calcium, no magnesium with 1 mM HEPES and 1% Penicillin-Streptomycin. The prefrontal cortex was dissected and placed in a cold HBSS EB buffer. After peeling the meninges and blood vessels, dissected the PFC was under a microscope. Discarded the HBSS EB buffer to around 500 μL, then cut the prefrontal cortex into 0.5-mm slices. Transfer the slices into a 15 mL tube, 70g 20s to discard the liquid, and then added 1-2mL Papain (Worthington, LK003178) in HBSS buffer with 10 U/μl DNase I. The PFC tissue was digested in a 37℃ oven with 10 rpm shaking for 30 minutes. Discarded the digestion solution as much as possible with 500g, 5 minutes. Resuspended cell pellet with 2-3 mL HABG culture medium: neurobasal medium (Invitrogen, 21103049) with 1X B27, 1X glutaMAX supplement. Pipetted 15 times in 45 s, then waited 2 minutes to collect single-cell suspension. Repeat 2-3 times. Centrifuged at 800g for 5 min to obtain a cell pellet. Re-suspended cell pellet in HABG culture medium: neurobasal medium (Invitrogen, 21103049) with 1X B27 (Invitrogen, 17504044), 1X glutaMAX supplement (Invitrogen, 35050-061), 1% Penicillin-Streptomycin. Seeded cell with 0.5-1 million/well for 6 well plates.  Cultured in a 37℃ incubator with 5% CO2. Checked cell situation every day and after 5 days changed HABG culture medium every two days with keeping one half of the old medium. Harvested cells on the needed day. The P0 mice cultured for 10 days.

extract_protocol:
Briefly, 1-2 million in vitro cultured cells were washed with PBS and then harvested with trizol, and follow normal RNA extraction protocols. The RNA concentration and purifity were detected. RNA integrity was assessed by obtaining a RIN score >8 on the Agilent 2100 Bioanalyzer.  Then constructed the library with VAHTS TM Total RNA-seq (H/M/R) Library Prep Kit for Illumina kit (Vazyme, NR603). Libraries were prepared according to the manufacturer’s protocol.
The labeled samples were immediately amplified by 9–10 cycles of polymerase chain reaction (PCR) with barcoded primers and sequenced with a NovaSeq 6000 instrument in a 150 bp/150 bp paired-end run using standard Illumina protocols.

treatment_protocol: 5ng/mL FGF2 were added for the treatment group.

value: P0 prefrontal cortex tissue

tag: cell sorting strategy

value: Prefrontal cortex tissue after in vitro culture 10 days

value: no FGF2


title: Mouse_P0_D10_noFGF2-RNAseq_B2


title: VAST6958414 ViTCV_nTD_D0.12h

value: whole blood


title: ICRMEFR1


title: Lung_Printex_Low_Day180_rep6

description: Gene expression in lung of rat exposed to Printex (5 mg/m3) 180 days post exposure

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 180, replicate 6


title: Mouse_P0_D10_FGF2-RNAseq_B2

value: WT


title: Lung_Printex_Low_Day180_rep3

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 180, replicate 3

value: Sprague Dawley


title: VAST6958401 ViTCV_TD_D0


title: VAST6958402 ViTCV_nTD_V0


title: Mouse_P0_D10_FGF2-RNAseq_B1


title: VAST6958408 ViTCV_nTD_V7


title: VAST6958398 ViTCV_TD_V7


title: VAST6958399 Control_nTD_D0


title: VAST6958397 ViTCV_TD_V1


title: VAST6958404 ViTCV_nTD_V1


title: E15.5 embryo, PDGFRa enriched

data_processing:
Reads from sequencing runs corresponding to a given sample were pooled and aligned using Cell Ranger software (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files containing feature names and cell barcodes and matrix files containing feature counts

source_name: Dorsal upper back

extract_protocol:
Embryos were collected at the specified timepoints and head and limbs were removed. The dorsal upper back portion was minced and digested with either 0.25% trypsin (Fisher) or Collagenase D: 6.1 mg ml−1 (Roche) and Dispase II: 2.4 mg ml−1 (Roche). Samples were placed at 37 °C with constant agitation (200 r.p.m), followed by quenching for 30 min with an equal volume of complete medium (DMEM/10% FBS). Dissociated cells were suspended using a P1000 pipette and filtered through a 100-μm filter. Cells were then pelleted at 400g for 4 min, and red blood cells were lysed in 155 mM NH4Cl, 12 mM NaHCO3 and 0.1 mM EDTA for 4 min. An equal volume of complete medium was added, and the cells were filtered through a 40-μm filter for downstream analyses. Isolated cells were suspended in FACS buffer (HBSS, 3% 0.45 µM filtered FBS; Thermo Fisher). Cells were stained in FACS buffer with antibodies for 1 h at 4 °C in the dark. Cells were washed twice with cold FACS buffer and sorted on a FACS Aria cell sorter (BD Biosciences) with a 100-μm nozzle. All compensation was performed at the time of acquisition in BD FACS DIVA software (8.0.1) using single stained cells and compensation beads. Single cells were flow sorted to isolate live (DAPI(−)) cells and remove debris. We enriched for mesenchymal, DM and brown adipose lineage cells as follows.  (i) E11.5 and E12.5 DM and mesenchymal cells based on cell surface expression of PDGFRa and/or LRIG1 [30% PDGFRa+, LRIG1(-) cells; 25% PDGFRa(-), LRIG1+ cells, 30% PDGFRa+, LRIG1+ cells, 15% PDGFRa(-), LRIG1(-) cells]. (ii) E13.5-E15.5 fibroblasts through selection of PDGFRa+ cells [75% PDGFRa+; 25% PDGFRa(-)]. (iii) E10.5, E14.5, and E15.5 brown adipose lineage cells based on expression of Early B Cell Factor-2 (Ebf2)-GFP [75% Ebf2-GFP+; 25% Ebf2-GFP(-)].
Single cell libraries were prepared  according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics) and sequenced on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000 by the University of Pennsylvania Next Gen Sequencing Core or CHOP Center for Applied Genomics Sequencing Core. Reads were aligned using Cell Ranger software from 10x Genomics.

value: Dorsal upper back

tag: developmental stage


title: E14.5 embryo, Ebf2-GFP enriched

description: Illumina NovaSeq 6000, Illumina HiSeq 4000


title: Lung_Printex_Low_Day180_rep4

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 180, replicate 4

value: accessory lobe of lung


title: AH3

city: Beijing

first: Hongwei

last: Li

address: 11 Ronghuanan Road, Yizhuang

institute: Chinese Academy of Inspection and Quarantine

data_processing:
Genomics Workbench v 11.0.1
The raw data of sequencing was evaluated by FastQC
TBEDTools was used to check the uniformity of distribution and statistical analysis of gene coverage
Salmon was used to calculate gene expression
DESeq2 was used to analyze gene expression differences
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Leptinotarsa decemlineata

source_name: head

extract_protocol:
RNA was harvested usinge PureLink™ RNA Mini Kit . 2 ug oftotal RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq w ere prepared using SMARTER mRNA-Seq Library Prep Kit follow ing manufacturer's protocols.

value: head

value: olfactory cell

value: Head olfactory cell

value: treatment with antibiotics


title: Lung_Printex_Low_Day180_rep1

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 180, replicate 1

value: female

value: 13 weeks-old (at the onset of instillation)


title: E15.5 embryo, Ebf2-GFP enriched


title: AH2


title: VAST6958395 Control_nTD_D7

value: Control


title: VAST6958400 ViPS_TD_D0

value: ViPS


title: Lung_Printex_Low_Day180_rep2

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 180, replicate 2


title: Lung_Printex_Low_Day180_rep5

source_name: Rat, Lung, Printex, Exposed to Low dose, Day 180, replicate 5


title: E14.5 embryo, PDGFRa enriched


title: Lung_Printex_Control_Day180_rep6

source_name: Rat, Lung, Printex, Control, Day 180, replicate 6


title: AH1


title: Lung_Printex_Control_Day180_rep5

source_name: Rat, Lung, Printex, Control, Day 180, replicate 5


title: VAST6958393 Control_TD_D0.12h

source_name: whole blood


title: E13.5 embryo, PDGFRa enriched


title: E12.5 embryo, PDGFRa/LRIG1 enriched


title: AA3

value: non-treatment


title: AA2


title: Lung_Printex_Control_Day180_rep4

source_name: Rat, Lung, Printex, Control, Day 180, replicate 4


title: Lung_Printex_Control_Day180_rep3

source_name: Rat, Lung, Printex, Control, Day 180, replicate 3


title: VAST6958392 ViTCV_TD_V0

value: ViTCV


title: AA1


title: E11.5 embryo, PDGFRa/LRIG1 enriched


title: Lung_Printex_Control_Day180_rep2

source_name: Rat, Lung, Printex, Control, Day 180, replicate 2


title: VAST6958396 ViPS_TD_V7


title: Lung_Printex_Control_Day180_rep1

source_name: Rat, Lung, Printex, Control, Day 180, replicate 1


title: VAST6958391 ViTCV_TD_D0.12h


title: VAST6958451 Control_TD_D0.12h


title: S. pseudintermedius cells, Erythritol added, biol rep 3

city: Toyoake

first: Tadashi

last: Fujii

state: Aichi

address: 1-98 Dengakugakubo Kutsukake-cho

department: School of Medicine, Gastroenterology and Hepatology

country: Japan

institute: FUJITA HEALTH UNIVERSITY

data_processing:
Bowtie2 (ver. 2.4.1) was used to read the alignment and mapping of the GCF_001792775.2 reference genomes.
After reading and writing the alignment data in the SAM and BAM formats with the SAMtools, the data were sorted and indexed.
The read counts per gene were obtained using the featureCounts (ver. 2.0.0).
The relative expression level of each gene was normalized by the RPKM (Reads per Kilobase Million) and Transcripts Per Million methods.
After normalization using the DEGES normalization method implemented in TCC (ver. 1.26.0), we performed a differential gene expression analysis using edgeR (ver. 3.28.1).
Supplementary files format and content: Exeel files include RPKM and TPM  values for each Sample

organism: Staphylococcus pseudintermedius

source_name: WT

growth_protocol: S. pseudintermedius cultured in 802 medium with or without 5% (w/w) erythritol, 60 or 30 µL of the above seed culture was inoculated into 3 mL of 802 medium, respectively, and incubated at 30°C until OD660 = 0.8–1.0 for three independent cultures under each condition.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
After removing rRNA in samples by riboPool (siTOOLs Biotech, Planegg, Germany), the NGS library was prepared by MGIEasy RNA Directional Library Prep Set (MGI Tech, Shenzhen, China) according to the manufacturer’s protocol.

treatment_protocol: After cooling 3 mL of the culture medium on ice, the cells were collected by centrifugation at 5,000 rpm for 5 min using the centrifuge MX-107 (Tomy Seiko, Tokyo, Japan), and 800 μl of RNA later (Thermo Fisher Scientific, MA, USA) was then added to cells for RNA extraction.

value: Erythritol added


title: S. pseudintermedius cells, Erythritol added, biol rep 2


title: Lung_Printex_High_Day30_rep6

description: Gene expression in lung of rat exposed to Printex (50 mg/m3) 30 days post exposure

source_name: Rat, Lung, Printex, Exposed to High dose, Day 30, replicate 6


title: VAST6958388 Control_nTD_D0.12h


title: S. pseudintermedius cells, Erythritol added, biol rep 1


title: VAST6958390 ViPS_TD_D0.12h


title: VBCS-762_AKO2

city: Grand Rapids

first: Ning

last: Wu

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Reads were trimmed with TrimGalore! v0.6.0.
Trimmed reads were aligned with STAR v2.7.8a against mm10 and gene counts were obtained based on GENCODE vM24 annotations.
Assembly: mm10
Supplementary files format and content: Gene counts in tab-delimited format.

source_name: eWAT macrophage mRNAseq of adipose specific TXNIP KO animals on ketogenic diet

extract_protocol:
Total RNA was extracted with a combination of TRIzol and PureLink RNA mini kit (Invitrogen).
For eWAT: Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA Stranded mRNA-Seq Kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA).
For macrophages: Libraries were prepared by the Van Andel Genomics Core from 1-5 ng of total RNA. Total RNA material was converted to dsDNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, v. 091817 (Takara Bio USA, Mountain View, CA, USA ). cDNA was sheared to 200–500 bp using a Covaris E220 Evolution ultrasonicator (Covaris Inc., Woburn, MA USA) and Illumina compatible sequencing libraries were generated using the Kapa HyperPrep kit, v6.17 (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex dual adapters (Bioo Scientific, Austin, TX, USA).

value: eWAT

value: F4/80+, CD11b+ and CD64+ macrophags

value: adipose specific TXNIP KO

value: ketogenic diet


title: VBCS-762_AKO3


title: VBCS-762_AKO1


title: S. pseudintermedius cells, Control, biol rep 3

value: WT

value: without erythritol


title: VAST6958387 ViPS_TD_V0

value: whole blood


title: S. pseudintermedius cells, Control, biol rep 2


title: VBCS-762_WT3

source_name: eWAT macrophage mRNAseq of WT animals on ketogenic diet


title: VAST6958386 ViPS_nTD_D0


title: Lung_Printex_High_Day30_rep5

source_name: Rat, Lung, Printex, Exposed to High dose, Day 30, replicate 5

value: Sprague Dawley

value: accessory lobe of lung


title: Lung_Printex_High_Day30_rep4

source_name: Rat, Lung, Printex, Exposed to High dose, Day 30, replicate 4


title: Lung_Printex_High_Day30_rep2

source_name: Rat, Lung, Printex, Exposed to High dose, Day 30, replicate 2


title: S. pseudintermedius cells, Control, biol rep 1


title: VBCS-762_WT2


title: VAST6958385 ViPS_nTD_D7


title: VBCS-762_WT1


title: Lung_Printex_High_Day30_rep1

source_name: Rat, Lung, Printex, Exposed to High dose, Day 30, replicate 1


title: VAST6958389 ViPS_TD_V1


title: VBCS-702_AKO6

source_name: eWAT macrophage mRNAseq of adipose specific TXNIP KO animals on control diet

value: control diet


title: SAA

city: Albany

first: Katherine

middle: C

last: MacNamara

state: New York

address: 47 New Scotland Avenue

department: Immunology and Microbial Disease

institute: Albany Medical College

description: 10x Genomics

data_processing:
Barcode processing, gene counting, and aggregation were done using Cell Ranger software v6.0.1.
Assembly: mm10

source_name: Bone marrow

extract_protocol:
Whole BM was flushed from femus and tibias into HBSS. After RBC lysis, cells suspensions were stained and 7-AAD- CD11b+ Ly6C+ Ly6G- cells were sorted on a BD FACSAria Cell Sorter. Cells from each experimental group (radiation and SAA, n = 3 mice per group) were pooled together.
Library construction was performed according to the manufacter's instructions (single cell 5' v2 protocol, 10x Genomics). Briefly, BM cells were resuspended in the master mix and loaded into the chromium chip with partioninig oil to generate the gel bead-in-emulsion (GEM). Reverse transcription was then performed and cDNA cleaned up with Silane DynaBeads and amplified by PCR. Library construction and sequencing was next performed by the Center for Functional Genomics at SUNY Albany.

value: Bone marrow

value: 300 rads + 6.5e7 B6 splenocytes


title: VAST6958383 ViPS_nTD_D0

city: Oxford

first: Henderson

last: Zhu

address: Oxford Vaccine Group, Old Road, Headington, Old Road, Headington

institute: University of Oxford


title: VBCS-702_AKO5


title: VAST6958382 ViPS_nTD_V1


title: Lung_Printex_Medium_Day30_rep5

description: Gene expression in lung of rat exposed to Printex (15 mg/m3) 30 days post exposure

source_name: Rat, Lung, Printex, Exposed to Medium dose, Day 30, replicate 5

value: female

value: 13 weeks-old (at the onset of instillation)


title: VBCS-702_AKO4