title: Control_Mus_Oocyte_1

status: Public on Nov 30 2024

type: SRA

city: Nan Jing

first: Qian

last: Gao

address: No 1, Weigang

country: China

institute: Nanjing Agricultural University

library_source: transcriptomic

data_processing:
uses the filtering software SOAPnuke V1.5.2 developed by BGI independently for filtering
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Bowtie2 V2.2.5 with -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RSEM) were calculated using a protocol from Li, B et al., BMC Bioinformatics, 2011. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: FPKM

molecule: total RNA

organism: Mus musculus

source_name: mouse oocyte

extract_protocol:
RNA contents in 100 oocytes from each group were extracted, and RNA quality was assessed by using Agilent bioanalyzer 2100. Transcriptome library was prepared following NEB Next Ultra RNA library Prep Kit. After mixing libraries based on the set concentration and the standard volume, Illumina Hi Seq platform was applied for sequencing and biological information analyzing.
RNA libraries were prepared for sequencing using standard illumina protocols

tag: cell type

value: mouse oocyte

tag: genotype

value: WT  ICR


title: SPE_Mus_Oocyte_1


title: Mouse kidney proximal tubule_KO, biological rep3

city: Kyoto

first: Yuichiro

last: Kitai

address: Yoshidakonoecho Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
The libraries were sequenced on a Nextseq 550 (Illumina) to generate 75 bp single-end reads at a read depth of at least 20 million reads per sample.
Reads were mapped to mouse (Ensembl 103; STAR version 2.6.0c) reference gene models.
The expected counts were calculated using RSEM verseion 1.3.1. Differential expression analyses were conducted using DESeq2 version 1.28.1.
Assembly: Ensembl 103

source_name: kidney proximal tubule

growth_protocol: C57BL/6 mice were purchased from Japan SLC.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (74106; Qiagen).
The RNA-Seq library was prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions.

treatment_protocol:
The fractions of the cortex of the kidney were homogenized in DMEM-based buffer containing 10% FBS, Hepes (0.01M), using the gentleMACS Dissociator (Miltenyi Biotec). After incubation at 37°C for 30 minutes, the lysates were forced through a 40-mm filter to remove cell clumps.
The cells were washed with ice-cold sorting buffer (HBSS with 3% BSA, and 2 mM EDTA), and then incubated with anti-prominin-1 antibody (130-092-442) for 15 minutes. Cells were then washed with ice-cold sorting buffer, and passed through an MS column (Miltenyi Biotec) under the effect of a magnetic field generated by the Mini MACS Separation Unit (Miltenyi Biotec).
The prominin-1-positive cells retained inside the column were washed 3 times and then eluted once the magnetic field was removed. RNA extraction was performed from the eluted cells, as described below.

tag: tissue

value: kidney proximal tubule

tag: strain

tag: gender

value: Female


title: Mouse kidney proximal tubule_KO, biological rep2


title: Mouse kidney proximal tubule_KO, biological rep1


title: Mouse kidney proximal tubule_Ctr, biological rep1


title: Mouse kidney proximal tubule_Ctr, biological rep2


title: Low dose, Pre-vaccination, NHP 10

city: Seattle

first: Maxwell

last: Neal

state: NY

address: 307 Westlake Ave N

country: USA

institute: Seattle Children's Research Institute

data_processing:
Raw sequencing data were aligned to the Macaca fascicularis reference genome from Ensembl (version 5.0) using STAR (version 2.6.1d) and gene counts were computed using featureCounts (version 1.5.2).
Assembly: Macaca_fascicularis_5.0 (Ensembl), INSDC AssemblyGCA_000364345.1
Supplementary files format and content: Tab-delimited text file of transcript counts for each Sample

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Blood

extract_protocol:
Whole-blood (250 µL) collected 18 days prior to vaccination and at 1- and 3-days post vaccination were stored at -80°C in DNA/RNA Shield (Zymo Research). Total RNA was isolated from whole blood samples using the Zymo Research Quick RNA Whole Blood Kit according to the manufacturer’s protocol.
Sample libraries were globin-depleted and prepared using the SMART-Seq® stranded kit (Takara Bio) which includes poly(A) selection.

treatment_protocol: Ten Chinese-origin cynomolgus macaques (Macaca fascicularis) were assigned to two vaccine groups of five animals each. Each group of vaccinated animals was composed of two males and three females. One group was administered a single dose of 2x10^7 PFU VSV∆G-LASV-GPC, the other group received a lower dose of 2x10^5 PFU, both by intramuscular (IM) injection. Animals were vaccinated once with 1 ml of virus injected into the caudal thigh. A control group of three animals (one female and two males) received an equivalent volume of vaccine diluent (PBS, 5% trehalose) delivered IM.

value: Blood

tag: treatment

value: Low dose


title: Low dose, Pre-vaccination, NHP 9


title: Low dose, Pre-vaccination, NHP 11


title: High dose, Pre-vaccination, NHP 6

value: High dose


title: Control, Pre-vaccination, NHP 1

value: Control


title: Control, Pre-vaccination, NHP 2

value: Male


title: High dose, Pre-vaccination, NHP 7


title: Control, Pre-vaccination, NHP 3


title: Low dose, Pre-vaccination, NHP 13


title: High dose, Pre-vaccination, NHP 8


title: Control, Day 1, NHP 1


title: Low dose, Pre-vaccination, NHP 12


title: High dose, Day 1, NHP 4


title: Low dose, Day 1, NHP 10


title: High dose, Day 1, NHP 8


title: High dose, Day 3, NHP 5


title: Low dose, Day 1, NHP 11


title: Low dose, Day 1, NHP 9


title: High dose, Day 1, NHP 5


title: Mouse kidney proximal tubule_Ctr, biological rep3


title: Control, Day 3, NHP 1


title: High dose, Pre-vaccination, NHP 5


title: High dose, Day 3, NHP 4


title: Low dose, Day 3, NHP 9


title: High dose, Day 1, NHP 6


title: High dose, Day 3, NHP 7


title: Low dose, Day 3, NHP 13


title: High dose, Pre-vaccination, NHP 4


title: Control, Day 3, NHP 2


title: Control, Day 3, NHP 3


title: Low dose, Day 3, NHP 12


title: High dose, Day 3, NHP 6


title: Low dose, Day 3, NHP 10


title: Control, Day 1, NHP 2


title: Low dose, Day 1, NHP 13


title: High dose, Day 1, NHP 7


title: Endothelial cells on micropatterned substrate replicate #4

city: Portland

first: Meghan

last: Fallon

state: Oregon

address: 3303 S Bond Ave

department: Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
Fastq files were trimmed for quality and adapter sequences using Timmomatic (ver. 0.39).
Trimmed reads were aligned to the baboon reference genome from Ensemble (Panu_3.0) with STAR (ver. 2.7.10b), specifying Ensemble annotation Panu_3.0.104.
Mapped reads were analyzed for differential expression using edgeR (ver. 3.28.0) with the input as the gene counts matrix (low count filtered genes).
Fastq files generated from base-call files using bcl2fastq (Illumina).
Differential gene expression analysis was performed using edgeR (v3.28.0) with low count filtered genes as the input.
Assembly: Trimmed reads from fastq files were aligned using STAR (ver. 2.7.10b) to the Papio anubis reference genome from Ensemble (Panu_3.0.104).
Supplementary files format and content: tab-delimited text file including the raw counts for each sample

organism: Papio anubis

source_name: carotid artery endothelial cells

growth_protocol: Endothelial cells were cultured for 24 hours in VascuLife VEGF Endothelial Medium kit (Lifeline Cell Technology) supplemented with an additional 8% vol/vol FBS (Hyclone) in a sterile incubator at 37C and 5% CO2.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen). 300 ng of total RNA was used to construct sequencing libraries.
RNA samples with a RIN >= 9.9 were used to construct sequencing libraries. Libraries were prepared for bulk RNA-seq using the TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: Endothelial cells were cultured for 24 hours on either fully non-patterned, planar polyurethane (NOA81) or topographically micropatterned polyurethane with features of 3 µm wide ridges and grooves at a depth of 1 µm.

value: carotid artery endothelial cells

value: micropatterned substrate


title: Endothelial cells on micropatterned substrate replicate #1


title: Endothelial cells on planar substrate replicate #4

value: planar substrate


title: High dose, Day 3, NHP 8


title: Endothelial cells on micropatterned substrate replicate #3


title: Endothelial cells on planar substrate replicate #2


title: Low dose, Day 3, NHP 11


title: Control, Day 1, NHP 3


title: Low dose, Day 1, NHP 12


title: AAV Day4 EGFP-1

type: RNA

city: TAIPEI

first: YU FEI

last: TSAI

address: No. 7, Chung-San S. Rd

country: Taiwan

institute: CLSMB, NTU

description: RMA expression value derived from Transcriptome Analysis Console (TAC) Software

hyb_protocol: Samples were hybridized with GeneChip MTA 1.0 Arrays (Affymetrix) and scanned at the NTU NGS & Microarray Core Lab.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Raw data were processed with the Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific) for background correction and normalization. Subsequent analyses, including Gene Ontology analysis and Functional Enrichment Analysis (FEA), were performed using the TAC software and the DAVID platform, leveraging WikiPathways. Gene Set Enrichment Analysis (GSEA) was conducted using GSAE software version 4.3.2. All the results, including the list of Differential Expression Genes (DEGs) and outcomes from the aforementioned analyses, have been documented in Supplementary Data 1 and 2 as Excel files.

label: biotin

source_name: Adult healthy male

label_protocol: Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0; one array per subject) according to the manufacturers instructions. WT cDNA Synthesis and Amplification kit and WT Sense Target Labelling and Control Reagents (Affymetrix) were used.

growth_protocol: About 100 mg liver tissue was grounded in liquid nitrogen with 1ml RLT lysis buffer form RNeasy mini kit (Qiagen, 74104).

extract_protocol: RNA extraction was conducted by RNeasy mini kit (Qiagen, 74104), according to the manufacturer’s instructions.

treatment_protocol: Not applicible.

value: Liver

tag: Sex

value: male


title: AAV Day4 EGFP-2


title: Endothelial cells on micropatterned substrate replicate #5


title: ATAC-seq in sea urchin whole embryos at 66 hpf, replicate 2

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

description: ATAC-seq

library_source: genomic

data_processing:
Alignment: reads were aligned to the reference genome using Bowtie2 software
Filtering duplicates: duplicated pairs were removed using Samtools software
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Visualization: bigWig files were visualized using UCSC Browser
Assembly: Strongylocentrotus purpuratus 2019 Assembly (strPur5/GCF_000002235.5)
Supplementary files format and content: narrowPeak files with peaks called using MACS2 with q<0.01

molecule: genomic DNA

organism: Strongylocentrotus purpuratus

source_name: whole embryo

growth_protocol: Embryos were grown at 15°C in ASW until desired developmental stage

extract_protocol:
Wild type embryos were lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109; Magri MS et al., 2020. Front Cell Dev Biol.24;7:372. doi: 10.3389/fcell.2019.00372; Magri MS et al., 2021. Methods Mol Biol. 2219:253-265. doi: 10.1007/978-1-0716-0974-3_16

value: whole embryo

value: WT

tag: time

value: 66 hpf


title: ATAC-seq in sea urchin whole embryos at 72 hpf, replicate 1

description: ATAC-seq

value: 72 hpf


title: ATAC-seq in sea urchin whole embryos at 72 hpf, replicate 2

description: ATAC-seq


title: AAV Day4 EGFP-3


title: AAV Day4 HPNWT-1


title: AAV Day2 EGFP-2


title: AAV Day2 EGFP-1


title: AAV Day2 HPNWT-3


title: AAV Day1 EGFP-3


title: AAV Day2 HPNWT-2


title: AAV Day4 HPNWT-2


title: ATAC-seq in sea urchin whole embryos at 24 hpf, replicate 2

description: ATAC-seq

value: 24 hpf


title: ATAC-seq in sea urchin whole embryos at 66 hpf, replicate 1

description: ATAC-seq


title: AAV Day1 EGFP-2


title: Endothelial cells on planar substrate replicate #3


title: AAV Day2 EGFP-3


title: ATAC-seq in sea urchin whole embryos at 11 hpf, replicate 2

description: ATAC-seq

value: 11 hpf


title: AAV Day4 HPNWT-3


title: AAV Day1 EGFP-1


title: Endothelial cells on planar substrate replicate #1


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4; UAS-brRNAi; UAS-E93RNAi rep2

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description:
Library name: Pupal_Wings_EP93Br_44h_b
A minimum of 40 pupal wings at 44H APF

data_processing:
vast-tools was used to map the reads to a library of mRNAs using vast-tools align --expr, for -sp dme. The libraries were analyzed using a pipeline described in Cruz et al.
Assembly: dm6
Supplementary files format and content: cRPKM files have raw read counts to each Drosophila gene annotated in vast-tools. They were generated using vast-tools align with --expr option.

organism: Drosophila melanogaster

source_name: pupal wings

growth_protocol: All fly stocks were cultured at 25ºC on standard flour/agar Drosophila media.

extract_protocol:
A minimum of 40 pupal wings were dissected in 1× PBS from the following genotypes at 24 and 44 hours APF: rn-Gal4 (control), rn-Gal4; UAS-E93RNAi and rn-Gal4; UAS-brRNAi; UAS-E93RNAi. Pupal wings were then transferred to ice for subsequent RNA extraction using the Roche High Pure RNA Tissue Kit (Cat# 12033674001).
Libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (ref. E7490, New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (ref. E7760) according to the manufacturer’s protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing. Briefly, 250 ng of total RNA was used for polyA‐mRNA selection using Oligo‐dT beads, performing two rounds of purification. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis. Immediately afterward, second strand cDNA was synthesized, incorporating dUTP in place of dTTP. dsDNA was then subjected to end repair and A‐tailing in a single reaction, and subsequent ligation of the NEB adapter. USER enzyme was used to excise the hairpin‐like adaptors. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, ref. E6440, E6442, E6444, E6446) and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter). Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref. 5067‐1504 or ref. DNF‐473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (ref. 07960204001, Roche). Libraries were sequenced 1 * 51 + 10 + 10 bp on Illumina’s NextSeq2000.

value: pupal wings

value: rn-Gal4; UAS-brRNAi; UAS-E93RNAi

tag: developmental stage

value: 44H APF


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4; UAS-brRNAi; UAS-E93RNAi rep1

description:
Library name: Pupal_Wings_EP93Br_44h_a
A minimum of 40 pupal wings at 44H APF


title: ATAC-seq in sea urchin whole embryos at 24 hpf, replicate 1

description: ATAC-seq


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4; UAS-brRNAi; UAS-E93RNAi rep3

description:
Library name: Pupal_Wings_EP93Br_44h_c
A minimum of 40 pupal wings at 44H APF


title: ATAC-seq in sea urchin whole embryos at 11 hpf, replicate 1

description: ATAC-seq


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4; UAS-brRNAi; UAS-E93RNAi rep2

description:
Library name: Pupal_Wings_EP93Br_24h_b
A minimum of 40 pupal wings at 24H APF

value: 24H APF


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4; UAS-brRNAi; UAS-E93RNAi rep3

description:
Library name: Pupal_Wings_EP93Br_24h_c
A minimum of 40 pupal wings at 24H APF


title: AAV Day2 HPNWT-1


title: nucleus pulposus cells, r-CRLF1-2

city: Guangzhou

first: Jian

last: Zhu

address: No.58, Zhongshan 2nd Road, Yuexiu District

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
HISAT2 v2.2.1 was used for comparison with the reference genome.
Filtering ribosomes using bowtie2 v2.5.1
Differential gene expression levels of samples with duplicate experiments were analysed using DESeq2_1.38.3
Assembly: GCF_015227675.2
Supplementary files format and content: Excel spreadsheet format showing raw counts, fpkm for each group

organism: Rattus norvegicus

source_name: Intervertebral disc

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)beads
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

value: Intervertebral disc

tag: cell line

value: primary cell

value: nucleus pulposus cells

value: r-CRLF1 for 3days


title: nucleus pulposus cells, Veh-3

value: Vehicle for 3days


title: nucleus pulposus cells, r-CRLF1-3


title: nucleus pulposus cells, Veh-2


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4; UAS-E93RNAi rep1

description:
Library name: Pupal_Wings_EP93_44h_a
A minimum of 40 pupal wings at 44H APF

value: rn-Gal4; UAS-E93RNAi


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4; UAS-E93RNAi rep3

description:
Library name: Pupal_Wings_EP93_44h_c
A minimum of 40 pupal wings at 44H APF


title: nucleus pulposus cells,Veh-1


title: AAV Day1 HPNWT-2

value: Liver

value: male


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4; UAS-E93RNAi rep3

description:
Library name: Pupal_Wings_EP93_24h_c
A minimum of 40 pupal wings at 24H APF


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4; UAS-E93RNAi rep1

description:
Library name: Pupal_Wings_EP93_24h_a
A minimum of 40 pupal wings at 24H APF


title: AAV Day1 HPNWT-1


title: AAV Day1 HPNWT-3


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4 rep3

description:
Library name: Pupal_Wings_Cont_44h_c
A minimum of 40 pupal wings at 44H APF


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4; UAS-E93RNAi rep2

description:
Library name: Pupal_Wings_EP93_24h_b
A minimum of 40 pupal wings at 24H APF


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4 rep2

description:
Library name: Pupal_Wings_Cont_44h_b
A minimum of 40 pupal wings at 44H APF


title: Splenic and bone marrow NK cells from CML mouse 3 - Cell Hashing

city: Birmingham

first: Valeriya

last: Kuznetsova

state: Al

department: Medicine

institute: The University of Alabama at Birmingham

description:
Library name: CML3 - FB
Chromium 10x

library_source: other

data_processing:
Bcl2fastq files were pre-processed with Cell Ranger mkfastq using a pipeline recommended by 10x Genomics. Cell Ranger multi, software v6.1.1, was used to align reads to reference mouse genome (mm10), assemble transcriptomic count matrices, and de-multiplex hashed samples. Partek Flow (https://www.partek.com/partek-flow/) was used for further analysis and data visualization, including QA/QC, normalization, noise reduction, DEG, clustering, and pathway enrichment analysis. First, cells with fewer than 500 or greater than 4000 detected genes, as well as the cells with ˃15% mitochondrial genes, were excluded. After noise-reduction filtering (excluding features with the value=0 in at least 99.0% of cells), log-normalization, and principal component analysis (PCA), contaminating lineages (either Il2rb- cells or cells with high counts of Cd3e, Cd19, Tmem179a/b, Cd14) were filtered out. Il2rb+Nkg7+ cells were classified as NK cells.
Assembly: Mouse mm10
Supplementary files format and content: h5 files

molecule: other

source_name: Bone marrow and spleen

extract_protocol:
For pooling purposes, bone marrow and spleen samples from (2) control and (3) CML mice were stained with TotalSeq-B hashtaging antibodies 1 (bone marrow of each mouse) and 2 (spleen of each mouse) according to the protocol provided by BioLegend. Live singlets gated on host CD45.1+ NK cells (CD3-IL2Rb+NK1.1+CD49b+) were sorted in DPBS 0.04% BSA before loading onto 10x Genomics instrument according to the manufacturer’s protocol. Tissues from each mouse were pooled together, while each individual mouse represented one sequencing sample. The recovery of bone marrow-derived NK cells of CML1 mouse was insufficient to proceed with scRNA-seq.
Gene expression and feature barcode libraries for single-cell RNA-seq were prepared using the Chromium Next GEM Single Cell 3’ Gene Expression v3 with modifications for hashtag libraries. Quality control for amplified cDNA libraries and sequencing libraries was performed using a BioAnalyzer High Sensitivity DNA kit (Agilent). GEX and Cell Hashing libraries were sequenced on Illumina NextSeq 500 with a sequencing depth of at least 50,000 reads per cell for 3’ GEX and 5,000 reads per cell for feature barcode.

value: Bone marrow and spleen

value: CD45.1+ (host) NK cells

tag: library type

value: Cell Hashing


title: Splenic and bone marrow NK cells from CML mouse 2 - Gene Expression

description:
Library name: CML2 - GEX
Chromium 10x

library_source: transcriptomic single cell

value: Gene Expression


title: Splenic and bone marrow NK cells from CML mouse 3 - Gene Expression

description:
Library name: CML3 - GEX
Chromium 10x


title: Splenic and bone marrow NK cells from CML mouse 2 - Cell Hashing

description:
Library name: CML2 - FB
Chromium 10x


title: nucleus pulposus cells, r-CRLF1-1

value: WT


title: Splenic and bone marrow NK cells from CML mouse 1 - Gene Expression

description:
Library name: CML1 - GEX
Chromium 10x

source_name: Spleen

value: Spleen


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4 rep1

description:
Library name: Pupal_Wings_Cont_44h_a
A minimum of 40 pupal wings at 44H APF

value: pupal wings


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4; UAS-brRNAi; UAS-E93RNAi rep1

description:
Library name: Pupal_Wings_EP93Br_24h_a
A minimum of 40 pupal wings at 24H APF

value: rn-Gal4; UAS-brRNAi; UAS-E93RNAi


title: Splenic and bone marrow NK cells from control mouse 1 - Cell Hashing

description:
Library name: Ctrl1 - FB
Chromium 10x


title: Splenic and bone marrow NK cells from control mouse 2 - Gene Expression

description:
Library name: Ctrl2 - GEX
Chromium 10x


title: Splenic and bone marrow NK cells from control mouse 2 - Cell Hashing

description:
Library name: Ctrl2 - FB
Chromium 10x


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4 rep3

description:
Library name: Pupal_Wings_Cont_24h_c
A minimum of 40 pupal wings at 24H APF

value: 24H APF


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4 rep2

description:
Library name: Pupal_Wings_Cont_24h_b
A minimum of 40 pupal wings at 24H APF


title: Pupal Wings at 44 after puparium formation (APF) of genotype rn-Gal4; UAS-E93RNAi rep2

description:
Library name: Pupal_Wings_EP93_44h_b
A minimum of 40 pupal wings at 44H APF

value: 44H APF


title: Splenic and bone marrow NK cells from control mouse 1 - Gene Expression

description:
Library name: Ctrl1 - GEX
Chromium 10x


title: KO2CD9POSATM

city: Rehovot

first: Paula

last: Abou Karam

address: Herzl St 234

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann institute of Science

data_processing:
RNA-Seq (3') UMI appears in Read2
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI
Assembly: Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Supplementary files format and content: Normalization and differential expression was performed using DESeq2
Supplementary files format and content: mm10

source_name: epiWAT

extract_protocol:
Animal experiments were performed with male adult mice (C57BL/6J background). Animals were maintained in specific pathogen-free animal facility, and experiments were performed according to protocols approved by the Animal Care Use Committee of the Sourasky Medical Center. Mice were housed with 12-h light cycles and a constant temperature of 22°C.
HFD for 12 weeks
ATM sorting was performed using the BD FACSAriaTM FUSION cell sorter (BD Bioscience) from SVF fraction directly to lysis buffer.
Bulk MARS-Seq protocol. In breif, mRNA was purified from ~100,000 cells of each sample using Dynabeads mRNA Direct purification kit (ThermoFisher), barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for mouse ActB gene. Sequencing was done on a Nextseq 75 cycles high output kit (Illumina).

value: epiWAT

value: Macrophage

value: HFD 12 weeks


title: KO4CD9POSATM


title: KO1CD9POSATM


title: Pupal Wings at 24 after puparium formation (APF) of genotype rn-Gal4 rep1

description:
Library name: Pupal_Wings_Cont_24h_a
A minimum of 40 pupal wings at 24H APF


title: WT5CD9POSATM


title: BMP4 treated micropatterns

city: Westmead

first: V. Pragathi

last: Masamsetti

state: NSW

address: 214 Hawkesbury rd

department: Embryology Unit

country: Australia

institute: Children's Medical Research Institute

description: 10X Genomics

data_processing:
see Aryamanesh 2022, DOI: 10.1007/978-1-0716-2281-0_10
The 10x samples were mapped to the human genome using cell Ranger package with default parameters. The reads were filtered using Seurat package with the following parameters - a minimum of 200 genes/features, minimum of 1000 reads per cell and maximum of 20% MT gene expression. The cells were annotated using clustifyr package using Tyser Atlas dataset.
Assembly: The 10x samples were mapped to the human genome using cell Ranger package with default parameters.
Supplementary files format and content: cellranger_PM1_outs_raw_feature_bc_matrix_features.tsv.gz
Supplementary files format and content: cellranger_PM2_outs_filtered_feature_bc_matrix_features.tsv.gz
Supplementary files format and content: cellranger_PM3_outs_filtered_feature_bc_matrix_features.tsv.gz

organism: Homo sapiens

source_name: cell line

growth_protocol: Differentiation of the cells on micropatterned coverslips was a protocol adapted from Warmflash et al. 2014 (Warmflash, Sorre et al. 2014).HES3 Mixl1:GFP cells were passaged as single cells with StemPro Accutase Cell Dissociation Reagent (ThermoFisher Scientific) and seeded on micropatterned coverslips at a density of 2.5x105 cells/cm2 with 10μM Y-27632 dihydrochloride Rock inhibitor (TOCRIS) in mTeSR Plus (StemCell Technologies) into a total volume of  0.5 mL per well of a 24-well plate. Cells were incubated at 37 °C with 5% CO2.

extract_protocol:
The micropatterned cells were lifted off the gelled coverslips by first washing with PBS to remove debris, followed by incubating in PBS at 37°C for 5 min and then by vigorous tapping of the plate. Whole micropatterned cells floating in PBS were visualized under a microscope and approximately 10 micropatterns for each treatment were picked up with a 200µl-capacity pipette tip. Cells were dissociated with StemPro Accutase Cell Dissociation Reagent (ThermoFisher Scientific) at 37°C for 5 min.
Cells were assessed for viability and concentration, before loading into a 10X Chromium Chip G (10X Genomics) for an output of 10,000 cells using single cell droplet capture performed on the Chromium Controller (10X Genomics). One channel per sample was used. After cell separation and reverse transcription reactions occurred, library preparation followed in accordance with the Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System (Agilent) and were sent to AGRF (https://www.agrf.org.au/) for sequencing. Samples were sequenced using paired-ended, dual indexing, using cycles 28, 10, 10, 90 (R1, i7, i5, R2), for an output of 200 million reads per sample. cDNA library preparation was performed in accordance with the Single-Cell 3’ v 3.0 or v3.1 protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System (Agilent).

treatment_protocol: After 24 hours, micropatterns were incubated with either 50 ng/mL recombinant human BMP-4 (R&D Systems), 6µM CHIR99021 (StemCell Technologies) alone or 3 µM CHIR99021 and 100 ng/ml recombinant h/m/rActivin A (R&D Systems) in mTeSR Plus and incubated for a further 48 hours at 37 °C with 5% CO2.

value: cell line

value: embryonic stem cells

value: HES3 Mixl1:GFP cells

value: BMP4 treated micropatterns


title: CHIR +Activin treated micropatterns

description: 10X Genomics

value: CHIR + Activin treated micropatterns


title: WT4CD9POSATM


title: WT3CD9POSATM


title: WT1CD9POSATM


title: PBMC derived macrophages-LCL161IFNg Treated Donor 4

city: Brookline

first: Li

last: Qiang

address: 1 Jimmy Fund Way

institute: Dana-Farber Cancer Institute

description: Library name: 4-LCLIFNg

data_processing:
Reads were trimmed for Illumina adapter sequences using cutadapt and aligned using STAR (v2.7.3a).
Feature counting was done in R using the package Rsubread allowing for fractional counting of multi-mapping reads.
Assembly: hg38
Supplementary files format and content: CSV matrix of raw (non-normalized) gene-level counts for each sample.

source_name: PBMC derived macrophages

extract_protocol:
PBMCs were isolated from eight individual donors and differentiated into macrophages. For each donor, macrophages were treated for 24 hours with either DMSO, rhLTα1/β2, IFN-γ, LCL-161 (500nM), LCL-161 + rhLTα1/β2, or LCL-161 + IFN-γ. After treatment, macrophages were harvested, and total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturer’s protocol. (company). Additionally, phagocytosis assays were performed on treated macrophages from all donors to ensure treatment response.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: PBMC derived macrophages

value: LCL161 IFNg


title: PBMC derived macrophages-LCL161IFNg Treated Donor 5

description: Library name: 5-LCLIFNg


title: PBMC derived macrophages-LCL161IFNg Treated Donor 7

description: Library name: 7-LCLIFNg


title: PBMC derived macrophages-LCL161IFNg Treated Donor 8

description: Library name: 8-LCLIFNg


title: WT2CD9POSATM


title: PBMC derived macrophages-LCL161 Treated Donor 7

description: Library name: 7-LCL


title: PBMC derived macrophages-LCL161IFNg Treated Donor 2

description: Library name: 2-LCLIFNg


title: PBMC derived macrophages-LCL161IFNg Treated Donor 1

description: Library name: 1-LCLIFNg


title: DNT cells, PBC_naive_1

city: Beijing

first: Tingting

last: Lv

address: No. 95 Yong-An Road

institute: Beijing Friendship Hospital

description: PBC patients

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean  reads then were mapped to  reference genome from ensembl (list as follow)using HISAT2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Supplementary_files_format_and_content: processed data.xls includes RPKM values for each Sample

source_name: Peripheral  double negative T cell

extract_protocol:
6 healthy controls and 13 PBC patients (4 treatment-naïve, 4 UDCA responders and 5 UDCA non-responders) who agreed to provide samples with written informed consent, were enrolled in this study. Peripheral DNT cells were collected from their blood with FACS Aria II. And then total RNA was harvested with RNeasy Micro Kit. All samples profiled the expression of mRNA by sequencing on an Illumina Hiseq platform (Illumina, San Diego, CA) according to manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Primary biliary cholangitis (PBC)

value: Peripheral  blood

value: Peripheral  double negative T cell

value: treatment-naïve

tag: drug response


title: PBMC derived macrophages-LCL161IFNg Treated Donor 6

description: Library name: 6-LCLIFNg


title: DNT cells, PBC_UR_5

description: PBC patients

value: UDCA

value: UDCA non-responder


title: PBMC derived macrophages-LCL161 Treated Donor 6

description: Library name: 6-LCL


title: PBMC derived macrophages-LCL161IFNg Treated Donor 3

description: Library name: 3-LCLIFNg


title: PBMC derived macrophages-LCL161 Treated Donor 8

description: Library name: 8-LCL


title: DNT cells, PBC_naive_3

description: PBC patients


title: DNT cells, PBC_naive_2

description: PBC patients


title: DNT cells, PBC_naive_4

description: PBC patients


title: DNT cells, PBC_UR_4

description: PBC patients


title: CHIR treated micropatterns

description: 10X Genomics

value: CHIR treated micropatterns


title: DNT cells, PBC_UR_3

description: PBC patients


title: PBMC derived macrophages-LCL161 Treated Donor 4

description: Library name: 4-LCL


title: DNT cells, PBC_R_4

description: PBC patients

value: UDCA responder


title: DNT cells, PBC_UR_1

description: PBC patients


title: PBMC derived macrophages-LCL161 Treated Donor 3

description: Library name: 3-LCL


title: PBMC derived macrophages-LCL161 Treated Donor 2

description: Library name: 2-LCL


title: PBMC derived macrophages-LCL161 Treated Donor 5

description: Library name: 5-LCL


title: DNT cells, PBC_UR_2

description: PBC patients


title: DNT cells, PBC_R_3

description: PBC patients


title: PBMC derived macrophages-LCL161 Treated Donor 1

description: Library name: 1-LCL


title: PBMC derived macrophages-IFNg Treated Donor 8

description: Library name: 8-IFNg

value: IFNg


title: DNT cells, HC_6

description: healthy control

value: control


title: PBMC derived macrophages-IFNg Treated Donor 6

description: Library name: 6-IFNg


title: DNT cells, PBC_R_1

description: PBC patients


title: DNT cells, PBC_R_2

description: PBC patients


title: DNT cells, HC_5

description: healthy control


title: PBMC derived macrophages-IFNg Treated Donor 7

description: Library name: 7-IFNg


title: PBMC derived macrophages-IFNg Treated Donor 4

description: Library name: 4-IFNg


title: Preimmune Chip-seq male

city: Moscow

first: Anastasia

last: Revel-Muroz

address: 34/5 Vavilov St.

country: Russia

institute: Institute of Gene Biology, Russian Academy of Sciences

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Peak calling was performed using MACS version 2 against preimmune control (Zhang et al. 2008) in paired-end mode (option format=BAMPE).
Peaks with p value less than 1x10-2 were passed to the IDR pipeline to access reproducibility of chip-seq replicates (https://sites.google.com/site/anshulkundaje/projects/idr).
Optimal set of reproduced peaks was chosen for each sample and passed to further analysis.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by MACS2 and deeptools bamCoverage (binSize 10) and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

source_name: whole organism

growth_protocol: Lines of Drosophila melanogaster were grown in population cages at 25 degrees. For chromatin preparation adult 3-day old flies were chosen.

extract_protocol:
Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL of nuclear lysis buffer (2 µL aliquots of such pre-cleared chromatin being stored as input material) were incubated overnight, at 4°C, with antibodies-Dynabeads complexes. After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl, and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted by the ChIP DNA Clean &Concentrator kit (Zymoresearch).
The ChIP-seq libraries were prepared with NEBNext®_Ultra™_II DNA Library Prep kit, as described in the manufacturer's instructions. Amplified libraries were quantified using fluorometry with DS-11 (DeNovix, United States) and Bioanalyzer 2100 (Agilent, United States). Diluted libraries were clustered on a pair-read flowcell and sequenced using a NovaSeq 6000 system (Illumina, United States).

treatment_protocol: Chromatin was prepared from two- to three-day-old adult males. A 1 g of adult flies was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized subsequently in a Potter and Dounce homogenizer with tight pestle, filtered through 100 µm Nylon Cell Strainer (Miltenyi Biotec, United States), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, protease inhibitors), one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, protease inhibitors). The suspension was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test extent of sonication and to measure DNA concentration. Debris was removed by centrifugation at 14 000 g, 4°C, for 10 min, and chromatin was pre-cleared with Protein A Dynabeads (Invitrogen). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein A (anti-Msl1, 1:100; anti-Msl2, 1:100; anti-Msl3, 1:500) Dynabeads (Invitrogen) mixed with 200 µL of PBST. Then antibodies-Dynabeads complexes were washed and equilibrated in nuclear lysis buffer.

tag: antibody source

value: rabbit

value: whole organism

value: wt

value: male

tag: chip antibody

value: IgG


title: DNT cells, HC_3

description: healthy control


title: DNT cells, HC_2

description: healthy control


title: Preimmune Chip-seq female, rep2

description: PI_female_merged.bam.10.RPKM.BedGraph.gz

value: female


title: PBMC derived macrophages-IFNg Treated Donor 5

description: Library name: 5-IFNg

value: PBMC derived macrophages


title: Preimmune Chip-seq female, rep1


title: PBMC derived macrophages-DMSO Treated Donor 7

description: Library name: 7-DMSO

value: DMSO


title: DNT cells, HC_1

description: healthy control

value: Peripheral  blood


title: PBMC derived macrophages-IFNg Treated Donor 1

description: Library name: 1-IFNg


title: PBMC derived macrophages-DMSO Treated Donor 5

description: Library name: 5-DMSO


title: PBMC derived macrophages-DMSO Treated Donor 3

description: Library name: 3-DMSO


title: PBMC derived macrophages-DMSO Treated Donor 4

description: Library name: 4-DMSO


title: DNT cells, HC_4

description: healthy control

value: Peripheral  double negative T cell


title: PBMC derived macrophages-DMSO Treated Donor 2

description: Library name: 2-DMSO


title: MSL3_male, rep1


title: PBMC derived macrophages-DMSO Treated Donor 1

description: Library name: 1-DMSO


title: PBMC derived macrophages-IFNg Treated Donor 2

description: Library name: 2-IFNg


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-CHES-1-like embryos, rep 4

city: Terre Haute

first: Shaad

middle: M.

last: Ahmad

state: IN

address: Science Building, Room 277, 600 Chestnut St.

department: Department of Biology

institute: Indiana State University

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-CHES-1-like insertion that constitutively expresses CHES-1-like within these Twist expressing cells
Sample_SH_19

data_processing:
TTophat 2, samtools sort, HTSeq count.
Assembly: dmel_r6.05_FB2015_02
Supplementary files format and content: Tab-delimated file with raw counts for each sample

source_name: FACS-sorted GFP positive cells (mesodermal cells)

growth_protocol: Embryos were aged to stage 11-early stage 12 at 25°C.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions of FACS-sorted mesodermal cells.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq stranded total RNA library prep kit following the manufacturer's protocols

tag: age

value: cell suspensions of stage 11/early stage 12 embryos

value: twi-GAL4 UAS-2EGFP/UAS-CHES-1-like


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-CHES-1-like embryos, rep 3

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-CHES-1-like insertion that constitutively expresses CHES-1-like within these Twist expressing cells
Sample_SH_13

value: FACS-sorted GFP positive cells (mesodermal cells)


title: PBMC derived macrophages-DMSO Treated Donor 8

description: Library name: 8-DMSO


title: PBMC derived macrophages-DMSO Treated Donor 6

description: Library name: 6-DMSO


title: PBMC derived macrophages-IFNg Treated Donor 3

description: Library name: 3-IFNg


title: MSL3_m1wt_male, rep1

description:
MSL3_m1wt_male.bam.10.RPKM.BedGraph.gz
MSL3_m1wt_male.narrowPeak.gz


title: KO vs WT - replica 2

city: Houston

first: Marco

last: Sardiello

state: TX

address: One Baylor Plaza

department: MHG

institute: Baylor College of Medicine

description: Transcriptional profiles of heterozygous and homozygous Pdp1-p205 larvae - replica 2

hyb_protocol: Genomics Solution GeneTAC hybridisation station with Ocimum hybridisation buffer. Hybridisation and washing described in detail at http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.php

scan_protocol: Axon 4000B scanner using standard protocols (http://www.flychip.org.uk/protocols/imaging/scanning2.php)

data_processing: Image analysis were conducted using the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/dapple-tr.pdf), data normalization were performed using the VSN statistical model (http://www.ncbi.nlm.nih.gov/pubmed/12169536), the CyberT framework (http://www.ncbi.nlm.nih.gov/pubmed/11395427) was used to assess the significance of the microarray results.

source_name: homozygous Pdp1-p205

label_protocol: Standard direct incorporation of Cy dyes during 1st strand cDNA synthesis (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.php)

extract_protocol: RNA extraction with TRIzol

value: larvae

value: homozygous Pdp1-p205

source_name: heterozygous Pdp1-p205

value: heterozygous Pdp1-p205


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-CHES-1-like embryos, rep 2

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-CHES-1-like insertion that constitutively expresses CHES-1-like within these Twist expressing cells
Sample_SH_7


title: KO vs WT - replica 3 - dye swap

description: Transcriptional profiles of heterozygous and homozygous Pdp1-p205 larvae - replica 3 - dye swap


title: VGH1650: M, AD, Subject ID: 655, Age: 66y

city: Taipei

first: Yi-Long

last: Huang

state: Not US or Canada

address: No.155, Sec.2, Linong Street, Peitou

department: Center for Healthy Longevity and Aging Sciences

institute: National Yang Ming Chiao Tung University

description: Library name: VGH1650

data_processing:
CLC Genomics Workbench 21.0.5
Sequence reads were trimmed for adaptor sequence/low-quality sequences (Q<20)
Trimmed clean reads were mapped onto the Homo sapiens (hg38) sequence using CLC Genomics Workbench (Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3;Length fraction = 0.8;  Similarity fraction = 0.8)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including TPM value for each gene (used for machine learning analysis)
Supplementary files format and content: Tab-delimited text file including expected count for each gene (used for DESeq2 analysis)

source_name: white blood cells

extract_protocol:
Total RNA extraction from white blood cells was performed through phenol/chloroform method using TRIzol (T9424, Sigma). 1 μg of total RNA was used for the construction of sequencing libraries
Sequencing library preparation was performed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction

value: white blood cells

value: M

value: AD

tag: subject id


title: VGH1588: F, AD, Subject ID: 553, Age: 69y

description: Library name: VGH1588

value: F


title: VGH1553: M, AD, Subject ID: 573, Age: 63y

description: Library name: VGH1553


title: MSL3_m1GS, rep2

value: rabbit

value: whole organism


title: VGH1634: M, AD, Subject ID: 648, Age: 67y

description: Library name: VGH1634


title: VGH1526: F, AD, Subject ID: 618, Age: 74y

description: Library name: VGH1526


title: MSL3_m1wt_male, rep2

value: male


title: VGH1489: M, P-MCI, Subject ID: 645, Age: 68y

description: Library name: VGH1489

value: P-MCI


title: MSL3_male, rep2

value: wt


title: VGH1435: M, P-MCI, Subject ID: 501, Age: 85y

description: Library name: VGH1435


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-CHES-1-like embryos, rep 1

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-CHES-1-like insertion that constitutively expresses CHES-1-like within these Twist expressing cells
Sample_SH_1

tag: cell type


title: VGH1525: F, AD, Subject ID: 659, Age: 68y

description: Library name: VGH1525


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-jumu embryos, rep 4

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-jumu insertion that constitutively expresses Jumu within these Twist expressing cells
Sample_SH_21

tag: genotype

value: twi-GAL4 UAS-2EGFP/UAS-jumu


title: MSL3_m1GS, rep1

tag: tissue

value: female


title: VGH1434: M, AD, Subject ID: 367, Age: 84y

description: Library name: VGH1434


title: KO vs WT - replica 1

description: Transcriptional profiles of heterozygous and homozygous Pdp1-p205 larvae - replica 1


title: MSL3_female, rep2

tag: strain


title: VGH1336: F, AD, Subject ID: 433, Age: 83y

description: Library name: VGH1336


title: VGH1401: F, AD, Subject ID: 493, Age: 83y

description: Library name: VGH1401


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-jumu embryos, rep 3

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-jumu insertion that constitutively expresses Jumu within these Twist expressing cells
Sample_SH_15

value: cell suspensions of stage 11/early stage 12 embryos


title: VGH1289: M, AD, Subject ID: 125, Age: 73y

description: Library name: VGH1289


title: VGH1264: M, AD, Subject ID: 384, Age: 83y

description: Library name: VGH1264


title: VGH1245: F, P-MCI, Subject ID: 553, Age: 67y

description: Library name: VGH1245


title: MSL3_female, rep1


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-jumu embryos, rep 2

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-jumu insertion that constitutively expresses Jumu within these Twist expressing cells
Sample_SH_9


title: MSL3_dwt, rep1

description:
MSL3_dwt.bam.10.RPKM.BedGraph.gz
MSL3_dwt.narrowPeak.gz


title: MSL3_dwt, rep2


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-jumu embryos, rep 1

description:
FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-jumu insertion that constitutively expresses Jumu within these Twist expressing cells
Sample_SH_3


title: VGH1130: M, S-MCI, Subject ID: 535, Age: 66y

description: Library name: VGH1130

value: S-MCI


title: VGH1117: M, S-MCI, Subject ID: 533, Age: 72y

description: Library name: VGH1117


title: VGH1092: M, AD, Subject ID: 497, Age: 78y

description: Library name: VGH1092


title: VGH1052: F, AD, Subject ID: 342, Age: 69y

description: Library name: VGH1052


title: MSL3_d41, rep2


title: VGH1110: M, AD, Subject ID: 125, Age: 72y

description: Library name: VGH1110


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 4

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are doubly homozygous for both the CHES-1-like and jumu null deficiencies Df(1)CHES-1-like1 and Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_20

value: FACS-sorted GFP positive cells (mesodermal cells)


title: MSL3_d41, rep1


title: VGH0951: M, AD, Subject ID: 125, Age: 71y

description: Library name: VGH0951


title: VGH0855: F, S-MCI, Subject ID: 461, Age: 65y

description: Library name: VGH0855


title: VGH0929: M, S-MCI, Subject ID: 478, Age: 67y

description: Library name: VGH0929


title: VGH0923: M, AD, Subject ID: 425, Age: 76y

description: Library name: VGH0923


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 1

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are doubly homozygous for both the CHES-1-like and jumu null deficiencies Df(1)CHES-1-like1 and Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_2


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 2

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are doubly homozygous for both the CHES-1-like and jumu null deficiencies Df(1)CHES-1-like1 and Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_8


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP/+ embryos, rep 4

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the CHES-1-like null deficiency Df(1)CHES-1-like1 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_23

value: Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP/+


title: MSL3_d15, rep1


title: MSL3_d15, rep2


title: MSL2_male, rep2


title: VGH0827: M, P-MCI, Subject ID: 238, Age: 86y

description: Library name: VGH0827


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP/+ embryos, rep 3

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the CHES-1-like null deficiency Df(1)CHES-1-like1 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_17


title: VGH1151: M, S-MCI, Subject ID: 432, Age: 66y

description: Library name: VGH1151


title: VGH0828: M, S-MCI, Subject ID: 448, Age: 74y

description: Library name: VGH0828


title: VGH0815: F, S-MCI, Subject ID: 307, Age: 69y

description: Library name: VGH0815


title: MSL2_male, rep1


title: MSL2_m1wt_male, rep2

description:
MSL2_m1wt_male.bam.10.RPKM.BedGraph.gz
MSL2_m1wt_male.narrowPeak.gz


title: VGH0797: M, S-MCI, Subject ID: 445, Age: 79y

description: Library name: VGH0797


title: VGH0749: M, S-MCI, Subject ID: 426, Age: 64y

description: Library name: VGH0749


title: VGH0750: F, S-MCI, Subject ID: 427, Age: 62y

description: Library name: VGH0750


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP/+ embryos, rep 1

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the CHES-1-like null deficiency Df(1)CHES-1-like1 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_5


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 3

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are doubly homozygous for both the CHES-1-like and jumu null deficiencies Df(1)CHES-1-like1 and Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_14


title: VGH0803: M, S-MCI, Subject ID: 444, Age: 63y

description: Library name: VGH0803


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP/+ embryos, rep 2

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the CHES-1-like null deficiency Df(1)CHES-1-like1 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_11


title: MSL2_m1wt_male, rep1


title: GFP-positive cells from twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 4

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the jumu null deficiency Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_22


title: VGH0745: F, AD, Subject ID: 50, Age: 89y

description: Library name: VGH0745


title: VGH0732: F, P-MCI, Subject ID: 409, Age: 79y

description: Library name: VGH0732


title: VGH0737: F, S-MCI, Subject ID: 294, Age: 61y

description: Library name: VGH0737


title: MSL2_m1GS, rep2


title: MSL2_m1GS, rep1


title: VGH0694: F, AD, Subject ID: 342, Age: 67y

description: Library name: VGH0694


title: VGH0715: M, S-MCI, Subject ID: 399, Age: 72y

description: Library name: VGH0715


title: VGH0707: M, AD, Subject ID: 468, Age: 68y

description: Library name: VGH0707


title: GFP-positive cells from twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 3

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the jumu null deficiency Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_16


title: MSL2_dwt, rep2

description:
MSL2_dwt.bam.10.RPKM.BedGraph.gz
MSL2_dwt.narrowPeak.gz


title: GFP-positive cells from twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 1

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the jumu null deficiency Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_4


title: VGH0616: M, AD, Subject ID: 344, Age: 77y

description: Library name: VGH0616


title: VGH0625: F, AD, Subject ID: 289, Age: 71y

description: Library name: VGH0625


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/+ embryos, rep 4

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_24

value: twi-GAL4 UAS-2EGFP/+


title: MSL2_dwt, rep1


title: VGH0611: M, S-MCI, Subject ID: 339, Age: 60y

description: Library name: VGH0611


title: GFP-positive cells from twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 2

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the jumu null deficiency Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_10


title: VGH0689: M, S-MCI, Subject ID: 257, Age: 76y

description: Library name: VGH0689


title: VGH0551: M, P-MCI, Subject ID: 422, Age: 76y

description: Library name: VGH0551


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/+ embryos, rep 3

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_18


title: VGH0521: F, P-MCI, Subject ID: 50, Age: 88y

description: Library name: VGH0521


title: MSL2_d41, rep1


title: VGH0649: F, P-MCI, Subject ID: 460, Age: 64y

description: Library name: VGH0649


title: MSL2_d15, rep2


title: VGH0514: M, S-MCI, Subject ID: 369, Age: 79y

description: Library name: VGH0514


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/+ embryos, rep 2

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_12


title: VGH0498: M, P-MCI, Subject ID: 233, Age: 86y

description: Library name: VGH0498


title: GIST 430/V654A cells, treated with SHP099 (20 µM) for 24 hours [SHP099-430-3]

city: Shenzhen

first: Chunxiao

last: He

address: No.628, Zhenyuan Rd, Guangming (New) Dist.

institute: The seventh affiliated hospital of Sun Yat-sen University

description:
430-654-SHP099.txt
SHP099-430-3

data_processing:
Reads obtained from the sequencing machines, including raw reads were further filtered by fastp (version 0.18.0). Reads containing adapters, containing more than 10% of unknown nucleotides, and low-quality reads containing more than 50% of low-quality bases were removed.
rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Assembly: rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Supplementary files format and content: FPKM values for each sample

growth_protocol: GIST cells were cultured in IMDM supplemented with 20% FBS, in a 5% CO2, 37 °C incubator.

extract_protocol:
Cells from each group were extracted by using the Trizol method. RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and checked using RNase-free agarose gel electrophoresis.
Total mRNA was enriched by Oligo(dT) beads. Then, the enriched mRNA was fragmented and reverse-transcripted into cDNA with random primers. Second-strand cDNA was synthesized by DNA polymerase I. The cDNA fragments were purified with the QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size-selected by agarose gel electrophoresis, PCR amplified and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (China).

treatment_protocol: In the control group, cells were cultured for 24 hours. In the treatment group, cells were treated with SHP099 (20 µM) for 24 hours. Total mRNA was extracted, processed, and analyzed.

value: Cell line, adherent

value: wild type


title: VGH0506: M, AD, Subject ID: 186, Age: 81y

description: Library name: VGH0506

value: white blood cells

value: M


title: MSL2_d41, rep2


title: VGH0440: F, AD, Subject ID: 293, Age: 71y

description: Library name: VGH0440

value: F

value: AD


title: VGH0503: F, P-MCI, Subject ID: 407, Age: 73y

description: Library name: VGH0503


title: MSL1_male, rep2

value: rabbit

value: whole organism


title: VGH0423: F, S-MCI, Subject ID: 248, Age: 74y

description: Library name: VGH0423


title: VGH0417: M, S-MCI, Subject ID: 163, Age: 65y

description: Library name: VGH0417


title: MSL2_d15, rep1


title: MSL1_male, rep1

value: male


title: GIST 430/V654A cells, control, cultured for 24 hours [ctrl-430-3]

description:
430 control.txt
ctrl-430-3

value: untreated


title: VGH0454: F, S-MCI, Subject ID: 338, Age: 68y

description: Library name: VGH0454


title: GIST T1/D816E cells, treated with SHP099 (20 µM) for 24 hours [SHP099-816-3]

description:
T1-816-SHP099.txt
SHP099-816-3

source_name: GIST T1/D816E

value: GIST T1/D816E


title: VGH0212: M, S-MCI, Subject ID: 328, Age: 60y

description: Library name: VGH0212


title: MSL1_m1wt_male

description:
MSL1_m1wt_male.bam.10.RPKM.BedGraph.gz
MSL1_m1wt_male.narrowPeak.gz


title: VGH0196: M, AD, Subject ID: 81, Age: 70y

description: Library name: VGH0196


title: VGH0013: M, S-MCI, Subject ID: 188

description: Library name: VGH0013


title: VGH1416: F, P-MCI, Subject ID: 553, Age: 68y

description: Library name: VGH1416

value: P-MCI


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/+ embryos, rep 1

description:
FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells
Sample_SH_6


title: GIST T1 cells, treated with SHP099 (20 µM) for 24 hours [T1-SHP099-3]

description:
T1-SHP099.txt
T1-SHP099-3

source_name: GIST T1

value: GIST T1


title: VGH1420: F, P-MCI, Subject ID: 618, Age: 74y

description: Library name: VGH1420


title: VGH1373: M, AD, Subject ID: 70, Age: 83y

description: Library name: VGH1373


title: VGH1361: M, AD, Subject ID: 591, Age: 67y

description: Library name: VGH1361


title: VGH1354: F, AD, Subject ID: 585, Age: 78y

description: Library name: VGH1354


title: MSL1_female, rep2

value: wt

value: female


title: VGH1352: M, AD, Subject ID: 583, Age: 66y

description: Library name: VGH1352


title: GIST T1/D816E cells, control, cultured for 24 hours [ctrl-816-3]

description:
T1-816-control.txt
ctrl-816-3


title: MSL1_m1GS, rep2


title: GIST 430/V654A cells, treated with SHP099 (20 µM) for 24 hours [SHP099-430-2]

description:
430-654-SHP099.txt
SHP099-430-2


title: MSL1_female, rep1


title: MSL1_m1GS, rep1


title: VGH1319: F, AD, Subject ID: 543, Age: 69y

description: Library name: VGH1319


title: VGH1350: F, AD, Subject ID: 581, Age: 82y

description: Library name: VGH1350


title: VGH1286: M, AD, Subject ID: 560, Age: 61y

description: Library name: VGH1286


title: GIST T1/D816E cells, control, cultured for 24 hours [ctrl-816-2]

description:
T1-816-control.txt
ctrl-816-2


title: MSL1_dwt, rep1

description:
MSL1_dwt.bam.10.RPKM.BedGraph.gz
MSL1_dwt.narrowPeak.gz


title: GIST T1/D816E cells, treated with SHP099 (20 µM) for 24 hours [SHP099-816-2]

description:
T1-816-SHP099.txt
SHP099-816-2


title: VGH0999: F, S-MCI, Subject ID: 307, Age: 71y

description: Library name: VGH0999

value: S-MCI


title: VGH1212: M, P-MCI, Subject ID: 367, Age: 82y

description: Library name: VGH1212


title: GIST 430/V654A cells, control, cultured for 24 hours [ctrl-430-2]

description:
430 control.txt
ctrl-430-2


title: MSL1_d41, rep1


title: VGH1388: M, AD, Subject ID: 605, Age: 81y

description: Library name: VGH1388


title: GIST T1 cells, treated with SHP099 (20 µM) for 24 hours [T1-SHP099-2]

description:
T1-SHP099.txt
T1-SHP099-2


title: VGH0958: M, P-MCI, Subject ID: 384, Age: 82y

description: Library name: VGH0958


title: GIST T1 cells, control, cultured for 24 hours [T1-ctrl-3]

description:
T1 control.txt
T1-ctrl-3


title: VGH0930: M, P-MCI, Subject ID: 497, Age: 77y

description: Library name: VGH0930


title: MSL1_d15, rep2


title: VGH0905: F, P-MCI, Subject ID: 409, Age: 80y

description: Library name: VGH0905


title: VGH0879: M, AD, Subject ID: 376, Age: 84y

description: Library name: VGH0879


title: VGH0866: F, AD, Subject ID: 228, Age: 79y

description: Library name: VGH0866


title: GIST T1 cells, control, cultured for 24 hours [T1-ctrl-2]

description:
T1 control.txt
T1-ctrl-2


title: VGH0860: M, P-MCI, Subject ID: 314, Age: 82y

description: Library name: VGH0860


title: GIST 430/V654A cells, treated with SHP099 (20 µM) for 24 hours [SHP099-430-1]

description:
430-654-SHP099.txt
SHP099-430-1


title: MSL1_dwt, rep2


title: MSL1_d15, rep1


title: VGH0861: F, AD, Subject ID: 417, Age: 77y

description: Library name: VGH0861


title: GIST T1/D816E cells, treated with SHP099 (20 µM) for 24 hours [SHP099-816-1]

description:
T1-816-SHP099.txt
SHP099-816-1


title: VGH0847: M, AD, Subject ID: 490, Age: 77y

description: Library name: VGH0847


title: VGH0770: M, P-MCI, Subject ID: 422, Age: 77y

description: Library name: VGH0770


title: VGH0845: M, AD, Subject ID: TADN1-RA001, Age: 62y

description: Library name: VGH0845


title: MSL1_d41, rep2


title: VGH0760: M, S-MCI, Subject ID: 478, Age: 66y

description: Library name: VGH0760


title: GIST T1 cells, treated with SHP099 (20 µM) for 24 hours [T1-SHP099-1]

description:
T1-SHP099.txt
T1-SHP099-1


title: VGH0748: F, P-MCI, Subject ID: 475, Age: 61y

description: Library name: VGH0748


title: VGH0729: F, P-MCI, Subject ID: 407, Age: 74y

description: Library name: VGH0729


title: GIST T1 cells, control, cultured for 24 hours [T1-ctrl-1]

description:
T1 control.txt
T1-ctrl-1


title: VGH0650: F, S-MCI, Subject ID: 461, Age: 64y

description: Library name: VGH0650


title: VGH0687: M, P-MCI, Subject ID: 376, Age: 83y

description: Library name: VGH0687


title: VGH0644: M, S-MCI, Subject ID: 458, Age: 67y

description: Library name: VGH0644


title: GIST 430/V654A cells, control, cultured for 24 hours [ctrl-430-1]

description:
430 control.txt
ctrl-430-1


title: VGH0628: M, S-MCI, Subject ID: 448, Age: 73y

description: Library name: VGH0628


title: D7-shAK2#2

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Blood

growth_protocol: HL60 cells were maintained in IMDM supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were synthesized by using the TruSeq® RNA sample preparation kit (Illumina, USA) following TruSeq® RNA sample preparation guide.

treatment_protocol: HL60 cells infected with lentivirus-shZDHHC21 (#1 and #2) or shAK2 (#1 and #2) for 4 and 7 days

value: Blood

value: AML

value: shAK2#2 at day 7


title: VGH0848: F, P-MCI, Subject ID: 460, Age: 65y

description: Library name: VGH0848

value: white blood cells


title: VGH0622: M, S-MCI, Subject ID: 447, Age: 71y

description: Library name: VGH0622

value: M


title: VGH0627: F, S-MCI, Subject ID: 38, Age: 72y

description: Library name: VGH0627

value: F


title: D7-shZDHHC21#2

value: shZDHCH21#2 at day 7


title: GIST T1/D816E cells, control, cultured for 24 hours [ctrl-816-1]

description:
T1-816-control.txt
ctrl-816-1

value: Cell line, adherent

value: wild type


title: VGH0608: M, P-MCI, Subject ID: 233, Age: 77y

description: Library name: VGH0608


title: Chickpea leaf 12 h rep2

city: Nanjing

first: xian-sheng

last: wang

address: Weigang No.1

institute: NJAU

description: Biological replicate 2, compare gene expression profiles of leaf 12h with leaf 0h

hyb_protocol: Standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

organism: Cicer arietinum

source_name: Total RNA from chickpea leaf at 0 h

label_protocol: Total RNA was reverse transcribed with Cbcscript reverse transcriptase and T7 oligo dT primer. 2nd-strand cDNA was synthesized by DNA polymerase. The double-stranded cDNA was in vitro transcribed into cRNA and purified by Nucleospin RNA Clean-up kit (Macherey-Nagel, Germany). The resulting cRNA was reverse transcribed by MMLV and purified with PCR Nucleospin Extract II kit (Macherey-Nagel, Germany). After reverse transcription, the cDNA was labeled by Cy5-dCTP or Cy3-dCTP (GE Healthcare, USA) with klenow enzyme at 37 °C for 60 min.

growth_protocol: Chickpea seedling were growthed in quartz sand in a growth chamber with a day/night cycle of 14 h/10 h at 28°C/20°C

extract_protocol: For drought treatment group, roots and leaves were harvested separately at 0.5, 1.5, 6, 12, and 24 h during drought stress treatment, frozen in liquid nitrogen, and kept at -80 °C. Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA)

treatment_protocol: When grew for 10 days, the seedlings were carefully transferred to one-off cups with water. 24 h later, the seedlings were separated into two groups: one was exposed to 60 mM PEG 4000 as drought treatment, and another was harvested immediately as control (0 h)

value: leaf

tag: time point

source_name: Total RNA from chickpea leaf at 12 h


title: VGH0576: F, AD, Subject ID: 433, Age: 78y

description: Library name: VGH0576

value: AD


title: Chickpea leaf 24 h rep1

description: Biological replicate 1, compare gene expression profiles of leaf 24h with leaf 0h

source_name: Total RNA from chickpea leaf at 24 h


title: VGH0556: F, S-MCI, Subject ID: 427, Age: 62y

description: Library name: VGH0556


title: Chickpea leaf 6 h rep2

description: Biological replicate 2, compare gene expression profiles of leaf 6h with leaf 0h

source_name: Total RNA from chickpea leaf at 6 h


title: Chickpea leaf 1.5 h rep2

description: Biological replicate 2, compare gene expression profiles of leaf 1.5h with leaf 0h

source_name: Total RNA from chickpea leaf at 1.5 h


title: Chickpea leaf 24 h rep2

description: Biological replicate 2, compare gene expression profiles of leaf 24h with leaf 0h


title: Chickpea leaf 6 h rep1

description: Biological replicate 1, compare gene expression profiles of leaf 6h with leaf 0h


title: D7-shCtrl

tag: treatment

value: shCtrl at day 7


title: VGH0555: M, S-MCI, Subject ID: 426, Age: 63y

description: Library name: VGH0555

tag: Sex


title: VGH0539: F, P-MCI, Subject ID: 417, Age: 76y

description: Library name: VGH0539

value: P-MCI


title: VGH0614: M, S-MCI, Subject ID: 444, Age: 62y

description: Library name: VGH0614


title: VGH0536: M, AD, Subject ID: 152, Age: 82y

description: Library name: VGH0536


title: D7-shAK2#1

value: shAK2#1 at day 7


title: D4-shAK2#2

value: shAK2#2 at day 4


title: VGH0515: F, S-MCI, Subject ID: 411, Age: 73y

description: Library name: VGH0515


title: VGH0516: M, AD, Subject ID: 260, Age: 62y

description: Library name: VGH0516


title: VGH0415: M, S-MCI, Subject ID: 389, Age: 60y

description: Library name: VGH0415


title: D7-shZDHHC21#1

value: shZDHHC21#1 at day 7


title: D4-shZDHHC21#1

value: shZDHHC21#1 at day 4


title: VGH0321: M, S-MCI, Subject ID: 72, Age: 77y

description: Library name: VGH0321

value: S-MCI


title: D4-shCtrl

value: Blood

value: AML

value: shCtrl at day 4


title: Chickpea leaf 0.5 h rep1

description: Biological replicate 1, compare gene expression profiles of leaf 0.5h with leaf 0h

source_name: Total RNA from chickpea leaf at 0.5 h


title: Chickpea leaf 0.5 h rep2

description: Biological replicate 2, compare gene expression profiles of leaf 0.5h with leaf 0h


title: Chickpea leaf 1.5 h rep1

description: Biological replicate 1, compare gene expression profiles of leaf 1.5h with leaf 0h


title: D4-shAK2#1

value: shAK2#1 at day 4


title: Chickpea leaf 0 h rep2

description: Biological replicate 2, compare gene expression profiles of leaf 0h with leaf 0h


title: Chickpea leaf 12 h rep1

description: Biological replicate 1, compare gene expression profiles of leaf 12h with leaf 0h


title: VGH0309: M, AD, Subject ID: 256, Age: 84y

description: Library name: VGH0309

value: white blood cells

value: M


title: VGH0293: M, P-MCI, Subject ID: 198, Age: 81y

description: Library name: VGH0293


title: liver,non-tumor tissue,biol rep8

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina HiSeq platform used for basecalling.
Raw image Data files obtained by Illumina HiSeq are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with RPKM values for every gene and every sample

source_name: liver

extract_protocol:
Total RNAs were extracted from cells using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: disease

value: HBV-infected hepatocellular cacinoma

tag: tumor stage

value: non-tumor


title: Chickpea leaf 0 h rep1

description: Biological replicate 1, compare gene expression profiles of leaf 0h with leaf 0h

value: leaf


title: VGH0459: F, S-MCI, Subject ID: 352, Age: 77y

description: Library name: VGH0459

value: F


title: D4-shZDHHC21#2

tag: cell line

value: shZDHCH21#2 at day 4


title: VGH0402: M, S-MCI, Subject ID: 241, Age: 78y

description: Library name: VGH0402


title: VGH0264: F, AD, Subject ID: 347, Age: 81y

description: Library name: VGH0264

value: AD


title: liver,non-tumor tissue,biol rep7


title: VGH0240: F, S-MCI, Subject ID: 338, Age: 67y

description: Library name: VGH0240


title: liver,non-tumor tissue,biol rep6


title: Chickpea root 24 h rep2

description: Biological replicate 2, compare gene expression profiles of root 24h with root 0h

source_name: Total RNA from chickpea root at 0 h

value: root

source_name: Total RNA from chickpea root at 24 h


title: VGH0310: F, AD, Subject ID: 79, Age: 83y

description: Library name: VGH0310


title: Chickpea root 24 h rep1

description: Biological replicate 1, compare gene expression profiles of root 24h with root 0h


title: VGH0329: M, S-MCI, Subject ID: 369, Age: 78y

description: Library name: VGH0329


title: VGH0216: M, AD, Subject ID: 16, Age: 83y

description: Library name: VGH0216


title: VGH0219: M, AD, Subject ID: 202, Age: 72y

description: Library name: VGH0219


title: Chickpea root 12 h rep2

description: Biological replicate 2, compare gene expression profiles of root 12h with root 0h

source_name: Total RNA from chickpea root at 12 h


title: liver,non-tumor tissue,biol rep5


title: VGH0203: M, AD, Subject ID: 42, Age: 85y

description: Library name: VGH0203


title: VGH0265: M, AD, Subject ID: 127, Age: 71y

description: Library name: VGH0265


title: Chickpea root 6 h rep2

description: Biological replicate 2, compare gene expression profiles of root 6h with root 0h

source_name: Total RNA from chickpea root at 6 h


title: liver,non-tumor tissue,biol rep4


title: Chickpea root 12 h rep1

description: Biological replicate 1, compare gene expression profiles of root 12h with root 0h


title: VGH0195: F, AD, Subject ID: 323, Age: 73y

description: Library name: VGH0195


title: VGH0089: F, AD, Subject ID: 91, Age: 78y

description: Library name: VGH0089


title: Chickpea root 6 h rep1

description: Biological replicate 1, compare gene expression profiles of root 6h with root 0h


title: VGH0146: M, P-MCI, Subject ID: 125, Age: 67y

description: Library name: VGH0146

value: P-MCI


title: VGH0075: F, P-MCI, Subject ID: 289, Age: 69y

description: Library name: VGH0075


title: liver,non-tumor tissue,biol rep3


title: VGH0252: F, S-MCI, Subject ID: 287, Age: 66y

description: Library name: VGH0252


title: liver,non-tumor tissue,biol rep2


title: liver,non-tumor tissue,biol rep1


title: Chickpea root 1.5 h rep2

description: Biological replicate 2, compare gene expression profiles of root 1.5h with root 0h

source_name: Total RNA from chickpea root at 1.5 h


title: Chickpea root 0.5 h rep1

description: Biological replicate 1, compare gene expression profiles of root 0.5h with root 0h

source_name: Total RNA from chickpea root at 0.5 h


title: Chickpea root 0.5 h rep2

description: Biological replicate 2, compare gene expression profiles of root 0.5h with root 0h


title: Treg_CAR_donor12

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
Library name: Sample 21
8457-MR-64_5_S1_L005_

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode v42). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Human GRCh38
Supplementary files format and content: Input tables are included as tab separated files.

source_name: Treg Tcell

extract_protocol:
Cells were immediately pelleted by centrifugation at 4°C and resuspended in Homogenization Buffer containing thioglycerol provided in the purification kit.  RNA was extracted with a Promega Maxwell RSC 16 using the Maxwell RSC simplyRNA Cells kit (Cat# AS1390) according to the manufacturer’s instructions and RNA concentration was measured using a NanoDrop 8000.  RNA quality was assessed using an Agilent 4200 TapeStation and RINe values ranged from 9.9 to10.
Total RNA (50 ng) was used the construction of libraries with the New England Biolabs NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# 7490L) and Ultra II Directional RNA Library Prep Kit for Illumina (Cat# 7760L) according to the manufacturer’s instructions.  Dual-indexed libraries were pooled to and sequenced at VANTAGE (Vanderbilt University) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 25 million paired-end 150 bp reads per library.

value: Treg Tcell


title: liver,tumor tissue,biol rep7

value: tumor


title: Teff_CAR_donor12

description:
Library name: Sample 22
8457-MR-64_6_S1_L005_

source_name: Teff Tcell

value: Teff Tcell


title: Teff_TCR_donor12

description:
Library name: Sample 20
8457-MR-64_4_S1_L005_


title: Treg_TCR_donor12

description:
Library name: Sample 19
8457-MR-64_3_S1_L005_


title: Teff_NoAct_donor12

description:
Library name: Sample 18
8457-MR-64_2_S1_L005_


title: liver,tumor tissue,biol rep6


title: Treg_NoAct_donor12

description:
Library name: Sample 17
8457-MR-64_1_S1_L005_


title: Treg_TCR_donor18

description:
Library name: Sample 16
8457-MR-32_0006_S1_L005_


title: Chickpea root 1.5 h rep1

description: Biological replicate 1, compare gene expression profiles of root 1.5h with root 0h


title: Treg_CAR_donor18

description:
Library name: Sample 15
8457-MR-32_0005_S1_L005_


title: liver,tumor tissue,biol rep5


title: H937

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

data_processing:
Accurate quantification was performed with the QuantiFluor dsDNA system (Promega).
The size range of the generated cDNA libraries was measured with the DNA 1000 chip on the Bioanalyzer 2100 (280 bp).
Amplification and sequencing of cDNA libraries were performed using the cBot and HiSeq 2000 (Illumina, SR, 1x51 bp, 8-9 gigabases, >40 mio reads per sample).
Sequence images were transformed with Illumina software BaseCaller to bcl-files, which were demultiplexed to fastq-files with CASAVA (v1.8.2).
Quality check was done via FastQC (v0.10.1, Babraham Bioinformatics).
Sequence reads were aligned with the reference genome GRCh37 using the STAR RNA-Seq alignment tool.
Gene-level abundances were estimated using the RNA-seq by expectation-maximization (RSEM) algorithm.
Assembly: hg19
Supplementary files format and content: Matrix table with RSEM gene counts for every gene and every sample.

source_name: brain metastases

growth_protocol: All brain metastases samples were obtained with informed consent as approved by the local ethics committee (24/10/05).

extract_protocol:
Total RNA was isolated with the Trizol reagent from fresh frozen tissue and RNA integrity was checked with the Bioanalyzer 2100 (Agilent Technologies).
cDNA library preparation was carried out using the TruSeq Stranded Total RNA sample preparation kit (Illumina).

treatment_protocol: Samples of brain metastases were collected from patients previously diagnosed with colorectal cancer during neurosurgical removal.

value: brain metastases

value: primary colon cancer

value: neurosurgical removal


title: H907


title: liver,tumor tissue,biol rep4


title: Teff_CAR_donor18

description:
Library name: Sample 12
8457-MR-32_0002_S1_L005_


title: Teff_NoAct_donor18

description:
Library name: Sample 11
8457-MR-32_0001_S1_L005_


title: liver,tumor tissue,biol rep3


title: Chickpea root 0 h rep1

description: Biological replicate 1, compare gene expression profiles of root 0h with root 0h


title: H857


title: Teff_TCR_donor18

description:
Library name: Sample 13
8457-MR-32_0003_S1_L005_


title: H616


title: Treg_CAR_CAT_donor33

description:
Library name: Sample 9
10282-MR-0016_04_S1_L005_


title: Treg_CAR_P2Y3_donor33

description:
Library name: Sample 10
10282-MR-0016_05_S1_L005_


title: liver,tumor tissue,biol rep2


title: D8_DTA_decidua_RNASeq_bio_rep_3

city: Xiamen

first: Yang

last: Sun

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR with default parameters
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: Decidua

growth_protocol: Mice were housed in the animal care facility of Xiamen University according to the guidelines for the care and use of laboratory animals. All experimental procedures were approved by the Animal Welfare Committee of Research Organization (X200811), Xiamen University.

extract_protocol:
After removing myometrium and embryo tissues from the whole uteri, the decidua were homogenized in TRIzol (Invitrogen, 15596018) to extract total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Decidua

value: D8 of early pregnancy

value: DTA


title: Chickpea root 0 h rep2

description: Biological replicate 2, compare gene expression profiles of root 0h with root 0h


title: NoDox_d4_rep3

data_processing:
Trimmed reads were aligned to the GRCm38/mm10 mouse reference genome using STAR aligner (Dobin, Davis et al. 2013) with the parameter `--outSAMtype BAM SortedByCoordinate` to output a coordinate-sorted BAM file for downstream processing. Transcript abundances were estimated from genome aligned sequences using featureCounts (Liao, Smyth et al. 2014) in paired-end mode keeping read pairs in which both reads aligned but excluding chimeric assignments `-p -B`. Differential expression and statistical analysis were done using the DESeq2 library (Love, Huber et al. 2014). Differentially expressed genes were identified based on the following criteria: absolute Fold change >= 2 and adjusted P-value < 0.05. Biological processes enriched in differentially expressed RNA-seq gene sets were identified using the clusterProfiler library (Yu, Wang et al. 2012).
Assembly: Trimmed reads were aligned to the GRCm38/mm10 mouse reference genome using STAR aligner (Dobin, Davis et al. 2013) with the parameter `--outSAMtype BAM SortedByCoordinate` to output a coordinate-sorted BAM file for downstream processing
Supplementary files format and content: text file

source_name: EpiSCs

extract_protocol:
Total RNA from flash frozen samples was extracted using ISOLATE II RNA Mini Kit as per manufacturer recommendations (Bioline). In short, samples were thawed on ice, lysed and passed through a column purification process and DNase treatment. Precipitated RNA was eluted into RNase-free water. RNA concentration, DNA and ethanol contamination were measured using the NanoDrop (Thermo Fisher) and adjusted using RNase-free water as required.
RNA-seq libraries were prepared from extracted RNA by Genewiz (Azenta, China) using the NEBNext Ultra II RNA Library Preparation Kit (NEB, E7770) as per manufacturer protocol and 150 bp paired-end sequenced on the HiSeq 4000 (Illumina).
150 bp paired-end reads were trimmed using Trim Galore (Felix 2021)  in paired mode `--paired` keeping reads with at least 50 bp `--length 50`.

treatment_protocol: Embryoid bodies (EB) were maintained in EB-medium consisting of Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 15% Fetal Calf Serum (Gibco), 1% Non-essential amino-acid supplement (Gibco) and 0.1 μM 2-Mercaptoethanol (Sigma). EpiSC colonies were collected after Collagenase IV (Gibco) treatment and transferred to EB-medium within non-tissue culture treated plates and placed at 37 ºC, 5% CO2 on an orbital-shaker under slight rotation to prevent single EBs from settling to the bottom of the plate or attaching to each other. Media was replenished every 48 h, unless otherwise noted. Doxycycline induction, where appropriate, was achieved by adding 1 μg/mL Doxycycline (Sigma) to the culture.

value: EpiSCs

value: -Dox


title: D6.5_DTA_decidua_RNASeq_bio_rep_3

value: D6.5 of early pregnancy


title: H558


title: D8_WT_decidua_RNASeq_bio_rep_3

value: WT


title: VGH1341: M, P-MCI, Subject ID: 573, Age: 62y

description: Library name: VGH1341

source_name: white blood cells

value: white blood cells

value: M


title: Treg_TCR_donor33

description:
Library name: Sample 7
10282-MR-0016_02_S1_L005_


title: liver,tumor tissue,biol rep1

value: liver

value: HBV-infected hepatocellular cacinoma


title: Treg_CAR_CD19_donor33

description:
Library name: Sample 8
10282-MR-0016_03_S1_L005_

value: Treg Tcell


title: NoDox_d4_rep2


title: D8_DTA_decidua_ RNASeq_bio_rep_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR with default parameters
Assembly: mm10
Supplementary files format and content: CSV UTF-8 file includes FPKM values for each Sample


title: Treg_NoAct_donor33

description:
Library name: Sample 6
10282-MR-0016_01_S1_L005_


title: NoDox_d4_rep1


title: Treg_CAR_P2Y3_donor31

description:
Library name: Sample 5
10282-MR-0014_5_S1_L005_


title: H194


title: D6.5_WT_decidua_RNASeq_bio_rep_3


title: H608


title: Treg_CAR_CD19_donor31

description:
Library name: Sample 4
10282-MR-0014_4_S1_L005_


title: H296


title: D8_DTA_decidua_ RNASeq_bio_rep_1


title: H1792


title: NoDox_d2_rep2


title: Treg_CAR_CAT_donor31

description:
Library name: Sample 3
10282-MR-0014_3_S1_L005_


title: D8_WT_decidua_ RNASeq_bio_rep_2


title: BM1169

value: primary rectal cancer


title: Treg_NoAct_donor18

description:
Library name: Sample 14
8457-MR-32_0004_S1_L005_


title: D6.5_DTA_decidua_ RNASeq_bio_rep_2


title: Treg_NoAct_donor31

description:
Library name: Sample 1
10282-MR-0014_1_S1_L005_


title: NoDox_d2_rep1


title: D3Dox_d4_rep3

value: +Dox


title: BM1153

value: brain metastases


title: D8_WT_decidua_ RNASeq_bio_rep_1


title: D3Dox_d4_rep2


title: BM1167

value: primary colon cancer


title: D6.5_DTA_decidua_ RNASeq_bio_rep_1


title: BM1118

value: neurosurgical removal


title: D3Dox_d4_rep1


title: BM1135


title: NoDox_d2_rep3


title: H100


title: D1Dox_d2_rep3


title: D6.5_WT_decidua_ RNASeq_bio_rep_1

value: Decidua


title: Teff_TCR_donor31

description:
Library name: Sample 2
10282-MR-0014_2_S1_L005_

value: Teff Tcell


title: D6.5_WT_decidua_ RNASeq_bio_rep_2


title: BM1117


title: S7D1PKM1_PEP

city: Guanggzhou

first: Haopeng

last: Lin

state: Guangdong Province

address: No. 9 XingDaoHuanBei Road

institute: Guangzhou national lab

description: 10x genomics

data_processing:
Raw FASTAQ files were processed using the Cell Ranger pipeline (v4.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references) with the default options
High quality cells (>300 genes, <10% mitochondrial genes, <3%red blood cell gene expression) were selected for data normalization, scaling and principal component analysis (PCA) with default methods. Top 3000 variable genes were identified from each sample. The Harmony method was applied on the first 30 principal components, using sample as a covariate to integrate different samples (52). The integrated principal components were used to construct the UMAP, identify neighboring cells (via shared nearest neighbor), and define cell clusters using default Seurat methods.
Assembly: GRCh38
Supplementary files format and content: Matrix files and Tab-separated values files

extract_protocol:
Briefly, cell clusters were dispersed with TrpLE. Single cells with more than 85% viability were adjusted to 1,000 cells per μL. Approximately 16,000 cells were added to each channel of a 10X loading chip and then approximately 10,000 cells were captured.
Single-cell libraries were constructed using the Single Cell 3 Library & Gel Bead Kit v.3 according to the manufacturer's instructions (10X Genomics)120. Briefly, cell clusters were dispersed with TrpLE. Single cells with more than 85% viability were adjusted to 1,000 cells per μL. Approximately 16,000 cells were added to each channel of a 10X loading chip and then approximately 10,000 cells were captured. The captured cells were divided into Gel Beads in Emulsion (GEMs) and lysed, and the isolated RNA was reverse transcribed, barcoded, and amplified.

value: islet cells

value: PKM1 overexpression treated with PEP from S7D1


title: S7D14Con

description: 10x genomics

value: Control from S7D14


title: S7D14PKM1

description: 10x genomics

value: PKM1 overexpression from S7D14


title: D1Dox_d2_rep1

value: EpiSCs


title: S7D1PKM1

description: 10x genomics

value: PKM1 overexpression from S7D1


title: BM1105


title: RNA-seq of cultured neurons: Tβ4-4 [P17]

city: beijin

last: Zhang

address: Beijin

institute: CIBR

data_processing:
RNA-seq raw data were initially filtered with “FastQC” to obtain clean data after quality control. Clean data were aligned to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT. Raw counts for each gene were calculated by FeatureCounts.
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
The heat map was generated by heatmap with the z-score of each gene. Gene Set Enrichment Analysis (GSEA) was performed using the ClusterProfiler package in R, with an adjusted p-value less than 0.05
Assembly: Hisat2 GRCm38
Supplementary files format and content: 20230221_cultured_neuron_withPipe_NP24vsctrl
Supplementary files format and content: 20230221_cultured_neuron_withPipe_tb10vsctrl
Supplementary files format and content: 20230221_cultured_neuron_withPipe_tb4vsctrl

source_name: Brain, P0

extract_protocol:
Total RNA was extracted from cultured neurons using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's protocol
DNA library for sequencing was prepared following the protocol of SMARTer Stranded Total RNA-Seq Kit v2

value: Brain, P0

value: Primary cultured neurons

value: Added with Tβ4


title: S7D1Con_PEP

description: 10x genomics

value: PEP treatment from S7D1


title: BM1103

value: primary rectal cancer


title: RNA-seq of cultured neurons: Tβ4-3 [P16]

description: 20230221_cultured_neuron_withPipe_tb4vsctrl