title: YNG_Btnl2-KO_SI 964940

description:
YNG_Btnl2-KO_SI
964940
Counts_7964.txt


title: BRA31

status: Public on Jun 16 2021

type: SRA

city: Bethesda

first: Thomas

middle: John

last: Pranzatelli

state: MD

address: 10 Center Dr

department: Molecular Physiology and Therapeutics Branch

country: USA

institute: National Institute of Dental and Craniofacial Research

library_source: transcriptomic

data_processing:
Samples were run on an Illumina NextSeq500 configured for 37 x 37 PE reads.
FASTQ files were extracted using bcl2fastq, and the FASTQ files were further processed using this SNAKEMAKE_FILE pipeline using the snakemake/3.8 utility in the Biowulf2 cluster.
Quality of the reads was evaluated using the FastQC software. The reads satisfy all critical parameters and are deemed of sufficient quality to proceed with further processing and analysis.
Read mapping against a recent ENCODE human release was performed using the STAR v2.5.2a aligner using the standard mode with mapping parameters derived from the GENCODE project
For read counting we used the quantMode utility of the STAR aligner.
Supplementary_files_format_and_content: The counts are generated during mapping, producing one count file per sample, which are then merged as RAWCOUNTFILE.
Supplementary_files_format_and_content: Normalized counts per gene (CPM, or counts per million reads) in the TMMNORMALIZEDCOUNTS file

molecule: total RNA

organism: Homo sapiens

source_name: minor salivary glands

extract_protocol:
Minor salivary glands were obtained from study participants and stored in RNAlater (Qiagen) until RNA extraction. Samples were homogenized with a Bullet-Blender (Next Advance) or an Omni TH (Omni International). Total RNA was extracted with an RNeasy Mini kit according to the instructions of the manufacturer (Qiagen). The quality of RNA was measured using a 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ribosomal RNA ratio of 1.7 and an RNA integrity number of ≥ 6.5 were used for the arrays.
The cDNA libraries were produced by the Genomics and Computational Biology Core (GCBC) using the Nextera XT method.

tag: tissue

value: minor salivary glands

tag: diagnosis

value: Healthy volunteer

tag: gender

value: Female

tag: age


title: MDA-MB-468 - c19ROW14

city: Shenzhen

first: Wenfei

last: Jin

state: Guangdong

address: 1088 Xueyuan Rd #faculty research building 1

department: Department of Biology

country: China

institute: Southern University of Science and Technology

data_processing:
Basecalling was performed with CASAVA v1.7 from Illumina.
Each column was demultiplexed to single cells using a script provided by Fluidigm (mRNASeqHT_demultiplex.pl).
Reads were filtered and trimmed using Trim Galore version 0.6.1.
Reads from each cell were mapped to human reference genome (hg19) or mouse GRCm38  by STAR version 2.5.2b.
Gene expression level was quantified by htseq-count version 0.11.2.
Genome_build: hg19 for human; GRCm38 for mouse
Supplementary_files_format_and_content: Counts matrix are tab-delimited files containing raw counts of each cell. Each column represents a sample/cell and each row represents a gene.

extract_protocol:
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System.
We started scPolyA-seq library preparation by cell lysis. Then we added primers containing polyT and cell barcode for labeling the 3’ end of transcripts. Full-length cDNA was synthesized by template-switching reverse transcription, amplification and tagmentation with Tn5 transposases. Nextera XT DNA Library Preparation Kit (Ilumina) was applied to construct scPolyA-seq library. DNA fragments at the 3’ end of the cDNA were captured by targeted PCR, and sequencing indexes were added for amplification. The quality of library was examined by Qubit 3.0 Fluorometer and Agilent 2100 Bioanalyzer. Libraries separated by columns were pooled together and sequenced on Illumina HiSeq2500 to obtain 150-bp paired-end reads.

tag: cell line


title: BRA4


title: BRA33


title: BRA3


title: YNG_WT_CO 964934

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description:
YNG_WT_CO
964934
Counts_7964.txt

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include read count for each sample

organism: Mus musculus

source_name: colon

extract_protocol:
Total RNA was purified using MagMAX™-96 Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen).
Strand-specific RNA-seq libraries were prepared using KAPA stranded mRNA-Seq Kit (KAPA Biosystems).

tag: strain

value: colon

tag: genotype

value: WT


title: MDA-MB-468 - c19ROW12


title: YNG_WT_CO 964937

description:
YNG_WT_CO
964937
Counts_7964.txt


title: YNG_WT_CO 964935

description:
YNG_WT_CO
964935
Counts_7964.txt


title: YNG_WT_CO 964933

description:
YNG_WT_CO
964933
Counts_7964.txt


title: YNG_WT_CO 964932

description:
YNG_WT_CO
964932
Counts_7964.txt


title: MDA-MB-468 - c19ROW10


title: YNG_Btnl2-KO_CO 964931

description:
YNG_Btnl2-KO_CO
964931
Counts_7964.txt


title: BRA2


title: YNG_WT_CO 964936

description:
YNG_WT_CO
964936
Counts_7964.txt


title: YNG_Btnl2-KO_SI 964939

description:
YNG_Btnl2-KO_SI
964939
Counts_7964.txt

source_name: small intestine

value: small intestine


title: Epicardial Cells from H9-ESCs-R3

city: Boston

first: Harald

middle: Christian

last: Ott

state: Massachusetts

address: 55 Fruit Street.

department: Surgery

institute: Mass General Hospital

description: Cells provided by Palecek lab. Same cell source as used in Bao et al. 2016 study.

data_processing:
Read and Trimming: Trimmometric
QC aggregation: MultiQC
Mapping: Burrow-Wheeler Alignment Tool for Short Sequence (<100 bps)
Analysis of BAM to gene count: featureCounts v1.6.4 based on simple Illumina Analysis Mode
DEG and GO: iDEP.90 integrated web application for gene with 5 counts per million (CPM)
Genome_build: hg38 Human Reference Genome

source_name: Epicardial Cells fro H9-ESCs

growth_protocol: Epicardial formation from pre-epicardial cells (PECs) is necessary for normal myocardial morphogenesis. Recapitulating the developmental processes for epicardial formation in vitro could enable the generation of myocardial constructs with enhanced function, cellular complexity, and tissue architecture. We directed lateral plate mesodermal fate from BJ RiPSCs with prolonged GSK β inhibition and PEC differentiation with BMP4, RA and VEGF for 4 days at high efficiency. We performed RNA sequencing on our PECs which was harvested at day 7 of differentiation, and its extended culture at passage 1, to compare the RNA expression profile with H9-embryonic stem cells-derived epicardial cells derived from Palecek Laboratory at UW-Madison (Bao et al., 2016). The RNA extraction and sequencing work were outsourced to Girihlet Inc.

extract_protocol:
RNA was extracted from cell lysates using Zymo's Direct-zol RNA Miniprep Kit (Zymo cat. 2050)
Libraries were prepared using Illumina mRNA library Prep Kit (Illumina cat.  RS-122-2001)
RNA was reverse transcribed to cDNA. cDNA libraries were prepared using 500ng of total RNA using the TruSeq mRNA library prep kit. mRNA-seq and data analysis cDNA libraries were sequenced on the Illumina Nextseq platform to obtain 80-bp single-end reads.

tag: cell type

value: Epicardial Cells

tag: psc source


title: MDA-MB-468 - c19ROW13


title: MDA-MB-468 - c19ROW07


title: YNG_Btnl2-KO_CO 964925

description:
YNG_Btnl2-KO_CO
964925
Counts_7964.txt


title: YNG_Btnl2-KO_CO 964928

description:
YNG_Btnl2-KO_CO
964928
Counts_7964.txt


title: YNG_Btnl2-KO_CO 964930

description:
YNG_Btnl2-KO_CO
964930
Counts_7964.txt


title: MDA-MB-468 - c19ROW08


title: TMM5_2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with  TMM5_2 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: ARS1

source_name: IRC mouse

extract_protocol:
C18-4 and TM4 cells were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: IRC

value: TM4 cells

tag: treatment


title: YNG_Btnl2-KO_SI 964941

description:
YNG_Btnl2-KO_SI
964941
Counts_7964.txt


title: Passage 1 Epicardial Cells -R3

source_name: Pre-epicardial Cells after Extended Culture

value: Pre-epicardial Cells

value: BJRiPSCs


title: Epicardial Cells from H9-ESCs-R1


title: MDA-MB-468 - c19ROW09


title: Passage 1 Epicardial Cells -R2


title: TM3NC_3

description: The group information is prefixed with  TM3NC_3 in the column of processed data file


title: YNG_Btnl2-KO_CO 964929

description:
YNG_Btnl2-KO_CO
964929
Counts_7964.txt


title: MDA-MB-468 - c19ROW04


title: Passage 1 Epicardial Cells -R1


title: Epicardial Cells from H9-ESCs-R2


title: MDA-MB-468 - c19ROW06


title: TM3NC_2

description: The group information is prefixed with  TM3NC_2 in the column of processed data file


title: YNG_Btnl2-KO_CO 964926

description:
YNG_Btnl2-KO_CO
964926
Counts_7964.txt


title: Day 7 Pre-epicardial Cells- R3

source_name: Pre-epicardial Cells from BJR-IPSCs


title: CM5_3

description: The group information is prefixed with  CM5_3 in the column of processed data file

value: C18-4 cells


title: TMM5_3

description: The group information is prefixed with  TMM5_3 in the column of processed data file


title: MDA-MB-468 - c19ROW03


title: TM3NC_1

description: The group information is prefixed with  TM3NC_1 in the column of processed data file


title: CM5_2

description: The group information is prefixed with  CM5_2 in the column of processed data file


title: YNG_Btnl2-KO_CO 964927

description:
YNG_Btnl2-KO_CO
964927
Counts_7964.txt


title: CM5_1

description: The group information is prefixed with  CM5_1 in the column of processed data file


title: Day 7 Pre-epicardial Cells- R1


title: TMM5_1

description: The group information is prefixed with  TMM5_1 in the column of processed data file


title: MDA-MB-468 - c16ROW40


title: MDA-MB-468 - c19ROW05


title: MDA-MB-468 - c19ROW01


title: c3NC_1

description: The group information is prefixed with C3NC_1 in the column of processed data file


title: c3NC_3

description: The group information is prefixed with C3NC_3 in the column of processed data file


title: BR3_C_PI3K

city: Dundee

first: Laura

last: Spinelli

address: Dow Street

department: Cell Signalling and Immunology

country: United Kingdom

institute: University of Dundee

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR3 FOXO1-GFP KO + PI3Kdi 24hr

data_processing:
raw reads aligned against the GRCm38.p6 (Ensembl) build on theMus Musculus reference genome using the STAR aligner (version 2.7.1a)
STAR quantMode GeneCounts option used to map align reads to genes to generate a gene counts matrix using the annotation file GRCm38.98 (Ensembl)
noise from low count genes reduced using the filterByExpr function.
resulting count matrix  normalised by the Trimmed Mean of M-values (TMM) method using the edgeR package
EdgeR RPKM function used on TMM-normalised counts to calculate FPKM values, with total exon length calculated using GenomicRanges (Lawrence, 2013) as the sum of the non-overlapping exonic regions for a gene.
Genome_build: GCRm38.p6 (Ensembl) build on the Mus Musculus reference genome
Supplementary_files_format_and_content: text file includes  FPKM values for each Sample/replicate

source_name: cytotoxic T lymphocytes (CTL)

growth_protocol: Cytotoxic T lymphocytes (CTL) were generated from WT or FOXO1-GFP KO mice. Cells were activated for 48hr, then washed out and cultured for further four days in complete RPMI media supplemented with 20 ng/mL IL-2 and 2 ng/mL IL-12. On day six cells were plated at a cell density of 0.5x106 live cells/mL in complete RPMI media supplemented with 20 ng/mL IL-2 and 2 ng/mL IL-12 andwith or without IC87114 inhibitor (10 µM) for 24hr.

extract_protocol:
Total RNA was extracted from cell pellets using Qiagen RNAeasy mini kit (Qiagen) as per manufacturer’s instructions.
Libraries preparation was started from 300 ng of total RNA using the Illumina TruSeq Stranded mRNA sample preparation kit (15031047) as per manufacturer’s instructions.

treatment_protocol: Some samples were treated with 10 µM PI3Kp110δ IC87114 inhibitor.

value: cytotoxic T lymphocytes (CTL)

value: FOXO1-GFPfl/fl Gzmb cre+

value: BR3 FOXO1-GFP KO + PI3Kdi 24hr


title: BR1_C_PI3K

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR1 FOXO1-GFP KO + PI3Kdi 24hr

value: BR1 FOXO1-GFP KO + PI3Kdi 24hr


title: MDA-MB-468 - c16ROW35


title: MDA-MB-468 - c16ROW37


title: BR1_C_DMSO

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR1 FOXO1-GFP KO

value: BR1 FOXO1-GFP KO


title: BR2_C_PI3K

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR2 FOXO1-GFP KO + PI3Kdi 24hr

value: BR2 FOXO1-GFP KO + PI3Kdi 24hr


title: MDA-MB-468 - c16ROW38


title: BR3_C_DMSO

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR3 FOXO1-GFP KO

value: BR3 FOXO1-GFP KO


title: BR2_C_DMSO

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR2 FOXO1-GFP KO

value: BR2 FOXO1-GFP KO


title: MDA-MB-468 - c16ROW31


title: BR1_YN_PI3K

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR1 WT+ PI3Kdi 24hr

value: GzmB cre+

value: BR1 WT+ PI3Kdi 24hr


title: BR2_YN_PI3K

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR2 WT+ PI3Kdi 24hr

value: BR2 WT+ PI3Kdi 24hr


title: MDA-MB-468 - c16ROW32


title: BR2_YN_DMSO

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR2 WT

value: BR2 WT


title: MDA-MB-468 - c16ROW34


title: BR1_YN_DMSO

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR1 WT

value: BR1 WT


title: MDA-MB-468 - c16ROW30


title: c3NC_2

description: The group information is prefixed with  C3NC_2 in the column of processed data file

value: IRC


title: MDA-MB-468 - c16ROW28


title: BR3_no_IL2

description: CTL with and without IL-2 24hr RNAseq FPKM processed data.txt

data_processing:
raw reads aligned against the Mus musculus mm10 reference genome using the STAR aligner (version 2.5.2b)
number of reads associated with each gene counted using subreads package (version 1.5.1)
noise from low count genes reduced using the filterByExpr function.
resulting count matrix  normalised by the Trimmed Mean of M-values (TMM) method using the edgeR package
EdgeR RPKM function used on TMM-normalised counts to calculate FPKM values, with total exon length calculated using GenomicRanges (Lawrence, 2013) as the sum of the non-overlapping exonic regions for a gene.
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: text file includes  FPKM values for each Sample/replicate

source_name: T cells

growth_protocol:
Cytotoxic T lymphocytes (CTL) were generated from P14 transgenic mice. Cells were activated for 48hr, then washed out and cultured for further four days in complete RPMI media supplemented with 20 ng/mL IL-2. On day six cells were washed out of IL-2 and then either added 20 ng/ml IL-2 back for the IL-2 maintained conditions or deprived the cells of IL-2 for 24 hours
For ex vivo naïve CD8+ T cells, 24hr TCR activated and 24hr TCR activated in the presence of the PI3Kp110δ inhibitor IC87114 (10 µM synthesized in-house), three mice were used per biological replicate. Cells from the three mice were pooled and then equally divided into the three conditions. Three biological replicates were generated per condition. Single cell suspensions were generated by mashing lymph nodes in RPMI media and filtered through a 70 µm cell strainer. For 24hr TCR activated CD8+ T cells, they were suspended in complete RPMI media with 100 ng/mL antigenic peptide (glycoprotein amino acids 33-41 (gp33-41)), 20 ng/mL interleukin-2 (IL-2; Proleukin, Novartis) and 2 ng/mL interleukin-12 (IL-12; PeproTech).

treatment_protocol: Some samples were treated with 10 µM PI3Kp110δ IC87114 inhibitor

value: LCMV-P14 TCR transgenic

value: BR1 cytotoxic T lymphocytes IL2 washout 24hr

tag: biological replicate


title: BR2_IL2

value: BR1 cytotoxic Tlymphocytes maintained in IL3


title: BR2_no_IL2


title: BR3_IL2

value: BR1 cytotoxic Tlymphocytes maintained in IL4


title: BR1_no_IL2


title: BR1_IL2

value: BR1 cytotoxic Tlymphocytes maintained in IL2


title: BR3_YN_PI3K

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR3 WT+ PI3Kdi 24hr

value: cytotoxic T lymphocytes (CTL)

value: BR3 WT+ PI3Kdi 24hr


title: BR3_TCR_PI3Ki

description:
BR3 TCR activated 24hr+PI3Kdi
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

growth_protocol: For ex vivo naïve CD8+ T cells, 24hr TCR activated and 24hr TCR activated in the presence of the PI3Kp110δ inhibitor IC87114 (10 µM synthesized in-house), three mice were used per biological replicate. Cells from the three mice were pooled and then equally divided into the three conditions. Three biological replicates were generated per condition. Single cell suspensions were generated by mashing lymph nodes in RPMI media and filtered through a 70 µm cell strainer. For 24hr TCR activated CD8+ T cells, they were suspended in complete RPMI media with 100 ng/mL antigenic peptide (glycoprotein amino acids 33-41 (gp33-41)), 20 ng/mL interleukin-2 (IL-2; Proleukin, Novartis) and 2 ng/mL interleukin-12 (IL-12; PeproTech).

value: BR3 TCR activated 24hr+PI3Kdi


title: MDA-MB-468 - c16ROW29


title: MDA-MB-468 - c16ROW27


title: BR2_TCR

description:
BR2 TCR activated 24hr
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

value: BR2 TCR activated 24hr


title: BR1_TCR

description:
BR1 TCR activated 24hr
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

value: BR1 TCR activated 24hr


title: MDA-MB-468 - c16ROW23


title: MDA-MB-468 - c16ROW25


title: MDA-MB-468 - c16ROW24


title: BR3_TCR

description:
BR3 TCR activated 24hr
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

value: BR3 TCR activated 24hr


title: BR1_TCR_PI3Ki

description:
BR1 TCR activated 24hr+PI3Kdi
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

value: BR1 TCR activated 24hr+PI3Kdi


title: MDA-MB-468 - c16ROW22


title: BR3_YN_DMSO

description:
BR: Biological Replicate
NAME IN SUPPLEMENTARY FILE:
BR3 WT

value: GzmB cre+

value: BR3 WT


title: pPDsHSrSNxi1963d200429PosE

city: Cambridge

first: Evan

last: Macosko

state: MA

address: 75 Ames St, Broad Institute

institute: Broad Institute

description:
Homo_bcd.tsv.gz
Homo_features.tsv.gz
Homo_matrix.tsv.gz

data_processing:
Sequencing was performed on either Illumina NovaSeq6000 or Illumina NextSeq
All sequencing reads from substantia nigra samples were demultiplexed and aligned to their respective animal genomes using Drop-Seq Tools
Digital gene expression matrices for all substantia nigra samples were generated from Drop-Seq Tools after alignment with the following genomes per species: human (hg19), rat (Rnor_6.0), macaque (Mmul_10), Tree shrew (tupBel1)
Digital gene expression matrices for all caudate samples were demultiplexed and aligned to hg38_premrna using CellRanger v3. Digital gene expression matrices were generated using CellRanger v3
Digital gene expression matrices were aggregated on a per individual or species basis and analyzed using Seurat v2.3.4, rliger v1.0.0, and Harmony
Genome_build: hg19, hg38
Genome_build: Rnor_6.0
Genome_build: Mmul_10
Genome_build: tupBel1
Supplementary_files_format_and_content: digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells
Supplementary_files_format_and_content: barcodes.txt: names of barcodes/cells for corresponding DGE matrix file
Supplementary_files_format_and_content: genes.txt: names of transcripts/genes for corresponding DGE matrix file
Supplementary_files_format_and_content: Each species (human; rat; macaque; tree shrew) were aggregated into a combined species' matrix

molecule: polyA RNA

source_name: Human Substantia nigra pars compacta

extract_protocol:
Please see: https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge
10X Chromium Single Cell 3' (V3), manufacturer's protocol

value: Substantia nigra pars compacta

tag: Sex

value: Male

tag: pmi

tag: disease

value: Disease

tag: status

value: PD

tag: Cause of death

value: Parkinson's disease

tag: facs classification

value: Positive

tag: 10x version

tag: genome build


title: MDA-MB-468 - c16ROW21


title: BR1_naive

description:
BR1 CD8 Naive
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

value: LCMV-P14 TCR transgenic

value: BR1 CD8 Naïve (ex vivo)


title: pPDsHSrSNxi3298d200429PosB

tag: tissue

value: Ctrl

value: Prostate cancer


title: BR3_naive

description:
BR3 CD8 Naive
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

value: BR3 CD8 Naïve (ex vivo)


title: pPDsHSrSNxi3298d200429PosA

tag: age


title: pPDCN3898DAPIA030419

source_name: Human Caudate nucleus

value: Caudate nucleus

value: Negative


title: MDA-MB-468 - c16ROW20

tag: cell line


title: BR2_TCR_PI3Ki

description:
BR2 TCR activated 24hr+PI3Kdi
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

tag: strain

value: BR2 TCR activated 24hr+PI3Kdi


title: pPDsHSrSNxi1963d200429PosC


title: Day 7 Pre-epicardial Cells- R2

value: Pre-epicardial Cells

value: BJRiPSCs


title: MDA-MB-468 - c16ROW18


title: pPDCN3898DAPIB030419


title: MDA-MB-468 - c16ROW12


title: pPDsHSrSNxi2561d200429DAPIA

value: Female

value: LBD

value: Lewy body dementia


title: pPDsHSrSNxi2569d200429DAPIB

value: Substantia nigra pars compacta

value: Male

value: Disease


title: pPDsHSrSNxi1963d200429PosA

value: PD

value: Parkinson's disease

value: Positive


title: BR2_naive

description:
BR2 CD8 Naive
CD88_Naive_and_TCRactivated_24hr_inibitor_RNAseq_FPKM_processed_data.txt

value: LCMV-P14 TCR transgenic

value: BR2 CD8 Naïve (ex vivo)


title: pPDsHSrSNxi1963d200429PosD


title: pPDsHSrSNxi1963d200429PosB


title: pPDsHSrSNxi6173d200429PosA

value: Ctrl

value: Not listed


title: pPDsHSrSNxi3298d200429DAPIB

value: Prostate cancer

value: Negative


title: pPDsHSrSNxi2142d200429DAPIB


title: MDA-MB-468 - c16ROW08


title: pPDsHSrSNxi2561d200429PosB


title: pPDsHSrSNxi2544d200429PosC


title: pPDsHSrSNxi3298d200429DAPIA


title: pPDsHSrSNxi2544d200429PosA


title: pPDCN5730DAPI22119

value: Caudate nucleus

value: Seizure disorder,congenital heart disease


title: MDA-MB-468 - c16ROW09


title: MDA-MB-468 - c16ROW03


title: MDA-MB-468 - c16ROW07


title: pPDsHSrSNxi3322d200429PosH

value: Female

value: Colon cancer


title: MDA-MB-468 - c16ROW14


title: pPDsHSrSNxi3322d200429PosB


title: pPDsHSrSNxi2561d200429DAPIB

value: LBD

value: Lewy body dementia


title: MDA-MB-468 - c16ROW02


title: pPDsHSrSNxi2561d200429PosA

value: Substantia nigra pars compacta


title: pPDsHSrSNxi3298d200429DAPIC

value: Male


title: pPDsHSrSNxi3322d200429PosA


title: pPDsHSrSNxi2569d200429DAPIA

value: Disease


title: MDA-MB-468 - c15ROW38


title: MDA-MB-468 - c15ROW39


title: pPDsHSrSNxi6173d200429PosB


title: pPDsHSrSNxi4956d200429PosB


title: MDA-MB-468 - c15ROW37


title: MDA-MB-468 - c15ROW36


title: MDA-MB-468 - c16ROW05


title: pPDsHSrSNxi1963d200429DAPIA

value: PD

value: Parkinson's disease


title: pPDsHSrSNxi1963d200429DAPIC


title: MDA-MB-468 - c15ROW35


title: pPDsHSrSNxi3322d200429DAPIC


title: pPDsHSrSNxi2569d200429PosA

value: Positive


title: MDA-MB-468 - c15ROW33


title: pPDsHSrSNxi4568d200429PosA


title: pPDsHSrSNxi2544d200429DAPIA


title: MDA-MB-468 - c15ROW34


title: pPDsHSrSNxi3887d200429DAPIA


title: pPDsHSrSNxi2544d200429PosB


title: MDA-MB-468 - c15ROW32


title: pPDsHSrSNxi1963d200429DAPIB


title: pPDsHSrSNxi4560d200429PosA


title: MDA-MB-468 - c15ROW31


title: pPDCN5730NeuN22119

value: NeuN


title: MDA-MB-468 - c15ROW29


title: pPDsHSrSNxi3322d200429DAPIB

value: Ctrl


title: pPDsHSrSNxi2142d200429DAPIA


title: pPDsHSrSNxi4560d200429PosC


title: MDA-MB-468 - c15ROW28


title: pPDsHSrSNxi5610d200429Neg

value: Smoke inhalation


title: pPDsHSrSNxi2142d200429PosA


title: pPDsHSrSNxi3345d200429PosA


title: MDA-MB-468 - c15ROW27


title: pPDsHSrSNxi4568d200429DAPIA


title: pPDsHSrSNxi4568d200429DAPIB


title: MDA-MB-468 - c15ROW26


title: pPDCN3839DAPIA030419

value: Colon cancer, cholangiocarcinoma


title: pPDsHSrSNxi2561d200429PosC


title: pPDsHSrSNxi4775d200429DAPIA

value: Negative


title: pPDsHSrSNxi4560d200429PosB


title: pPDsHSrSNxi4568d200429PosB


title: pPDsHSrSNxi4560d200429DAPIA


title: pPDsHSrSNxi4775d200429DAPIC


title: MDA-MB-468 - c15ROW21


title: pPDsHSrSNxi4775d200429PosB


title: pPDsHSrSNxi3322d200429PosD


title: pPDsHSrSNxi3345d200429DAPIC


title: MDA-MB-468 - c15ROW24


title: pPDsHSrSNxi4775d200429DAPIB


title: pPDsHSrSNxi3873d200429PosC


title: MDA-MB-468 - c15ROW20


title: MDA-MB-468 - c15ROW19


title: MDA-MB-468 - c15ROW18


title: pPDsHSrSNxi4560d200429PosE


title: pPDsHSrSNxi3887d200429PosA


title: pPDsHSrSNxi3873d200429DAPIB


title: MDA-MB-468 - c15ROW17


title: pPDsHSrSNxi3873d200429PosB


title: pPDsHSrSNxi3322d200429PosC


title: pPDsHSrSNxi3887d200429DAPIB


title: pPDsHSrSNxi4560d200429PosD


title: pPDsHSrSNxi4956d200429DAPIA

value: Prostate cancer


title: MDA-MB-468 - c15ROW13


title: pPDsHSrSNxi3322d200429DAPIA


title: MDA-MB-468 - c15ROW14


title: MDA-MB-468 - c15ROW25


title: MDA-MB-468 - c15ROW16


title: pPDsHSrSNxi3873d200429PosD


title: pPDsHSrSNxi2544d200429DAPIB


title: pPDsHSrSNxi3873d200429DAPIA


title: MDA-MB-468 - c15ROW08


title: MDA-MB-468 - c15ROW12


title: pPDsHSrSNxi4956d200429DAPIB


title: pPDsHSrSNxi6173d200429DAPIA

value: Not listed


title: pPDsHSrSNxi3346d200429DAPIB

value: Female

value: Congestive Heart failure


title: MDA-MB-468 - c15ROW07


title: MDA-MB-468 - c15ROW09


title: pPDsHSrSNxi4560d200429DAPIB


title: pPDsHSrSNxi3322d200429PosF

value: Colon cancer


title: pPDsHSrSNxi3345d200429DAPIA


title: MDA-MB-468 - c15ROW06


title: MDA-MB-468 - c15ROW04


title: pPDsHSrSNxi3482d200429DAPIB

value: Coronary artery disease


title: MDA-MB-468 - c15ROW05


title: pPDsHSrSNxi4956d200429PosA

value: Substantia nigra pars compacta


title: pPDsHSrSNxi3887d200429PosB

value: Male


title: pPDsHSrSNxi4775d200429PosA

value: Disease

value: LBD


title: pPDsHSrSNxi3345d200429DAPIB


title: pPDsHSrSNxi3346d200429PosA


title: pPDsHSrSNxi3873d200429PosF

value: PD

value: Parkinson's disease


title: MDA-MB-468 - c14ROW39


title: pPDCN3839DAPIB030419

value: Caudate nucleus


title: pPDsHSrSNxi5610d200429Pos

value: Ctrl

value: Positive


title: MDA-MB-468 - c14ROW40


title: pPDsHSrSNxi3322d200429PosG


title: pPDsHSrSNxi3482d200429DAPIA


title: pPDCN4340DAPIB030419

value: Esophageal cancer with liver mets


title: pPDsHSrSNxi3346d200429PosB


title: pPDsHSrSNxi3346d200429PosC


title: MDA-MB-468 - c14ROW29


title: MDA-MB-468 - c14ROW34


title: MDA-MB-468 - c14ROW30


title: MDA-MB-468 - c14ROW36


title: MDA-MB-468 - c14ROW37


title: pPDsHSrSNxi3322d200429PosE


title: pPDsHSrSNxi3873d200429PosA


title: MDA-MB-468 - c14ROW28


title: pPDCN4340DAPIA030419

value: Negative


title: pPDsHSrSNxi3482d200429PosB


title: MDA-MB-468 - c14ROW38


title: 147_GS0638_CD4

city: San Diego

first: Hao

last: Wang

state: CA

address: 9452 Medical Center Dr

institute: University of California, San Diego

description:
X147_GS0638_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5) and features with 0 counts across all samples were removed
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
PBMCs were stained with anti-human CD3, CD4, CD8, CD14, CD19, CD56, and live/dead viability antibodies (see Supplemental Table S2 for antibody details). Subsequently, live CD4+ single positive (SP) (CD14-CD19-CD56-CD3+CD4+CD8-), CD8+ SP (CD14-CD19-CD56-CD3+CD4-CD8+), and CD4+CD8+ DP (CD14-CD19-CD56-CD3+CD4+CD8+) cells were sorted into TRIzol LS Reagent (Invitrogen, Carlsbad, CA) using a BD FACSAria cell sorter (BD Biosciences, San Jose, CA). Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (5 ng) was amplified following the Smart-seq2 protocol. cDNA was purified using AMPure XP beads (1:1 ratio; Beckman Coulter, Carlsbad, CA). From this step, 1 ng cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA library preparation kit and index kit (set B and C, respectively), Illumina, San Diego, CA).

treatment_protocol: No specific treatment involved

value: Cryopreserved PBMC

tag: disease group

value: dengue patient with warning signs of plasma leakage

tag: cell subtype


title: 148_GS0638_CD8

description:
X148_GS0638_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 145_GS0638_PBMC

description:
X145_GS0638_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: PBMC


title: 149_GS0638_CD4_CD8

description:
X149_GS0638_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: pPDsHSrSNxi3873d200429PosE

value: Female


title: 146_GS0638_CD3

description:
X146_GS0638_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW26


title: 144_GS0635_CD4_CD8

description:
X144_GS0635_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 142_GS0635_CD4

description:
X142_GS0635_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW25


title: 143_GS0635_CD8

description:
X143_GS0635_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 140_GS0635_PBMC

description:
X140_GS0635_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW24


title: 138_GS0611_CD8

description:
X138_GS0611_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW22


title: 135_GS0611_PBMC

description:
X135_GS0611_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW20


title: 137_GS0611_CD4

description:
X137_GS0611_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 136_GS0611_CD3

description:
X136_GS0611_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW21


title: 132_GS0330_CD4

description:
X132_GS0330_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 131_GS0330_CD3

description:
X131_GS0330_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 133_GS0330_CD8

description:
X133_GS0330_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 134_GS0330_CD4_CD8

description:
X134_GS0330_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 129_GS1795_CD4_CD8

description:
X129_GS1795_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage


title: 130_GS0330_PBMC

description:
X130_GS0330_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW16


title: 126_GS1795_CD3

description:
X126_GS1795_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 125_GS1795_PBMC

description:
X125_GS1795_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 127_GS1795_CD4

description:
X127_GS1795_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 141_GS0635_CD3

description:
X141_GS0635_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW15


title: MDA-MB-468 - c14ROW14


title: MDA-MB-468 - c14ROW12


title: MDA-MB-468 - c14ROW19


title: MDA-MB-468 - c14ROW18


title: 128_GS1795_CD8

description:
X128_GS1795_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW09


title: MDA-MB-468 - c14ROW17


title: 113_GS2139_CD8

description:
X113_GS2139_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 116_GS1641_CD3

description:
X116_GS1641_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 115_GS1641_PBMC

description:
X115_GS1641_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 117_GS1641_CD4

description:
X117_GS1641_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 121_GS1737_CD3

description:
X121_GS1737_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 123_GS1737_CD8

description:
X123_GS1737_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 120_GS1737_PBMC

description:
X120_GS1737_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 118_GS1641_CD8

description:
X118_GS1641_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 122_GS1737_CD4

description:
X122_GS1737_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 114_GS2139_CD4_CD8

description:
X114_GS2139_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 119_GS1641_CD4_CD8

description:
X119_GS1641_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 124_GS1737_CD4_CD8

description:
X124_GS1737_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 108_GS2137_CD8

description:
X108_GS2137_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 109_GS2137_CD4_CD8

description:
X109_GS2137_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 112_GS2139_CD4

description:
X112_GS2139_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 111_GS2139_CD3

description:
X111_GS2139_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 107_GS2137_CD4

description:
X107_GS2137_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 106_GS2137_CD3

description:
X106_GS2137_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW10


title: MDA-MB-468 - c14ROW05


title: MDA-MB-468 - c14ROW08


title: MDA-MB-468 - c14ROW02


title: 104_GS1845_CD4_CD8

description:
X104_GS1845_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW37


title: 103_GS1845_CD8

description:
X103_GS1845_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW38


title: 102_GS1845_CD4

description:
X102_GS1845_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 105_GS2137_PBMC

description:
X105_GS2137_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW36


title: 097_GS1798_CD4

description:
X097_GS1798_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 099_GS1798_CD4_CD8

description:
X099_GS1798_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW34


title: MDA-MB-468 - c13ROW32


title: 095_GS1798_PBMC

description:
X095_GS1798_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 096_GS1798_CD3

description:
X096_GS1798_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c14ROW07


title: MDA-MB-468 - c13ROW35


title: 094_GS1467_CD4_CD8

description:
X094_GS1467_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 100_GS1845_PBMC

description:
X100_GS1845_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 098_GS1798_CD8

description:
X098_GS1798_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 093_GS1467_CD8

description:
X093_GS1467_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 091_GS1467_CD3

description:
X091_GS1467_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW31


title: 092_GS1467_CD4

description:
X092_GS1467_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW30


title: 089_GS1869_CD4_CD8

description:
X089_GS1869_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 090_GS1467_PBMC

description:
X090_GS1467_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW29


title: 088_GS1869_CD8

description:
X088_GS1869_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW27


title: 101_GS1845_CD3

description:
X101_GS1845_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW26


title: 085_GS1869_PBMC

description:
X085_GS1869_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 086_GS1869_CD3

description:
X086_GS1869_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 087_GS1869_CD4

description:
X087_GS1869_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 084_GS1867_CD4_CD8

description:
X084_GS1867_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW21


title: 082_GS1867_CD4

description:
X082_GS1867_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW19


title: 083_GS1867_CD8

description:
X083_GS1867_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 078_GS1850_CD4

description:
X078_GS1850_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW16


title: 081_GS1867_CD3

description:
X081_GS1867_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 077_GS1850_CD3

description:
X077_GS1850_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 080_GS1867_PBMC

description:
X080_GS1867_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW15


title: 076_GS1850_PBMC

description:
X076_GS1850_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW10


title: 074_GS1830_CD8

description:
X074_GS1830_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 072_GS1830_CD3

description:
X072_GS1830_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW08


title: MDA-MB-468 - c13ROW09


title: 069_GS1817_CD8

description:
X069_GS1817_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 073_GS1830_CD4

description:
X073_GS1830_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW06


title: 066_GS1817_PBMC

description:
X066_GS1817_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 065_GS1796_CD4_CD8

description:
X065_GS1796_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 079_GS1850_CD8

description:
X079_GS1850_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 067_GS1817_CD3

description:
X067_GS1817_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW07


title: 064_GS1796_CD8

description:
X064_GS1796_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 063_GS1796_CD4

description:
X063_GS1796_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW03


title: 071_GS1830_PBMC

description:
X071_GS1830_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 061_GS1796_PBMC

description:
X061_GS1796_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW40


title: 059_GS2134_CD8

description:
X059_GS2134_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 062_GS1796_CD3

description:
X062_GS1796_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 075_GS1830_CD4_CD8

description:
X075_GS1830_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW39


title: 058_GS2134_CD4

description:
X058_GS2134_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW38


title: 068_GS1817_CD4

description:
X068_GS1817_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 057_GS2134_CD3

description:
X057_GS2134_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 055_GS2114_CD4_CD8

description:
X055_GS2114_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW36


title: 056_GS2134_PBMC

description:
X056_GS2134_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 054_GS2114_CD8

description:
X054_GS2114_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW35


title: 052_GS2114_CD3

description:
X052_GS2114_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 051_GS2114_PBMC

description:
X051_GS2114_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c13ROW02


title: 050_GS1676_CD4_CD8

description:
X050_GS1676_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 049_GS1676_CD8

description:
X049_GS1676_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 048_GS1676_CD4

description:
X048_GS1676_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW33


title: 047_GS1676_CD3

description:
X047_GS1676_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW31


title: 060_GS2134_CD4_CD8

description:
X060_GS2134_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 046_GS1676_PBMC

description:
X046_GS1676_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 044_GS1514_CD8

description:
X044_GS1514_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 053_GS2114_CD4

description:
X053_GS2114_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 043_GS1514_CD4

description:
X043_GS1514_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW28


title: MDA-MB-468 - c12ROW29


title: 040_GS1904_CD4_CD8

description:
X040_GS1904_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 041_GS1514_PBMC

description:
X041_GS1514_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 039_GS1904_CD8

description:
X039_GS1904_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 038_GS1904_CD4

description:
X038_GS1904_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW27


title: 037_GS1904_CD3

description:
X037_GS1904_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 036_GS1904_PBMC

description:
X036_GS1904_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: pPDsHSrSNxi3482d200429PosA

description:
Homo_bcd.tsv.gz
Homo_features.tsv.gz
Homo_matrix.tsv.gz

value: Coronary artery disease


title: MDA-MB-468 - c12ROW25


title: 035_GS1866_CD4_CD8

description:
X035_GS1866_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW34


title: 034_GS1866_CD8

description:
X034_GS1866_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 033_GS1866_CD4

description:
X033_GS1866_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW24


title: 032_GS1866_CD3

description:
X032_GS1866_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 0.5h_input

city: Shanghai

first: Chen

last: Lin

address: NO.2005 Songhu road

institute: Fudan university

description: whiB4-0.5h.q0.05_peaks.narrowPeak.annotation

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the M.marinum genome assembly using Bowtie2
Data were filtered using the IDR
The peaks were significantly enriched in ChIP samples compared with input genomic DNA, as determined by MACS2(Zhang et al, 2008) with a cutoff of enrichment fold larger than 1.5, q-value<0.05.
Genome_build: NC_010612.1
Supplementary_files_format_and_content: narrowPeak

molecule: genomic DNA

organism: Mycobacterium marinum

source_name: mycobacteria marinum 1218R OE WhiB4

growth_protocol: For ChIP-seq, 50 ml M. marinum cultures grown to log phase (OD600=0.8) under normoxia, or 100 ml M. marinum cultures grown under hypoxia (7 days) or 0.5 h after reaeration.

extract_protocol:
Lysates were clarified from sonicated bacteria and protein-DNA complexes were isolated with antibody.
DNA was purified using phenol–chloroform extraction.Sequencing was performed on the Illumina HiSeq platform. Coverage along the genome was calculated using Bowtie2(Langmead & Salzberg, 2012). Input genomic DNA without IP was used as a control.

value: mycobacteria marinum 1218R OE WhiB4

tag: chip antibody

value: 0.5hours reaeration


title: 0h_input

description: whiB4-0h.q0.05_peaks.narrowPeak.annotation

tag: treatment

value: 7 days hypoxia


title: MDA-MB-468 - c12ROW30


title: 028_GS1844_CD4

description:
X028_GS1844_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 029_GS1844_CD8

description:
X029_GS1844_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 042_GS1514_CD3

description:
X042_GS1514_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 027_GS1844_CD3

description:
X027_GS1844_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW19


title: 031_GS1866_PBMC

description:
X031_GS1866_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW23


title: MDA-MB-468 - c12ROW15


title: 026_GS1844_PBMC

description:
X026_GS1844_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW12


title: 0h_ChIPseq

value: Anti-FLAG® M2 Magnetic Beads (Sigma)


title: MDA-MB-468 - c12ROW11


title: 0.5h_ChIPseq


title: logarithmic phase_input

description: whiB4-logphase.q0.05_peaks.narrowPeak.annotation

value: normoxia conditioned logarithmic phase


title: logarithmic phase_ChIPseq


title: ΔwhiB4-48_rep3

data_processing:
High-throughput sequencing was carried out on an Illumina HiSeq 2500 system according to the  manufacturer’s instructions (Illumina HiSeq 2500 User Guide)
The raw reads were fltered by Seqtk and then mapped to the M. marinum M strain reference sequence (GenBank  GCA_000018345.1) using Bowtie2 (version: 2–2.0.5)
Counting of reads per gene was performed using HTSeq followed by TMM (trimmed mean of M-values) normalization
Genome_build: M. marinum M strain reference sequence (GenBank  GCA_000018345.1)
Supplementary_files_format_and_content: Excel file include FPKM values for all differential expression genes during reaeration between wild type and whiB4 mutant strain

growth_protocol: Cultures of M. marinum were grown to mid-log phase (OD600 0.4–0.45), and then transferred to a hypoxia culture based on the Wayne model with a headspace ratio of 0.5.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and purifed using the RNAClean XP Kit (Beckman Coulter) and  RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions.
Purifed RNA was used to construct cDNA library according to the TruSeq Stranded RNA LT Guide from Illumina.

treatment_protocol: cultures were sealed and incubated with slow stirring in the dark at 30°C in a conical flask for 7 days. Samples were taken 0, 0.5, 4, 24, and 48 h after reaeration

value: 7 days hypoxia, 48 hours reaeration

tag: genotype

value: whiB4 mutant


title: MDA-MB-468 - c12ROW08


title: 024_GS1841_CD8

description:
X024_GS1841_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW06


title: ΔwhiB4-48_rep1


title: 022_GS1841_CD3

description:
X022_GS1841_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 021_GS1841_PBMC

description:
X021_GS1841_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW20


title: ΔwhiB4-24_rep3

value: 7 days hypoxia, 24 hours reaeration


title: MDA-MB-468 - c12ROW05


title: MDA-MB-468 - c12ROW04


title: 019_GS1763_CD8

description:
X019_GS1763_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 020_GS1763_CD4_CD8

description:
X020_GS1763_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 025_GS1841_CD4_CD8

description:
X025_GS1841_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468 - c12ROW03


title: ΔwhiB4-24_rep1


title: ΔwhiB4-24_rep2


title: MDA-MB-468 - c12ROW02


title: HeLa_sync - c9ROW15

description: HeLa cells in this mixture were syncronized by TdR.

value: HeLa


title: ΔwhiB4-4_rep3

value: 7 days hypoxia, 4 hours reaeration


title: 023_GS1841_CD4

description:
X023_GS1841_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: ΔwhiB4-48_rep2


title: 016_GS1763_PBMC

description:
X016_GS1763_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c9ROW14


title: 017_GS1763_CD3

description:
X017_GS1763_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 014_GS1723_CD8

description:
X014_GS1723_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: ΔwhiB4-4_rep2


title: ΔwhiB4-0.5_rep3

value: 7 days hypoxia, 0.5 hours reaeration


title: ΔwhiB4-4_rep1


title: HeLa_sync - c9ROW08


title: HeLa_sync - c8ROW12


title: HeLa_sync - c9ROW04


title: ΔwhiB4-0.5_rep2


title: 012_GS1723_CD3

description:
X012_GS1723_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: Cryopreserved PBMC


title: MDA-MB-468 - c12ROW07


title: 018_GS1763_CD4

description:
X018_GS1763_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: ΔwhiB4-0.5_rep1


title: 011_GS1723_PBMC

description:
X011_GS1723_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c7ROW27


title: ΔwhiB4-0_rep3


title: 010_GS1698_CD4_CD8

description:
X010_GS1698_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c3ROW35


title: 009_GS1698_CD8

description:
X009_GS1698_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: ΔwhiB4-0_rep1


title: HeLa_sync - c7ROW12


title: HeLa_sync - c3ROW04


title: ΔwhiB4-0_rep2


title: 008_GS1698_CD4

description:
X008_GS1698_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 007_GS1698_CD3

description:
X007_GS1698_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: WT-1218R-48_rep3

value: wild type


title: 006_GS1698_PBMC

description:
X006_GS1698_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: PBMC


title: WT-1218R-48_rep2


title: WT-1218R-48_rep1


title: 013_GS1723_CD4

description:
X013_GS1723_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 005_GS1674_CD4_CD8

description:
X005_GS1674_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c3ROW02


title: WT-1218R-24_rep3


title: 004_GS1674_CD8

description:
X004_GS1674_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c2ROW02


title: HeLa_sync - c10ROW34


title: 003_GS1674_CD4

description:
X003_GS1674_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: WT-1218R-24_rep2


title: HeLa_sync - c2ROW15

description: HeLa cells in this mixture were syncronized by TdR.


title: HeLa_sync - c10ROW30


title: WT-1218R-4_rep3


title: 001_GS1674_PBMC

description:
X001_GS1674_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c05ROW33


title: 559_4_0595_CD4CD8

description:
X2_GS0595_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient with warning signs of plasma leakage


title: WT-1218R-24_rep1


title: WT-1218R-4_rep2


title: HeLa_sync - c05ROW31


title: WT-1218R-4_rep1


title: WT-1218R-0.5_rep3


title: 558_4_0595_CD8

description:
X2_GS0595_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 557_4_0595_CD4

description:
X2_GS0595_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c2ROW19


title: 556_4_0595_CD3

description:
X2_GS0595_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c05ROW02


title: 555_4_0595_PBMCs

description:
X2_GS0595_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 554_4_0591_CD4CD8

description:
X2_GS0591_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c04ROW06


title: 002_GS1674_CD3

description:
X002_GS1674_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage


title: HeLa_sync - c04ROW14


title: 553_4_0591_CD8

description:
X2_GS0591_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: WT-1218R-0_rep2


title: WT-1218R-0.5_rep1


title: WT-1218R-0_rep1


title: WT-1218R-0_rep3


title: 552_4_0591_CD4

description:
X2_GS0591_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 551_4_0591_CD3

description:
X2_GS0591_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c01ROW31


title: 550_4_0591_PBMCs

description:
X2_GS0591_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: pPDsTreeShrewrSNxixd200314x

description:
Tupaia_bcd.tsv.gz
Tupaia_features.tsv.gz
Tupaia_matrix.tsv.gz

organism: Tupaia belangeri

source_name: Tree Shrew Substantia nigra pars compacta

value: Substantia nigra pars compacta

tag: Sex

value: Male

value: Positive


title: HeLa_sync - c05ROW19


title: MT-D706

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

institute: Shandong University

description:
Processed data files:
SNP DiR-seq MDA-MB-468-rep1.txt
SNP DiR-seq MDA-MB-468-rep2.txt
SNP DiR-seq MDA-MB-468-rep3.txt
SNP DiR-seq BT-549-rep1.txt
SNP DiR-seq BT-549-rep2.txt
SNP DiR-seq BT-549-rep3.txt
SNP DiR-seq plasmid2-rep1.txt
SNP DiR-seq plasmid2-rep2.txt
SNP DiR-seq plasmid2-rep3.txt

data_processing:
The next-generation sequencing Data quality statistical software Cutadapt (version 1.9.1) was used to remove the adapters and low-quality sequences from the original sequencing Data (Pass Filter Data) to obtain Clean Data for subsequent information analysis.
The overlap area between read1 and read2 of Clean Reads was combined using Pandaseq (version 2.7) to produce complete sequences.
According to the Barcode sequence of read1 of each sample, the spliced Tag starting position is split into the corresponding sample with perfect matching, and the result is saved in FASTQ file.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every barcode and every sample (bundled into a tar archive)
Supplementary_files_format_and_content: SNP_barcode_id.txt
Supplementary_files_format_and_content: Samples to library relationships information.txt

molecule: other

organism:
Homo sapiens
synthetic construct

source_name: MDA-MB-468, BT-549, plasmid library

extract_protocol:
Twenty-four hours post-transfection, cells were washed twice and harvested in 1 × PBS, and Total RNA was extracted from all surviving cells using RNeasy Plus Mini Kit (74136, QIAGEN). We treated the mRNA with RapidOut DNA Removal Kit (K2981, Thermo Scientific) to remove the trace amount of genomic DNA residue according to the product manual. The purified RNA was then subjected to reverse transcription with High-Capacity cDNA Reverse Transcription Kits (4374967, Applied Biosystems). Briefly, 1.5μg RNA was added into 10μl of 2× RT Master Mix and made up to the final 20μl with nuclease-free water. The reactions were incubated at 25°C for 10 min, followed by 120 min at 37°C, then were inactivated Reverse Transcriptase by heating to 85°C for 5 min. The cDNA products were stored at -20°C or -80°C and ready for qPCR analysis and preparing the NGS sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols
We combined the 35 libraries into seven i7 indexes for Illumina sequencing.
To help the user demultiplex the raw data, we provided all the necessary information in "Sample to library relationship information.txt".

value: breast cancer cell lines MDA-MB-468, BT-549, plasmid library 2

tag: sample type

value: multiplexed

tag: molecule

value: total RNA and plasmid mixture


title: HeLa_sync - c01ROW24


title: HeLa_sync - c05ROW14


title: 549_4_0579_CD4CD8

description:
X2_GS0579_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_sync - c01ROW12


title: WT-1218R-0.5_rep2


title: 548_4_0579_CD8

description:
X2_GS0579_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c19ROW34


title: Sample 30: CRY2 F428D; high density  – Biological replicate 3

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

data_processing:
Basecalling was performed by the BGI Group.
Transcript abundance was estimated using Kallisto
Genome_build: GRCh37.p13 human genome reference assembly

source_name: mouse embryonic fibroblasts

growth_protocol: Cry2−/− mouse embryonic fibroblasts were grown in complete Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen cat #10569) supplemented with 15% FBS and 1% penicillin and streptomycin.  MEF cells were grown in a 37 °C incubator maintained at 5% CO2 and 3% O2 (low oxygen).

extract_protocol:
The cells from two wells were combined and collected for RNA extraction 11 days (high) and 14 days (low) after plating. RNA was extracted using RNeasy mini kit (Qiagen, Hilden, Germany, cat # 74106) according to the manufacturer’s protocol. The QIAGEN RNase-Free DNase Set was used for on-column DNA digestion according to the manufacturer’s protocol (Qiagen, Hilden, Germany,  cat # 79256).
Total RNA samples were sent to BGI Group, Beijing, China, for library preparation and sequencing. Reads (single-end 50bp at a sequencing depth of 20 million reads per sample) were generated by BGISEQ-500.

treatment_protocol: Cry2−/− primary MEFs stably overexpressing c-MYC and EV, WT, D325H, S510L, or F428D were plated in biological triplicate, two wells per replicate, in 6-well plates at two plating densities – 150 cells/ well (low) or 500 cells/ well (high).

tag: cell type

value: MEFs

tag: genotype/variation

value: stable overexpression of c-MYC and CRY2 F428D with 500 cells/well


title: Sample 29: CRY2 F428D; high density  – Biological replicate 2


title: HeLa_sync - c01ROW07

description: HeLa cells in this mixture were syncronized by TdR.


title: HeLa_normal - c19ROW32


title: Sample 28: CRY2 F428D; high density  – Biological replicate 1


title: 547_4_0579_CD4

description:
X2_GS0579_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 546_4_0579_CD3

description:
X2_GS0579_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 27: CRY2 S510L; high density  – Biological replicate 3

value: stable overexpression of c-MYC and CRY2 S510L with 500 cells/well


title: HeLa_sync - c01ROW35

value: HeLa


title: HeLa_normal - c19ROW24


title: Sample 26: CRY2 S510L; high density  – Biological replicate 2


title: HeLa_normal - c19ROW28


title: 545_4_0579_PBMCs

description:
X2_GS0579_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 543_4_0578_CD8

description:
X2_GS0578_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c19ROW21


title: 544_4_0578_CD4CD8

description:
X2_GS0578_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c16ROW39


title: 542_4_0578_CD4

description:
X2_GS0578_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 541_4_0578_CD3

description:
X2_GS0578_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c16ROW33


title: Sample 24: CRY2 D325H; high density  – Biological replicate 3

value: stable overexpression of c-MYC and CRY2 D325H with 500 cells/well


title: Sample 23: CRY2 D325H; high density  – Biological replicate 2


title: Sample 21: CRY2; high density  – Biological replicate 3

value: stable overexpression of c-MYC and CRY2 WT with 500 cells/well


title: Sample 22: CRY2 D325H; high density  – Biological replicate 1


title: HeLa_normal - c16ROW36


title: HeLa_normal - c16ROW26


title: Sample 20: CRY2; high density  – Biological replicate 2


title: HeLa_normal - c16ROW17


title: 540_4_0578_PBMCs

description:
X2_GS0578_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: Cryopreserved PBMC


title: Sample 19: CRY2; high density  – Biological replicate 1


title: HeLa_normal - c16ROW16


title: 537_4_0572_CD4

description:
X2_GS0572_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 18: empty vector control; high density – Biological replicate 3

value: stable overexpression of c-MYC and empty vector with 500 cells/well


title: Sample 25: CRY2 S510L; high density  – Biological replicate 1


title: 538_4_0572_CD8

description:
X2_GS0572_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 17: empty vector control; high density – Biological replicate 2


title: HeLa_normal - c16ROW11


title: 536_4_0572_CD3

description:
X2_GS0572_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 539_4_0572_CD4CD8

description:
X2_GS0572_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 16: empty vector control; high density – Biological replicate 1


title: HeLa_normal - c16ROW10


title: 533_4_1128_CD8

description:
X3_GS1128_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c16ROW15


title: HeLa_normal - c15ROW40


title: 532_4_1128_CD4CD8

description:
X3_GS1128_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c15ROW30


title: 531_4_1128_CD3

description:
X3_GS1128_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c15ROW22


title: Sample 12: CRY2 S510L; low density  – Biological replicate 3

value: stable overexpression of c-MYC and CRY2 S510L with 150 cells/well


title: 519_4_1128_CD4

description:
X3_GS1128_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient with warning signs of plasma leakage


title: Sample 11: CRY2 S510L; low density  – Biological replicate 2


title: HeLa_normal - c14ROW31


title: 530_4_1099_CD4CD8

description:
X3_GS1099_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 535_4_0572_PBMCs

description:
X2_GS0572_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage

value: PBMC


title: Sample 9: CRY2 D325H; low density  – Biological replicate 3

value: stable overexpression of c-MYC and CRY2 D325H with 150 cells/well


title: Sample 10: CRY2 S510L; low density  – Biological replicate 1


title: Sample 15: CRY2 F428D; low density  – Biological replicate 3

value: stable overexpression of c-MYC and CRY2 F428D with 150 cells/well


title: 529_4_1099_CD3

description:
X3_GS1099_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c13ROW24


title: HeLa_normal - c14ROW06


title: 518_4_1099_PBMCs

description:
X3_GS1099_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 7: CRY2 D325H; low density  – Biological replicate 1


title: Sample 8: CRY2 D325H; low density  – Biological replicate 2


title: Sample 14: CRY2 F428D; low density  – Biological replicate 2


title: HeLa_normal - c13ROW22


title: 528_4_1086_PBMCs

description:
X3_GS1086_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 13: CRY2 F428D; low density  – Biological replicate 1


title: Sample 6: CRY2; low density  – Biological replicate 3

value: stable overexpression of c-MYC and CRY2 WT with 150 cells/well


title: 516_4_1099_CD4

description:
X3_GS1099_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 5: CRY2; low density  – Biological replicate 2


title: HeLa_normal - c13ROW12


title: HeLa_normal - c14ROW35


title: 526_4_1086_CD3

description:
X3_GS1086_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c13ROW04


title: Sample 4: CRY2; low density  – Biological replicate 1


title: 527_4_1086_CD4

description:
X3_GS1086_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 517_4_1099_CD8

description:
X3_GS1099_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sample 3: empty vector control; low density – Biological replicate 3

value: stable overexpression of c-MYC and empty vector with 150 cells/well


title: HeLa_normal - c12ROW26


title: HeLa_normal - c12ROW17


title: Sample 2: empty vector control; low density – Biological replicate 2


title: Sample 1: empty vector control; low density – Biological replicate 1


title: HeLa_normal - c12ROW16


title: 515_4_1086_CD8

description:
X3_GS1086_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 514_4_1086_CD4CD8

description:
X3_GS1086_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 525_4_1035_CD4CD8

description:
X3_GS1035_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: eGFP/tdTomato-biological replicate 5

city: Toulouse

first: David

last: OHAYON

state: Haute-Garonne

address: Université Paul Sabatier 118 Route de Narbonne

country: France

institute: CNRS

data_processing:
All files were aligned to the reference mouse genome (Ensembl mus musculus GRCm38.91; gtf(mm10)) using STAR aligner (Version Galaxy Tool: V2.1)  with parameters --alignIntronMin 20 --alignIntronMax 1000000 --outFilterMismatchNmax 10
Read count per sample was computed using HT-seq count (Version Galaxy Tool: V1.0) with parameters  "--stranded=no -a 0 -t exon -i gene_id -m union -rpos -f bam -q"
Genome_build: mm10
Supplementary_files_format_and_content: ht-seq read counts output

source_name: eGFP/tdTomato_spinal cord

extract_protocol:
Spinal cords from Aldh1L1-GFP/Olig2td-tomato mice were harvested at postnatal day 7, only the brachial and thoracic levels were isolated. Tissue was digested using Papain dissociation kit and GFP/tdTomato+ cells were sorted on a FACS Aria sorter.
RNA libraries were prepared for sequencing using BGISEQ platform (BGISEQ-500)

tag: strain background

value: post natal day 7

value: spinal cord


title: 513_4_1035_PBMCs

description:
X3_GS1035_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: tdTomato-biological replicate 5

source_name: tdTomato_spinal cord


title: 511_4_1035_CD4

description:
X3_GS1035_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: eGFP-biological replicate 5

source_name: eGFP_spinal cord


title: 512_4_1035_CD8

description:
X3_GS1035_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: eGFP/tdTomato-biological replicate 3


title: MDA-MB-468_bulk 1

source_name: cell line MDA-MB-468


title: 510_4_1035_CD3

description:
X3_GS1035_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0390_CD8_Deng1

description:
X3_GS0390_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MDA-MB-468_bulk 2


title: 3_GS0300_CD8_Deng1

description:
X3_GS0300_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: eGFP-biological replicate 3


title: 3_GS0297_CD8_Deng1

description:
X3_GS0297_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: tdTomato-biological replicate 3


title: HeLa_normal - c12ROW10


title: 509_4_0389_PBMCs

description:
X2_GS0389_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: eGFP/tdTomato-biological replicate 2


title: 508_4_0389_CD8

description:
X2_GS0389_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0287_CD8_Deng1

description:
X3_GS0287_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 507_4_0389_CD4CD8

description:
X2_GS0389_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0372_CD8_Deng1

description:
X3_GS0372_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 506_4_0389_CD4

description:
X2_GS0389_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: tdTomato-biological replicate 2


title: eGFP-biological replicate 2


title: 3_GS0284_CD8_Deng1

description:
X3_GS0284_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 505_4_0389_CD3

description:
X2_GS0389_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 501_1_0340_PBMCs

description:
X1_GS0340_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0365_CD8_Deng1

description:
X3_GS0365_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: tdTomato-biological replicate 1


title: eGFP/tdTomato-biological replicate1


title: 3_GS0502_CD8_Deng1

description:
X3_GS0502_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0324_CD8_Deng1

description:
X3_GS0324_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 500_1_0340_CD8

description:
X1_GS0340_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0386_CD8_Deng1

description:
X3_GS0386_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 499_1_0340_CD4CD8

description:
X1_GS0340_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 497_1_0340_CD3

description:
X1_GS0340_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0489_CD8_Deng1

description:
X2_GS0489_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0603_CD8_Deng1

description:
X2_GS0603_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HeLa_normal - c14ROW27


title: Hypha_biorep1

city: Yokohama

first: Shuta

last: Asai

address: 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN

data_processing:
Illumina sequence was quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50, and reads containing “N” are discarded.
Quality-filtered libraries were aligned to the FocnCong:1-1 genome using CLC Genomic Workbench 20.
Genome_build: RSAI00000000 (genome accession at NCBI)
Supplementary_files_format_and_content: Tab-delimited text files include the transcription levels for each transcript as TPM (transcripts per million).  Only Fusarium oxysporum reads were evaluated in each sample.

organism: Fusarium oxysporum

source_name: hypha

extract_protocol:
RNAs were extracted by RNeasy Plant Mini Kit (QIAGEN).
library was constructed using a custom high-throughput method (Front Plant Sci 2012, 3:202)

value: hypha

tag: strain/cultivar

tag: condition

value: NO3 media


title: Hypha_biorep2

tag: tissue


title: Bud_cell_biorep3

source_name: bud cells

value: bud cells


title: 495_1_0336_CD8

description:
X1_GS0336_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Hypha_biorep3


title: 494_1_0336_CD4CD8

description:
X1_GS0336_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 496_1_0336_PBMCs

description:
X1_GS0336_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Bud_cell_biorep1


title: 2_GS0510_CD8_Deng1

description:
X2_GS0510_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0478_CD8_Deng1

description:
X2_GS0478_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 492_1_0336_CD3

description:
X1_GS0336_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: PDA_biorep2

source_name: mycelia

value: mycelia

value: PDA


title: Bud_cell_biorep2


title: 491_1_0328_PBMCs

description:
X1_GS0328_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: Cryopreserved PBMC


title: HeLa_normal - c12ROW37

value: HeLa


title: PDA_biorep1


title: 2_GS0366_CD8_Deng1

description:
X2_GS0366_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0497_CD8_Deng1

description:
X2_GS0497_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 10dpi_in_cabbage_biorep3

organism: Brassica oleracea

source_name: root

value: root

value: cv. Shosyu

value: infections


title: 490_1_0328_CD8

description:
X1_GS0328_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage


title: 10dpi_in_cabbage_biorep2


title: 489_1_0328_CD4CD8

description:
X1_GS0328_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: PDA_biorep3


title: 1_GS0475_CD8_Deng1

description:
X1_GS0475_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0330_CD8_Deng1

description:
X2_GS0330_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient with warning signs of plasma leakage


title: 10dpi_in_cabbage_biorep1


title: 488_1_0328_CD4

description:
X1_GS0328_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 493_1_0336_CD4

description:
X1_GS0336_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0337_CD8_Deng1

description:
X1_GS0337_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0351_CD8_Deng1

description:
X1_GS0351_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3dpi_in_cabbage_biorep3


title: 523_1_0322_CD8

description:
X1_GS0322_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 487_1_0328_CD3

description:
X1_GS0328_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3dpi_in_cabbage_biorep2


title: 2_GS0445_CD8_Deng1

description:
X2_GS0445_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3dpi_in_cabbage_biorep1


title: 486_1_0322_PBMCs

description:
X1_GS0322_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: PBMC


title: 1_GS0326_CD8_Deng1

description:
X1_GS0326_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0530_CD8_Deng1

description:
X1_GS0530_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 484_1_0322_CD3

description:
X1_GS0322_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 485_1_0322_CD4

description:
X1_GS0322_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0406_CD8_Deng1

description:
X1_GS0406_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0336_CD8_Deng1

description:
X1_GS0336_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 522_1_0322_CD4CD8

description:
X1_GS0322_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 483_1_0321_PBMCs

description:
X1_GS0321_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0393_CD8_Deng1

description:
X1_GS0393_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0392_CD8_Deng1

description:
X1_GS0392_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0300_CD4CD8_Deng1

description:
X3_GS0300_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0373_CD8_Deng1

description:
X1_GS0373_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 480_1_0321_CD4

description:
X1_GS0321_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 481_1_0321_CD4CD8

description:
X1_GS0321_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 479_1_0321_CD3

description:
X1_GS0321_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 482_1_0321_CD8

description:
X1_GS0321_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0287_CD4CD8_Deng1

description:
X3_GS0287_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 521_1_0315_CD4CD8

description:
X1_GS0315_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: DG_replicate1-4

city: Kyoto

first: Shinya

last: Oki

address: 53 Kawahara-cho, Shogoin

institute: Kyoto University

description:
UMI_count_Hippo_PIC.csv
cell_barcode_Hippocampus_sample.csv

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix:CSV

source_name: Hippocampal region

extract_protocol: Lysis solution(0.1% Tween and 400 ug/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55℃. cDNA;mRNA hybrids were purified with QIAGEN Mini Elute PCR Purification Kit.

tag: mice strain

value: ICR

tag: week old

value: 8 weeks

value: male


title: 478_1_0315_PBMCs

description:
X1_GS0315_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: CA3_replicate1-4


title: 3_GS0297_CD4CD8_Deng1

description:
X3_GS0297_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 477_1_0315_CD8

description:
X1_GS0315_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: CA1_replicate1-4


title: 2_GS0603_CD4CD8_Deng1

description:
X2_GS0603_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0372_CD4CD8_Deng1

description:
X3_GS0372_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0489_CD4CD8_Deng1

description:
X2_GS0489_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 476_1_0315_CD4

description:
X1_GS0315_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Low_input_1000  replicate1-3

description:
multiplexed sample: cell barcodes for each replicate are included in the file "cell_barcode_sample.csv"
UMI_count_Low_input.csv
cell_barcode_sample.csv
CEL-seq2 protocol
Each fastq file contains multiple samples with cell-barcodes and UMIs at read-1.
Low_input_1000_1-3_S57

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38 or GRCh38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Genome_build: GRCh38 or GRCm38
Supplementary_files_format_and_content: count matrix:CSV

growth_protocol: HeLa cells were cultured in E-MEM+NEAA+10%FBS (KAC: DSGM105 ) with 1% penicillin/streptomycin. NIH3T3 cells were cultured  in high glucose DMEM supplemented with 10%  calf serum, 1% penicilling/streptomycin, and 1% L-Glutamin .These cells were grown at 37°C in a humidified 5% CO2 atmosphere. For PIC experiments, these cells were grown on cover slips.

extract_protocol: Lysis solution(0.1% Tween and 400 ug/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55°C cDNA;mRNA hybrids were purified with QIAGEN Mini Elute PCR Purification Kit.

treatment_protocol: Stress granules were induced by addition of 75 mM NaAsO2 for 30 min.

value: NIH3T3 cells

value: UV + NIH3T3_Low_input

tag: stimulation

value: non-stimulation


title: 2_GS0330_CD4CD8_Deng1

description:
X2_GS0330_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

tag: disease group


title: Esophageal carcinoma after radiotherapy_4

type: RNA

city: changzhou

first: Jianlin

state: jiangsu

address: Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical Univ

institute: hospital

description: Gene expression data before and after radiotherapy and chemotherapy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Esophageal carcinoma after radiotherapy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: individual

value: patient 4

value: Esophageal carcinoma tissue

tag: time

value: after radiotherapy


title: Esophageal carcinoma after radiotherapy_2

value: patient 2


title: Esophageal carcinoma before radiotherapy_3

value: patient 3

value: before radiotherapy


title: Low_input_100  replicate1-3

description:
multiplexed sample: cell barcodes for each replicate are included in the file "cell_barcode_sample.csv"
UMI_count_Low_input.csv
cell_barcode_sample.csv
CEL-seq2 protocol
Each fastq file contains multiple samples with cell-barcodes and UMIs at read-1.
Low_input_100_1-3_S56


title: Esophageal carcinoma after radiotherapy_1

value: patient 1


title: Esophageal carcinoma before radiotherapy_2


title: Esophageal carcinoma before radiotherapy_4


title: Esophageal carcinoma after radiotherapy_3


title: 2_GS0388_CD4CD8_Deng1

description:
X2_GS0388_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: Cryopreserved PBMC

tag: cell subtype


title: 474_1_0304_PBMCs

description:
X1_GS0304_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage


title: Low_input_10  replicate1-5

description:
multiplexed sample: cell barcodes for each replicate are included in the file "cell_barcode_sample.csv"
UMI_count_Low_input.csv
cell_barcode_sample.csv
CEL-seq2 protocol
Each fastq file contains multiple samples with cell-barcodes and UMIs at read-1.
Low_input_10_1-5_S55


title: 2_GS0510_CD4CD8_Deng1

description:
X2_GS0510_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient with warning signs of plasma leakage


title: 473_1_0304_CD8

description:
X1_GS0304_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Esophageal carcinoma before radiotherapy_1


title: Low_input_1  replicate1-10

description:
multiplexed sample: cell barcodes for each replicate are included in the file "cell_barcode_sample.csv"
UMI_count_Low_input.csv
cell_barcode_sample.csv
CEL-seq2 protocol
Each fastq file contains multiple samples with cell-barcodes and UMIs at read-1.
Low_input_1_1-10_S54


title: 2_GS0366_CD4CD8_Deng1

description:
X2_GS0366_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 472_1_0304_CD4CD8

description:
X1_GS0304_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 475_1_0315_CD3

description:
X1_GS0315_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0336_CD4CD8_Deng1

description:
X1_GS0336_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 471_1_0304_CD4

description:
X1_GS0304_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0392_CD4CD8_Deng1

description:
X1_GS0392_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 5000 μm diameter replicate 4 [5000-4]

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix:(CSV) zipped

source_name: photo-irradiation 5000 μm diameter

extract_protocol:
Lysis solution(0.1% Tween and 400 μg/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55℃.
cDNA;mRNA hybrids were purified with QIAGEN Mini Elute PCR Purification Kit.

tag: strain

tag: developmental stage

value: Neural tube

value: UV+ Neural tube

tag: size

value: Diameter 5000 um


title: 445_4_0985_CD4CD8

description:
X3_GS0985_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 470_1_0304_CD3

description:
X1_GS0304_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 439_4_0985_PBMCs

description:
X3_GS0985_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: PBMC


title: 1_GS0326_CD4CD8_Deng1

description:
X1_GS0326_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 5000 μm diameter replicate 2 [5000-2]

value: ICR

tag: sample type


title: 426_4_0985_CD4

description:
X3_GS0985_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0297_CD4_Deng1

description:
X3_GS0297_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 427_4_0985_CD8

description:
X3_GS0985_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0287_CD4_Deng1

description:
X3_GS0287_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 425_4_0985_CD3

description:
X3_GS0985_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Low_input_0  replicate1-3

description:
multiplexed sample: cell barcodes for each replicate are included in the file "cell_barcode_sample.csv"
UMI_count_Low_input.csv
cell_barcode_sample.csv
CEL-seq2 protocol
Each fastq file contains multiple samples with cell-barcodes and UMIs at read-1.
Low_input_0_1-3_S58 (UVplus_ROImin)

value: NIH3T3 cells

value: UV + NIH3T3_Low_input


title: photo-irradiation 5000 μm diameter replicate 1 [5000-1]


title: photo-irradiation 75 μm diameter VM region replicate 5 [75VM-5]

value: UV+ VentroMedial

value: Diameter 75 um


title: Low_input_nonUV  replicate1-3

description:
multiplexed sample: cell barcodes for each replicate are included in the file "cell_barcode_sample.csv"
UMI_count_Low_input.csv
cell_barcode_sample.csv
CEL-seq2 protocol
Each fastq file contains multiple samples with cell-barcodes and UMIs at read-1.
Low_input_nonUV_1-3_S53

value: UV -

value: non-stimulation


title: 3_GS0372_CD4_Deng1

description:
X3_GS0372_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 444_4_0860_CD8

description:
X3_GS0860_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter VM region replicate 4 [75VM-4]


title: 443_4_0860_CD4CD8

description:
X3_GS0860_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0284_CD4_Deng1

description:
X3_GS0284_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter VM region replicate 3 [75VM-3]


title: photo-irradiation 5000 μm diameter replicate 3 [5000-3]


title: 3_GS0390_CD4_Deng1

description:
X3_GS0390_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 442_4_0860_CD3

description:
X3_GS0860_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0365_CD4_Deng1

description:
X3_GS0365_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0300_CD4_Deng1

description:
X3_GS0300_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0324_CD4_Deng1

description:
X3_GS0324_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter VM region replicate 1 [75VM-1]


title: photo-irradiation 75 μm diameter VM region replicate 6 [75VM-6]


title: 3_GS0386_CD4_Deng1

description:
X3_GS0386_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 423_4_0860_CD4

description:
X3_GS0860_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0502_CD4_Deng1

description:
X3_GS0502_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 422_4_0850_PBMCs

description:
X3_GS0850_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter MM region replicate 4 [75MM-4]

value: UV+ MedioMedial


title: photo-irradiation 75 μm diameter MM region replicate 2 [75MM-2]


title: 421_4_0850_CD8

description:
X3_GS0850_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0603_CD4_Deng1

description:
X2_GS0603_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 420_4_0850_CD4CD8

description:
X3_GS0850_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter MM region replicate 1 [75MM-1]


title: 2_GS0489_CD4_Deng1

description:
X2_GS0489_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 419_4_0850_CD4

description:
X3_GS0850_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0478_CD4_Deng1

description:
X2_GS0478_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter DL region replicate 6 [75DL-6]

value: UV+ DorsoLateral


title: photo-irradiation 75 μm diameter VM region replicate 2 [75VM-2]


title: 520_4_1128_PBMCs

description:
X3_GS1128_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0330_CD4_Deng1

description:
X2_GS0330_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter DL region replicate 5 [75DL-5]


title: 418_4_0850_CD3

description:
X3_GS0850_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 424_4_0860_PBMCs

description:
X3_GS0860_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 417_4_0843_PBMCs

description:
X3_GS0843_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0510_CD4_Deng1

description:
X2_GS0510_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0388_CD4_Deng1

description:
X2_GS0388_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 75 μm diameter MM region replicate 3 [75MM-3]


title: photo-irradiation 75 μm diameter DL region replicate 4 [75DL-4]


title: photo-irradiation 75 μm diameter DL region replicate 3 [75DL-3]


title: photo-irradiation 75 μm diameter DL region replicate 2 [75DL-2]


title: 2_GS0445_CD4_Deng1

description:
X2_GS0445_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0382_CD4_Deng1

description:
X2_GS0382_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 414_4_0843_CD4

description:
X3_GS0843_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 415_4_0843_CD4CD8

description:
X3_GS0843_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0382_CD8_Deng1

description:
X2_GS0382_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0366_CD4_Deng1

description:
X2_GS0366_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: eGFP-biological replicate 1

tag: age

value: post natal day 7

value: spinal cord


title: 413_4_0843_CD3

description:
X3_GS0843_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: Cryopreserved PBMC


title: photo-irradiation 75 μm diameter DL region replicate 1 [75DL-1]


title: 498_1_0340_CD4

description:
X1_GS0340_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage


title: 411_4_0818_CD8

description:
X3_GS0818_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient with warning signs of plasma leakage


title: photo-irradiation 250 μm diameter replicate 4 [250-4]

source_name: photo-irradiation 250 μm diameter

value: Neural tube

value: UV+ Neural tube

value: Diameter 250 um


title: 412_4_0818_PBMCs

description:
X3_GS0818_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

source_name: Cryopreserved PBMC

value: PBMC


title: 1_GS0351_CD4_Deng1

description:
X1_GS0351_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0475_CD4_Deng1

description:
X1_GS0475_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 410_4_0818_CD4CD8

description:
X3_GS0818_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 250 μm diameter replicate 2 [250-2]

value: ICR


title: 416_4_0843_CD8

description:
X3_GS0843_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0337_CD4_Deng1

description:
X1_GS0337_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 409_4_0818_CD4

description:
X3_GS0818_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: None photo-irradiation replicate 4 [None-4]

source_name: None photo-irradiation

value: UV-


title: 408_4_0818_CD3

description:
X3_GS0818_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 250 μm diameter replicate 1 [250-1]


title: 1_GS0336_CD4_Deng1

description:
X1_GS0336_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: None photo-irradiation replicate 3 [None-3]


title: 407_4_0632_PBMCs

description:
X2_GS0632_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0326_CD4_Deng1

description:
X1_GS0326_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: None photo-irradiation replicate 2 [None-2]


title: 1_GS0530_CD4_Deng1

description:
X1_GS0530_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 406_4_0632_CD8

description:
X2_GS0632_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0406_CD4_Deng1

description:
X1_GS0406_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 405_4_0632_CD4

description:
X2_GS0632_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: None photo-irradiation replicate 1 [None-1]


title: 2_GS0497_CD4_Deng1

description:
X2_GS0497_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: photo-irradiation 250 μm diameter replicate 3 [250-3]


title: 1_GS0393_CD4_Deng1

description:
X1_GS0393_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 404_4_0632_CD3

description:
X2_GS0632_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0392_CD4_Deng1

description:
X1_GS0392_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0373_CD4_Deng1

description:
X1_GS0373_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: VCPFF-CAMK2_1M-9: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3' gene counting, Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

tag: mouse genotype

value: nuclei of brain

value: 1 month


title: VCPFF-CAMK2_1M-8: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice


title: 441_4_0614_CD8

description:
X3_GS0614_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 403_4_0614_PBMCs

description:
X3_GS0614_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: VCPFF-CAMK2_2M-5: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice

value: 2 months


title: VCPFF-CAMK2_1M-7: Isolated single nuclei from cortex of 1 month old VCPfl/fl;Camk2-Cre mice


title: VCPFF-CAMK2_2M-6: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice


title: 3_GS0390_CD3_Deng1

description:
X3_GS0390_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 440_4_0614_CD4CD8

description:
X3_GS0614_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0300_CD3_Deng1

description:
X3_GS0300_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 402_4_0614_CD4

description:
X3_GS0614_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: VCPFF-CAMK2_2M-4: Isolated single nuclei from cortex of 2 month old VCPfl/fl;Camk2-Cre mice


title: VCPFF-3: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice

value: VCPfl/fl


title: 3_GS0287_CD3_Deng1

description:
X3_GS0287_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq