title: SM45.Complete_Responder.A8, Clinically stable MS, 8MU IFN-beta (250 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM45.Complete_Responder.A8, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM31.Complete_Responder.A6, Clinically stable MS, 8MU IFN-beta (250 ug), 0  h after IFN-beta injection

status: Public on Sep 27 2019

type: RNA

city: Chicago

first: Riyue

last: Bao

state: IL

address: 900 E 57 Street

department: Center for Research Informatics

country: USA

institute: University of Chicago

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM31.Complete_Responder.A6, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection

hyb_protocol: The fragmented and labeled single stranded cDNA was hybridized to Human Clariom D array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix  GeneChip WT Plus Reagent Kit guide (Thermo Fisher Scientific, Inc).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by GeneChip Command Console Software (AGCC, Thermo Fisher Scientific, Inc).  The Cel. files were then used to analyze the data with TAC console (Affymetrix).

data_processing: Raw CEL files were imported, log2-transformed, and normalized using GC Correction and Space Transformation Robust Multi-array Average (GC-STT-RMA) algorithms in Affymetrix Power Tools (APT, version 1·17·0).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human peripheral blood mononuclear cells

label_protocol: 250 ng of total RNA was used to generate double stranded cDNA and cRNA. 5.5ug of single stranded cDNA synthesized from cRNA was fragmented and biotin labeled according to Affymetrix  GeneChip WT Plus Reagent Kit manual (Thermo Fisher Scientific, Inc).

growth_protocol: mononuclear cells, extracted on ficoll gradients

extract_protocol: Total RNA extracted, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN).  Before affymetrix genechip Human ClariomD microarray analysis, the quality and quantity of each RNA sample were checked using a 2100 BioAnalyzer (Agilent, inc). High-quality RNA (RNA integrity number>9.0) was used for whole transcript microarray analysis

treatment_protocol: Blood obtained before, and 4 and 24  h after, in vivo injection of 8 or 16 million units (250 or 500 micrograms)) of interferon-b, subcutaneous.

tag: tissue

value: peripheral blood mononuclear cells

tag: age


title: SM32.Complete_Responder.A6, Clinically stable MS, 8MU IFN-beta (250 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM32.Complete_Responder.A6, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: LN, CD4 T cells, EM, 620043

type: SRA

first: Carole

last: Ober

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the human genome using STAR version 2.5.0
Reads aligning to genes were determined using the STAR using "--quantMode GeneCounts" command
The number of reads for each gene and each sample was summed across all sample sequencing files in R.
Counts per million (CPM) reads was calculated in R and genes with more than 1 CPM in 10 or more samples were included
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file of CPM

source_name: LN

extract_protocol:
Cells sorted into RLT buffer were extractued uwing Qiagen column purification
Takara SMART-seq v4 ultra low input RNA kit and Nextera XT DNA library preparation kit

value: LN

tag: cell type

value: CD4 T cells

tag: cell subset

value: EM

tag: individual

value: donor 620

tag: Sex

value: Female

tag: reported race

value: White


title: Lung, CD4 T cells, EM, 618143

source_name: Lung

value: Lung

value: donor 618

value: Male

value: Black


title: LN, CD8 T cells, EM, 618083

value: CD8 T cells


title: SM30.Complete_Responder.A5, Clinically stable MS, 16MU IFN-beta (500 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM30.Complete_Responder.A5, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: LN, CD4 T cells, TRM, 500044

value: TRM

value: donor 500


title: SM36.Complete_Responder.A6, Clinically stable MS, 16MU IFN-beta (500 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM36.Complete_Responder.A6, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: LN, CD4 T cells, EM, 618043


title: SM38.Complete_Responder.A7, Clinically stable MS, 8MU IFN-beta (250 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM38.Complete_Responder.A7, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: LN, CD4 T cells, EM, 576043

value: donor 576


title: Lung, CD4 T cells, EM, 576143


title: Lung, CD4 T cells, EM, 574143

value: donor 574


title: LN, CD8 T cells, EM, 616083

value: donor 616


title: Lung, CD4 T cells, EM, 571143

value: donor 571


title: LN, CD4 T cells, EM, 574043

value: LN


title: Lung, CD8 T cells, EM, 574183


title: SM29.Complete_Responder.A5, Clinically stable MS, 16MU IFN-beta (500 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM29.Complete_Responder.A5, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection

value: peripheral blood mononuclear cells


title: SM28.Complete_Responder.A5, Clinically stable MS, 16MU IFN-beta (500 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM28.Complete_Responder.A5, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: LN, CD8 T cells, EM, 571083

value: EM


title: SM27.Complete_Responder.A5, Clinically stable MS, 8MU IFN-beta (250 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM27.Complete_Responder.A5, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: LN, CD4 T cells, EM, 571043

value: CD4 T cells


title: Lung, CD8 T cells, EM, 515183

value: donor 515


title: LN, CD4 T cells, EM, 515043

value: White


title: SM25.Complete_Responder.A5, Clinically stable MS, 8MU IFN-beta (250 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM25.Complete_Responder.A5, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM24.Complete_Responder.A4, Clinically stable MS, 16MU IFN-beta (500 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM24.Complete_Responder.A4, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM23.Complete_Responder.A4, Clinically stable MS, 16MU IFN-beta (500 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM23.Complete_Responder.A4, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM19.Complete_Responder.A4, Clinically stable MS, 8MU IFN-beta (250 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM19.Complete_Responder.A4, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM21.Complete_Responder.A4, Clinically stable MS, 8MU IFN-beta (250 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM21.Complete_Responder.A4, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM17.Complete_Responder.A3, Clinically stable MS, 16MU IFN-beta (500 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM17.Complete_Responder.A3, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: LN, CD8 T cells, EM, 510083

value: donor 510

value: Female


title: SM26.Complete_Responder.A5, Clinically stable MS, 8MU IFN-beta (250 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM26.Complete_Responder.A5, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM18.Complete_Responder.A3, Clinically stable MS, 16MU IFN-beta (500 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM18.Complete_Responder.A3, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: LN, CD4 T cells, EM, 508043

value: donor 508

value: Male


title: Lung, CD4 T cells, EM, 508143

value: Lung

value: Black


title: Lung, CD8 T cells, EM, 500183

value: CD8 T cells

value: donor 500


title: LN, CD4 T cells, EM, 510043


title: SM20.Complete_Responder.A4, Clinically stable MS, 8MU IFN-beta (250 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM20.Complete_Responder.A4, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: Lung, CD4 T cells, EM, 515143


title: LN, CD8 T cells, EM, 500083


title: LN, CD4 T cells, EM, 500043


title: Lung, CD4 T cells, CM, 620142

value: CM

value: donor 620


title: SM22.Complete_Responder.A4, Clinically stable MS, 16MU IFN-beta (500 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM22.Complete_Responder.A4, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM16.Complete_Responder.A3, Clinically stable MS, 16MU IFN-beta (500 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM16.Complete_Responder.A3, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM14.Complete_Responder.A3, Clinically stable MS, 8MU IFN-beta (250 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM14.Complete_Responder.A3, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM13.Complete_Responder.A3, Clinically stable MS, 8MU IFN-beta (250 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM13.Complete_Responder.A3, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM11.Complete_Responder.A2, Clinically stable MS, 16MU IFN-beta (500 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM11.Complete_Responder.A2, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: Lung, CD4 T cells, CM, 618142

value: donor 618


title: SM8.Complete_Responder.A2, Clinically stable MS, 8MU IFN-beta (250 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM8.Complete_Responder.A2, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM6.Complete_Responder.A1, Clinically stable MS, 16MU IFN-beta (500 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM6.Complete_Responder.A1, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM5.Complete_Responder.A1, Clinically stable MS, 16MU IFN-beta (500 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM5.Complete_Responder.A1, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: dDC_Thymus

city: Erlangen

first: David

last: Vöhringer

state: Bavaria

address: Wassersturmstr 3-5

department: Microbiology

country: Germany

institute: University Hospital Erlangen

hyb_protocol: 600 ng Cy3-labeled fragmented cRNA were hybridized over night (17 hours, 65°C) in hybridization buffer to Agilent Whole Mouse Genome Oligo Microarrays 8x60K. Then, microarrays were washed once with Agilent Gene Expression Wash BUffer 1 for 1 min at 25°C followed by a second wash for 1 min in 37°C Agilent Gene Expression Wash Buffer 2

scan_protocol: Scanning was done with an Agilent's Microarray Scanner System.

data_processing: Agilent Feature Extraction Software (FES) was utilized to generate numeric values from the image files.

organism: Mus musculus

source_name: deltaDC Tregs from Thymus

label_protocol: RNA quality was determined with the Agilent 2100 Bioanalyzer (Agilent technologies) and revealed RIN values between 8.4 and 9.9. 10 ng total RNA was then used to produce Cy3-labeled cRNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies).

growth_protocol: cells from spleens and thymi of 3 mice per genotype were isolated, CD4 T cells of spleens were isolated with the Negative selection EasySep Mouse CD4 T cell isolation kit (StemCell Technologies), CD4 T cells of thymi were enriched by incubating with anti-CD8 antibody followed by streptavidin-coupled beads (StemCell Technologies), cells were pooled per genotype and Tregs were sorted as DAPI negative, CD4 positive, CD25 positive

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: strain

value: male

value: Thymus

value: deltaDC Tregs


title: Lung, CD4 T cells, EM, 500143

value: CD4 T cells

value: EM


title: LN, CD4 T cells, CM, 618042

value: LN


title: dDC_Spleen

source_name: deltaDC Tregs from Spleen

value: Spleen


title: SM12.Complete_Responder.A2, Clinically stable MS, 16MU IFN-beta (500 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM12.Complete_Responder.A2, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection

value: peripheral blood mononuclear cells


title: SM15.Complete_Responder.A3, Clinically stable MS, 8MU IFN-beta (250 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM15.Complete_Responder.A3, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: LN, CD4 T cells, CM, 616042

value: donor 616

value: Female

value: White


title: SM10.Complete_Responder.A2, Clinically stable MS, 16MU IFN-beta (500 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM10.Complete_Responder.A2, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM9.Complete_Responder.A2, Clinically stable MS, 8MU IFN-beta (250 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM9.Complete_Responder.A2, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: Lung, CD4 T cells, CM, 576142

value: Lung

value: donor 576

value: Black


title: WT_Spleen

source_name: wild type Tregs from Spleen

value: Wild-type Tregs


title: LN, CD8 T cells, TRM, 515084

value: CD8 T cells

value: TRM

value: donor 515

value: Male


title: LN, CD4 T cells, CM, 620042

value: CM

value: donor 620


title: SM7.Complete_Responder.A2, Clinically stable MS, 8MU IFN-beta (250 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM7.Complete_Responder.A2, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: Lung, CD4 T cells, CM, 574142

value: CD4 T cells

value: donor 574


title: LN, CD8 T cells, CM, 574082

value: LN


title: SM1.Complete_Responder.A1, Clinically stable MS, 8MU IFN-beta (250 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM1.Complete_Responder.A1, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection

value: peripheral blood mononuclear cells


title: LN, CD4 T cells, CM, 576042


title: SM2.Complete_Responder.A1, Clinically stable MS, 8MU IFN-beta (250 ug), 4  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM2.Complete_Responder.A1, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM3.Complete_Responder.A1, Clinically stable MS, 8MU IFN-beta (250 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM3.Complete_Responder.A1, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM4.Complete_Responder.A1, Clinically stable MS, 16MU IFN-beta (500 ug), 0  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM4.Complete_Responder.A1, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: LN, CD4 T cells, CM, 574042


title: Lung, CD8 T cells, CM, 571182

value: donor 571


title: LN, CD8 T cells, CM, 516082

value: donor 516

value: Female


title: Lung, CD4 T cells, CM, 571142

value: Lung


title: LN, CD4 T cells, CM, 571042


title: Lung, CD4 T cells, CM, 508142

value: donor 508


title: Lung, CD4 T cells, CM, 515142

value: White


title: LN, CD4 T cells, CM, 508042

value: Black


title: Lung, CD4 T cells, CM, 510142

value: donor 510


title: LN, CD4 T cells, CM, 510042


title: KO3_rep2_2

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Biomedicine

country: Switzerland

institute: University of Basel

description: BSSE_QGF_41410_C87PPANXX_5_9K_N2CKO_rep2_new_cDNA_Jan2016_GGAGCTAC_CTAAGCCT_S12_L005_R1_001.fastq

data_processing:
For data processing with Bowtie2 and Htseq go to https://github.com/mboareto/Notch2KO
Genome_build: Mus Musculus GRCm38

source_name: Hippocampal stem cells

extract_protocol:
Hes5::CreERT2 derived cells were isolated by sorting of Rosa26R-CAG::GFP recombined GFP+ cells after 5 days of Tamoxifen treatment and 1 day chase. Sorted cells from pools of wild type or Notch2 CKO animals were lysed into Trisol and RNA extracted.
Nextera XT DNA Library Preparation Kit (Illumina)
Smart-Seq2 (Illumina) RNA-Seq

treatment_protocol: Hes5::CreERT2, Notch2 flox/flox, Rosa26R-CAG::GFP mice (Notch2 CKO) and  Hes5::CreERT2, Notch2 wt/wt Rosa26R-CAG::GFP mice (wild type) were treated 5 days with Tamoxifen  and GFP+ cells isolated after a 1 day chase.

value: Hippocampus

value: Adult

tag: genotype

value: Notch2 CKO


title: KO3_rep1_1

description: BSSE_QGF_41404_C87PPANXX_4_9K_N2CKO_rep1_new_cDNA_Jan2016_ACTCGCTA_CTAAGCCT_S6_L004_R1_001.fastq


title: KO3_rep1_2

description: BSSE_QGF_41404_C87PPANXX_5_9K_N2CKO_rep1_new_cDNA_Jan2016_ACTCGCTA_CTAAGCCT_S6_L005_R1_001.fastq


title: KO3_rep2_1

description: BSSE_QGF_41410_C87PPANXX_4_9K_N2CKO_rep2_new_cDNA_Jan2016_GGAGCTAC_CTAAGCCT_S12_L004_R1_001.fastq


title: LN, CD4 T cells, CM, 500042

value: CM

value: donor 500


title: Lung, CD4 T cells, CM, 500142

value: CD4 T cells


title: P1 p75NTR(+) cells

city: Tokyo

first: Yasuhiro

last: Nakano

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University (TMDU)

description: p75NTR-positive sorting

hyb_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent), according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

scan_protocol: Scaned using microarray scanner G2690D

data_processing: All scanned images were analyzed using Agilent feature extraction software (v11.5.1.1). Raw data were imported with GeneSpring GX software (v14.9, Agilent Technologies, CA, USA) with adapted by 75 percentile shift normalization

source_name: mouse newborn liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using NucleoSpin RNA XS (Takara, Japan) and quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: liver

tag: developmental stage


title: Lung, CD8 T cells, naive, 620181

value: CD8 T cells

value: naive

value: donor 620


title: MEFs

description: cultured embryonic skin fibroblasts

source_name: mouse embryonic fibroblasts

value: skin

value: cultured embryonic skin fibroblasts


title: LN, CD4 T cells, CM, 516042

value: LN

value: donor 516

value: Female


title: E11.5 p75NTR(+) cells

description: p75NTR-positive sorting

source_name: mouse embryonic liver


title: MSCs

description: purified MSCs

source_name: mouse adult mesenchymal stem cells

value: bone marrow

value: purified MSCs


title: E17.5 p75NTR(+) cells

description: p75NTR-positive sorting


title: E13.5 p75NTR(+) cells

description: p75NTR-positive sorting


title: KO2_rep1_2

description: BSSE_QGF_41403_C87PPANXX_5_4K_N2CKO_rep1_new_cDNA_Jan2016_ACTCGCTA_AAGGAGTA_S5_L005_R1_001.fastq

value: Hippocampus


title: KO2_rep1_1

description: BSSE_QGF_41403_C87PPANXX_4_4K_N2CKO_rep1_new_cDNA_Jan2016_ACTCGCTA_AAGGAGTA_S5_L004_R1_001.fastq

value: Adult


title: KO2_rep2_1

description: BSSE_QGF_41409_C87PPANXX_4_4K_N2CKO_rep2_new_cDNA_Jan2016_GGAGCTAC_AAGGAGTA_S11_L004_R1_001.fastq

value: Notch2 CKO


title: Adult HSCs

description: vitamin A-positive sorting

source_name: mouse adult HSCs

value: vitamin A-positive


title: E14.5 p75NTR(+) cells

description: p75NTR-positive sorting


title: KO1_rep2_2

description: BSSE_QGF_41408_C87PPANXX_5_19K_N2CKO_rep2_new_cDNA_Jan2016_GGAGCTAC_ACTGCATA_S10_L005_R1_001.fastq


title: LN, CD8 T cells, naive, 620081

value: White


title: KO1_rep2_1

description: BSSE_QGF_41408_C87PPANXX_4_19K_N2CKO_rep2_new_cDNA_Jan2016_GGAGCTAC_ACTGCATA_S10_L004_R1_001.fastq


title: Lung, CD4 T cells, naive, 620141

value: Lung

value: CD4 T cells


title: LN, CD4 T cells, naive, 620041


title: KO1_rep1_2

description: BSSE_QGF_41402_C87PPANXX_5_19K_N2CKO_rep1_new_cDNA_Jan2016_ACTCGCTA_ACTGCATA_S4_L005_R1_001.fastq


title: Lung, CD8 T cells, naive, 618181

value: CD8 T cells

value: donor 618

value: Male

value: Black


title: KO1_rep1_1

description: BSSE_QGF_41402_C87PPANXX_4_19K_N2CKO_rep1_new_cDNA_Jan2016_ACTCGCTA_ACTGCATA_S4_L004_R1_001.fastq


title: WT3_rep2_2

description: BSSE_QGF_41407_C87PPANXX_5_2K_CAG_rep2_new_cDNA_Jan2016_GGAGCTAC_GTAAGGAG_S9_L005_R1_001.fastq

value: Wild type


title: WT3_rep2_1

description: BSSE_QGF_41407_C87PPANXX_4_2K_CAG_rep2_new_cDNA_Jan2016_GGAGCTAC_GTAAGGAG_S9_L004_R1_001.fastq


title: Lung, CD4 T cells, naive, 618141

value: naive


title: LN, CD4 T cells, naive, 618041

value: LN


title: LN, CD8 T cells, naive, 618081


title: KO2_rep2_2

description: BSSE_QGF_41409_C87PPANXX_5_4K_N2CKO_rep2_new_cDNA_Jan2016_GGAGCTAC_AAGGAGTA_S11_L005_R1_001.fastq


title: WT3_rep1_2

description: BSSE_QGF_41401_C87PPANXX_5_2K_CAG_rep1_new_cDNA_Jan2016_ACTCGCTA_GTAAGGAG_S3_L005_R1_001.fastq


title: WT3_rep1_1

description: BSSE_QGF_41401_C87PPANXX_4_2K_CAG_rep1_new_cDNA_Jan2016_ACTCGCTA_GTAAGGAG_S3_L004_R1_001.fastq


title: Lung, CD4 T cells, naive, 616141

value: donor 616

value: Female


title: Lung, CD8 T cells, naive, 616181


title: WT2_rep2_2

description: BSSE_QGF_41406_C87PPANXX_5_12K_CAGGFP_rep2_new_cDNA_Jan2016_GGAGCTAC_TATCCTCT_S8_L005_R1_001.fastq


title: WT2_rep1_2

description: BSSE_QGF_41400_C87PPANXX_5_12K_CAGGFP_rep1_new_cDNA_Jan2016_ACTCGCTA_TATCCTCT_S2_L005_R1_001.fastq


title: LN, CD8 T cells, naive, 616081


title: LN, CD4 T cells, naive, 616041


title: WT2_rep2_1

description: BSSE_QGF_41406_C87PPANXX_4_12K_CAGGFP_rep2_new_cDNA_Jan2016_GGAGCTAC_TATCCTCT_S8_L004_R1_001.fastq


title: WT2_rep1_1

description: BSSE_QGF_41400_C87PPANXX_4_12K_CAGGFP_rep1_new_cDNA_Jan2016_ACTCGCTA_TATCCTCT_S2_L004_R1_001.fastq


title: WT1_rep2_2

description: BSSE_QGF_41405_C87PPANXX_5_20K_CAGGFP_rep2_new_cDNA_Jan2016_GGAGCTAC_CTCTCTAT_S7_L005_R1_001.fastq


title: Lung, CD8 T cells, naive, 576181

value: donor 576


title: LN, CD4 T cells, naive, 576041


title: LN, CD8 T cells, naive, 576081


title: WT1_rep2_1

description: BSSE_QGF_41405_C87PPANXX_4_20K_CAGGFP_rep2_new_cDNA_Jan2016_GGAGCTAC_CTCTCTAT_S7_L004_R1_001.fastq

value: Hippocampus


title: Lung, CD4 T cells, naive, 574141

value: donor 574


title: LN, CD8 T cells, naive, 574081


title: LN, CD4 T cells, naive, 574041


title: Lung, CD4 T cells, naive, 571141

value: donor 571


title: Lung, CD8 T cells, naive, 571181


title: Lung, CD4 T cells, naive, 516141

value: donor 516


title: CleanTag E 3

city: Oslo

first: Fatima

last: Heinicke

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: Oslo University Hospital

description:
TriLink-15
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

data_processing:
Primary base calling and quality scoring was performed using RTA v1.18.66.4 (Illumina)
demultiplexing and processing with Bcl2fastq v2.18.0.12 (Illumina)
3' adapter were trimmed using cutadapt v1.15 with parameter -m 10
Remaining reads were mapped to the synthetic miRNA reference or customized miRNA reference based on miRBase v21 using Bowtie v1.1.2 with parameter -a and --norc, no mismatches allowed
Reads were counted a custom python script
Genome_build: synthetic miRNA reference and customized miRNA reference based on miRBase v21
Supplementary_files_format_and_content: Raw count table, Downsampled count table, rlog transformed, downsampled count table, Mapping_reference

organism: synthetic RNA

source_name: Synthetic miRNA

extract_protocol:
Synthetic miRNA samples: no RNA extraction needed, human samples: RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
CATS, Small RNA-Seq Library Prep kit (srLp), QIAseq, TailorMix,SMARTer, CleanTag

tag: library prep kit

value: CleanTag

tag: mix type/state

value: E

tag: replicate

tag: molecule subtype

value: Synthetic miRNA


title: LN, CD8 T cells, naive, 516081

value: CD8 T cells


title: Lung, CD4 T cells, naive, 576141

value: Lung

value: CD4 T cells


title: CleanTag E 2

description:
TriLink-14
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: LN, CD8 T cells, naive, 515081

value: donor 515

value: Male

value: White


title: LN, CD4 T cells, naive, 571041

value: LN

value: naive

value: Black


title: Lung, CD8 T cells, naive, 515181


title: WT1_rep1_2

description: BSSE_QGF_41399_C87PPANXX_5_20K_CAGGFP_rep1_new_cDNA_Jan2016_ACTCGCTA_CTCTCTAT_S1_L005_R1_001.fastq

value: Adult

value: Wild type


title: CleanTag D 2

description:
TriLink-11
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: D


title: Lung, CD8 T cells, naive, 510181

value: donor 510

value: Female


title: CleanTag D 3

description:
TriLink-12
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: CleanTag


title: LN, CD4 T cells, naive, 515041


title: CleanTag E 1

description:
TriLink-13
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: E


title: Lung, CD8 T cells, naive, 574181

value: donor 574


title: CleanTag C 3

description:
TriLink-9
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: C

value: Synthetic miRNA


title: Lung, CD4 T cells, naive, 515141

value: Lung

value: CD4 T cells


title: LN, CD8 T cells, naive, 510081

value: CD8 T cells


title: LN, CD4 T cells, naive, 510041

value: White


title: WT_Thy

source_name: wild type Tregs from Thymus

value: male

value: Thymus

value: Wild-type Tregs


title: CleanTag C 1

description:
TriLink-7
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CleanTag B 3

description:
TriLink-6
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: B


title: Lung, CD8 T cells, naive, 508181

value: naive

value: donor 508

value: Male

value: Black


title: WT1_rep1_1

description: BSSE_QGF_41399_C87PPANXX_4_20K_CAGGFP_rep1_new_cDNA_Jan2016_ACTCGCTA_CTCTCTAT_S1_L004_R1_001.fastq

value: Hippocampus

value: Adult

value: Wild type


title: Lung, CD4 T cells, naive, 510141

value: donor 510

value: Female


title: Lung, CD8 T cells, naive, 516181

value: Lung

value: donor 516


title: CleanTag B 2

description:
TriLink-5
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: CleanTag

value: Synthetic miRNA


title: Lung, CD4 T cells, naive, 508141

value: CD4 T cells


title: LN, CD4 T cells, naive, 516041

value: LN


title: CleanTag B 1

description:
TriLink-4
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: LN, CD8 T cells, naive, 508081

value: CD8 T cells


title: CleanTag D 1

description:
TriLink-10
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: D


title: LN, CD4 T cells, naive, 508041

value: naive


title: CleanTag A 3

description:
TriLink-3
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: A


title: CleanTag A 2

description:
TriLink-2
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CleanTag A 1

description:
TriLink-1
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CleanTag C 2

description:
TriLink-8
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: C


title: Lung, CD8 T cells, naive, 500181

value: donor 500

value: Black


title: SMARTer E 3

description:
Takara-15
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: SMARTer

value: E


title: Lung, CD4 T cells, naive, 500141


title: CleanTag HC 3

description:
TriLink-21
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta

source_name: Lymphocytes

value: Healthy control

value: total RNA


title: SMARTer E 1

description:
Takara-13
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: LN, CD4 T cells, naive, 500041

value: Female


title: SMARTer D 2

description:
Takara-11
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: SMARTer D 3

description:
Takara-12
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CleanTag HC 1

description:
TriLink-19
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer D 1

description:
Takara-10
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CleanTag RA 2

description:
TriLink-17
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta

value: Disease state


title: LN, CD8 T cells, naive, 500081


title: CleanTag HC 2

description:
TriLink-20
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta

value: CleanTag


title: SMARTer C 2

description:
Takara-8
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: Synthetic miRNA


title: CleanTag RA 3

description:
TriLink-18
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer C 1

description:
Takara-7
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CleanTag RA 1

description:
TriLink-16
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer HC 3

description:
Takara-21
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer B 3

description:
Takara-6
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: B


title: SMARTer B 2

description:
Takara-5
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: SMARTer HC 2

description:
Takara-20
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer HC 1

description:
Takara-19
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer A 3

description:
Takara-3
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: SMARTer B 1

description:
Takara-4
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: SMARTer RA 2

description:
Takara-17
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer A 2

description:
Takara-2
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: SMARTer E 2

description:
Takara-14
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: SMARTer RA 1

description:
Takara-16
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer RA 3

description:
Takara-18
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer C 3

description:
Takara-9
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix D 3

description:
SeqMatic-12
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: TailorMix


title: TailorMix E 3

description:
SeqMatic-15
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix RA 2

description:
SeqMatic-17
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: TailorMix D 1

description:
SeqMatic-10
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix D 2

description:
SeqMatic-11
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix RA 3

description:
SeqMatic-18
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: TailorMix HC 3

description:
SeqMatic-21
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: TailorMix RA 1

description:
SeqMatic-16
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq RA 3

description:
Qiagen-18
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta

value: QIAseq


title: TailorMix C 3

description:
SeqMatic-9
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq HC 2

description:
Qiagen-20
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq HC 3

description:
Qiagen-21
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: SMARTer A 1

description:
Takara-1
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix C 2

description:
SeqMatic-8
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix HC 2

description:
SeqMatic-20
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: TailorMix E 2

description:
SeqMatic-14
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix C 1

description:
SeqMatic-7
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix B 1

description:
SeqMatic-4
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix A 3

description:
SeqMatic-3
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq RA 1

description:
Qiagen-16
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: TailorMix B 3

description:
SeqMatic-6
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: TailorMix B 2

description:
SeqMatic-5
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: srLp HC 2

description:
Lexogen-20
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta

value: srLp


title: srLp HC 3

description:
Lexogen-21
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: TailorMix E 1

description:
SeqMatic-13
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq RA 2

description:
Qiagen-17
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: TailorMix HC 1

description:
SeqMatic-19
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq HC 1

description:
Qiagen-19
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: srLp HC 1

description:
Lexogen-19
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: srLp RA 3

description:
Lexogen-18
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq E 2

description:
Qiagen-14
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: srLp RA 2

description:
Lexogen-17
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: srLp RA 1

description:
Lexogen-16
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: CATS RA 3

description:
Diagenode-18
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta

value: CATS


title: CATS HC 1

description:
Diagenode-19
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq E 1

description:
Qiagen-13
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CATS HC 3

description:
Diagenode-21
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq C 3

description:
Qiagen-9
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq E 3

description:
Qiagen-15
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CATS RA 1

description:
Diagenode-16
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq D 2

description:
Qiagen-11
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: D


title: QIAseq B 2

description:
Qiagen-5
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq D 1

description:
Qiagen-10
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq B 3

description:
Qiagen-6
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq C 1

description:
Qiagen-7
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: C


title: TailorMix A 2

description:
SeqMatic-2
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: A


title: CATS HC 2

description:
Diagenode-20
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq B 1

description:
Qiagen-4
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: Current Smoker 4

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene Expression from single bronchial cells from a current smoker.

data_processing:
Illumina’s CASAVA software (version 1.8.2) was used to process base calls and de-multiplex the sequencing output to 12 pairs of plate-level FASTQ files (1 per 96-well plate), where the first read contains the UMI (bases 1-5) and the cell barcode (bases 6-11), the second read contains the target RNA molecule, and the last base in each read was trimmed off.
A python-based pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was then utilized to: 1) de-multiplex each plate-level FASTQ file to 96 cell-level FASTQ files, trim 51 nucleotide reads to 35 nucleotides, and append UMI information from read 1 (R1) to the header of read 2 (R2); 2) perform genomic alignment of R2 with Bowtie2 (v2.2.2) using a concatenated hg19/ERCC reference assembly; and 3) convert aligned reads to gene-level counts using a modified version of the HTSeq (v0.5.4p1) python library that identifies reads aligning to the same location with identical UMIs and reduces them to a single count. One UMI-corrected count was then referred to as a “transcript”. The pipeline was configured with the following settings: alignment quality (min_bc_quality) = 10, barcode length (bc_length) = 6, UMI length (umi_length) = 5, cut_length = 35.
Genome_build: hg19
Supplementary_files_format_and_content: count_matrix.txt

molecule: polyA RNA

source_name: Bronchial brushings

extract_protocol:
Bronchial brushings from 12 subjects (6 never smokers and 6 current smokers) were treated with 0.25% Trypsin/EDTA for 20 minutes and stained for sorting (FACS) into 96-well PCR plates containing lysis buffer (0.2% Triton-X 100, 2.5% RNaseOUT) compatible with downstream RNA library preparation. In each 96-well PCR plate for each subject, we sorted 84 ALCAM+ cells, 11 CD45+ cells, and maintained one empty well as a negative control.
Single-cell RNA-Seq of human bronchial airway cells was performed using a modified version of the CEL-Seq RNA library preparation protocol. For each of the 12 subjects, one frozen 96-well PCR plate containing sorted cells was thawed on ice and RNA was directly reverse transcribed from whole cell lysate using primers composed of an anchored poly(dT), the 5’ Illumina adaptor sequence, a 6-nucleotide well-specific barcode, a 5-nucleotide unique molecular identifier (UMI), and a T7 RNA polymerase promoter. Samples were additionally supplemented with ERCC RNA Spike-In mix (1:1,000,000 dilution) for quality control. cDNA generated from each of the 96 cells per plate was pooled, subjected to second strand synthesis and amplified by in vitro transcription. Amplified RNA was chemically fragmented and ligated to the Illumina RNA 3’ adapter. Samples were again reverse transcribed using a 3’ adaptor-specific primer and amplified using indexed Illumina RNA PCR primers.
Samples were sequenced on an Illumina HiSeq 2500 in rapid mode, generating paired-end reads (15 nucleotides for Read 1, 7 nucleotides for index, 52 nucleotides for Read 2).

tag: smoking status

value: Current Smoker

tag: pack years

tag: co ppm

value: female


title: QIAseq A 3

description:
Qiagen-3
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: Current Smoker 6


title: Current Smoker 5

value: male


title: TailorMix A 1

description:
SeqMatic-1
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: CATS RA 2

description:
Diagenode-17
processed data, mapping reference file:
countTable_biological.tsv
countTable_biological_downsampled.csv
countTable_biological_rlog_downsampled.csv
Composer.biologic.matureRef.fasta


title: QIAseq C 2

description:
Qiagen-8
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: QIAseq A 2

description:
Qiagen-2
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: Current Smoker 1


title: Never Smoker 6

description: Gene Expression from single bronchial cells from a never smoker.

value: Never Smoker


title: srLp E 3

description:
Lexogen-15
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: E


title: QIAseq A 1

description:
Qiagen-1
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: Never Smoker 5


title: srLp D 3

description:
Lexogen-12
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: Never Smoker 4


title: Current Smoker 3


title: srLp E 1

description:
Lexogen-13
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: srLp E 2

description:
Lexogen-14
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: srLp D 2

description:
Lexogen-11
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: Never Smoker 3


title: Never Smoker 2


title: Current Smoker 2


title: RH4 Entinostat AQuA-HiChIP

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

library_source: genomic

data_processing:
Library strategy: AQuA-HiChIP
Paired end reads were mapped once to the human genome (hg19), and in parallel also mapped to the mouse genome (mm10), using bowtie2 within the HiC-pro pipeline
Mapped read pairs were then filtered first for junction validity (containing two fragments from restriction digestion), then duplicates were removed, using HiC-pro pipeline
AQuA factor incorporation was done by calculating the Contacts Per Million (CPM=Raw contact frequency matrix*1,000,000/total valid contacts), then converting to Reference normalized Contacts Per Million (RCPM=CPM*hg19 valid contacts/mm10 valid contacts).
Contact maps were converted to Juicebox compatible *.hic file format using the hicpro2juicebox.sh tool (https://github.com/nservant/HiC-Pro) provided with HiC-pro, and matrices were extracted using the Juicer33 dump tool (https://github.com/theaidenlab/juicer/wiki/Data-Extraction).
Genome_build: Hg19
Supplementary_files_format_and_content: processed file is in Juicer and Juicebox compatible .hic format, that is a contact matrix

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: RH4, spike in NIH3T3

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
Nuclei were then pelleted, sonicated (11 minutes shearing ‘on’ time with 30 seconds ‘on’ 30 seconds off, using Active Motif Epi-shear probe sonicator at 30% power), and immunoprecipitated with cross-species reactive antibody against H3K27ac (Active Motif, Cat# 39133). After overnight incubation (rotating, 4 °C), the ChIP reactions were buffer exchanged into Dynabeads Protein A (ThermoFischer Scientific, Cat# 10002D) and incubated (2 hours, 4 °C).  ChIP reaction was then washed, eluted, treated with Proteinase K (45 minutes at 55 °C), and crosslinks reversed by increasing temperature to 67 °C for 2 hours, and purified.
Biotin capture and washing was performed with Dynabeads M-280 Streptavidin (ThermoFischer Scientific, Cat# 11205D), followed by on-bead library preparation (end repair, A-tailing, adapter ligation and library amplification)31.  Amplified library DNA was purified with AMPure beads, quantified and multiplexed, and paired-end sequenced with Illumina NextSeq High Output v2 kit (150 cycles, Cat# FC-404-2002) to generate 100-200 million read pairs per condition.

treatment_protocol: NIH3T3 (mouse) cells were grown and fixed in parallel with human cancer cells (RH4) treated with DMSO or Entinostat for 6 hours. 2 million fixed mouse cells were mixed with 7 million fixed RH4 cells, for each condition.  Gentle lysis was used to release the nuclei that were then permeabilized in 0.5% SDS (10 minutes at 62 °C) and then quenched with 10% Triton X-100, followed by digestion with Mbol restriction enzyme (2 hours at 37 °C) and heat inactivated (20 minutes at 62 °C).  Biotin was incorporated (biotin-14-dATP, Thermo Scientific, Cat# 19524-016) with DNA Polymerase I, Large (Klenow) Fragment (NEB, Cat# M0210) for 1 hour at 37 °C, followed by in situ ligation with T4 DNA ligase (4 hours, room temperature).

tag: antibody

value: anti-H3K27ac antibody  (Active Motif, 39133)

tag: enrichment target

tag: digestion enzyme

value: Mbol

tag: treatment

value: Entinostat, 1 µM, 6 hours


title: srLp D 1

description:
Lexogen-10
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

value: Synthetic miRNA


title: QIAseq D 3

description:
Qiagen-12
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: srLp C 3

description:
Lexogen-9
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta


title: NoHCC [Single-cell]

city: San Francisco

first: Kimberley

middle: Jane

last: Evason

state: CA

address: 513 Parnassus Ave, Room M545

department: Pathology

institute: University of California, San Francisco

data_processing:
10x Genomics’ Cell Ranger software (v2.2.0) executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 (26 bp) and R2 (100 bp)  FASTQ files.
Custom transgenic genomic reference was built with ‘cellranger mkref’, but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene_biotypes matching ‘protein_coding’, ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added.
Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘--expect-cells=3000’
In attempt to recover those (perhaps lower quality) GEM partitions, the raw gene-barcode matrices from ‘cellranger count’ (located in ‘outs/raw_gene_bc_matrices’) was processed with the EmptyDrops algorithm (R package DropletUtils v1.2.2) to discriminate cells from background GEM partitions at a false discovery rate (FDR) of 1% (Lun ATL et al., 2019). GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells, while those with at least 10,000 UMI counts were automatically considered to be cells.
Cell-based QC metrics were calculated with R package scater (v1.10.1) using the calculateQCMetrics function (McCarthy DJ et al., 2017). Principal component analysis (PCA) on the cell-based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect (P. Filzmoser et al., 2008). Cells with extremely low UMI counts, extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally, cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis.
Genome_build: GRCz11
Supplementary_files_format_and_content: MTX

organism: Danio rerio

source_name: Liver

growth_protocol: Fish were raised following IACUC-approved protocols in insititutional zebrafish facility.

extract_protocol:
Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis (HCC or no HCC). The remaining half of each liver was dissociated into single-cell suspensions and prepared for single-tube single-cell RNA sequencing (scRNA-seq) based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum (FBS) in Hank’s Buffered Saline Solution (HBSS) without phenol red, with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re-suspended in 1 mL of 5%FBS+5mM EDTA in HBSS-Free solution. Cells were then filtered through a 40 micron membrane filter, and the filtrate was centrifuged at 1200 RPM, 4C for 5 minutes. The cell pellet was then re-suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single-cell suspension.
Viability and cell count were assessed on Countess I (Thermo Scientific).  The Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 2 (PN-120237) was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier (UMI) according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6,000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip (PN-120236) to form Gel-Bead-In EMulsions (GEMs), the micro-droplets.  Within individual GEMs, cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min.  Subsequent A tailing, end repair, adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode.
Single-cell 3' RNA-Sequencing

treatment_protocol: Larvae for Samples 2 and 3 were treated with 10micromolar 4-hydroxytamoxifen from 3 to 6 days post fertilization.

tag: transgenic line

tag: age

value: 6 months post fertilization

tag: treatment at larval stage

tag: diagnosis

value: No HCC


title: HCCCreLox [Single-cell]

description: Tg(fabp10a-CreERT2;fabp10a-flox-β-catenin)

value: 10micromolar 4-hydroxytamoxifen from 3 to 6 days post fertilization.

value: HCC


title: RH4 DMSO AQuA-HiChIP

value: DMSO, 6 hours


title: C2

city: Qingdao

first: Liu

last: Jun

address: Binhai Road 72

country: China

institute: Shandong University

data_processing:
In this project, Oligo(dT) magnetic beads were used to enrich the mRNA with polyA structure in total RNA, and the RNA was interrupted by ion interrupting to a fragment of about 300 bp in length. The first strand of cDNA was synthesized using a 6-base random primer and reverse transcriptase using RNA as a template, and the second strand cDNA was synthesized using the first strand cDNA as a template. After the library construction was completed, the library fragments were enriched by PCR amplification, and then the library selection was performed according to the fragment size, and the library size was 450 bp. Next, the library was subjected to a quality test by Agilent 2100 Bioanalyzer, and the total library concentration and the effective concentration of the library were examined. Then, according to the effective concentration of the library and the amount of data required for the library, the libraries containing different Index sequences (each sample plus a different index, and finally the index data of each sample are classified according to Index) are mixed in proportion. The mixed library was uniformly diluted to 2 nM and denatured by alkali to form a single-stranded library. After RNA extraction, purification, and library construction, these libraries were subjected to Paired-end (PE) sequencing based on the Illumina HiSeq sequencing platform using Next-Generation Sequencing (NGS).
Genome_build: Starmerella bombicola CGMCC 1576 genomic sequence
Supplementary_files_format_and_content: One matrix table in text format including FPKM values for each genes.

organism: Starmerella bombicola

source_name: Cryptococcus

growth_protocol: All strains were first pre-incubated overnight in YEPD medium containing 2% glucose to OD600 = 1, then transferred to fermentation medium and incubated at 30 ° C, 200 rpm for 72 hours.

extract_protocol: Total RNA was prepared from the cells by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.

treatment_protocol: Cell pellet obtained by centrifugation at 4 °

tag: strain

value: gme3787_g deletion mutant delta3787

tag: carbon source

value: glucose and oleic acid


title: C3


title: C1


title: srLp C 2

description:
Lexogen-8
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

tag: library prep kit

value: srLp

value: C


title: B3

value: gme3596_g deletion mutant delta3596


title: srLp C 1

description:
Lexogen-7
processed data, mapping reference file:
countTable_synthetic.tsv
countTable_synthetic_downsampled.csv
countTable_synthetic_rlog_downsampled.csv
Composer.synthetic.matureRef.fasta

tag: mix type/state


title: B2


title: B1


title: Never Smoker 1

tag: Sex

value: female


title: 317E11

description:
15743R_counts.txt
15743X10

data_processing:
The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab-delimited matrix where each column denotes a sample and each row corresponds to a gene.

extract_protocol:
Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis (HCC or no HCC). The other half of each dissected liver was flash-frozen on dry ice and stored in -80C prior to RNA extraction. RNA was isolated using TriReagent (Cat# R2050-1-50, Zymo Research) and Direct-Zol RNA Mini prep kit (Cat# R2050, Zymo Research) including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase-/DNase-free water.
Sample quality control, library preparation, sequencing and alignments were performed by the Huntsman Cancer Institute (HCI) High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired-read, 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell.
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10)

treatment_protocol: Larvae were treated with either 0.1% ethanol or 10micromolar 4-hydroxytamoxifen from 3 to 6 days post fertilization.

value: No treatment


title: 317E9

description:
15743R_counts.txt
15743X8


title: 317E10

description:
15743R_counts.txt
15743X9


title: A3

value: bro1 deletion mutant deltabro1