title: SM111.Partial_Responder.B5, 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.
SM111.Partial_Responder.B5, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM126.Partial_Responder.B7, Clinically stable MS, 8MU IFN-beta (250 ug), 24  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.
SM126.Partial_Responder.B7, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  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: SM134.Partial_Responder.B8, 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.
SM134.Partial_Responder.B8, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM131.Partial_Responder.B8, Clinically active MS 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.
SM131.Partial_Responder.B8, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM116.Partial_Responder.B6, 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.
SM116.Partial_Responder.B6, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM114.Partial_Responder.B6, Clinically active MS 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.
SM114.Partial_Responder.B6, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM129.Partial_Responder.B7, 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.
SM129.Partial_Responder.B7, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM107.Partial_Responder.B5, Clinically active MS 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.
SM107.Partial_Responder.B5, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM104.Partial_Responder.B4, 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.
SM104.Partial_Responder.B4, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM105.Partial_Responder.B4, 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.
SM105.Partial_Responder.B4, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM97.Partial_Responder.B3, 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.
SM97.Partial_Responder.B3, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM103.Partial_Responder.B4, 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.
SM103.Partial_Responder.B4, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM101.Partial_Responder.B4, Clinically active MS 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.
SM101.Partial_Responder.B4, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM106.Partial_Responder.B5, Clinically active MS 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.
SM106.Partial_Responder.B5, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM96.Partial_Responder.B3, 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.
SM96.Partial_Responder.B3, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM99.Partial_Responder.B3, 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.
SM99.Partial_Responder.B3, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM100.Partial_Responder.B4, Clinically active MS 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.
SM100.Partial_Responder.B4, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM98.Partial_Responder.B3, 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.
SM98.Partial_Responder.B3, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM108.Partial_Responder.B5, Clinically active MS 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.
SM108.Partial_Responder.B5, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM95.Partial_Responder.B3, 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.
SM95.Partial_Responder.B3, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM93.Partial_Responder.B3, Clinically active MS 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.
SM93.Partial_Responder.B3, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM82.Partial_Responder.B2, Clinically active MS 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.
SM82.Partial_Responder.B2, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM85.Partial_Responder.B2, 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.
SM85.Partial_Responder.B2, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM92.Partial_Responder.B3, Clinically active MS 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.
SM92.Partial_Responder.B3, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM87.Partial_Responder.B2, 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.
SM87.Partial_Responder.B2, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM84.Partial_Responder.B2, Clinically active MS 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.
SM84.Partial_Responder.B2, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM102.Partial_Responder.B4, Clinically active MS 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.
SM102.Partial_Responder.B4, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM89.Partial_Responder.B2, 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.
SM89.Partial_Responder.B2, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM83.Partial_Responder.B2, Clinically active MS 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.
SM83.Partial_Responder.B2, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM81.Partial_Responder.B1, 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.
SM81.Partial_Responder.B1, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM90.Partial_Responder.B2, 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.
SM90.Partial_Responder.B2, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: LR35_H3K27me3

type: SRA

city: Guangzhou

first: Delin

last: Mo

address: Xingang Road

country: China

institute: Sun Yat-sen University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Sus scrofa genome assembly using EasyAlign version 3.2.
Data were filtered using Sickle
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: Sus scrofa reference genome buid 10.23
Supplementary_files_format_and_content: wig files were generated using Bigwig

molecule: genomic DNA

organism: Sus scrofa

source_name: Muscle

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Muscle

tag: breed

value: Landrace

tag: antibody

value: H3K27me3 (Millipore, 17-622)

tag: Stage

value: 35 dpc


title: SM91.Partial_Responder.B3, Clinically active MS 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.
SM91.Partial_Responder.B3, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM88.Partial_Responder.B2, 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.
SM88.Partial_Responder.B2, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM86.Partial_Responder.B2, 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.
SM86.Partial_Responder.B2, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM109.Partial_Responder.B5, 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.
SM109.Partial_Responder.B5, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: LR28_H3K27me3

value: 28 dpc


title: WZS35_H3K27me3

value: Wuzhishan


title: WZS28_H3K27me3


title: SM94.Partial_Responder.B3, 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.
SM94.Partial_Responder.B3, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: LR35_H3K4me3

value: H3K4me3 (Millipore, 05-745R)


title: LR28_H3K4me3


title: WZS35_H3K4me3


title: WZS28_H3K4me3


title: SM113.Partial_Responder.B6, Clinically active MS 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.
SM113.Partial_Responder.B6, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM78.Partial_Responder.B1, 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.
SM78.Partial_Responder.B1, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM79.Partial_Responder.B1, 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.
SM79.Partial_Responder.B1, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM80.Partial_Responder.B1, 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.
SM80.Partial_Responder.B1, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: Lung, CD4 T cells, TRM, 618144

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: Lung

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: Lung

tag: cell type

value: CD4 T cells

tag: cell subset

value: TRM

tag: individual

value: donor 618

tag: Sex

value: Male

tag: reported race

value: Black


title: Lung, CD8 T cells, TRM, 618184

value: CD8 T cells


title: LN, CD8 T cells, TRM, 620084

source_name: LN

value: LN

value: donor 620

value: Female

value: White


title: Lung, CD8 T cells, TRM, 620184


title: Lung, CD4 T cells, TRM, 620144


title: Lung, CD4 T cells, TRM, 616144

value: donor 616


title: LN, CD8 T cells, TRM, 618084


title: LN, CD4 T cells, TRM, 618044


title: Lung, CD8 T cells, TRM, 616184


title: LN, CD4 T cells, TRM, 620044


title: SM73.Partial_Responder.B1, Clinically active MS 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.
SM73.Partial_Responder.B1, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection

value: peripheral blood mononuclear cells


title: SM70.Complete_Responder.A12, 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.
SM70.Complete_Responder.A12, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM71.Complete_Responder.A12, 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.
SM71.Complete_Responder.A12, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM77.Partial_Responder.B1, 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.
SM77.Partial_Responder.B1, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM64.Complete_Responder.A11, 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.
SM64.Complete_Responder.A11, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM74.Partial_Responder.B1, Clinically active MS 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.
SM74.Partial_Responder.B1, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM62.Complete_Responder.A11, 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.
SM62.Complete_Responder.A11, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM66.Complete_Responder.A11, 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.
SM66.Complete_Responder.A11, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM76.Partial_Responder.B1, 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.
SM76.Partial_Responder.B1, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM72.Complete_Responder.A12, 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.
SM72.Complete_Responder.A12, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM68.Complete_Responder.A12, 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.
SM68.Complete_Responder.A12, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM69.Complete_Responder.A12, 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.
SM69.Complete_Responder.A12, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM63.Complete_Responder.A11, 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.
SM63.Complete_Responder.A11, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: LN, CD4 T cells, TRM, 616044


title: SM67.Complete_Responder.A12, 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.
SM67.Complete_Responder.A12, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM65.Complete_Responder.A11, 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.
SM65.Complete_Responder.A11, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: Lung, CD8 T cells, TRM, 574184

value: donor 574


title: Lung, CD8 T cells, TRM, 576184

value: donor 576


title: LN, CD4 T cells, TRM, 576044


title: Lung, CD4 T cells, TRM, 574144


title: Lung, CD4 T cells, TRM, 576144


title: LN, CD4 T cells, TRM, 574044


title: Lung, CD8 T cells, TRM, 571184

value: donor 571


title: LN, CD8 T cells, TRM, 616084


title: LN, CD8 T cells, TRM, 574084


title: Lung, CD4 T cells, TRM, 571144


title: SM60.Complete_Responder.A10, 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.
SM60.Complete_Responder.A10, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: LN, CD8 T cells, TRM, 571084


title: LN, CD4 T cells, TRM, 571044


title: Lung, CD8 T cells, TRM, 516184

value: donor 516


title: Lung, CD4 T cells, TRM, 516144

value: Lung


title: SM61.Complete_Responder.A11, 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.
SM61.Complete_Responder.A11, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: LN, CD8 T cells, TRM, 516084


title: LN, CD4 T cells, TRM, 516044

value: CD4 T cells


title: SM53.Complete_Responder.A9, 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.
SM53.Complete_Responder.A9, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM55.Complete_Responder.A10, 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.
SM55.Complete_Responder.A10, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM54.Complete_Responder.A9, 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.
SM54.Complete_Responder.A9, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM56.Complete_Responder.A10, 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.
SM56.Complete_Responder.A10, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: Lung, CD4 T cells, TRM, 515144

value: TRM

value: donor 515


title: SM47.Complete_Responder.A8, 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.
SM47.Complete_Responder.A8, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: Lung, CD8 T cells, TRM, 515184

value: Male


title: SM58.Complete_Responder.A10, 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.
SM58.Complete_Responder.A10, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM59.Complete_Responder.A10, 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.
SM59.Complete_Responder.A10, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM50.Complete_Responder.A9, 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.
SM50.Complete_Responder.A9, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM57.Complete_Responder.A10, 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.
SM57.Complete_Responder.A10, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM49.Complete_Responder.A9, 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.
SM49.Complete_Responder.A9, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM48.Complete_Responder.A8, 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.
SM48.Complete_Responder.A8, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM44.Complete_Responder.A8, 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.
SM44.Complete_Responder.A8, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 4  h after IFN-b injection


title: SM46.Complete_Responder.A8, 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.
SM46.Complete_Responder.A8, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM52.Complete_Responder.A9, 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.
SM52.Complete_Responder.A9, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM51.Complete_Responder.A9, 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.
SM51.Complete_Responder.A9, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM43.Complete_Responder.A8, 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.
SM43.Complete_Responder.A8, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: Lung, CD8 T cells, TRM, 508184

value: donor 508

value: Black


title: Lung, CD8 T cells, TRM, 510184

value: CD8 T cells

value: donor 510


title: Lung, CD4 T cells, TRM, 510144

value: Female


title: LN, CD8 T cells, TRM, 508084

value: LN


title: Lung, CD4 T cells, TRM, 508144


title: LN, CD4 T cells, TRM, 515044

value: White


title: Lung, CD8 T cells, TRM, 500184

value: donor 500


title: LN, CD4 T cells, TRM, 508044


title: Lung, CD4 T cells, TRM, 500144


title: SM42.Complete_Responder.A7, 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.
SM42.Complete_Responder.A7, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection

value: peripheral blood mononuclear cells


title: Lung, CD8 T cells, EM, 620183

value: EM

value: donor 620


title: Lung, CD4 T cells, EM, 620143


title: SM41.Complete_Responder.A7, 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.
SM41.Complete_Responder.A7, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: LN, CD8 T cells, EM, 620083


title: SM37.Complete_Responder.A7, 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.
SM37.Complete_Responder.A7, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 0  h after IFN-b injection


title: SM35.Complete_Responder.A6, 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.
SM35.Complete_Responder.A6, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 4  h after IFN-b injection


title: SM39.Complete_Responder.A7, 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.
SM39.Complete_Responder.A7, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM75.Partial_Responder.B1, Clinically active MS 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.
SM75.Partial_Responder.B1, Clinically active MS (exacerbation), 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


title: SM33.Complete_Responder.A6, 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.
SM33.Complete_Responder.A6, Clinically stable MS, 8MU (8 million units IFN-b (250 ug)), 24  h after IFN-b injection


title: SM40.Complete_Responder.A7, 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.
SM40.Complete_Responder.A7, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection


title: SM34.Complete_Responder.A6, 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.
SM34.Complete_Responder.A6, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 0  h after IFN-b injection