title: NormalDonor3_untreated_PBMC_047


title: Blood P181

status: Public on Jan 01 2021

type: genomic

city: Tianjin

first: huanxin

last: chen

address: No.61, third avenue, tianjin economic and technolo

country: China

institute: Teda International Cardiovascular Hospital

description: Hybridized to Affymetrix SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The overall hybridization quality was estimated by the call rate obtained from Genotyping Console Software 4.2 (birdseed algorithm with default parameter settings). Partek Genomics Suite (version 6.5, Partek Inc., St. Louis, MO) was used for copy number analysis. Regions of CNV were detected using a Hidden Markov Model (HMM) algorithm in the Partek workflow for unpaired samples.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: TOF patient_blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood for each patient and control subject, using QIAamp® DNA blood mini kit according to the manufacturer’s instruction

tag: group

value: TOF patient

tag: tissue

value: blood


title: Newly diagnosed elderly multiple myeloma 165

type: RNA

city: Rotterdam

first: P

last: Sonneveld

address: Wytemaweg 80

department: Department of Hematology

country: Netherlands

institute: ErasmusMC cancer institute

hyb_protocol: 13 ug of fragmented and biotin labeled cRNA hybridized to the microarray in an Affymetrix GeneChip® Hybridization Oven 645 and washed / stained in Affymetrix GeneChip Fluidics Station FS450DX2v2.

scan_protocol: Affymetrix GeneChip® System 3000Dx v.2

data_processing: MAS5.0 (Bioconductor affy package v1.36.2) default values with a  trimmed mean target intensity value set to 1500. Values below 30 were truncated. Log2 transformed.

molecule: total RNA

source_name: CD138 purified myeloma plasma cells

label_protocol: Affymetrix GeneChip® 3' IVT PLUS Reagent Kit or Gene Profiling MDx IVD Expression Reagent Kit in accordance with Affymetrix protocols.

extract_protocol: Bone marrow aspirates were processed by CD138 based magnetic bead sorting (Stem Cell Technologies) to a purity of >80% plasma cells as verified by CD38 positivity by flowcytometry. Purified cells are prepared for RNA isolation using Qiagen Allprep.

tag: diagnosis

value: multiple myeloma

value: bone marrow

tag: cell type

value: CD138 purified myeloma plasma cells

tag: sky92 status

value: Standard risk

tag: reagents

value: GPR


title: Blood P174

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 164


title: NormalDonor3_untreated_PBMC_046

type: SRA

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

source_name: Blood

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

tag: who classification

value: Normal

value: Peripherial blood mononuclear cells


title: NormalDonor3_untreated_PBMC_049


title: Blood P177

description: Hybridized to Affymetrix SNP 6.0


title: Blood P176

description: Hybridized to Affymetrix SNP 6.0


title: Blood P172

description: Hybridized to Affymetrix SNP 6.0


title: Blood P169

description: Hybridized to Affymetrix SNP 6.0


title: Blood P179

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_044


title: Blood P175

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_045


title: Blood P170

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 163


title: Blood P173

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_048


title: Blood P171

description: Hybridized to Affymetrix SNP 6.0


title: Blood P168

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_043


title: Newly diagnosed elderly multiple myeloma 158


title: Blood P166

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 160


title: Newly diagnosed elderly multiple myeloma 161


title: NormalDonor3_untreated_PBMC_042


title: Newly diagnosed elderly multiple myeloma 162


title: Newly diagnosed elderly multiple myeloma 159

value: High risk


title: NormalDonor3_untreated_PBMC_041


title: Blood P167

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_040


title: Blood P160

description: Hybridized to Affymetrix SNP 6.0


title: Blood P161

description: Hybridized to Affymetrix SNP 6.0


title: Blood P163

description: Hybridized to Affymetrix SNP 6.0


title: Blood P158

description: Hybridized to Affymetrix SNP 6.0


title: Blood P162

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 156


title: Blood P159

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 157


title: NormalDonor3_untreated_PBMC_038


title: Blood P157

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_039


title: NormalDonor3_untreated_PBMC_056


title: Newly diagnosed elderly multiple myeloma 155


title: Blood P165

description: Hybridized to Affymetrix SNP 6.0


title: Blood P164

description: Hybridized to Affymetrix SNP 6.0


title: Blood P156

description: Hybridized to Affymetrix SNP 6.0


title: Blood P155

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_037


title: Blood P154

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_036


title: Blood P153

description: Hybridized to Affymetrix SNP 6.0


title: Blood P152

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 151


title: Newly diagnosed elderly multiple myeloma 153


title: Newly diagnosed elderly multiple myeloma 150


title: NormalDonor3_untreated_PBMC_035


title: Blood P149

description: Hybridized to Affymetrix SNP 6.0


title: Blood P151

description: Hybridized to Affymetrix SNP 6.0


title: Blood P146

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_034


title: NormalDonor3_untreated_PBMC_032


title: Blood P145

description: Hybridized to Affymetrix SNP 6.0


title: Blood P148

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 148


title: Newly diagnosed elderly multiple myeloma 152


title: Blood P147

description: Hybridized to Affymetrix SNP 6.0


title: Blood P144

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_031


title: Blood P143

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_030


title: Newly diagnosed elderly multiple myeloma 149


title: Newly diagnosed elderly multiple myeloma 143


title: Newly diagnosed elderly multiple myeloma 144


title: Newly diagnosed elderly multiple myeloma 146


title: Blood P141

description: Hybridized to Affymetrix SNP 6.0


title: Blood P140

description: Hybridized to Affymetrix SNP 6.0


title: Blood P142

description: Hybridized to Affymetrix SNP 6.0


title: Blood P139

description: Hybridized to Affymetrix SNP 6.0


title: Blood P150

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 147


title: NormalDonor3_untreated_PBMC_029


title: Blood P137

description: Hybridized to Affymetrix SNP 6.0


title: Blood P138

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_028


title: Blood P135

description: Hybridized to Affymetrix SNP 6.0


title: Blood P134

description: Hybridized to Affymetrix SNP 6.0


title: Blood P133

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 142


title: NormalDonor3_untreated_PBMC_026


title: NormalDonor3_untreated_PBMC_027


title: NormalDonor3_untreated_PBMC_025


title: Blood P131

description: Hybridized to Affymetrix SNP 6.0


title: Blood P136

description: Hybridized to Affymetrix SNP 6.0


title: Blood P129

description: Hybridized to Affymetrix SNP 6.0


title: Blood P128

description: Hybridized to Affymetrix SNP 6.0


title: Blood P127

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 170


title: NormalDonor3_untreated_PBMC_024


title: NormalDonor3_untreated_PBMC_023


title: Newly diagnosed elderly multiple myeloma 140


title: Newly diagnosed elderly multiple myeloma 137


title: Newly diagnosed elderly multiple myeloma 141


title: Newly diagnosed elderly multiple myeloma 139


title: Blood P126

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 134


title: NormalDonor3_untreated_PBMC_022


title: Blood P132

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 136


title: NormalDonor3_untreated_PBMC_021


title: Newly diagnosed elderly multiple myeloma 135


title: Blood P122

description: Hybridized to Affymetrix SNP 6.0


title: Blood P121

description: Hybridized to Affymetrix SNP 6.0


title: Blood P130

description: Hybridized to Affymetrix SNP 6.0


title: Blood P119

description: Hybridized to Affymetrix SNP 6.0


title: Blood P120

description: Hybridized to Affymetrix SNP 6.0


title: Blood P117

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_019


title: Blood P118

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_033


title: Blood P123

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 131


title: Blood P113

description: Hybridized to Affymetrix SNP 6.0


title: Blood P114

description: Hybridized to Affymetrix SNP 6.0


title: Blood P115

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 130


title: NormalDonor3_untreated_PBMC_017


title: NormalDonor3_untreated_PBMC_018


title: NormalDonor3_untreated_PBMC_020


title: Blood P112

description: Hybridized to Affymetrix SNP 6.0


title: Blood P111

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_016


title: Blood P110

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_015


title: Blood P116

description: Hybridized to Affymetrix SNP 6.0


title: Blood P109

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_013


title: NormalDonor3_untreated_PBMC_012


title: Blood P107

description: Hybridized to Affymetrix SNP 6.0


title: Blood P108

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_011


title: Blood P106

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_010


title: Newly diagnosed elderly multiple myeloma 129


title: Newly diagnosed elderly multiple myeloma 133


title: Blood P105

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_009


title: Newly diagnosed elderly multiple myeloma 127


title: Blood P104

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 126


title: Newly diagnosed elderly multiple myeloma 124


title: Blood P103

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 128


title: NormalDonor3_untreated_PBMC_007


title: Blood QTOF14

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_014


title: Newly diagnosed elderly multiple myeloma 120


title: Newly diagnosed elderly multiple myeloma 121


title: Blood QTOF12

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 123


title: Newly diagnosed elderly multiple myeloma 119


title: Newly diagnosed elderly multiple myeloma 125


title: NormalDonor3_untreated_PBMC_005


title: Newly diagnosed elderly multiple myeloma 117


title: NormalDonor3_untreated_PBMC_006


title: Newly diagnosed elderly multiple myeloma 118


title: Blood QTOF11

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_004


title: Blood QTOF10

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 116


title: abdominal lipo; tissue; F62

city: Stanford

first: Heather

last: Clemons

state: CA

address: Beckman Center

department: Dept of Biochemistry

institute: Stanford School of Medicine

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79515.gif

hyb_protocol: not provided

scan_protocol: Model: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Human Universal Reference

source_name: abdominal lipo; tissue; F62, 10 ug labeled aRNA

extract_protocol:
Adipose Tissue Samples; Specimen Collection Adipose tissue specimens were collected either from the Stanford Tissue Bank, Stanford Dermatology Clinic, Stanford Surgical Pathology or directly from the surgeon at the time of surgery. All surgeries were performed at Stanford Hospital and Clinics. When necessary a trained pathologist dissected the desired adipose specimen from the organ/limb/skin to which it was attached. Samples acquired by Stanford Tissue Bank or Surgical Pathology may have been stored at 4C for up to several hours but were always processed on the same day as the surgery was performed. All samples are considered normal human tissues and were originally collected under the IRB Study of Messenger RNA Expression in Normal Human Tissues ID: 76363, which did not require patient consent as very little patient information (age, gender, procedure) was provided. Subsequently it was determined that our sample collection does not meet the definitions of human subject research under Stanfords Human Research Protection Program and therefore an IRB protocol was no longer required.
Tissue Fractionation - Clemons; Tissue Fractionation Adipose tissue samples were thoroughly rinsed with 70% ethanol to minimize risk of microbial contamination of cell cultures. Tissues were then rinsed with Hanks Balanced Salt Solution (HBSS) and transferred to a clean dish. At this time 1-4 g of tissue were removed and stored at -80C. Additionally a thin slice of each tissue was placed in 10% formalin for paraffin embedding. The remainder of each tissue sample was minced using surgical scissors. Tissue pieces were transferred to 50 ml conical tubes (up to 25 ml tissue per tube), and an equivalent volume of collagenase solution* was added to the tube. Tissue was again minced with scissors until no large pieces remained. Tubes were shaken to mix and incubated at 37C for 30 min to 4 hours, until pieces of tissue were no longer visible. Shin/calf adipose tissue in general took the longest and abdominal and thigh lipoaspirate the shortest time to digest. Digested tissues were then passed through a 180-micron nylon net filter and centrifuged at 100g for 5 minutes to pellet stromal-vascular cells. A 16-gauge needle attached to a 20 ml syringe was passed through the top visible lipid/adipocyte layer and the entire bottom layer containing buffer, cell pellet and blood cells was aspirated from the bottom and transferred to a new conical, tube. This cell suspension (stromal-vascular fraction) was thoroughly mixed by pipetting and divided equally into 2 conical tubes. One of these was set aside for cell culture (see Cell Culture) and the other was centrifuged at 400g for 7 minutes. Buffer was carefully aspirated with a pipette to avoid losing pelleted cells and 15 ml Trizol was added. The remaining lipid/adipocyte layer was washed 1-2 times depending on the amount of visible blood cells: 25 ml HBSS was added to the adipocytes, and gently inverted to mix. Adipocytes were centrifuged at 100g and excess buffer along with contaminating cells was aspirated from the bottom using a needle and syringe as described above. An equal volume of Trizol was added to the washed adipocytes. The stromal-vascular pellet sample and the adipocyte sample were stored in Trizol at -80C.  Collagenase Solution: For stock solution 1000 U/ml Sigma Type II Collagenase (Cat# C6885) was dissolved in HBSS and centrifuged at 1000g for 20 minutes. Resulting liquid fraction was filtered (.22 micron) and stored at -20C and pelleted crystals were discarded. For working solution 1000 U/ml collagenase stock solution was diluted 3x in HBSS containing 5mM CaCl2
Amplification 1 ug of each total RNA sample was amplified using Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821) according to manufacturers protocol

tag: age

value: 62 years

tag: organism part

value: abdominal lipo

tag: sample fraction

value: tissue

tag: Sex

value: female


title: shin/calf; adipocyte; F63

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79510.gif

source_name: shin/calf; adipocyte; F63, 10 ug labeled aRNA

value: 63 years

value: shin/calf

value: adipocyte


title: Newly diagnosed elderly multiple myeloma 115


title: shin/calf; adipocyte; M51

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79568.gif

scan_protocol: Model: GenePix 4000A

source_name: shin/calf; adipocyte; M51, 10 ug labeled aRNA

value: 51 years

value: Male


title: abdominal; stromal pellet; F59a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79564.gif

source_name: abdominal; stromal pellet; F59a, 10 ug labeled aRNA

value: 59 years

value: abdominal

value: stromal pellet


title: Blood QTOF9

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: Newly diagnosed elderly multiple myeloma 114

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

value: Standard risk

value: GPR


title: Blood QTOF8

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_003

value: Normal

value: Peripherial blood mononuclear cells


title: Blood QTOF7

description: Hybridized to Affymetrix SNP 6.0


title: Blood QTOF6

description: Hybridized to Affymetrix SNP 6.0


title: shin/calf; tissue; F63

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79511.gif

value: Stratagene Human Universal Reference

source_name: shin/calf; tissue; F63, 10 ug labeled aRNA

value: 63 years

value: tissue

value: female


title: Newly diagnosed elderly multiple myeloma 112


title: NormalDonor2_untreated_PBMC_094


title: Newly diagnosed elderly multiple myeloma 113

value: High risk


title: NormalDonor3_untreated_PBMC_002


title: NormalDonor3_untreated_PBMC_001


title: shin/calf; stromal pellet; M55c

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79538.gif

source_name: shin/calf; stromal pellet; M55c, 10 ug labeled aRNA

value: 55 years

value: shin/calf

value: Male


title: abdominal lipo; stromal pellet; F62

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79514.gif

source_name: abdominal lipo; stromal pellet; F62, 10 ug labeled aRNA

value: 62 years

value: abdominal lipo

value: stromal pellet


title: Blood QTOF5

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: abdominal; adipocyte; F62a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79557.gif

source_name: abdominal; adipocyte; F62a, 10 ug labeled aRNA

value: abdominal

value: adipocyte


title: abdominal; adipocyte; F42

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79513.gif

source_name: abdominal; adipocyte; F42, 10 ug labeled aRNA

value: 42 years


title: Newly diagnosed elderly multiple myeloma 109

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

value: GPR


title: NormalDonor2_untreated_PBMC_093

value: Normal

value: Peripherial blood mononuclear cells


title: Newly diagnosed elderly multiple myeloma 110

value: Standard risk


title: Newly diagnosed elderly multiple myeloma 108


title: shin/calf; adipocyte; M84

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79507.gif

value: Stratagene Human Universal Reference

source_name: shin/calf; adipocyte; M84, 10 ug labeled aRNA

value: 84 years

value: shin/calf


title: abdominal; tissue; F36

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79517.gif

source_name: abdominal; tissue; F36, 10 ug labeled aRNA

value: 36 years

value: tissue

value: female


title: Newly diagnosed elderly multiple myeloma 106


title: omentum (stomach); adipocyte; F73

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79532.gif

source_name: omentum (stomach); adipocyte; F73, 10 ug labeled aRNA

value: 73 years

value: omentum (stomach)


title: NormalDonor2_untreated_PBMC_091


title: omentum (colon); tissue; F59

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79531.gif

source_name: omentum (colon); tissue; F59, 10 ug labeled aRNA

value: 59 years

value: omentum (colon)


title: Blood QTOF4

description: Hybridized to Affymetrix SNP 6.0

source_name: TOF patient_blood

value: TOF patient

value: blood


title: Blood QTOF3

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_092


title: Blood QTOF2

description: Hybridized to Affymetrix SNP 6.0


title: Blood QTOF1

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_089


title: NormalDonor2_untreated_PBMC_090


title: NormalDonor2_untreated_PBMC_088


title: NormalDonor3_untreated_PBMC_008


title: Blood GTOF60

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_087


title: NormalDonor2_untreated_PBMC_086


title: abdominal; tissue; M34

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79530.gif

source_name: abdominal; tissue; M34, 10 ug labeled aRNA

value: 34 years

value: abdominal

value: Male


title: Newly diagnosed elderly multiple myeloma 103

source_name: CD138 purified myeloma plasma cells

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

value: GPR


title: abdominal; tissue; F59a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79547.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: Stratagene Human Universal Reference

source_name: abdominal; tissue; F59a, 10 ug labeled aRNA


title: Newly diagnosed elderly multiple myeloma 105

value: Standard risk


title: Newly diagnosed elderly multiple myeloma 102

value: High risk


title: Newly diagnosed elderly multiple myeloma 104


title: Blood GTOF58

description: Hybridized to Affymetrix SNP 6.0


title: shin; stromal pellet; F76

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79508.gif

source_name: shin; stromal pellet; F76, 10 ug labeled aRNA

value: 76 years

value: shin

value: stromal pellet

value: female


title: Blood GTOF57

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_084

source_name: Blood

value: Normal

value: Peripherial blood mononuclear cells


title: shin; tissue; F76

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79527.gif

source_name: shin; tissue; F76, 10 ug labeled aRNA

value: tissue


title: Blood GTOF55

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: Blood GTOF52

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_083


title: Blood GTOF51

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 132


title: Newly diagnosed elderly multiple myeloma 101


title: Blood GTOF50

description: Hybridized to Affymetrix SNP 6.0


title: shin; adipocyte; F76

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79509.gif

source_name: shin; adipocyte; F76, 10 ug labeled aRNA

value: adipocyte


title: Blood GTOF49

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_082


title: NormalDonor2_untreated_PBMC_081


title: NormalDonor2_untreated_PBMC_080


title: Newly diagnosed elderly multiple myeloma 98

value: multiple myeloma

value: IVT


title: NormalDonor2_untreated_PBMC_079


title: abdominal; adipocyte; F36

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79523.gif

source_name: abdominal; adipocyte; F36, 10 ug labeled aRNA

value: 36 years

value: abdominal


title: Blood GTOF48

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 97

value: bone marrow

value: CD138 purified myeloma plasma cells


title: omentum (colon); adipocyte; UUf

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79544.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); adipocyte; UUf, 10 ug labeled aRNA

value: unknown

value: omentum (colon)


title: shin/calf; stromal pellet; F81

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79542.gif

source_name: shin/calf; stromal pellet; F81, 10 ug labeled aRNA

value: 81 years

value: shin/calf

value: stromal pellet


title: shin/calf; adipocyte; F81a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79571.gif

source_name: shin/calf; adipocyte; F81a, 10 ug labeled aRNA

value: female


title: abdominal; adipocyte; M60

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79536.gif

source_name: abdominal; adipocyte; M60, 10 ug labeled aRNA

value: 60 years

value: Male


title: Newly diagnosed elderly multiple myeloma 100

value: Standard risk

value: GPR


title: abdominal lipo; adipocyte; F62

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79525.gif

source_name: abdominal lipo; adipocyte; F62, 10 ug labeled aRNA

value: 62 years

value: abdominal lipo

value: adipocyte


title: Newly diagnosed elderly multiple myeloma 99

value: multiple myeloma

value: IVT


title: Newly diagnosed elderly multiple myeloma 95

value: bone marrow

value: CD138 purified myeloma plasma cells


title: Newly diagnosed elderly multiple myeloma 96


title: Newly diagnosed elderly multiple myeloma 93


title: Newly diagnosed elderly multiple myeloma 94


title: NormalDonor2_untreated_PBMC_077

value: Normal

value: Peripherial blood mononuclear cells


title: Blood GTOF46

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: Blood GTOF47

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_076


title: NormalDonor2_untreated_PBMC_078


title: Newly diagnosed elderly multiple myeloma 92


title: Blood GTOF45

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF44

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_075


title: omentum (colon); adipocyte; F47

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79556.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); adipocyte; F47, 10 ug labeled aRNA

value: 47 years

value: omentum (colon)


title: Blood GTOF59

description: Hybridized to Affymetrix SNP 6.0


title: pericolonic; tissue; F44

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79631.gif

source_name: pericolonic; tissue; F44, 10 ug labeled aRNA

value: 44 years

value: pericolonic

value: tissue

value: female


title: NormalDonor2_untreated_PBMC_085


title: Blood GTOF42

description: Hybridized to Affymetrix SNP 6.0

source_name: TOF patient_blood


title: shin/calf; adipocyte; M55c

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79569.gif

source_name: shin/calf; adipocyte; M55c, 10 ug labeled aRNA

value: 55 years

value: shin/calf

value: Male


title: NormalDonor2_untreated_PBMC_074


title: Newly diagnosed elderly multiple myeloma 90

source_name: CD138 purified myeloma plasma cells

value: multiple myeloma

value: Standard risk

value: IVT


title: shin/calf; stromal pellet; M84

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79506.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: shin/calf; stromal pellet; M84, 10 ug labeled aRNA

value: 84 years

value: stromal pellet


title: Newly diagnosed elderly multiple myeloma 91

value: bone marrow

value: CD138 purified myeloma plasma cells


title: shin/calf; tissue; M17a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79567.gif

value: Stratagene Human Universal Reference

source_name: shin/calf; tissue; M17a, 10 ug labeled aRNA

value: 17 years


title: Blood GTOF41

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: NormalDonor2_untreated_PBMC_072

source_name: Blood

value: Normal

value: Peripherial blood mononuclear cells


title: Blood GTOF43

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 88


title: NormalDonor2_untreated_PBMC_071


title: NormalDonor2_untreated_PBMC_073


title: Newly diagnosed elderly multiple myeloma 89


title: shin/calf; stromal pellet; M55

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79504.gif

source_name: shin/calf; stromal pellet; M55, 10 ug labeled aRNA


title: Newly diagnosed elderly multiple myeloma 87


title: shin/calf; tissue; F71

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79520.gif

source_name: shin/calf; tissue; F71, 10 ug labeled aRNA

value: 71 years

value: tissue

value: female


title: Blood GTOF40

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_070


title: NormalDonor2_untreated_PBMC_069


title: omentum (stomach); adipocyte; F52d

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79573.gif

source_name: omentum (stomach); adipocyte; F52d, 10 ug labeled aRNA

value: 52 years

value: omentum (stomach)

value: adipocyte


title: Newly diagnosed elderly multiple myeloma 86

value: multiple myeloma

value: Standard risk

value: IVT


title: Blood GTOF37

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_068


title: Blood GTOF38

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_067


title: Newly diagnosed elderly multiple myeloma 85

value: bone marrow


title: abdominal (deep); adipocyte; F33

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79554.gif

source_name: abdominal (deep); adipocyte; F33, 10 ug labeled aRNA

value: 33 years

value: abdominal (deep)


title: Blood GTOF36

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_066


title: abdominal; tissue; M60

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79565.gif

value: Stratagene Human Universal Reference

source_name: abdominal; tissue; M60, 10 ug labeled aRNA

value: 60 years

value: abdominal

value: Male


title: Newly diagnosed elderly multiple myeloma 83

value: CD138 purified myeloma plasma cells

value: High risk


title: Newly diagnosed elderly multiple myeloma 82


title: abdominal; tissue; F62a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79537.gif

source_name: abdominal; tissue; F62a, 10 ug labeled aRNA

value: 62 years

value: tissue


title: NormalDonor2_untreated_PBMC_065

value: Normal

value: Peripherial blood mononuclear cells


title: shin/calf; stromal pellet; M51

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79540.gif

source_name: shin/calf; stromal pellet; M51, 10 ug labeled aRNA

value: 51 years

value: shin/calf

value: stromal pellet


title: NormalDonor2_untreated_PBMC_064


title: Newly diagnosed elderly multiple myeloma 84

value: multiple myeloma

value: Standard risk

value: IVT


title: Blood GTOF35

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: abdominal (superficial); tissue; F33

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79552.gif

value: Stratagene Human Universal Reference

source_name: abdominal (superficial); tissue; F33, 10 ug labeled aRNA

value: 33 years

value: abdominal (superficial)

value: female


title: Blood GTOF33

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 81

value: bone marrow

value: CD138 purified myeloma plasma cells


title: Newly diagnosed elderly multiple myeloma 79


title: Blood GTOF32

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_063


title: Newly diagnosed elderly multiple myeloma 80


title: abdominal (deep); stromal pellet; F33

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79548.gif

source_name: abdominal (deep); stromal pellet; F33, 10 ug labeled aRNA

value: abdominal (deep)


title: NormalDonor2_untreated_PBMC_062

value: Normal


title: calf; adipocyte; M44

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79563.gif

source_name: calf; adipocyte; M44, 10 ug labeled aRNA

value: 44 years

value: calf

value: adipocyte

value: Male


title: NormalDonor2_untreated_PBMC_061

value: Peripherial blood mononuclear cells


title: Blood GTOF31

description: Hybridized to Affymetrix SNP 6.0

source_name: TOF patient_blood


title: Newly diagnosed elderly multiple myeloma 78

value: multiple myeloma

value: Standard risk


title: shin; tissue; F31

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79533.gif

source_name: shin; tissue; F31, 10 ug labeled aRNA

value: 31 years

value: shin

value: tissue


title: NormalDonor2_untreated_PBMC_060


title: Newly diagnosed elderly multiple myeloma 76

source_name: CD138 purified myeloma plasma cells

value: IVT


title: abdominal lipo; adipocyte; M58a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79512.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: Stratagene Human Universal Reference

source_name: abdominal lipo; adipocyte; M58a, 10 ug labeled aRNA

value: 58 years

value: abdominal lipo


title: Newly diagnosed elderly multiple myeloma 77

value: bone marrow

value: CD138 purified myeloma plasma cells


title: Blood GTOF29

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: Newly diagnosed elderly multiple myeloma 75


title: Blood GTOF28

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_058

value: Normal


title: NormalDonor2_untreated_PBMC_059


title: Blood GTOF30

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF27

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 73


title: NormalDonor2_untreated_PBMC_057


title: omentum (stomach); stromal pellet; F52d

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79543.gif

source_name: omentum (stomach); stromal pellet; F52d, 10 ug labeled aRNA

value: 52 years

value: omentum (stomach)

value: stromal pellet

value: female


title: Blood GTOF26

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF25

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF39

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_056

source_name: Blood

value: Peripherial blood mononuclear cells


title: shin/calf; tissue; M51

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79539.gif

source_name: shin/calf; tissue; M51, 10 ug labeled aRNA

value: 51 years

value: shin/calf

value: Male


title: Blood GTOF24

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_054


title: Newly diagnosed elderly multiple myeloma 72

value: multiple myeloma

value: Standard risk

value: IVT


title: shin/calf; adipocyte; F81

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79559.gif

value: Stratagene Human Universal Reference

source_name: shin/calf; adipocyte; F81, 10 ug labeled aRNA

value: 81 years

value: adipocyte


title: Blood GTOF23

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient


title: Newly diagnosed elderly multiple myeloma 69

value: bone marrow

value: CD138 purified myeloma plasma cells


title: NormalDonor2_untreated_PBMC_055

value: Normal


title: NormalDonor2_untreated_PBMC_053


title: shin/calf; tissue; F81

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79560.gif

source_name: shin/calf; tissue; F81, 10 ug labeled aRNA

value: tissue


title: Blood GTOF22

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: shin/calf; stromal pellet; F12

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79541.gif

source_name: shin/calf; stromal pellet; F12, 10 ug labeled aRNA

value: 12 years

value: stromal pellet

value: female


title: Newly diagnosed elderly multiple myeloma 67

value: High risk


title: Newly diagnosed elderly multiple myeloma 71


title: Blood GTOF34

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_052

value: Peripherial blood mononuclear cells


title: shin/calf; tissue; M84

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79528.gif

source_name: shin/calf; tissue; M84, 10 ug labeled aRNA

value: 84 years

value: shin/calf

value: Male


title: abdominal; stromal pellet; M34

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79529.gif

value: Stratagene Human Universal Reference

source_name: abdominal; stromal pellet; M34, 10 ug labeled aRNA

value: 34 years

value: abdominal


title: Blood GTOF21

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient


title: NormalDonor2_untreated_PBMC_051


title: Blood GTOF20

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_050


title: abdominal; adipocyte; M34

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79524.gif

source_name: abdominal; adipocyte; M34, 10 ug labeled aRNA

value: adipocyte


title: Newly diagnosed elderly multiple myeloma 68

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

value: IVT


title: shin/calf; tissue; F81a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79558.gif

source_name: shin/calf; tissue; F81a, 10 ug labeled aRNA

value: 81 years

value: tissue


title: Newly diagnosed elderly multiple myeloma 65

value: Standard risk


title: shin/calf; stromal pellet; M17a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79553.gif

source_name: shin/calf; stromal pellet; M17a, 10 ug labeled aRNA

value: 17 years

value: stromal pellet


title: Newly diagnosed elderly multiple myeloma 66


title: abdominal; stromal pellet; F33

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79534.gif

source_name: abdominal; stromal pellet; F33, 10 ug labeled aRNA

value: 33 years

value: female


title: Newly diagnosed elderly multiple myeloma 70


title: Newly diagnosed elderly multiple myeloma 74


title: Newly diagnosed elderly multiple myeloma 64


title: NormalDonor2_untreated_PBMC_049

value: Normal

value: Peripherial blood mononuclear cells


title: abdominal; stromal pellet; F62a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79555.gif

value: Stratagene Human Universal Reference

source_name: abdominal; stromal pellet; F62a, 10 ug labeled aRNA

value: 62 years


title: omentum (colon); tissue; F23a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79518.gif

source_name: omentum (colon); tissue; F23a, 10 ug labeled aRNA

value: 23 years

value: omentum (colon)


title: NormalDonor2_untreated_PBMC_048


title: Blood GTOF16

description: Hybridized to Affymetrix SNP 6.0

source_name: TOF patient_blood

value: TOF patient

value: blood


title: Blood GTOF19

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_047


title: NormalDonor2_untreated_PBMC_046


title: Blood GTOF15

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_045


title: shin/calf; tissue; M23

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79505.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: shin/calf; tissue; M23, 10 ug labeled aRNA

value: shin/calf

value: Male


title: abdominal (deep); tissue; F33

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79576.gif

source_name: abdominal (deep); tissue; F33, 10 ug labeled aRNA

value: abdominal (deep)


title: omentum (stomach); tissue; F52d

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79572.gif

source_name: omentum (stomach); tissue; F52d, 10 ug labeled aRNA

value: 52 years

value: omentum (stomach)

value: tissue


title: Blood GTOF14

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 62

source_name: CD138 purified myeloma plasma cells

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

value: Standard risk

value: IVT


title: NormalDonor2_untreated_PBMC_044

source_name: Blood

value: Normal

value: Peripherial blood mononuclear cells


title: SSA(100ng mL -1, 6 hr) treated HeLa S3 cells

city: Toyoake

first: Rei

last: Yoshimoto

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using Tophat2
bigwig files were generated using bam2wig then followed by wigToBigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: HeLa S3 cells

growth_protocol: HeLa S3 cells were cultured in DMEM media

extract_protocol:
HeLa cells were collected, and then cytoplasmic RNAs were purified using PARIS kit (Life technologies) according to the manufacturer’s instruction.
Poly(A)+ RNA-seq library was prepared as previously reported (Kawaji et al. 2014). We constructed sequencing libraries starting from 1 µg of total RNA. The library was sequenced Illumina GAIIx using custom sequencing primer.

treatment_protocol: cytoplasmica RNAs derived from HeLa S3 cells treated either with MeOH or SSA (100 ng mL-1)

tag: cell line

value: HeLa

tag: treatment

value: SSA(100ng mL -1, 6 hr)


title: Newly diagnosed elderly multiple myeloma 61


title: Blood GTOF13

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient


title: Newly diagnosed elderly multiple myeloma 58


title: Blood GTOF12

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: NormalDonor2_untreated_PBMC_043


title: Control(MeOH) treated HeLa S3 cells

value: Control(MeOH)


title: Newly diagnosed elderly multiple myeloma 60


title: Pediatric Patient 25

city: Richmond

first: Maren

middle: Lydia

last: Smith

state: Virginia

address: 1217 E Marshall St

department: Pharmacology and Toxicology

institute: Virginia Commonwealth University

data_processing:
Illumina software used for basecalling.
Sequence reads were mapped to GRC38.91 using STAR v2.6.
Count data was generated from STAR produced BAM files using HTSeq v0.61p1.
Count data was corrected for batch effects using ComBat (Johnson et al. PMID: 16632515) and transformed to positive whole numbers.
Genome_build: GRC38.91
Supplementary_files_format_and_content: Tab-deliminted text files countaining count values for each sample after batch correction by ComBat and transformation to positive, whole numbers.

source_name: whole blood

extract_protocol:
Whole blood (2 mL) was collected from study participants in Tempus Blood RNA tubes at the time of diagnosis or flareup. RNA was extracted from blood using the Tempus Spin RNA Isolation Kit (Thermo Fisher), and polyA enrichment was conducted using the NEBNEXT Poly(A) mRNA magnetic isolation kit (New England BioSciences).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole blood

tag: disease state

value: ANCA-associated vasculitis

tag: rna-cluster

value: Endotype A

tag: anca status


title: Blood GTOF10

description: Hybridized to Affymetrix SNP 6.0

tag: group


title: Newly diagnosed elderly multiple myeloma 57

tag: tissue


title: NormalDonor2_untreated_PBMC_042


title: omentum (colon); tissue; F72

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79522.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); tissue; F72, 10 ug labeled aRNA

value: 72 years

value: omentum (colon)

value: female


title: Pediatric Patient 24


title: Pediatric Patient 23


title: Newly diagnosed elderly multiple myeloma 56

tag: diagnosis

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells


title: shin/calf; stromal pellet; F63

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79526.gif

source_name: shin/calf; stromal pellet; F63, 10 ug labeled aRNA

value: 63 years

value: shin/calf

value: stromal pellet


title: Newly diagnosed elderly multiple myeloma 53

tag: cell type

value: Standard risk

value: IVT


title: Newly diagnosed elderly multiple myeloma 55

tag: sky92 status


title: NormalDonor2_untreated_PBMC_041

value: Normal

value: Peripherial blood mononuclear cells


title: abdominal; adipocyte; F50

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79535.gif

source_name: abdominal; adipocyte; F50, 10 ug labeled aRNA

value: 50 years

value: abdominal

value: adipocyte


title: NormalDonor2_untreated_PBMC_040


title: Blood GTOF7

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: abdominal; tissue; M51a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79519.gif

value: Stratagene Human Universal Reference

source_name: abdominal; tissue; M51a, 10 ug labeled aRNA

value: 51 years

value: tissue

value: Male


title: Newly diagnosed elderly multiple myeloma 49

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

tag: reagents


title: abdominal; stromal pellet; F50

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79549.gif

source_name: abdominal; stromal pellet; F50, 10 ug labeled aRNA

value: stromal pellet

value: female


title: Blood GTOF4

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF17

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF8

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF3

description: Hybridized to Affymetrix SNP 6.0


title: abdominal; stromal pellet; F36

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79516.gif

source_name: abdominal; stromal pellet; F36, 10 ug labeled aRNA

value: 36 years


title: NormalDonor2_untreated_PBMC_039

tag: who classification

value: Normal


title: abdominal; tissue; F50

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79550.gif

tag: reference

source_name: abdominal; tissue; F50, 10 ug labeled aRNA


title: Newly diagnosed elderly multiple myeloma 47

value: High risk

value: IVT


title: Pediatric Patient 7

value: whole blood

value: ANCA-associated vasculitis

value: Endotype A


title: Blood GTOF18

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: NormalDonor2_untreated_PBMC_035

value: Peripherial blood mononuclear cells


title: Blood GTOF6

description: Hybridized to Affymetrix SNP 6.0


title: Blood GTOF2

description: Hybridized to Affymetrix SNP 6.0


title: Pediatric Patient 20

value: Endotype B

value: MPO


title: Pediatric Patient 19


title: Newly diagnosed elderly multiple myeloma 46

value: multiple myeloma


title: Pediatric Patient 10


title: Newly diagnosed elderly multiple myeloma 51

value: bone marrow

value: Standard risk


title: NormalDonor2_untreated_PBMC_037


title: omentum (colon); tissue; F75

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79503.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); tissue; F75, 10 ug labeled aRNA

tag: age

value: 75 years

value: omentum (colon)

value: tissue


title: Blood GTOF5

description: Hybridized to Affymetrix SNP 6.0

source_name: TOF patient_blood


title: Blood S20

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_033

value: Normal


title: NormalDonor2_untreated_PBMC_036


title: NormalDonor2_untreated_PBMC_032


title: Newly diagnosed elderly multiple myeloma 48

value: CD138 purified myeloma plasma cells

value: IVT


title: HiC: K562 siMAZ

city: Bethesda

first: Tiaojiang

last: XIao

state: MD

address: rockville Pike

institute: NIDDK, NIH

library_source: genomic

data_processing:
Library strategy: HiC
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for ChIP-seq data. Hic files for Hi-C data.

growth_protocol: K562 cells (ATCC® CCL-243™) were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 10 mM HEPES (pH 7.3), and 1% penicillin-streptomycin.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed with a ChIP-IT Express kit.
ChIP-Seq libraries were prepared using the “NEBNext® Ultra™ II DNA Library Prep Kit”. K562 cells were used to prepare the Hi-C library. The enzyme DpnII was used for restriction digestion. Biotin-14-dATP  was used to fill in the 5’ overhang of DNAs. Hi-C Libraries were prepared with the “NEBNext® Ultra™ II DNA Library Prep Kit”.

treatment_protocol: Knockdown of MAZ and/or CTCF in K562 cells was conducted by using an electroporation system. SiRNAs against MAZ  were On-TARGET plus SMARTpool siRNA oligonucleotides purchased from Dhmarcon Inc.

value: 85% confluent cultured cells

tag: genotype

value: siMAZ


title: NormalDonor2_untreated_PBMC_031


title: Input: k562CtrInp91418

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for ChIP-seq data. Hic files for Hi-C data.


title: Blood S19

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient


title: NormalDonor2_untreated_PBMC_034


title: Newly diagnosed elderly multiple myeloma 44


title: Pediatric Patient 2

value: whole blood

value: ANCA-associated vasculitis

value: Other


title: Newly diagnosed elderly multiple myeloma 43


title: Input: TxInpK562Ctr6217


title: Pediatric Patient 9

value: Endotype B

value: NEGATIVE


title: Blood GTOF1

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: Newly diagnosed elderly multiple myeloma 52

value: multiple myeloma

value: bone marrow

value: High risk


title: Blood S16

description: Hybridized to Affymetrix SNP 6.0


title: Input: TxK562CtrInpJ3117


title: Newly diagnosed elderly multiple myeloma 45


title: NormalDonor2_untreated_PBMC_028

value: Peripherial blood mononuclear cells


title: Blood S18

description: Hybridized to Affymetrix SNP 6.0


title: ChIPSeq: S2PSiMazK562Sept2018

description:
19.ChIPSeq_S2PSiMazK562Sept2018
INPUT SAMPLE: ChIPseqk562CtrInp91418


title: NormalDonor2_untreated_PBMC_030


title: Newly diagnosed elderly multiple myeloma 40


title: HiC: K562 wild type

description: 20.HiC_K562Ctr_J2425F15Comb_HiCJuicer_inter

value: wild type


title: Blood S15

description: Hybridized to Affymetrix SNP 6.0


title: ChIPSeq: S2PK562CtrSept252018

description:
18.ChIPSeq_S2PK562CtrSept252018
INPUT SAMPLE: ChIPseqk562CtrInp91418


title: Newly diagnosed elderly multiple myeloma 39

value: Standard risk


title: Newly diagnosed elderly multiple myeloma 42

value: CD138 purified myeloma plasma cells


title: Blood S13

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 41

value: IVT


title: NormalDonor2_untreated_PBMC_026

value: Normal


title: Newly diagnosed elderly multiple myeloma 37


title: ChIPSeq: MazK562CtrSept252018

description:
17.ChIPSeq_MazK562CtrSept252018
INPUT SAMPLE: ChIPseqk562CtrInp91418

value: 85% confluent cultured cells


title: Blood S17

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient


title: Blood S14

description: Hybridized to Affymetrix SNP 6.0


title: ChIPSeq: Rad21K562siDKsiCTCF&MAZ_Oct102018

description:
16.ChIPSeq_Rad21K562siDKsiCTCF&MAZ_Oct102018
INPUT SAMPLE: ChIPseqk562CtrInp91418

value: SiCTCF&MAZ


title: NormalDonor2_untreated_PBMC_025


title: Newly diagnosed elderly multiple myeloma 63


title: NormalDonor2_untreated_PBMC_024


title: ChIPSeq: Rad21K562SiMazSept252018

description:
15.ChIPSeq_Rad21K562SiMazSept252018
INPUT SAMPLE: ChIPseqk562CtrInp91418

value: SiMAZ


title: Blood S10

description: Hybridized to Affymetrix SNP 6.0


title: abdominal; stromal pellet; M60

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79575.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: Stratagene Human Universal Reference

source_name: abdominal; stromal pellet; M60, 10 ug labeled aRNA

value: 60 years

tag: organism part

value: abdominal

tag: sample fraction

value: stromal pellet

value: Male


title: NormalDonor2_untreated_PBMC_023


title: Newly diagnosed elderly multiple myeloma 35

value: multiple myeloma

value: bone marrow


title: ChIPSeq: Rad21K562CtrSept252018

description:
13.ChIPSeq_Rad21K562CtrSept252018
INPUT SAMPLE: ChIPseqk562CtrInp91418

tag: cell line


title: Newly diagnosed elderly multiple myeloma 36


title: Newly diagnosed elderly multiple myeloma 33

value: High risk


title: Blood S9

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: Blood S8

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_022

value: Peripherial blood mononuclear cells


title: Newly diagnosed elderly multiple myeloma 38

value: CD138 purified myeloma plasma cells

value: Standard risk


title: NormalDonor2_untreated_PBMC_020

value: Normal


title: Blood S7

description: Hybridized to Affymetrix SNP 6.0


title: Blood S12

description: Hybridized to Affymetrix SNP 6.0


title: ChIPSeq: Rad21K562SiCTCFSept252018

description:
14.ChIPSeq_Rad21K562SiCTCFSept252018
INPUT SAMPLE: ChIPseqk562CtrInp91418

value: 85% confluent cultured cells

value: SiCTCF


title: NormalDonor2_untreated_PBMC_021


title: NormalDonor2_untreated_PBMC_019


title: Newly diagnosed elderly multiple myeloma 32

value: IVT


title: NormalDonor2_untreated_PBMC_018


title: NormalDonor2_untreated_PBMC_038


title: Blood S6

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient


title: ChIPSeq: CTCFMiK562SiCTCFSept252018

description:
12.ChIPSeq_CTCFMiK562SiCTCFSept252018
INPUT SAMPLE: ChIPseqk562CtrInp91418

value: siCTCF


title: Newly diagnosed elderly multiple myeloma 31


title: Blood S5

description: Hybridized to Affymetrix SNP 6.0


title: ChIPSeq: S2PK562siMazJ312017

description:
10.ChIPSeq_S2PK562siMazJ312017
INPUT SAMPLE: TxK562CtrInpJ3117

value: siMAZ


title: ChIPSeq: S2PK562CtrJ312017

description:
9.ChIPSeq_S2PK562CtrJ312017
INPUT SAMPLE: TxK562CtrInpJ3117

value: wild type


title: NormalDonor2_untreated_PBMC_017


title: ChIPSeq: MazK562SiMaz6212017

description:
8.ChIPSeq_MazK562SiMaz6212017
INPUT SAMPLE: TxInpK562Ctr6217


title: Blood S4

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 34


title: Newly diagnosed elderly multiple myeloma 29


title: ChIPSeq: MazK562Ctr6212017

description:
7.ChIPSeq_MazK562Ctr6212017
INPUT SAMPLE: TxInpK562Ctr6217


title: Newly diagnosed elderly multiple myeloma 30


title: Blood S1

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_014


title: NormalDonor2_untreated_PBMC_015


title: ChIPSeq: Rad21K562DKDSiCTCF&MAZJuly312017

description:
6.ChIPSeq_Rad21K562DKDSiCTCF&MAZJuly312017
INPUT SAMPLE: TxK562CtrInpJ3117

value: wild typsiCTCF&MAZe


title: ChIPSeq: Rad21K562SiMAZJuly312017

description:
5.ChIPSeq_Rad21K562SiMAZJuly312017
INPUT SAMPLE: TxK562CtrInpJ3117


title: Newly diagnosed elderly multiple myeloma 28


title: Newly diagnosed elderly multiple myeloma 27


title: NormalDonor2_untreated_PBMC_013


title: Blood 20

description: Hybridized to Affymetrix SNP 6.0


title: ChIPSeq: Rad21K562SiCTCFJuly312017

description:
4.ChIPSeq_Rad21K562SiCTCFJuly312017
INPUT SAMPLE: TxK562CtrInpJ3117


title: ChIPSeq: CTCFMiK562CtrSept252018

description:
11.ChIPSeq_CTCFMiK562CtrSept252018
INPUT SAMPLE: ChIPseqk562CtrInp91418


title: ChIPSeq: Rad21K562CtrJuly312017

description:
3.ChIPSeq_Rad21K562CtrJuly312017
INPUT SAMPLE: TxK562CtrInpJ3117


title: Newly diagnosed elderly multiple myeloma 25


title: NormalDonor2_untreated_PBMC_012


title: NormalDonor2_untreated_PBMC_011


title: NormalDonor2_untreated_PBMC_016


title: Blood S3

description: Hybridized to Affymetrix SNP 6.0


title: ChIPSeq: CTCFK562siCTCFJ312017

description:
2.ChIPSeq_CTCFK562siCTCFJ312017
INPUT SAMPLE: TxK562CtrInpJ3117


title: Blood 18

description: Hybridized to Affymetrix SNP 6.0


title: Blood S2

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 22


title: Newly diagnosed elderly multiple myeloma 24


title: ChIPSeq: CTCFK562CtrJ312017

description:
1.ChIPSeq_CTCFK562CtrJ312017
INPUT SAMPLE: TxK562CtrInpJ3117


title: NormalDonor2_untreated_PBMC_010


title: Newly diagnosed elderly multiple myeloma 23


title: Blood 17

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_008


title: Blood 19

description: Hybridized to Affymetrix SNP 6.0


title: Blood 15

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 21


title: Newly diagnosed elderly multiple myeloma 26


title: NormalDonor2_untreated_PBMC_006


title: Blood 13

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_005


title: Blood 16

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor2_untreated_PBMC_007


title: NormalDonor2_untreated_PBMC_009


title: NormalDonor2_untreated_PBMC_029


title: Newly diagnosed elderly multiple myeloma 20


title: NormalDonor2_untreated_PBMC_004


title: NormalDonor2_untreated_PBMC_003


title: Blood 14

description: Hybridized to Affymetrix SNP 6.0


title: PBMC_HC4 (array)

city: Beijing

first: Boyang

last: Xu

address: No.8 Xi Shi Ku Street, Xi Cheng District

institute: Peking University First Hospital

description:
SAMPLE 9
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.

hyb_protocol: cRNA was hybridized at 58°C for 16 hours to the Illumina HumanHT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA).

scan_protocol: BeadChips were scanned using an Illumina BeadArray Reader and the Bead Scan Software (Illumina, San Diego, CA, USA).

data_processing:
The data were normalized using average normalization.
Genomestudio software computed normalized signal intensity.

source_name: PBMC

label_protocol: Illumina Total Prep RNA Amplification Kit (Applied Biosystems, Foster City, CA, USA) was used to transcribe 200 ng of RNA according to the manufacture's recommendation.

extract_protocol: Total RNA, including small RNA fractions, was extracted from PBMC using TRIZOL® Reagent (Invitrogen, Carlsbad, CA, USA), and then eluted with ribonuclease-free water.

tag: gender

value: female

value: healthy control

value: PBMC


title: Blood 11

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 19

value: multiple myeloma

value: bone marrow


title: PBMC_HC2 (array)

description:
SAMPLE 7
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.

tag: disease state


title: Blood 10

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: Newly diagnosed elderly multiple myeloma 17

value: CD138 purified myeloma plasma cells


title: Newly diagnosed elderly multiple myeloma 16

value: Standard risk

value: GPR


title: PBMC_HC3 (array)

description:
SAMPLE 8
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.

value: male


title: Newly diagnosed elderly multiple myeloma 18


title: Blood 9

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 15


title: PBMC_HC1 (array)

description:
SAMPLE 6
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.


title: NormalDonor2_untreated_PBMC_002

value: Normal

value: Peripherial blood mononuclear cells


title: PBMC_IgAN5 (array)

description:
SAMPLE 5
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.

value: IgAN patient


title: Blood 12

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient


title: PBMC_IgAN4 (array)

description:
SAMPLE 4
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.


title: Newly diagnosed elderly multiple myeloma 13


title: PBMC_IgAN3 (array)

description:
SAMPLE 3
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.


title: Blood 8

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 14


title: NormalDonor2_untreated_PBMC_001


title: NormalDonor1_untreated_PBMC_093


title: NormalDonor1_untreated_PBMC_092


title: NormalDonor1_untreated_PBMC_094


title: Blood 6

description: Hybridized to Affymetrix SNP 6.0


title: hSODG93A, corticospinal motor neurons, rep3

city: Chicago

first: Hande

last: Ozdinler

state: Illinois

address: 4141 N. Lawndale Ave

department: Neurology

institute: Northwestern University

hyb_protocol: Biotinylated cRNA (100 ng) was hybridized to Illumina MouseWG-6 v2 Expression BeadChips at 58 °C overnight, according to the manufacturer's instructions (Illumina Inc., San Diego, CA, USA).

scan_protocol: Slides scanned using the Illumina BeadArray Reader.

data_processing:
Data was generated through the Illumina BeadStudio 3.0 software (Illumina Inc.) and probe signal intensities were quantile normalized and log transformed. The exon microarray analyses were performed 3 independent times and the averages of exon readings are presented here. They were also color coded to improve visualization and data analyses. These procedures were performed by the Genomics Core Facility of Northwestern University.
[exon_analyses_complete.txt]  quantile normalized and log2-transformed signals

organism: Mus musculus

source_name: hSODG93A, motor cortex

label_protocol: RNA isolated from two littermate pups with the same genotype was used, and total RNA was converted into biotinylated cRNA (Ambion Illumina RNA amplification kit; Ambion, Austin, TX, USA), it was quantified (ND-1000 Spectrophotometer ; NanoDrop, Wilmington, DE, USA).

extract_protocol: Total RNA was extracted from CSMN that are retrogradely labeled and FACS-purified from P30 WT and hSOD1G93A mice, using TRIZOL reagent (Invitrogen Life Technologies, Grand Island, NY, USA) with DNase digestion to prevent DNA contamination. RNA was reprecipitated in ethanol, integrity and quantity was assessed (Agilent 2100 Bioanalyzer; Agilent Technologies, Palo Alto, CA, USA). Only high quality RNA (OD260/280 ≥ 1.8, RIN > 7.0) were used.

value: motor cortex

value: FACS-purified corticospinal motor neuron (CSMN)


title: hSODG93A, corticospinal motor neurons, rep1


title: wild type, corticospinal motor neurons, rep3

source_name: wild type, motor cortex

value: wild type


title: Blood 7

description: Hybridized to Affymetrix SNP 6.0


title: Blood 4

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 12

source_name: CD138 purified myeloma plasma cells


title: hSODG93A, corticospinal motor neurons, rep2


title: wild type, corticospinal motor neurons, rep2


title: Blood 3

description: Hybridized to Affymetrix SNP 6.0


title: PBMC_IgAN2 (array)

description:
SAMPLE 2
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.

value: female


title: Newly diagnosed elderly multiple myeloma 10


title: NormalDonor1_untreated_PBMC_091

source_name: Blood


title: Newly diagnosed elderly multiple myeloma 11


title: Newly diagnosed elderly multiple myeloma 9


title: Blood 5

description: Hybridized to Affymetrix SNP 6.0


title: wild type, corticospinal motor neurons, rep1


title: Newly diagnosed elderly multiple myeloma 7


title: NormalDonor1_untreated_PBMC_088


title: PBMC_IgAN1 (array)

description:
SAMPLE 1
patient's PBMC were collected before receiving glucocorticoid or immunosuppressive therapy.


title: NormalDonor2_untreated_PBMC_027


title: Blood S11

description: Hybridized to Affymetrix SNP 6.0


title: Blood 1

description: Hybridized to Affymetrix SNP 6.0


title: Blood 2

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_087


title: SG142_12

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

data_processing:
libraries and downstream sequencing was performed by genewiz
Supplementary_files_format_and_content: Data was normalized in Python / R using Deseq2.  Non-normalized and normalized data is supplied in .csv format and contains read information for all 12 samples along with official gene symbol information.

source_name: iCD103+ DC

growth_protocol: bone marrow stem cells were harvested from the femurs of C57Bl/6j mice and grown in RPMI suplemented with 10% FBS, 50 μM 2-βMercaptoethanol, 5 ng / mL murine GMCSF and 200 ng / mL murine FLT ligand.  Medium was changed at 4 days and suspension cells were replated into fresh plates at 9 days.  16 days post isolation DCs were used for downstream experiments.

extract_protocol:
RNA was harvested using RNAeasy columns
libraries and downstream sequencing was performed by genewiz

treatment_protocol: 16 days post isolation cells were treated with γHV-68 (MOI of 1.0) w/ or w/o 200 μM kyn for 24 hours

tag: treatment 2

tag: treatment 3

value: 200 μM kynurenine


title: SG142_11


title: Newly diagnosed elderly multiple myeloma 6


title: Newly diagnosed elderly multiple myeloma 5


title: Newly diagnosed elderly multiple myeloma 8


title: Newly diagnosed elderly multiple myeloma 4


title: Blood QC392

description: Hybridized to Affymetrix SNP 6.0

source_name: healthy control_blood

tag: group

value: healthy control


title: NormalDonor1_untreated_PBMC_090


title: SG142_9


title: NormalDonor1_untreated_PBMC_086


title: NormalDonor1_untreated_PBMC_085


title: Blood QC368

description: Hybridized to Affymetrix SNP 6.0

tag: tissue


title: NormalDonor1_untreated_PBMC_084


title: SG142_10


title: NormalDonor1_untreated_PBMC_089


title: Blood QC313

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_083


title: Blood QC272

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC365

description: Hybridized to Affymetrix SNP 6.0


title: SG142_6

tag: treatment 1

value: Vehicle (DMSO)


title: Blood QC271

description: Hybridized to Affymetrix SNP 6.0


title: SG142_8


title: SG142_7


title: Blood QC270

description: Hybridized to Affymetrix SNP 6.0


title: SG142_5


title: NormalDonor1_untreated_PBMC_081

tag: cell type


title: Blood QC269

description: Hybridized to Affymetrix SNP 6.0


title: SG142_4


title: SG142_3


title: BC_case7_Int-ID_1228

city: Hannover

first: Janin

last: Bublitz

address: Carl-Neuberg-Str. 1

department: Human Genetics

country: Germany

institute: Medizinische Hochschule Hannover

description: hybridized to [OncoScan] Affymetrix OncoScan array

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files were generated after scanning by the Affymetrix GeneChip Command Console (AGCC).
Data was processed and analyzed using Chromosome Analysis Suite (ChAS) version 4.0.0.385
Primary data description: Copy number data

source_name: adj. BC

label_protocol: as given by the manufacturer

growth_protocol: Primary formalin fixed parafffin embedded tissue

extract_protocol: Tissue areas were macrodissected from FFPE tissue blocks.Genomic DNA was extracted with the Maxwell RSC DNA FFPE kits (Promega, Madison, U.S.A.) on a Maxwell RSC instrument (Promega) according to the manufacturer’s recommendations. DNA was quantified using a Qubit 2.0 fluorometer (Invitrogen, Darmstadt, Germany) and the Qubit dsDNA HS assay kit (Life Technologies, Carlsbad, U.S.A.)

tag: condition

value: breast cancer (adjacent)

value: breast tumor tissue


title: NormalDonor1_untreated_PBMC_080


title: NormalDonor1_untreated_PBMC_082


title: BC_case5_Int-ID_1227


title: NormalDonor1_untreated_PBMC_079


title: Blood QC268

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: BC_case1_Int-ID_1225


title: BC_case2_Int-ID_1226


title: SG142_2


title: Blood QC267

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC266

description: Hybridized to Affymetrix SNP 6.0


title: MGA_case8_Int-ID_491

source_name: MGA

value: microglandular adenosis


title: Newly diagnosed elderly multiple myeloma 2

tag: diagnosis

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

tag: sky92 status

value: Standard risk

tag: reagents

value: GPR


title: NormalDonor1_untreated_PBMC_077

tag: who classification

value: Normal

value: Peripherial blood mononuclear cells


title: Newly diagnosed elderly multiple myeloma 3


title: NormalDonor1_untreated_PBMC_078


title: NormalDonor1_untreated_PBMC_076


title: Homozygous VCP Rep4

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

data_processing:
Reads were mapped to the mouse genome (mm10) using the RNASeq Unified Mapper (RUM)
Gene expression differences were analyzed using EdgeR with statistical significance set at a false discovery rate (FDR) of <5%.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene/transcript identifiers, Edge-R output values (A,M,p-value,FDR) for WT vs HET comparison, Edge-R output values (A,M,p-value,FDR) for WT vs HOM comparison, quantile normalized lg read counts, and raw read counts

source_name: Mouse

extract_protocol:
RNA from anterior cortex were extracted using RNeasy RNA extraction kit (Qiagen) following manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: anterior cortex

tag: strain

tag: age

value: 15 months

tag: genotype

value: DG/DG

tag: mouse number


title: NormalDonor1_untreated_PBMC_075


title: Homozygous VCP Rep3


title: Blood QC263

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_074


title: MGA_case5_Int-ID_40


title: Blood QC264

description: Hybridized to Affymetrix SNP 6.0


title: Homozygous VCP Rep2


title: Blood QC262

description: Hybridized to Affymetrix SNP 6.0


title: MGA_case4_Int-ID_490


title: NormalDonor1_untreated_PBMC_073


title: MGA_case2_Int-ID_489


title: Homozygous VCP Rep1


title: NormalDonor1_untreated_PBMC_072


title: SG142_1


title: Heterozygous VCP Rep6

value: DG/+


title: MGA_case1_Int-ID_34


title: Blood QC261

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: MGA_case6_Int-ID_41


title: Blood QC265

description: Hybridized to Affymetrix SNP 6.0


title: Heterozygous VCP Rep5


title: NormalDonor1_untreated_PBMC_071


title: Blood QC260

description: Hybridized to Affymetrix SNP 6.0


title: SCCOHT1_BRG1_RNAseq_Rep3

city: Chapel Hill

first: Bernard

middle: E.

last: Weissman

state: NC

address: 450 West Drive

department: Pathology and Laboratory Medicine

institute: University of North Carolina at Chapel Hill

description: SCCOHT1 Parental cells, BRG1 transfected - Rep 3

data_processing:
Fastq files were initially analyzed by fastqc (v0.11.5). Reads were aligned with STAR (v2.5.3a) to GENCODE v24 (hg38) using the 2-pass method.  Aligned reads were quantified by salmon (v0.8.2) for transcripts per million (TPM) counts. TPMs were summarized to gene level using tximport (v1.10.1) in R. Differentially expressed genes between BRG1 and Control samples using DESeq2 (v1.22.2).
Genome_build: hg38 (GENCODE v24)
Supplementary_files_format_and_content: scaled counts = normalized counts (TPMs) summarized to gene level using tximport (countsFromAbundance = "lengthScaledTPMs").

source_name: Cell Line

growth_protocol: SCCOHT1 cells were cultured in RPMI-1640 (Gibco #11875-093) supplemented with 10% FBS and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA from frozen cell pellets was extracted using the Zymo Quick-RNA Miniprep Kit (Zymo cat# R1054).
Total RNA was prepared using the Illumina TruSeq mRNA v2 kit with an input of 500ng of RNA for each sample to produce unstranded RNA libraries following the manufacturer’s protocol. Final RNA libraries were quantified using the Qubit High Sense Reagent kit and Agilent Tapestation HSD1000 tapes. Libraries were equimolar pooled and paired end sequenced across three lanes of a HiSeq4000 (paired end x 78 bp).

tag: cell line

tag: transfected vector


title: NormalDonor1_untreated_PBMC_069


title: SCCOHT1_BRG1_RNAseq_Rep2

description: SCCOHT1 Parental cells, BRG1 transfected - Rep 2


title: NormalDonor1_untreated_PBMC_070


title: Heterozygous VCP Rep3


title: Heterozygous VCP Rep4


title: NormalDonor1_untreated_PBMC_068


title: SCCOHT1_BRG1_RNAseq_Rep1

description: SCCOHT1 Parental cells, BRG1 transfected - Rep 1


title: Heterozygous VCP Rep2


title: NormalDonor1_untreated_PBMC_067


title: SCCOHT1_Control_RNAseq_Rep3

description: SCCOHT1 Parental cells, control transfected - Rep 3

value: Control


title: Blood QC258

description: Hybridized to Affymetrix SNP 6.0


title: Heterozygous VCP Rep1


title: Blood QC257

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC256

description: Hybridized to Affymetrix SNP 6.0


title: Wild-type VCP Rep3

value: Wild-type


title: Blood QC255

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_066


title: Blood QC259

description: Hybridized to Affymetrix SNP 6.0


title: SCCOHT1_Control_RNAseq_Rep1

description: SCCOHT1 Parental cells, control transfected - Rep 1


title: Wild-type VCP Rep2


title: NormalDonor1_untreated_PBMC_065


title: SCCOHT1_Control_RNAseq_Rep2

description: SCCOHT1 Parental cells, control transfected - Rep 2


title: COV434_Parent_BRG1_RNAseq_Rep3

description: COV434 Parental cells, BRG1 transfected - Rep 3

data_processing:
Fastq files were initially analyzed by fastqc (v0.11.5). Reads were aligned with STAR (v2.5.3a) to GENCODE v24 (hg38) using the 2-pass method.  Aligned reads were quantified by salmon (v0.8.2) for transcripts per million (TPM) counts. TPMs were summarized to gene level using tximport (v1.10.1) in R. Differentially expressed genes between BRG1 and Control samples using DESeq2 (v1.22.2).
Genome_build: hg38 (GENCODE v24)
Supplementary_files_format_and_content: scaledCounts = normalized counts (TPMs) summarized to gene level using tximport (countsFromAbundance = "lengthScaledTPMs").

growth_protocol: COV434 cells were cultured in RPMI-1640 (Gibco #11875-093) supplemented with 10% FBS and maintained at 37°C in a humidified incubator with 5% CO2.


title: Blood QC254

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_064


title: Blood QC253

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_063


title: Wild-type VCP Rep4


title: Blood QC252

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_062


title: COV434_Parent_BRG1_RNAseq_Rep1

description: COV434 Parental cells, BRG1 transfected - Rep 1


title: Wild-type VCP Rep1


title: Blood QC251

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_061


title: p88_Calv: Mouse calvaria (sample p88)

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Adapter trimmed reads were obtained from raw reads using Cutadapt v0.9.5
Bowtie v0.12.7 was used to aglign the reads.
mirDeep2 along with miRBase v20 was used to identify novel miRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each miRNA per sample

source_name: Calvaria (parietal and frontal bones)

extract_protocol:
Direct-zol™ RNA kit (Zymo Research)
NEBNext Small RNA library prep kit

value: Primary calvaria tissue

value: 2 to 3 days old


title: p73_Calv: Mouse calvaria (sample p73)


title: Blood QC249

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: COV434_Parent_Control_RNAseq_Rep2

description: COV434 Parental cells, control transfected - Rep 2


title: COV434_Parent_BRG1_RNAseq_Rep2

description: COV434 Parental cells, BRG1 transfected - Rep 2


title: p64_Calv: Mouse calvaria (sample p64)


title: NormalDonor1_untreated_PBMC_060


title: D24: Day 24 differentiated MC3T3 cells

source_name: Cell line

value: MC3T3 E1 sc4

value: Passage 10 to 15


title: A427_RNAseq_BRG1_Rep3

description: A427 cells with doxycyline inducible BRG1 expression

data_processing:
Fastq files were initially analyzed by fastqc (v0.11.5). Reads were aligned with STAR (v2.5.3a) to GENCODE v24 (hg38) using the 2-pass method.  Aligned reads were quantified by salmon (v0.8.2) for transcripts per million (TPM) counts. TPMs were summarized to gene level using tximport (v1.10.1) in R. Differentially expressed genes between BRG1 and Control samples using DESeq2 (v1.22.2).
IGV browser tracks (bigwig) were generated on the merged biological replicates by deeptools (v3.2.) bamCoverage with a binsize of 30 and normalized using RPKMs.
Genome_build: hg38 (GENCODE v24)
Supplementary_files_format_and_content: scaled counts = normalized counts (TPMs) summarized to gene level using tximport (countsFromAbundance = "lengthScaledTPMs").

growth_protocol: A427 pINDUCER20-BRG1 cells were cultured in RPMI-1640 (Gibco #11875-093) supplemented with 10% TET-FREE FBS (GenminiBio# 100-106) +400 ug/ml G418 and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA from frozen cell pellets was extracted using the Zymo Quick-RNA Miniprep Kit (Zymo cat# R1054).
Library construction and sequncing was performed by Novogene Inc.

treatment_protocol: A427 pINDUCER20-BRG1 cells were induced +/- DOX (+/- BRG1 expression) for 48 hours prior to harvest for RNAseq.

tag: treatment

value: Doxycycline (DOX)

tag: expression

tag: construct


title: COV434_Parent_Control_RNAseq_Rep1

description: COV434 Parental cells, control transfected - Rep 1


title: Blood QC250

description: Hybridized to Affymetrix SNP 6.0

data_processing: The overall hybridization quality was estimated by the call rate obtained from Genotyping Console Software 4.2 (birdseed algorithm with default parameter settings). Partek Genomics Suite (version 6.5, Partek Inc., St. Louis, MO) was used for copy number analysis. Regions of CNV were detected using a Hidden Markov Model (HMM) algorithm in the Partek workflow for unpaired samples.

tag: group

tag: tissue


title: COV434_Parent_Control_RNAseq_Rep3

description: COV434 Parental cells, control transfected - Rep 3


title: NormalDonor1_untreated_PBMC_058

tag: cell type


title: Blood QC248

description: Hybridized to Affymetrix SNP 6.0


title: A427_RNAseq_BRG1_Rep2


title: D17: Day 17 differentiated MC3T3 cells


title: D10: Day 10 differentiated MC3T3 cells


title: Blood QC247

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC246

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_059


title: A427_RNAseq_BRG1_Rep1


title: D6: Day 6 differentiated MC3T3 cells


title: Blood QC245

description: Hybridized to Affymetrix SNP 6.0


title: D0: Day 0 (undifferentiated) MC3T3 cells


title: NormalDonor1_untreated_PBMC_056


title: NormalDonor1_untreated_PBMC_054


title: A427_RNAseq_Control_Rep1


title: T-Rheb -/- CD8+ cells from spleen

city: Baltimore

first: Jonathan

middle: D.

last: Powell

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University

description: Total mouse spleen was mashed through a 70um filter and red blood cells removed via hypotonic lysis. Then CD4+ and CD8+ cells were isolated.

hyb_protocol: The standard Affymetrix hybridization protocol was followed.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw data were extracted from Affymetrix CEL files. This file was then normalized using an Robust Multiarray Analysis algorithm.

source_name: T-Rheb -/- spleen

label_protocol: The standard Affymetrix labeling protocol was followed.

extract_protocol: RNA was isolated via Trizol. cDNA was synthesized with M-MuLV Reverse Transcriptase.

treatment_protocol: The microarray procedure was performed by the Johns Hopkins Deep Sequencing & Microarray Core.

value: 6 weeks

value: spleen

value: T-Rheb -/-

value: CD8+ cells


title: A427_RNAseq_Control_Rep3


title: HSCs aged in old niche 1

city: los angeles

first: Du

last: Jiang

state: ca

address: 1425 san pablo st bcc 305

department: stem cell

institute: university of southern california

data_processing:
raw fastq files were generated by Illumina bcl2fastq software with default parameters
fastq files of each sample were processed separately using cellranger software (v2.1.0) "cellranger count" with default settings
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file containing UMI matrix of each gene in each cell

source_name: hematopoietic stem cells

extract_protocol: Chromium Single Cell 3’ Library (10X Genomics, V2)

value: bone marrow

tag: developmental stage

value: adult


title: NormalDonor1_untreated_PBMC_057

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

value: Normal

value: Peripherial blood mononuclear cells


title: HSCs aged in old niche 2


title: Blood QC244

description: Hybridized to Affymetrix SNP 6.0

extract_protocol: Genomic DNA was extracted from peripheral blood for each patient and control subject, using QIAamp® DNA blood mini kit according to the manufacturer’s instruction

value: healthy control


title: NormalDonor1_untreated_PBMC_052

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.


title: Blood QC243

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_053


title: A427_RNAseq_Control_Rep2

value: Control


title: Blood QC241

description: Hybridized to Affymetrix SNP 6.0


title: HD_66Q_Luc_R2

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

description:
HD sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
31_CS02iHD66n4_D37_LucLNP_R2

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence, and then mapped to mm10 or GRCh37 whole genome using Tophat2
gene counts were quantified using featureCounts and raw counts were used for normalization and differential stats using deseq2
Genome_build: mm10 or GRCh37
Supplementary_files_format_and_content: csv or tab-delimited text file includes raw count data for each Sample

source_name: medium spiny neuron-like

growth_protocol: iPSC were grown and matrigel and in mTESR and then differentiated into medium spiny neuron-like cells using a combination of growth factors, growth medium, and chemical inhibitors. Mouse tissues were collected at 8 and 13.5 Mos on GFP-positive microdissected striatal tissue

extract_protocol:
For iPSC-derived neurons, RNA was extracted from day 37 cell pellets using Qiagen RNeasy kit and QIAshredders, 1 µg of RNA with Rin values >8 for each sample were utilized for library preparation and RNAseq using illumina Truseq stranded polyA+ mRNA kit. For zQ175 mice, GFP+ micro-dissected flash frozen brain regions were homogenized in TRIzol reagent (Invitrogen) and RNA was extracted according to manufacturer’s protocol. RNA was then purified using RNEasy Mini kit (QIAGEN). Residual DNA was removed by DNase treatment incorporated into the RNEasy protocol as per manufacturer’s
RNA libraries were prepared for sequencing using standard Illumina Truseq protocols for stranded mRNAseq

treatment_protocol: Mice were treated with AAV2/1 expressing either a miRNA against Pias1 (miPias1.3), a control scrambled miRNA (miSafe) or a vehicle control (Saline) through bilateral stereotaxic striatal injections. The human iPSCs were differentiated into neural progenitors and then treated with siRNA against PIAS1 (or luciferase) via lipid nanoparticles at the iPSC stage.

value: iPSC-derived MSN-like

tag: condition

value: HD

tag: polyq length

tag: treatement

value: Luc

tag: replicate


title: Wt C57B6J -/- CD4+ cells from spleen

source_name: Wt C57B6J spleen

growth_protocol: Total mouse spleen was mashed through a 70um filter and red blood cells removed via hypotonic lysis. Then CD4+ and CD8+ cells were isolated.

value: Wt C57B6J

value: CD4+ cells


title: Wt C57B6J -/- CD8+ cells from spleen


title: Blood QC242

city: Tianjin

first: huanxin

last: chen

address: No.61, third avenue, tianjin economic and technolo

institute: Teda International Cardiovascular Hospital

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: control_33Q_Luc_R2

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
25_CS83iCTR33n1_D37_LucLNP_R2

value: control


title: T-Rheb -/- CD4+ cells from spleen

value: 6 weeks


title: HD_66Q_Pias_R2

description:
HD sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
32_CS02iHD66n4_D37_PIAS1LNP_R2

value: Pias


title: HSCs aged in young niche 2

tag: strain


title: RXRDM_14

city: New Haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

institute: Yale University School of Medicine

data_processing:
Paired-end reads were mapped against Mouse assembly GRCm38 using STAR-2.6
Counts calculated with FeatureCounts version 1.6.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for each sample

source_name: brain

extract_protocol:
Rneasy plus micro kit (Qiagen)
SMART-seq v4 Ultra Low Input Kit (Takara) and Nextera XT DNA library Prep Kit (Illumina)

tag: brain region

value: Medial

tag: index

value: Index sequences N506 N702

value: RXRg, RARb double mutant


title: RXRDO_13

value: Orbital

value: Index sequences N506 N701

tag: genotype


title: NormalDonor1_untreated_PBMC_048

city: Boston

first: Birgit

last: Knoechel

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

tag: who classification

value: Normal

value: Peripherial blood mononuclear cells


title: NormalDonor1_untreated_PBMC_051


title: HD_109Q_Pias_R1

description:
HD sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
18_CS09iHD109n4_D37_PIAS1LNP_R1


title: NormalDonor1_untreated_PBMC_050


title: Blood QC237

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: HSCs aged in young niche 1

value: bone marrow

value: adult


title: Blood QC240

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC236

description: Hybridized to Affymetrix SNP 6.0


title: control_33Q_Pias_R2

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
26_CS83iCTR33n1_D37_PIAS1LNP_R2

value: iPSC-derived MSN-like


title: RXRWM_10

value: Index sequences N505 N702


title: RXRDD_15

value: Dorsal

value: Index sequences N506 N705


title: Blood QC239

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: Blood QC235

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_055


title: NormalDonor1_untreated_PBMC_049


title: NormalDonor1_untreated_PBMC_045


title: NormalDonor1_untreated_PBMC_046


title: RXRWD_11

value: Index sequences N505 N705

value: control


title: control_18Q_Luc_R2

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
19_CS25iCTR18n6_D37_LucLNP_R2

value: Luc


title: NormalDonor1_untreated_PBMC_047


title: Blood QC234

description: Hybridized to Affymetrix SNP 6.0


title: RXRDD_7

value: Index sequences N504 N705


title: control_18Q_Pias_R2

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
20_CS25iCTR18n6_D37_PIAS1LNP_R2

value: Pias


title: Blood QC238

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC233

description: Hybridized to Affymetrix SNP 6.0


title: control_28Q_Pias_R1

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
6_CS14iCTR28n6_D37_PIAS1LNP_R1


title: NormalDonor1_untreated_PBMC_044


title: HD_109Q_Luc_R1

description:
HD sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
17_CS09iHD109n4_D37_LucLNP_R1

value: HD


title: NormalDonor1_untreated_PBMC_043


title: Blood QC232

description: Hybridized to Affymetrix SNP 6.0


title: HD_109Q_Pias_R2

description:
HD sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
36_CS09iHD109n4_D37_PIAS1LNP_R2


title: RXRDM_6

value: Medial

value: Index sequences N504 N702

value: RXRg, RARb double mutant


title: Blood QC231

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: HD_109Q_Luc_R2

description:
HD sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
35_CS09iHD109n4_D37_LucLNP_R2


title: control_28Q_Luc_R1

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
5_CS14iCTR28n6_D37_LucLNP_R1


title: Blood QC230

description: Hybridized to Affymetrix SNP 6.0


title: RXRDO_5

value: Orbital

value: Index sequences N504 N701


title: control_28Q_Pias_R2

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
24_CS14iCTR28n6_D37_PIAS1LNP_R2

value: iPSC-derived MSN-like


title: RXRWD_3

value: Index sequences N503 N705


title: NormalDonor1_untreated_PBMC_040

value: Normal

value: Peripherial blood mononuclear cells


title: RXRWM_2

value: Index sequences N503 N702


title: Blood QC229

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: RXRW0_9

value: Index sequences N505 N701

value: control


title: Blood QC228

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_039


title: control_28Q_Luc_R2

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
23_CS14iCTR28n6_D37_LucLNP_R2

value: Luc


title: NormalDonor1_untreated_PBMC_038


title: HD_71Q_Pias_R1

description:
HD sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
16_CS81iHD71n3_D37_PIAS1LNP_R1

value: Pias


title: RARDDO7

value: Dorsal

value: Index sequences N504 N705


title: Blood QC227

description: Hybridized to Affymetrix SNP 6.0


title: RXRW0_1

value: Index sequences N503 N701


title: NormalDonor1_untreated_PBMC_042


title: control_20Q_Pias_R1

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
4_CS71iCTR20n6_D37_PIAS1LNP_R1


title: RARMDO6

value: Medial

value: Index sequences N504 N702

value: RXRg, RARb double mutant


title: HD_71Q_Luc_R1

description:
HD sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
15_CS81iHD71n3_D37_LucLNP_R1

value: HD


title: NormalDonor1_untreated_PBMC_041


title: Blood QC225

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: Blood QC226

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC223

description: Hybridized to Affymetrix SNP 6.0


title: RARDWT3

value: Index sequences N503 N705


title: RARODO5

value: Orbital

value: Index sequences N504 N701


title: RAROWT1


title: NormalDonor1_untreated_PBMC_032

value: Normal

value: Peripherial blood mononuclear cells


title: NormalDonor1_untreated_PBMC_036


title: HD_71Q_Luc_R2

description:
HD sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
33_CS81iHD71n3_D37_LucLNP_R2

value: iPSC-derived MSN-like


title: NormalDonor1_untreated_PBMC_037


title: control_20Q_Luc_R2

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
21_CS71iCTR20n6_D37_LucLNP_R2

value: control


title: NormalDonor1_untreated_PBMC_035


title: control_20Q_Pias_R2

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
22_CS71iCTR20n6_D37_PIAS1LNP_R2


title: Blood QC220

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: RARMWT2

value: Index sequences N503 N702


title: HD_66Q_Pias_R1

description:
HD sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
14_CS02iHD66n4_D37_PIAS1LNP_R1

value: Pias


title: HD_71Q_Pias_R2

description:
HD sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
34_CS81iHD71n3_D37_PIAS1LNP_R2


title: control_20Q_Luc_R1

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
3_CS71iCTR20n6_D37_LucLNP_R1

value: Luc


title: NormalDonor1_untreated_PBMC_031


title: Blood QC222

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_030