title: post-vaccination blood sample from donor 822653 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d822653_post_92TH023ENV_15h


title: post-vaccination blood sample from donor 117102 stimulate 15 hours with 92TH023ENV

status: Public on Feb 15 2019

type: RNA

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

country: USA

institute: Northwestern University

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).

data_processing: Raw probe intensities were preprocessed using the R (version 3.3.2) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.48.0). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.30.7).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Blood sample from donor 117102

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: RNA was isolated using the Rneasy micro kit (Qiagen) and the quality of the RNA was conﬁrmed using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.

treatment_protocol: Peripheral blood mononuclear cells were stimulated in vitro for 15 hours with short peptides (15-mers) of HIV-1 Env or for 15 hours with the vehicle (DMSO).

tag: donor

tag: scanning note

value: ok

tag: rna extraction protocol

value: Micro kit

tag: stimulation

tag: stimulation time

tag: stimulation time unit

value: hours

tag: treatment

value: VACCINE

tag: hiv infection

value: No


title: pre-vaccination blood sample from donor 822653 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d822653_pre_92TH023ENV_15h

source_name: Blood sample from donor 822653

tag: post-thraw resting

value: no

tag: visit

value: pre


title: post-vaccination blood sample from donor 816509 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d816509_post_92TH023ENV_15h

source_name: Blood sample from donor 816509

value: post

value: RV144 vaccine


title: post-vaccination blood sample from donor 818754 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d818754_post_92TH023ENV_15h

source_name: Blood sample from donor 818754


title: pre-vaccination blood sample from donor 726470 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d726470_pre_92TH023ENV_15h

source_name: Blood sample from donor 726470


title: pre-vaccination blood sample from donor 719845 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d719845_pre_DMSO_15h

source_name: Blood sample from donor 719845

value: DMSO


title: post-vaccination blood sample from donor 726470 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d726470_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 719845 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d719845_pre_92TH023ENV_15h


title: KPC tumor #1

type: SRA

city: La Jolla

first: Michael

last: Hamilton

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

description: cell barcodes for this sample end in "-1"

library_source: transcriptomic

data_processing:
Cellranger 2.1.1 – for alignment, filtering, barcode counting, and UMI counting
Seurat 3.0 – for secondary analysis of feature-barcode matrices
Genome_build: Mus38
Supplementary_files_format_and_content: .csv, .tsv, .mtx, differential gene expression between clusters, UMI counts

organism: Mus musculus

source_name: KPC tumor cells

extract_protocol:
10x genomics manufacturer's protocol
10x genomics 3' expression gene profiling v2

treatment_protocol: Sorted and sequenced KPC cells that were CD45-, CD31- and PDGFRa-

tag: strain

value: KPf/fC

tag: cell type

value: KPC tumor cells


title: post-vaccination blood sample from donor 726470 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d726470_post_DMSO_15h


title: post-vaccination blood sample from donor 804141 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d804141_post_DMSO_15h

source_name: Blood sample from donor 804141


title: post-vaccination blood sample from donor 719845 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d719845_post_DMSO_15h


title: post-vaccination blood sample from donor 804141 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d804141_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 816509 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d816509_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 719845 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d719845_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 804141 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d804141_pre_92TH023ENV_15h


title: pre-vaccination blood sample from donor 816509 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d816509_pre_DMSO_15h


title: pre-vaccination blood sample from donor 726470 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d726470_pre_DMSO_15h


title: pre-vaccination blood sample from donor 642334 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d642334_pre_92TH023ENV_15h

source_name: Blood sample from donor 642334


title: pre-vaccination blood sample from donor 638110 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d638110_pre_DMSO_15h

source_name: Blood sample from donor 638110


title: pre-vaccination blood sample from donor 804141 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d804141_pre_DMSO_15h


title: pre-vaccination blood sample from donor 642334 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d642334_pre_DMSO_15h


title: post-vaccination blood sample from donor 642334 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d642334_post_DMSO_15h

value: RV144 placebo


title: post-vaccination blood sample from donor 638110 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d638110_post_DMSO_15h


title: N90

city: West Point

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45oC with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: The data were analyzed by RMA with Affymetrix Power Tools package using Affymetrix default analysis settings.

source_name: Normal from patient 90

label_protocol: standard Affymetrix protocol

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: tissue

value: normal gastric tissue

tag: patient


title: Rorc sgRNA replicate 3

data_processing:
Kallisto – transcript quantification
Sleuth – gene differential expression analysis/gene normalized abundance measurements
GSVA R package – pathway enrichment analysis
Genome_build: Hg38
Supplementary_files_format_and_content: .xls, TPM values and sleuth output

source_name: Human FG pancreatic cancer cells

extract_protocol:
Rneasy Micro Plus kit
Illumina's Stranded Truseq

tag: condition

value: Rorc sgRNA

tag: cell line

value: FG

value: pancreatic cancer cells


title: N93

source_name: Normal from patient 93


title: Rorc sgRNA replicate 2


title: N97

source_name: Normal from patient 97


title: N96

source_name: Normal from patient 96


title: pre-vaccination blood sample from donor 638110 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d638110_pre_92TH023ENV_15h


title: Rorc sgRNA replicate 1


title: post-vaccination blood sample from donor 642334 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV
RV144_d642334_post_92TH023ENV_15h


title: N91

source_name: Normal from patient 91


title: N85

source_name: Normal from patient 85


title: post-vaccination blood sample from donor 818754 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d818754_post_DMSO_15h


title: pre-vaccination blood sample from donor 630802 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d630802_pre_92TH023ENV_15h

source_name: Blood sample from donor 630802


title: N84

source_name: Normal from patient 84


title: post-vaccination blood sample from donor 628785 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d628785_post_DMSO_15h

source_name: Blood sample from donor 628785


title: N88

source_name: Normal from patient 88


title: pre-vaccination blood sample from donor 630802 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d630802_pre_DMSO_15h


title: pre-vaccination blood sample from donor 627471 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d627471_pre_92TH023ENV_15h

source_name: Blood sample from donor 627471


title: N86

source_name: Normal from patient 86


title: pre-vaccination blood sample from donor 627471 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d627471_pre_DMSO_15h


title: pre-vaccination blood sample from donor 628785 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d628785_pre_DMSO_15h


title: pre-vaccination blood sample from donor 628785 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d628785_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 638110 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d638110_post_92TH023ENV_15h


title: post-vaccination blood sample from donor 816509 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d816509_post_DMSO_15h

source_name: Blood sample from donor 816509


title: post-vaccination blood sample from donor 630802 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d630802_post_92TH023ENV_15h


title: post-vaccination blood sample from donor 628785 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV
RV144_d628785_post_92TH023ENV_15h


title: Control sgRNA replicate 3

value: Control sgRNA


title: Control sgRNA replicate 1


title: N80

source_name: Normal from patient 80


title: KPC tumor #2

description: cell barcodes for this sample end in "-2"

source_name: KPC tumor cells


title: N81

source_name: Normal from patient 81


title: BJfibroblastsp63_RNA_rep1

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Reads were mapped to the reference human genome assembly GRCh37/hg19 using splice-aware tool STAR (maximum fragment size set to be 2000 bp). Alignments with a MAPQ score over ten were counted towards RefSeq genes using featureCounts (default parameters).
Fragment pileup per ten million reads for each RNA library were generated by BedTools (“genomecov -split -bg -scale”) and UCSC tool package (“bedGraphToBigWig”).
Pairwise differential expression analysis was implemented using R package DESeq2 with FDR cutoff set to be 0.05 and fold-change cutoff set to be 1.5.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each library.

molecule: polyA RNA

source_name: BJ ATCC ® CRL-2522™

growth_protocol: Trans-differentiated and control BJ fibroblasts (population doubling 20-30) were lysed in TRIzol (ThermoFischer Scientific, #15596018) and snap frozen for RNA isolation.

extract_protocol:
Snapfrozen RNA samples were further extracted using chloroform and QIAGEN RNeasy Mini Kit (#74106) including DNase digestion. Purified RNA was then reverse transcribed to cDNA using High Capacity cDNA Reverse Transcription Kit from Applied Biosystems (4368814), cDNA was then quantified and used to construct sequencing libraries.
Poly(A) + RNA was isolated using double selection with poly-dT beads, followed by first and second-strand synthesis.

value: skin; foreskin normal

tag: growth protocol

value: cell culture, 37˚C

tag: vector


title: BJfibroblastsp63KLF4_RNA_rep1


title: BJfibroblastsp63_RNA_rep2


title: BJfibroblastsp63KLF4_RNA_rep2


title: post-vaccination blood sample from donor 627471 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d627471_post_DMSO_15h

tag: donor

value: Micro kit

value: hours


title: pre-vaccination blood sample from donor 617107 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d617107_pre_92TH023ENV_15h

source_name: Blood sample from donor 617107

value: no

tag: rna extraction protocol

value: No


title: N49

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Normal from patient 49


title: N4

source_name: Normal from patient 4


title: pre-vaccination blood sample from donor 615235 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d615235_pre_DMSO_15h

source_name: Blood sample from donor 615235

tag: stimulation

value: pre


title: Control sgRNA replicate 2

source_name: Human FG pancreatic cancer cells


title: pre-vaccination blood sample from donor 611510 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d611510_pre_92TH023ENV_15h

source_name: Blood sample from donor 611510

tag: stimulation time


title: BJfibroblastsmtp63SAMKLF4_RNA_rep2


title: post-vaccination blood sample from donor 617107 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d617107_post_DMSO_15h

tag: stimulation time unit

value: post

value: RV144 vaccine


title: post-vaccination blood sample from donor 615235 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d615235_post_DMSO_15h

value: DMSO

tag: treatment


title: N47

source_name: Normal from patient 47


title: N45

source_name: Normal from patient 45


title: BJfibroblastsmtp63SAMKLF4_RNA_rep1


title: pre-vaccination blood sample from donor 617107 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d617107_pre_DMSO_15h

tag: hiv infection


title: BJfibroblastsmtp63DBDKLF4_RNA_rep2


title: post-vaccination blood sample from donor 611510 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d611510_post_DMSO_15h

tag: post-thraw resting


title: N41

source_name: Normal from patient 41


title: pre-vaccination blood sample from donor 610097 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d610097_pre_DMSO_15h

source_name: Blood sample from donor 610097

tag: visit


title: pre-vaccination blood sample from donor 611459 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d611459_pre_92TH023ENV_15h

source_name: Blood sample from donor 611459


title: post-vaccination blood sample from donor 610097 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d610097_post_DMSO_15h


title: N42

source_name: Normal from patient 42


title: pre-vaccination blood sample from donor 615235 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d615235_pre_92TH023ENV_15h


title: BJfibroblastsmtp63DBDKLF4_RNA_rep1


title: N55

source_name: Normal from patient 55


title: BJfibroblastsctrl_RNA_rep2

value: control


title: N3

source_name: Normal from patient 3


title: post-vaccination blood sample from donor 611459 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d611459_post_DMSO_15h


title: pre-vaccination blood sample from donor 611510 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d611510_pre_DMSO_15h


title: BJfibroblastsctrl_RNA_rep1


title: N39

source_name: Normal from patient 39


title: pre-vaccination blood sample from donor 611459 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d611459_pre_DMSO_15h


title: pre-vaccination blood sample from donor 605022 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d605022_pre_DMSO_15h

source_name: Blood sample from donor 605022


title: pre-vaccination blood sample from donor 610097 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d610097_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 605022 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d605022_post_DMSO_15h


title: pre-vaccination blood sample from donor 601471 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d601471_pre_DMSO_15h

source_name: Blood sample from donor 601471


title: pre-vaccination blood sample from donor 601471 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d601471_pre_92TH023ENV_15h


title: pre-vaccination blood sample from donor 605022 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d605022_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 601471 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d601471_post_DMSO_15h


title: pre-vaccination blood sample from donor 503384 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d503384_pre_DMSO_15h

source_name: Blood sample from donor 503384


title: N38

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Normal from patient 38


title: pre-vaccination blood sample from donor 600077 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d600077_pre_92TH023ENV_15h

source_name: Blood sample from donor 600077


title: post-vaccination blood sample from donor 503474 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d503474_post_92TH023ENV_15h

source_name: Blood sample from donor 503474


title: BJfibroblastsp63_p63ChIP_rep2

library_source: genomic

data_processing:
Reads were mapped to the reference human genome assembly GRCh37/hg19 using Bowtie2 (maximum fragment size set to be 2000 bp).
Properly aligned, non-duplicated pairs were retained for peak calling using MACS2 (q-value cutoff set to be 0.01).
Fragment pileup per million reads for each ChIP library and corresponding input were also generated and subtracted by MACS2 for visualization. Only overlapping peaks shared by biological replicates were used for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: enrichment regions in bed format and read pileup in bigwig format

molecule: genomic DNA

source_name: BJ ATCC ® CRL-2522™

growth_protocol: Trans-differentiated and control BJ fibroblasts (population doubling 20-30) were crosslinked with formaldehyde (1% final) for 5 min at room temperature.

extract_protocol:
Crosslinked cells were quenched with glycine (125mM final) for 5 min, followed by 2 x washes in cold PBS. Nuclei were then isolated from 20 million cells as previously described (Shah et at. 2013), and chromatin  was sheared to 250bp average size using a Covaris S220. Immunoprecipitations were performed using 500µg sheared chromatin lysate and 5 µg antibodies preconjugated to Protein G beads (Invitrogen): H3K27ac (Active Motif, 39133), Flag (Sigma, M2, F1804) and hKLF4 (R&D Systems, AF3640). ChIP reactions were incubated for 16 hours at 4˚C with rotation and then washed 4x in wash buffer (50mM HEPES-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurylsarcosine), followed by 1 wash in ChIP final wash buffer (1xTE, 50mM NaCl). Immunoprecipitated DNA was eluted from washed beads, reverse crosslinked overnight, purified and used to construct libraries.
Sequencing libraries for ChIP experiments were prepared using NEBNext Ultra reagents (New England Biolabs). All ChIP samples and input were double-end sequenced on an Illumina NextSeq 500.

tag: growth

tag: chip antibody

value: antiFlag(Sigma M2 #F1804)


title: post-vaccination blood sample from donor 503384 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d503384_post_DMSO_15h


title: N33

source_name: Normal from patient 33

tag: tissue

value: normal gastric tissue


title: N34

source_name: Normal from patient 34

tag: patient


title: N35

source_name: Normal from patient 35


title: pre-vaccination blood sample from donor 503384 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d503384_pre_92TH023ENV_15h


title: BJfibroblastsp63KLF4_p63ChIP_rep2


title: N32

source_name: Normal from patient 32


title: N36

source_name: Normal from patient 36


title: post-vaccination blood sample from donor 503384 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d503384_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 600077 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d600077_pre_DMSO_15h


title: pre-vaccination blood sample from donor 503474 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d503474_pre_DMSO_15h


title: BJfibroblastsp63_p63ChIP_rep1


title: BJfibroblastsp63KLF4_p63ChIP_rep1


title: pre-vaccination blood sample from donor 503474 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d503474_pre_92TH023ENV_15h


title: BJfibroblastsp63KLF4_KLF4ChIP_rep2

value: R&D Systems #AF3640


title: pre-vaccination blood sample from donor 501766 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d501766_pre_DMSO_15h

source_name: Blood sample from donor 501766


title: BJfibroblastsp63KLF4_InputChIP_rep2


title: BJfibroblastsp63KLF4_H3K27acChIP_rep2

value: Active Motif #39133


title: BJfibroblastsp63KLF4_KLF4ChIP_rep1


title: N31

source_name: Normal from patient 31


title: BJfibroblastsp63KLF4_H3K27acChIP_rep1


title: pre-vaccination blood sample from donor 501766 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d501766_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 501766 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d501766_post_DMSO_15h


title: N30

source_name: Normal from patient 30


title: N26

source_name: Normal from patient 26


title: pre-vaccination blood sample from donor 453859 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d453859_pre_DMSO_15h

source_name: Blood sample from donor 453859


title: N29

source_name: Normal from patient 29


title: post-vaccination blood sample from donor 501766 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d501766_post_92TH023ENV_15h


title: N27

source_name: Normal from patient 27


title: post-vaccination blood sample from donor 446015 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d446015_post_DMSO_15h

source_name: Blood sample from donor 446015


title: post-vaccination blood sample from donor 453859 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d453859_post_DMSO_15h


title: post-vaccination blood sample from donor 453859 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d453859_post_92TH023ENV_15h


title: BJfibroblastsp63_InputChIP_rep1


title: BJfibroblastsp63_InputChIP_rep2


title: N28

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Normal from patient 28


title: post-vaccination blood sample from donor 444677 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d444677_post_92TH023ENV_15h

source_name: Blood sample from donor 444677


title: post-vaccination blood sample from donor 446015 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d446015_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 453859 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d453859_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 444677 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d444677_post_DMSO_15h


title: pre-vaccination blood sample from donor 444677 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d444677_pre_92TH023ENV_15h


title: pre-vaccination blood sample from donor 444677 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d444677_pre_DMSO_15h


title: pre-vaccination blood sample from donor 446015 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d446015_pre_DMSO_15h


title: pre-vaccination blood sample from donor 446015 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d446015_pre_92TH023ENV_15h


title: N24

source_name: Normal from patient 24


title: N20

source_name: Normal from patient 20


title: pre-vaccination blood sample from donor 443620 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d443620_pre_DMSO_15h

source_name: Blood sample from donor 443620


title: post-vaccination blood sample from donor 443620 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d443620_post_DMSO_15h


title: N22

source_name: Normal from patient 22


title: N25

source_name: Normal from patient 25


title: pre-vaccination blood sample from donor 443620 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d443620_pre_92TH023ENV_15h


title: BJfibroblastsp63_H3K27acChIP_rep1

source_name: BJ ATCC ® CRL-2522™


title: BJfibroblastsmtp63SAMKLF4_p63ChIP_rep2


title: BJfibroblastsmtp63SAMKLF4_p63ChIP_rep1


title: alms1MUT-1

city: Baltimore

first: Norann

middle: A

last: Zaghloul

state: MD

address: 670 W. Baltimore Street; HSF3 Room 4176

institute: University of Maryland School of Medicine

data_processing:
trimmed to remove low-quality bases at ends
mapping to ref genome using CLC Genomics Workbench v 10.0.1
calculated total gene hit counts and RPKM values
Genome_build: GRCz10
Supplementary_files_format_and_content: tab delineated text files of gene expression for each sample set

organism: Danio rerio

source_name: beta-cells

growth_protocol: 5 dpf zebrafish animals of either Tg(ins:mCherry) or alms1 mutants carrying Tg(ins:mCherry)

extract_protocol:
single cell dissociation of whole embryo and FACS sort for mCherry fluorescence (Hostelley et al., 2017)
Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.

tag: cell marker

value: FACS-isolated mCherry+ cells

tag: cell type

value: beta-cell enriched

tag: genotype

tag: age

value: 5 dpf


title: WT-2

value: wildtype


title: BJfibroblastsmtp63SAMKLF4_KLF4ChIP_rep2

value: skin; foreskin normal

value: cell culture, 37˚C

tag: vector


title: BJfibroblastsmtp63SAMKLF4_KLF4ChIP_rep1


title: BJfibroblastsmtp63SAMKLF4_InputChIP_rep2


title: BJfibroblastsmtp63SAMKLF4_InputChIP_rep1


title: alms1MUT-2


title: N1

source_name: Normal from patient 1


title: post-vaccination blood sample from donor 443620 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d443620_post_92TH023ENV_15h

tag: donor

value: no

tag: rna extraction protocol

value: Micro kit

value: hours


title: RNA-mNPC-Ctrl replicate 4

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: RNA-mNPC.all.counts.txt.gz

data_processing:
Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (vM9) (Harrow et al., 2012).
Genome_build: mm9(NCBIM37_um)
Supplementary_files_format_and_content: raw reads count by HTSEQ

source_name: Neural Tube Embryonic day 14

growth_protocol: Animal experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. The Trp53bp1tm1Jc KO mouse, stock 006495, was from the Jackson Laboratory. KO and wild-type embryos at embryonic day 14 were used for comparison studies.

extract_protocol:
Deletion/KO and wild-type embryos at embryonic day 14 were dissected, their neural tubes were dissociated by collagenase type 2 to yield single cells, and mNPCs isolated by FACS using NeuroFluor CDr3 (STEMCELL Technologies, #01800). Isolated mNPCs were analyzed or cultured in differentiation media (NeuroCult differentiation, STEMCELL Technologies, #05704) for further analyses
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)

treatment_protocol: To derive 53bp1 mutant mouse, C57BL/6J zygotes were micro-injected with 100ng/ul Cas9 mRNAs and 25ng/ul CRISPR RNAs diluted in IDTE and transferred into the oviducts of pseudo-pregnant CD-1 females. Targeted region in 53bp1 locus of the resultant pups were sequenced to identify in-frame deletions. Males containing the deletions were mated to Trp53bp1tm1Jc females to generate embryos, whose 53bp1 locus was sequenced to identify deletion/KO embryos.

tag: genotype/variation

value: Control

value: Mouse Neural Progenitor cells

tag: strain

tag: developmental stage

value: Embryonic day 14


title: BJfibroblastsp63KLF4_InputChIP_rep1


title: N18

source_name: Normal from patient 18


title: WT-1


title: pre-vaccination blood sample from donor 438404 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d438404_pre_DMSO_15h

source_name: Blood sample from donor 438404

tag: stimulation

value: DMSO

tag: stimulation time

tag: stimulation time unit

value: pre

tag: hiv infection

value: No


title: post-vaccination blood sample from donor 438404 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d438404_post_DMSO_15h

tag: post-thraw resting

tag: visit

value: post

tag: treatment

value: RV144 vaccine


title: N19

source_name: Normal from patient 19

tag: tissue

value: normal gastric tissue

tag: patient


title: pre-vaccination blood sample from donor 438404 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d438404_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 424473 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d424473_post_DMSO_15h

source_name: Blood sample from donor 424473


title: pre-vaccination blood sample from donor 424473 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d424473_pre_DMSO_15h


title: N15

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Normal from patient 15


title: RNA-mNPC-Ctrl replicate 2

description: RNA-mNPC.all.counts.txt.gz

tag: cell type


title: BJfibroblastsmtp63SAMKLF4_H3K27acChIP_rep2

tag: growth

tag: chip antibody

value: Active Motif #39133


title: N17

source_name: Normal from patient 17


title: pre-vaccination blood sample from donor 424473 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d424473_pre_92TH023ENV_15h

tag: donor


title: N12

source_name: Normal from patient 12


title: post-vaccination blood sample from donor 438404 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d438404_post_92TH023ENV_15h

tag: rna extraction protocol


title: BJfibroblastsmtp63SAMKLF4_H3K27acChIP_rep1

tag: vector


title: RNA-mNPC-Ctrl replicate 3

description: RNA-mNPC.all.counts.txt.gz

tag: genotype/variation

tag: strain


title: N129

source_name: Normal from patient 129


title: pre-vaccination blood sample from donor 417655 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d417655_pre_DMSO_15h

source_name: Blood sample from donor 417655

tag: stimulation


title: BJfibroblastsctrl_p63ChIP_rep1

value: antiFlag(Sigma M2 #F1804)

value: control


title: N11

source_name: Normal from patient 11


title: post-vaccination blood sample from donor 424473 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d424473_post_92TH023ENV_15h

tag: stimulation time


title: pre-vaccination blood sample from donor 417655 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d417655_pre_92TH023ENV_15h

tag: stimulation time unit


title: post-vaccination blood sample from donor 417655 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d417655_post_DMSO_15h

tag: hiv infection


title: RNA-mNPC-Ctrl replicate 1

description: RNA-mNPC.all.counts.txt.gz

tag: developmental stage


title: BJfibroblastsctrl_p63ChIP_rep2

value: skin; foreskin normal


title: RNA-mNPC-53BP1KO replicate 4

description: RNA-mNPC.all.counts.txt.gz

value: 53BP1 KO


title: RNA-mNPC-53BP1KO replicate 3

description: RNA-mNPC.all.counts.txt.gz


title: BJfibroblastsctrl_KLF4ChIP_rep2

value: cell culture, 37˚C

value: R&D Systems #AF3640


title: RNA-mNPC-53BP1KO replicate 1

description: RNA-mNPC.all.counts.txt.gz


title: RNA-mNPC-53BP1KO replicate 2

description: RNA-mNPC.all.counts.txt.gz


title: N118

source_name: Normal from patient 118


title: BJfibroblastsctrl_InputChIP_rep2


title: BJfibroblastsctrl_KLF4ChIP_rep1


title: 60m: Secondary meningioma

city: Olomouc

first: Josef

last: Srovnal

address: Hnevotinska 5

department: IMTM

country: Czech Republic

institute: Palacky University

hyb_protocol: Total RNA was polyadenylated, labeled, ligated by FlashTag and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidic station 450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (version 4.0.0.1567G).
CEL files (all 59 meningioma samples) were loaded with read.celfiles() function from oligo Bioconductor package (ver. 1.44.0) with usage of pd.mirna.4.0 annotation package (ver 3.12.0) and normalized by quantile normalization method with rma() function from oligo package. Subset of 6094 stem-loops, miRNAs and snoRNAs normalized expressions corresponding to „Homo sapiens“ were then used as an input file for subsequent analysis.

label: Biotin

source_name: Tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA  was extracted from macrodissected FFPE tumor tissue using miRNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: meningioma tumor

tag: recurrence

value: pair to 45m

tag: gender

value: F


title: BJfibroblastsctrl_InputChIP_rep1

tag: tissue


title: 59m: Secondary meningioma

value: pair to 44m

value: M


title: 58m: Secondary meningioma

value: pair to 43m


title: BJfibroblastsctrl_H3K27acChIP_rep2


title: pre-vaccination blood sample from donor 408280 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d408280_pre_92TH023ENV_15h

source_name: Blood sample from donor 408280

tag: post-thraw resting

value: no

value: Micro kit

value: hours

tag: visit

value: pre

value: No


title: N117

source_name: Normal from patient 117

value: normal gastric tissue

tag: patient


title: BJfibroblastsctrl_H3K27acChIP_rep1

source_name: BJ ATCC ® CRL-2522™

tag: growth

tag: chip antibody

value: Active Motif #39133

value: control


title: N115

source_name: Normal from patient 115


title: post-vaccination blood sample from donor 417655 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d417655_post_92TH023ENV_15h

tag: donor

tag: rna extraction protocol

value: post

tag: treatment

value: RV144 vaccine


title: pre-vaccination blood sample from donor 408280 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d408280_pre_DMSO_15h

value: DMSO


title: 57m: Secondary meningioma

value: meningioma tumor

value: pair to 42m


title: N113

source_name: Normal from patient 113


title: post-vaccination blood sample from donor 408280 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d408280_post_DMSO_15h


title: N116

source_name: Normal from patient 116


title: pre-vaccination blood sample from donor 407053 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d407053_pre_DMSO_15h

source_name: Blood sample from donor 407053


title: 56m: Secondary meningioma

value: pair to 41m


title: post-vaccination blood sample from donor 408280 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d408280_post_92TH023ENV_15h


title: 55m: Secondary meningioma

value: pair to 40m

value: F


title: N112

source_name: Normal from patient 112


title: pre-vaccination blood sample from donor 407053 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d407053_pre_92TH023ENV_15h


title: N114

source_name: Normal from patient 114


title: 54m: Secondary meningioma

value: pair to 39m

value: M


title: BJfibroblastsp63KLF4_ATAC_rep2

data_processing:
Reads were mapped to the reference human genome assembly GRCh37/hg19 using Bowtie2 (maximum fragment size set to be 2000 bp).
Properly aligned, non-duplicated pairs were retained and reads mapped to mitochondria or ENCODE blacklist regions were excluded. For peak calling, we adjusted the read start sites to represent the center of the transposon binding event (all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the - strand were offset -5 bp). Broad peaks were called using MACS2 (q-value cutoff set to be 0.01).
Fragment pileup per million reads for each ATAC library were also generated by MACS2 for visualization. Similar to the ChIP-seq data, only overlapping peaks shared by biological replicates were used for analysis. To acquire sub-nucleosomal peaks, only fragments shorter than 120 nt were used.
Genome_build: hg19
Supplementary_files_format_and_content: enrichment regions in bed format and read pileup in bigwig format

growth_protocol: Trans-differentiated and control BJ fibroblasts (population doubling 20-30) were crosslinked with formaldehyde (1% final) for 5 min at room temperature or lysed in TRIzol (ThermoFischer Scientific, #15596018) and snap frozen for RNA isolation.

extract_protocol:
ATACseq experiments were performed as previously described (Buenrostro et al) using 100,000 cells and 5µL Tn5 transposase (Nextera XT Kit, Illumina) to tagment intact nuclei.
ATACseq experiments were performed as previously described (Buenrostro et al) using 100,000 cells and 5µL Tn5 transposase (Nextera XT Kit, Illumina) to tagment intact nuclei.

value: skin; foreskin normal

value: cell culture, 37˚C

tag: vector


title: BJfibroblastsp63_ATAC_rep1


title: BJfibroblastsp63KLF4_ATAC_rep1


title: 53m: Secondary meningioma

value: pair to 38m


title: N105

source_name: Normal from patient 105


title: BJfibroblastsmtp63SAMKLF4_ATAC_rep2


title: BJfibroblastsmtp63SAMKLF4_ATAC_rep1


title: N101

source_name: Normal from patient 101


title: pre-vaccination blood sample from donor 356632 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d356632_pre_DMSO_15h

source_name: Blood sample from donor 356632

value: no

value: Micro kit

tag: stimulation

value: hours

value: pre

value: No


title: post-vaccination blood sample from donor 407053 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d407053_post_DMSO_15h

tag: stimulation time

value: post

value: RV144 vaccine


title: N106

source_name: Normal from patient 106

value: normal gastric tissue


title: post-vaccination blood sample from donor 407053 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d407053_post_92TH023ENV_15h

tag: stimulation time unit


title: N94

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Normal from patient 94


title: N95

source_name: Normal from patient 95


title: 51m: Secondary meningioma

value: meningioma tumor

value: pair to 36m


title: post-vaccination blood sample from donor 356632 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d356632_post_92TH023ENV_15h

tag: hiv infection


title: 50m: Secondary meningioma

value: pair to 35m


title: BJfibroblastsctrl_ATAC_rep2

value: control


title: pre-vaccination blood sample from donor 356632 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d356632_pre_92TH023ENV_15h


title: 52m: Secondary meningioma

value: pair to 37m

value: F


title: post-vaccination blood sample from donor 356632 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d356632_post_DMSO_15h

value: DMSO


title: pre-vaccination blood sample from donor 333892 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d333892_pre_92TH023ENV_15h

source_name: Blood sample from donor 333892


title: N89

source_name: Normal from patient 89


title: 49m: Secondary meningioma

source_name: Tumor tissue

value: pair to 34m


title: BJfibroblastsp63_ATAC_rep2

value: skin; foreskin normal

value: cell culture, 37˚C


title: pre-vaccination blood sample from donor 333892 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d333892_pre_DMSO_15h

value: no

value: Micro kit


title: BJfibroblastsctrl_ATAC_rep1


title: N82

source_name: Normal from patient 82


title: N87

source_name: Normal from patient 87


title: Rag2null_E14_5_WholeThy_rep1

city: Neuherberg

first: David

middle: Sebastian

last: Fischer

address: Ingolstaedter Landstr. 1

department: ICB

country: Germany

institute: Helmholtz Zentrum Munich

description: Drop-seq

data_processing:
Base calling was performed using Illumina RTA version 2.4.11.
FASTQ's from resequenced runs were concatenated prior to processing.
Alignment and quantification were performed using the STAR aligner v2.4.2, Picard tools v1.96, Samtools v1.3, and Drop-seq tools v1.0.
Analysis step: Convert to SAM  Software package:  Picard tools   Command name:  FastqToSam.jar Parameters used:  --
Analysis step: Tag cell barcode  Software package:  DropSeq tools  Command name: TagBamWithReadSequenceExtended  Parameters used:  BASE_QUALITY=10, BARCODED_READ=1, NUM_BASES_BELOW_QUALITY=1,  DISCARD_READ=False
Analysis step: Tag molecular barcode  Software package:  DropSeq tools  Command name: TagBamWithReadSequenceExtended Parameters used:  BASE_QUALITY=10, BARCODED_READ=1, NUM_BASES_BELOW_QUALITY=1,  DISCARD_READ=True
Analysis step: Remove low-quality barcodes  Software package:  DropSeq tools  Command name:   FilterBAM  Parameters used:     --
Analysis step: Remove polyA tail  Software package:  DropSeq tools  Command name:   PolyATrimmer               Parameters used:  MISMATCHES=0, NUM_BASES=6
Analysis step: Convert to FASTQ  Software package:  Picard tools   Command name:   SamToFastq.jar             Parameters used:     --
Analysis step: Align reads to exome  Software package:  STAR  Command name:   --  Parameters used: --
Analysis step: Sort BAM to speed merging  Software package:  Picard tools  Command name:   SortSam.jar                 Parameters used:     --
Analysis step: Merge barcode and alignment info  Software package:  Picard tools  Command name:   MergeBamAlignment.jar       Parameters used:  INCLUDE_SECONDARY_ALIGNMENTS=False
Analysis step: Label read with exon  Software package:  DropSeq tools  Command name:   TagReadWithGeneExon        Parameters used:     --
Analysis step: Screen for bead errors  Software package:  DropSeq tools  Command name:  DetectBeadSynthesisErrors  Parameters used: NUM_BARCODES=2000
Analysis step: Form DGE matrix  Software package:  DropSeq tools  Command name:   DigitalExpression          Parameters used: MIN_NUM_GENES_PER_CELL=1000
The procedure was repeated with a TCR contig added to the reference genome and the following two steps were used to generate improved TCR counts.
Analysis step: Subset reads aligning to TCR contig Software package: Samtools Command name: view Parameters used:  -bh
Analysis step: Form TCR-specific DGE matrix  Software package:  DropSeq tools  Command name:   DigitalExpression          Parameters used: MIN_NUM_GENES_PER_CELL=1 READ_MQ=1
Genome_build: For initial DGE calculations, mm10 was used. For TCR-specific DGE's, an artificial TCR contig was added.
Supplementary_files_format_and_content: Processed files are digital gene expression matrices containing UMI counts. They are represented as dense matrices in (gzipped) tab-delimited text files. Each column is labeled with a cell barcode and each row is labeled with a gene.

growth_protocol: Thymic lobes were isolated from timed mouse embryos.

extract_protocol:
Thymic lobes were mechanically isolated, dissociated in trypsin, depleted of RBC's (only some samples), washed and stained with 7AAD cell viability dye, and 7AAD negative single cells were sorted on a BD FACSARIA.
Libraries were prepared according to the Drop-seq lab protocol version 3.1 (Macosko and Goldman, December 2015, McCarroll Lab).  Final libraries were sequenced on an Illumina NextSeq 500 using high-output 75-cycle kits.

tag: genotype

tag: source tissue

value: embryo

tag: developmental day

tag: rbc lysis buffer

tag: cell type

value: mixed sample (non-demultiplexed) [whole thymus, including mesenchyme, endothelium, epithelium, thymocytes, and other lymphocytes]


title: 48m: Secondary meningioma

tag: tissue

tag: recurrence

value: pair to 33m

tag: gender

value: M


title: 45m: Primary meningioma

value: yes


title: post-vaccination blood sample from donor 333892 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d333892_post_DMSO_15h

tag: post-thraw resting

value: hours

tag: visit

value: post

value: RV144 vaccine

value: No


title: BJfibroblastsp63_H3K27acChIP_rep2

source_name: BJ ATCC ® CRL-2522™

tag: growth

tag: chip antibody

value: Active Motif #39133


title: 47m: Secondary meningioma

value: meningioma tumor

value: pair to 32m


title: 46m: Secondary meningioma

value: pair to 31m


title: 42m: Primary meningioma

value: F


title: N75

source_name: Normal from patient 75

value: normal gastric tissue

tag: patient


title: 44m: Primary meningioma


title: post-vaccination blood sample from donor 333892 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d333892_post_92TH023ENV_15h

tag: donor

value: no

tag: rna extraction protocol

tag: stimulation

tag: treatment


title: pre-vaccination blood sample from donor 321087 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d321087_pre_DMSO_15h

source_name: Blood sample from donor 321087

value: Micro kit

value: DMSO

tag: stimulation time

tag: stimulation time unit

value: pre

tag: hiv infection


title: post-vaccination blood sample from donor 328351 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d328351_post_DMSO_15h

source_name: Blood sample from donor 328351


title: post-vaccination blood sample from donor 328351 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d328351_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 328351 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d328351_pre_DMSO_15h


title: N61

source_name: Normal from patient 61


title: 39m: Primary meningioma


title: N68

source_name: Normal from patient 68


title: N78

source_name: Normal from patient 78


title: N79

source_name: Normal from patient 79


title: 41m: Primary meningioma


title: N60

source_name: Normal from patient 60


title: 37m: Primary meningioma


title: N57

source_name: Normal from patient 57


title: N58

source_name: Normal from patient 58


title: post-vaccination blood sample from donor 321087 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d321087_post_DMSO_15h


title: pre-vaccination blood sample from donor 321087 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d321087_pre_92TH023ENV_15h


title: 40m: Primary meningioma


title: N56

source_name: Normal from patient 56


title: 38m: Primary meningioma


title: N238

source_name: Normal from patient 238


title: N236

source_name: Normal from patient 236


title: pre-vaccination blood sample from donor 309403 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d309403_pre_DMSO_15h

source_name: Blood sample from donor 309403


title: post-vaccination blood sample from donor 321087 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d321087_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 316054 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d316054_pre_DMSO_15h

source_name: Blood sample from donor 316054


title: post-vaccination blood sample from donor 316054 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d316054_post_DMSO_15h


title: pre-vaccination blood sample from donor 309403 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d309403_pre_92TH023ENV_15h


title: 36m: Primary meningioma

source_name: Tumor tissue


title: N213

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Normal from patient 213


title: pre-vaccination blood sample from donor 316054 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d316054_pre_92TH023ENV_15h


title: N202

source_name: Normal from patient 202


title: 35m: Primary meningioma


title: N228

source_name: Normal from patient 228


title: N197

source_name: Normal from patient 197


title: N205

source_name: Normal from patient 205


title: N227

source_name: Normal from patient 227


title: post-vaccination blood sample from donor 316054 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d316054_post_92TH023ENV_15h


title: post-vaccination blood sample from donor 309403 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d309403_post_DMSO_15h

value: PLACEBO


title: 33m: Primary meningioma

value: M


title: 32m: Primary meningioma

value: yes


title: 31m: Primary meningioma


title: N192

source_name: Normal from patient 192


title: N201

source_name: Normal from patient 201


title: pre-vaccination blood sample from donor 308636 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d308636_pre_DMSO_15h

source_name: Blood sample from donor 308636

value: hours


title: pre-vaccination blood sample from donor 308157 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d308157_pre_DMSO_15h

source_name: Blood sample from donor 308157


title: N193

source_name: Normal from patient 193


title: 26m: Primary meningioma


title: 30m: Primary meningioma


title: 28m: Primary meningioma


title: 29m: Primary meningioma


title: post-vaccination blood sample from donor 309403 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV
RV144_d309403_post_92TH023ENV_15h

value: post


title: pre-vaccination blood sample from donor 308157 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d308157_pre_92TH023ENV_15h


title: N189

source_name: Normal from patient 189


title: post-vaccination blood sample from donor 308636 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d308636_post_DMSO_15h


title: post-vaccination blood sample from donor 308157 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d308157_post_DMSO_15h

value: RV144 vaccine


title: pre-vaccination blood sample from donor 308636 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d308636_pre_92TH023ENV_15h

value: No


title: 22m: Primary meningioma


title: 27m: Primary meningioma


title: N175

source_name: Normal from patient 175


title: N172

source_name: Normal from patient 172


title: N185

source_name: Normal from patient 185


title: N180

source_name: Normal from patient 180


title: 24m: Primary meningioma

source_name: Tumor tissue


title: post-vaccination blood sample from donor 308636 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV
RV144_d308636_post_92TH023ENV_15h


title: N188

source_name: Normal from patient 188


title: 20m: Primary meningioma


title: N187

source_name: Normal from patient 187


title: 25m: Primary meningioma


title: 23m: Primary meningioma


title: pre-vaccination blood sample from donor 305900 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d305900_pre_DMSO_15h

source_name: Blood sample from donor 305900


title: pre-vaccination blood sample from donor 328351 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d328351_pre_92TH023ENV_15h

source_name: Blood sample from donor 328351


title: 17m: Primary meningioma


title: 19m: Primary meningioma


title: 15m: Primary meningioma


title: pre-vaccination blood sample from donor 305900 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d305900_pre_92TH023ENV_15h


title: 14m: Primary meningioma


title: 43m: Primary meningioma


title: N151

source_name: Normal from patient 151


title: N150

source_name: Normal from patient 150


title: pre-vaccination blood sample from donor 234806 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d234806_pre_92TH023ENV_15h

source_name: Blood sample from donor 234806


title: post-vaccination blood sample from donor 305900 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d305900_post_92TH023ENV_15h


title: post-vaccination blood sample from donor 305900 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d305900_post_DMSO_15h


title: N157

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

source_name: Normal from patient 157


title: N146

source_name: Normal from patient 146


title: post-vaccination blood sample from donor 234806 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d234806_post_92TH023ENV_15h


title: 21m: Primary meningioma


title: 18m: Primary meningioma


title: pre-vaccination blood sample from donor 234806 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d234806_pre_DMSO_15h


title: 13m: Primary meningioma


title: N144

source_name: Normal from patient 144


title: N141

source_name: Normal from patient 141


title: N136

source_name: Normal from patient 136


title: post-vaccination blood sample from donor 215604 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d215604_post_92TH023ENV_15h

source_name: Blood sample from donor 215604


title: 16m: Primary meningioma


title: post-vaccination blood sample from donor 215604 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d215604_post_DMSO_15h


title: N138

source_name: Normal from patient 138


title: post-vaccination blood sample from donor 234806 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d234806_post_DMSO_15h


title: pre-vaccination blood sample from donor 215604 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d215604_pre_DMSO_15h


title: KPC Rorc shRNA replicate 3

data_processing:
Kallisto – transcript quantification
Sleuth – gene differential expression analysis/gene normalized abundance measurements
Data were also analyzed with CuffDiff. The reads were aligned with STAR and analyzed using cuffdiff with a FDR cutoff of 5%.
GSVA R package – pathway enrichment analysis
Genome_build: Mus38
Supplementary_files_format_and_content: .txt, TPM values and sleuth output
Supplementary_files_format_and_content: Excel file: cuffdiff output and the calculated FPKM values for the each of the samples

source_name: KPC epithelial cells

tag: condition

value: Rorc shRNA

tag: strain

value: KPf/fC


title: 12m: Primary meningioma

tag: tissue

value: meningioma tumor


title: 11m: Primary meningioma

tag: recurrence


title: 10m: Primary meningioma

tag: gender


title: KPC Rorc shRNA replicate 1


title: GBM30

city: New York

first: Kam

last: Leong

state: NY

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

data_processing:
Sequencing data was generated on Illumina HiSeq 2500 instrument, same as GSE109535.
Casava 1.8.2 and bcl2fastq2 v2.19.0 were used for fastq generation.
Sequenced reads were trimmed for adaptor sequence, preprocessed for cell barcodes and unique molecular index, and  then mapped to hg19 genome(STAR v2.5.2b).
Digital expression matrix was generated for the cells with over 10,000 reads per cell.
Genome_build: hg19
Supplementary_files_format_and_content: Text files of expression matrix used in analysis.  The Seurat package (V2.3.0) in R (V3.4.1) was applied to identify differentially expressed genes among 26,027 single cells from 10 samples. Cells were considered in the analysis only if they met the following quality control criteria: 1) expression of more than 1,000 genes and fewer than 5,000 genes; 2) low expression of mitochondrial genes (<10% of total counts in a cell). After filtering, 24,120 genes in 21,750 cells were left for clustering analysis. Different batches of the same patient were combined in one txt file. The name of each column indicates the batch and cell barcode. For example, the column name "GBM1A_ATGCAGCGCTGA" represents the mRNA expression data from GBM1 patient, the first batch "A", and from the cell "ATGCAGCGCTGA".

source_name: Human Glioblastoma Cells

growth_protocol: Human glioblastoma cells were maintained in neural basal medium supplemented with B27 (Gibco), FGF (20ng/ml, Peprotech), and EGF (20ng/ml, Peprotech).

extract_protocol:
Brain tumor-derived neurospheres were mechanically dissociated into single cells using a pipette and then loaded to a microwell-based chip (sc-FTDseq) for mRNA capture by uniquely barcoded beads. The cells were lysed using three cycles of freeze-thaw .
The single cell mRNA libraries were prepared using the DropSeq protocol (GSE63473), tagged with Illumina nextera single indexes (N701, N702, N703, N704, N705, N706). We used the same protocol as in scFTD-seq(GSE109535), where each mRNA captured was end-paired with an unique molecular index(UMI) and a cell barcode. We prepared 2 to 4 biological repeats of each patient sample for library construction and sequenced 26,027 single cells in 26 batches.

treatment_protocol: no treatment

tag: subject status

value: glioblastoma patient

value: brain

tag: cell type

value: Patient-derived glioblastoma stem-like cells


title: GBM24


title: 7m: Primary meningioma

source_name: Tumor tissue

value: no

value: F


title: KPC Control shRNA replicate 2

value: Control shRNA


title: KPC Control shRNA replicate 3


title: GS5


title: 9m: Primary meningioma


title: N135

source_name: Normal from patient 135

value: normal gastric tissue


title: N133

source_name: Normal from patient 133


title: KPC Rorc shRNA replicate 2


title: GBM16


title: pre-vaccination blood sample from donor 201390 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d201390_pre_DMSO_15h

source_name: Blood sample from donor 201390

tag: post-thraw resting

value: Micro kit

value: DMSO

tag: visit

value: pre


title: N140

source_name: Normal from patient 140

tag: patient


title: GBM14


title: N134

source_name: Normal from patient 134


title: N132

source_name: Normal from patient 132


title: 6m: Primary meningioma

value: yes


title: 5m: Primary meningioma


title: pre-vaccination blood sample from donor 126294 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d126294_pre_DMSO_15h

source_name: Blood sample from donor 126294

tag: donor

value: hours


title: post-vaccination blood sample from donor 201390 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d201390_post_DMSO_15h

tag: rna extraction protocol

value: post

value: RV144 vaccine


title: 8m: Primary meningioma


title: 4m: Primary meningioma


title: post-vaccination blood sample from donor 126294 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d126294_post_DMSO_15h

tag: stimulation

value: No


title: pre-vaccination blood sample from donor 126294 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d126294_pre_92TH023ENV_15h


title: KPC4 shRorc

data_processing:
Bowtie2 2.1.0 for alignment to genome, removed reads with quality score <15
Samtools 0.1.19 to remove non-unique reads
Picard 1.98 to remove duplicate reads
BEDTools 2.17.0 to combine replicates
Absolute H3K27ac occupancy determined by SICER 1.1 with redundancy threshold of 1, a window size of 200bp, a fragment size of 150, an effective genome fraction of 0.75, a gap size of 200bp and an FDR <0.05
ROSE algorithm to determine super-enhancers
getSeq function from the ‘BSGenome.MMusculus.UCSC.mm10’ R package to extract peak sequences
Map RORC binding sites with RORG_MOUSE.H10MO.C.pcm (HOCOMOCO database) as a reference, along with the ‘matchPWM’ function in R at 90% stringency
‘GenomicRanges’ and ‘ChIPpeakAnno’ to assess peak overlap (min overlap of 1bp)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for each ChIP sample. Summary data on series record.

source_name: KPC epithelial cells KPC4

growth_protocol: KPC4 and KCP9 are lines derived from independent KPC tumors

extract_protocol: KAPA Hyper Prep Kit

tag: chip antibody

value: anti-H3K27ac (ab4729 abcam)

tag: genotype

value: Rorc shRNA

value: KPf/fC

tag: cell line


title: GBM12

value: glioblastoma patient

value: brain


title: KPC Control shRNA replicate 1


title: KPC4 shCtrl


title: 2m: Primary meningioma

value: meningioma tumor

value: no


title: 3m: Primary meningioma

value: F


title: GBM6

value: Patient-derived glioblastoma stem-like cells


title: GBM5


title: pre-vaccination blood sample from donor 201390 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d201390_pre_92TH023ENV_15h

value: Micro kit

tag: stimulation time

tag: stimulation time unit

tag: hiv infection


title: post-vaccination blood sample from donor 201390 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d201390_post_92TH023ENV_15h

tag: treatment


title: KPC9 shRorc

source_name: KPC epithelial cells KPC9

tag: strain


title: GBM4

tag: tissue


title: post-vaccination blood sample from donor 126294 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d126294_post_92TH023ENV_15h


title: 5NK: Healthy control

description: Healthy control samples were not included in the final analysis.

source_name: Meninges

value: Meninges

tag: recurrence

tag: gender


title: 1m: Primary meningioma


title: H3K79me2-Ctrl-hESC

data_processing:
Basecalls performed using CASAVA
Single-end reads of 50 bp were obtained. BWA (version 0.5.9-r26-dev, default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard (version 1.65(1160)), and uniquely mapped reads were retained by SAMtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). When clear peaks were observed by inspection on Integrated Genomics Viewer (Broad Institute)  and there was high consistency among replicates, peaks for each replicate were called by MACS2 (version 2.0.9 20111102). Peaks within 100 bp were merged by bedtools (version 2.17.0).
Almost every CHIPSEQ sample have 20M unique mapped reads, only few have less but more than 15M unique mapped reads. We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size and converted to bigwig files.  With clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates. We further extend reads to the estimated fragment size and counted at each called peaks, pearson correlation coefficients were calculated among replicates suggested high reproducibility.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig

source_name: Cell Line

growth_protocol: H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies, #85850) at 37°C and 5% CO2. To induce neural lineage, cells were plated in PSC neural induction medium (Life Technologies) at 15–25% confluency, with medium changed every other day. On day 7, cells were harvested or expanded for further analyses.

extract_protocol:
Approximately 2 mg of nuclear extracts was incubated with primary antibody overnight at 4°C. Extract and antibody were added to protein A and protein G Dynabeads™ (ThermoFisher Scientific, #10002D and 10004D) for 4 h at 4°C, washed with PBST, and eluted with 0.1 M glycine (pH 2.3). Eluates were neutralized with 1.5 M Tris buffer (pH 8.8).
Cells were harvested in PBS. Cytoplasmic fractions were extracted using buffer A with 1× protease inhibitors and 1 mM DTT. Nuclear pellets were cross-linked by 1.1% formaldehyde in buffer B with 1× protease inhibitors and 1 mM DTT; washed; and lysed in lysis buffer 3 with 1× protease inhibitors, 1 mM DTT, and 1 mM PMSF. The fixed and lysed nuclear extract was sonicated with Bioruptor® Pico (Diagenode) 10 times for 15 s each , with 45-s intervals. Chromatin was added to Dynabeads™ (Life Technologies) prebound with 4 µg of antibodies. For UTX chromatin immunoprecipitation (ChIP), chromatin and antibodies were incubated overnight, followed by 4 h of recapture with Dynabeads™ the next day. After incubation, beads were washed and immunoprecipitates were eluted.  DNA from eluates was recovered by the GeneJET FFPE DNA purification kit (ThermoFisher Scientific, #K0882). ChIP-qPCR signals were calculated as the percentage of input. DNA libraries were generated using the NEBNext™ Ultra DNA Library Prep kit (NEB, #E7370S) and sequenced at the St. Jude Hartwell Center.

treatment_protocol: Neuronal maturation assay was performed using STEMdiff™ neuron differentiation kit (STEMCELL Technologies, #08500) and STEMdiff™ neuron maturation kit (STEMCELL Technologies, #08510). ES cells were seeded onto AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs). On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation started from day 11 to day 16. On day 17, cells were treated with Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium till days 22–24. RNA samples were collected on days 10, 11, and 22 for deep-sequencing analysis. Cells were also seeded onto multi-chamber slides for immunofluorescence (IF) analysis.

tag: cell type

value: Human Embryonic Stem cell H9

tag: genotype/variation

value: Control

value: H3K79me2 (Abcam,ab3594)


title: GBM1

tag: subject status


title: pre-vaccination blood sample from donor 215604 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d215604_pre_92TH023ENV_15h

tag: donor

tag: post-thraw resting

value: hours

tag: visit

value: pre


title: 3NK: Healthy control


title: 2NK: Healthy control


title: H3K79me2-53BP1KO-hESC replicate 2

value: 53BP1 KO

tag: chip antibody


title: H3K79me2-53BP1KO-hESC replicate 1


title: hESC_53BP1-Novus-UTXKD replicate 3

value: UTX KD


title: KPC9 input

value: none (input)


title: KPC9 shCtrl

value: anti-H3K27ac (ab4729 abcam)

tag: genotype

value: Control shRNA

value: KPf/fC


title: 4NK: Healthy control


title: HG_MDL_rep1

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

country: China

institute: University of Macau

data_processing:
hisat2
featureCounts
DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Text. Normalized; VSD; log2.

source_name: iPSC-EC

growth_protocol: iPSCs were differentiated into endothelial cells (iPSC-ECs) using a monolayer chemically-defined methods.

extract_protocol:
RNA was then extracted using the miRNeasy Mini Kit with DNA digestion, and collected total RNA was used for RNA-sequencing.
RNA-seq construction protocol of Illumina.

treatment_protocol: iPSC-ECs (passage 3) were seeded into 6-well plates. 24 hours later, iPSC-Ecs were exposed to normoglycemia (5.5mM glucose) or hyperglycemia (33mM glucose with 10nM ET-1) with and without MDL-28170 (2.5 uM) for 72 hours.

tag: cell line

value: iPSC-EC

value: Hyperglycemia


title: HG_MDL_rep2


title: hESC_53BP1-Novus-UTXKD replicate 1


title: hESC_53BP1-Novus-UTXKD replicate 2


title: pre-vaccination blood sample from donor 124184 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d124184_pre_92TH023ENV_15h

source_name: Blood sample from donor 124184

value: no

tag: rna extraction protocol

tag: stimulation

tag: stimulation time

value: No


title: HG_vehicle_rep2

tag: treatment

value: Vehicle


title: L-Thr-treatment_36h_rep2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custum Fusarium graminearum Microarray 8x15K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The images were analyzed using Feature Extraction Software (Ver. 10.7.3.1; Agilent Technologies). These data were analyzed further with GeneSpring GX12.0 software (Agilent Technologies).  Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array

organism: Fusarium graminearum

source_name: mycellium at 36 h after L-Thr-treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input  Quick Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fusarium graminearum strain JCM9873 was cultured on brown rice flour medium with or without L-Thr treatment  at 25°C. Mycelia were grown for 36 or 72 hrs on the medium.

extract_protocol: Mycellium were ground in liquid nitrogen. Total RNA was prepared using a Qiagen Plant RNA Isolation Kit.

treatment_protocol: The L-Thr solution was added to brown rice flour  medium after autoclave sterilization and mixed well before turning into a hard mass by cooling at room temperature.  The treated medium was  immediately used for inoculation of conidia. After incubating at  25°C in a sealed container for 36 or 72 hrs, the culture was used for  RNA isolation.

tag: strain

value: L-Thr-treatment

tag: time after spraying

value: mycellium


title: NG_MDL_rep2

value: Normoglycemia


title: pre-vaccination blood sample from donor 124184 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d124184_pre_DMSO_15h

data_processing: Raw probe intensities were preprocessed using the R (version 3.3.2) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.48.0). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.30.7).

value: Micro kit

value: DMSO

tag: stimulation time unit

tag: hiv infection


title: Non-treatment_72h_rep1

source_name: mycellium at 72 h after non-treatment

value: non-treatment

tag: tissue


title: L-Thr-treatment_72h_rep1

source_name: mycellium at 72 h after L-Thr-treatment


title: hNeuron_UTX-Bethyl-53BP1KO replicate 1

tag: cell type

value: Human Neuron Cell

value: derived from H9

tag: genotype/variation

value: 53BP1 KO

value: UTX (Bethyl,A302-374A)


title: L-Thr-treatment_36h_rep1


title: hNeuron_UTX-Bethyl-Ctrl

value: Control


title: Non-treatment_72h_rep2


title: post-vaccination blood sample from donor 124184 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d124184_post_92TH023ENV_15h

tag: donor

value: hours

value: post

value: RV144 vaccine


title: NG_MDL_rep1

value: iPSC-EC


title: HG_vehicle_rep1

value: Hyperglycemia


title: L-Thr-treatment_72h_rep2


title: 1NK: Healthy control

value: Meninges

tag: recurrence

tag: gender


title: VAT Pool 2 sample treated with KO- LysM

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

source_name: KO-LysM VAT NCD

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Adipose tissue-derived macrophages (ATMs) from 19-21 week-old mice were obtained from the subcutaneous and visceral adipose tissue. Briefly, scWAT and vWAT was washed extensively with PBS to remove debris and treated with 0.1% collagenase in PBS and 1% BSA for 1 hr at 37ºC with gentle agitation. Digested samples were centrifuged at 300 ×g at 4ºC for 5 min to separate adipocytes from SVF. The SVF from sc and vWAT was resuspended in red-blood-cells lysis buffer. To isolate ATMs, SVF was incubated with CD11b MicroBeads for 30 min, and positive selection was performed by autoMACS separator (MiltenyiBiotec).

extract_protocol: RNA was isolated using magnetic beads from 300000 cells. Library preparation and cDNA amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 24 cycles.

treatment_protocol: Magnetically isolated F4/80+ cells were washed with PBS and RNA isolation was performed

value: visceral adipose tissue

value: KO-LysM

tag: day

tag: pool

value: adipose tissue-derived macrophages (ATMs)


title: VAT Pool 4 sample treated with KO- LysM

tag: genotype


title: NG_vehicle_rep1

tag: cell line

value: Normoglycemia

value: Vehicle


title: N142

description:
ACRG Gastric cohort: microarray profiles from 300 gastric tumors and 100 patient matched normal tissue from gastric cancer patients
Nugen amplification protocol

data_processing: The data were analyzed by RMA with Affymetrix Power Tools package using Affymetrix default analysis settings.

source_name: Normal from patient 142

value: normal gastric tissue

tag: patient


title: VAT Pool 3 sample treated with KO- LysM


title: Non-treatment_36h_rep2

source_name: mycellium at 36 h after non-treatment

value: non-treatment

value: mycellium


title: VAT Pool 1 sample treated with KO- LysM


title: NG_vehicle_rep2


title: Non-treatment_36h_rep1


title: RNA-Organoid-D45_Ctrl replicate 1

data_processing:
Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on NovaSeq 6000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (v24) (Harrow et al., 2012).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: raw reads count by HTSEQ

growth_protocol: Cerebral organoids were generated based on previously published methods with minor modifications20,21. In brief, hESCs were dissociated to single cell suspension using Accutase and seeded onto low-attachment 96-well plates (Costar, 7007) at a density of 9,000 cells per well to aggregate into embryoid bodies (EBs).

extract_protocol:
RNA was purified with the GeneJET RNA purification kit (ThermoFisher Scientific, K0732). The cDNA was reverse transcribed from 300 ng of RNA, using SuperScript IV reverse transcriptase (ThermoFisher Scientific, #18090050) with random hexamers. RT reactions were performed in triplicate to minimize variability.
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)

treatment_protocol: The EB formation medium (DMEM/F12 with 20% knockout serum replacement, 3% ESC-quality FBS, 2 mM GlutaMAX, 0.1 mM nonessential amino acides,) was supplemented with Dorsomorphin (2 µM), WNT inhibitor (IWR1, 3 µM), TGF-ß inhibitor (SB431542, 5 µM) and Rho Kinase inhibitor (Y-27623, 20 µM). Starting form Day4, EBs were fed with cortical differentiation medium (Glasgow-MEM, 20% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM ß-ME, 1% anti-anti), supplement with WNT inhibitor (IWR1, 3 µM), TGF-ß inhibitor (SB431542, 5 µM), Cyclopamine (2.5 µM) and Rho Kinase inhibitor (Y-27623, 20 µM). On Day17, EBs were embedded in matri-gel droplets and transferred onto low-attachemnt 6-wells and cultured in suspension using DMEM/F-12 supplemented with 1% N2 supplement, 1% Lipid concentrate, 2% B27suppmenent without Vitamin A, and 1% anti-anti under 40% O2/5% CO2 conditions on shaker. Starting from Day30, medium was changed to 50% DMED/F-12, 50% Neurobasal media, 0.5% N2 supplement, 1% GlutaMax, 0.05 mM NEAA, 0.025% human insulin, 0.1 mM ß-ME and 1% anti-anti, supplemented with 2% B27.

value: Human Organoid D45

value: derived from H9 (day 45)


title: RNA-Organoid-D45_53BP1KO3 replicate 1

value: 53BP1 KO


title: SREBP1-siRNA_serum-free_normoxia

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: gene expression in cells transfected with SREBP1-siRNA, and then cultured under serum-free and normoxia condition

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: ovarian cancer cell line, OVSAYO

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Total RNA was isolated using SV total RNA isolation system (Promega).

treatment_protocol: OVSAYO cells were transfected with non-specific (Silencer negative control siRNA (Ambion)) or SREBP1 (SMRT pool (Dharmacon)) siRNA using lipofectamine 2000 (Life technologies, Carlsbad, CA,USA) and cultured for 30 h in RPMI1640 medium (10% fetal calf serum). Cells were washed once with serum-free medium. Cells were further cultured under serum-free condition for 16 h under normoxia and hypoxia.

value: female


title: SREBP1-siRNA_serum-free_1%O2

description: gene expression in cells transfected with SREBP1-siRNA, and then cultured under serum-free and 1%O2 condition


title: SAT Pool 4 sample treated with KO- LysM

source_name: KO-LysM SAT NCD

value: subcutaneous adipose tissue


title: NS-siRNA_serum-free_1%O2

description: gene expression in cells transfected with NS-siRNA, and then cultured under serum-free and 1%O2 condition


title: SAT Pool 3 sample treated with KO- LysM


title: RNA-Organoid-D45_53BP1KO2 replicate 2


title: NS-siRNA_serum-free_normoxia

description: gene expression in cells transfected with NS-siRNA, and then cultured under serum-free and normoxia condition


title: RNA-Organoid-D45_53BP1KO2 replicate 1


title: SAT Pool 2 sample treated with KO- LysM


title: SAT Pool 1 sample treated with KO- LysM


title: hNeuron_UTX-Bethyl-53BP1KO replicate 2

value: Human Neuron Cell

value: derived from H9

tag: chip antibody

value: UTX (Bethyl,A302-374A)


title: RNA-Organoid-D45_53BP1KO1 replicate 2


title: RNA-Organoid-D45_53BP1KO3 replicate 2


title: RNA-Organoid-D45_53BP1KO1 replicate 1