title: K9920.CD38.p.sIgD.p._naive


title: K9920.CD38.dp.sIgD.p_pre_GC.B

status: Public on Sep 03 2019

type: RNA

city: Shinjuku-ku

first: Jun

last: Inamo

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Following fragmentation, cDNAs were hybridized on the Human Genome U133 Plus 2.0 Array using GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Fluidics Station 450Dx v.2

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000Dx v.2 with AutoLoaderDX.

data_processing: Probe set expression values were estimated using frozen RMA, and their presence call was calculated with the MAS5 algorithm. Stepwise quality control for probes was conducted. First, probes that did not match any genes or that targeted multiple genes were removed. Then, probes that were called absent in all samples, were filtered out. In the case where multiple probes hybridized the same gene and those probes were positively correlated with a Pearson’s correlation coefficient of more than 0.3, the probe exhibiting the maximum average signals across samples was kept. Lastly, less variable probes whose interquartile ranges were in the bottom 20% of all probes were filtered out.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: pSS_Naive B cell

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted from B cell subsets and transcribed to cDNA using NucleoSpin RNA (Macherey Nagel) and ReverTra Ace qPCR RT Master Mix (TOYOBO).

tag: subject status

value: healthy control

tag: subject id

tag: cell type

value: peripheral blood B cell

tag: cell subtype

value: Naive B cell


title: K9920.CD38.n.sIgD.p


title: K8262.CD38.p.n.sIgD.n_memory


title: K5251.CD38.dp.sIgD.p_pre_GC.B


title: K5251.CD38.p.n.sIgD.n_memory


title: HC-AE.CD38.dp.sIgD.p_pre_GC.B

source_name: HC_Memory B cell

value: Memory B cell


title: K5251.CD38.n.sIgD.p


title: K8262.CD38.dp.sIgD.p_pre_GC.B


title: HC-AD.CD38.p.sIgD.p._naive

source_name: HC_Pre-GC B cell

value: Pre-GC B cell


title: HC-AE.CD38.p.n.sIgD.n_memory


title: HC-AE.CD38.p.sIgD.p._naive


title: HC-AC.CD38.n.sIgD.p

source_name: HC_Naive B cell


title: HC-AF.CD38.dp.sIgD.p_pre_GC.B


title: K5251.CD38.p.sIgD.p._naive


title: K8262.CD38.n.sIgD.p


title: HC-AD.CD38.dp.sIgD.p_pre_GC.B


title: HC-AC.CD38.dp.sIgD.p_pre_GC.B


title: HC-AC.CD38.p.sIgD.p._naive


title: HC-AC.CD38.p.n.sIgD.n_memory


title: HC-AB.CD38.p.n.sIgD.n_memory


title: HC-AD.CD38.n.sIgD.p


title: HC-AF.CD38.p.n.sIgD.n_memory


title: HC-AE.CD38.n.sIgD.p


title: HC-AF.CD38.n.sIgD.p


title: HC-AF.CD38.p.sIgD.p._naive


title: HC-AB.CD38.dp.sIgD.p_pre_GC.B


title: HC-AB.CD38.n.sIgD.p


title: HC-AD.CD38.p.n.sIgD.n_memory


title: K8262.CD38.p.sIgD.p._naive


title: HC-AB.CD38.p.sIgD.p._naive


title: HC-AA.CD38.p.n.sIgD.n_memory


title: HC-AA.CD38.dp.sIgD.p_pre_GC.B


title: DGM-00568_lg (array)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.6 using default analysis settings and robust multi-array (RMA) normalization method.

source_name: large airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: nonsmoker

tag: age

tag: gender

value: M

tag: ethnicity

value: Hisp

tag: tissue

value: large airway epithelium brushing


title: DGM-00465_lg (array)

value: Afr


title: DGM-00551_lg (array)

value: Cauc


title: DGM-00529_lg (array)

value: F


title: HC-AA.CD38.p.sIgD.p._naive


title: DGM-00661_sm (array)

source_name: small airway epithelium brushing

value: small airway epithelium brushing


title: HC-AA.CD38.n.sIgD.p


title: DGM-00661_lg (array)


title: DGM-00551_sm (array)


title: DGM-00568_sm (array)


title: DGM-00268_lg (array)


title: DGM-00073_lg (array)


title: DGM-00529_sm (array)


title: DGM-00465_sm (array)


title: DGM-00041_sm (array)


title: DGM-00568_tr (array)

source_name: trachea brushing

value: trachea brushing


title: DGM-00036_lg (array)


title: DGM-00551_tr (array)


title: DGM-00661_tr (array)


title: mir156abcdfghikl seedling shoots [D216]

type: SRA

city: Shanghai

first: Jian-Kang

last: Zhu

address: No. 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology

description:
mir156abcdfghikl-seedling (D216)
NIPvsD216.DiffExpGene.anno.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with SOAPnuke1.3.0; Clean reads were aligned to reference genomes (TIGR release 7) using Hisat2 with default parameters.
Mapped reads from three biological replicates for rice were merged and then assembled with Cufflinks (v2.2.1).
Genome_build: Rice TIGR release 7
Supplementary_files_format_and_content: FPKM and Annotation of DEGs as indicated in the file name

organism: Oryza sativa

source_name: Seedling shoots

growth_protocol: The seeds of all rice materials were sowed in early June in the paddy field on natural condition in Hangzhou of the year 2017, and then the materials were sampled at indicated times

extract_protocol:
Total RNAs were extracted with RNAprep pure Plant kit (TIANGEN, Cat. no. DP432).
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.

tag: cultivar/ecotype

value: Nipponbare (NIP)

tag: developmental stage

value: Two-week-old

tag: genotype/variation

value: mir156abcdfghikl mutant

value: Seedling shoots


title: DGM-00073_sm (array)


title: DGM-00036_sm (array)


title: DGM-00268_sm (array)


title: Wild-type seedling shoots

description: NIP-shoot

value: wild type


title: Wild-type fresh seed embryos

description: NIP-embryo

source_name: The embryos of fresh wet seeds

value: Just after the seed-filling stage

value: The embryos of fresh wet seeds


title: DGM-00268_tr (array)


title: DGM-00465_tr (array)


title: DGM-00073_tr (array)


title: DGM-00529_tr (array)


title: mir156abcdfghikl fresh seed embryos [C403]

description:
mir156abcdfghikl-embryo (C403)
NIPvsC403.DiffExpGene.anno.txt


title: Unelongated culm of 20-day-old mir156defghi seedlings [D265]

description:
mir156defghi-base (D265)
NIPvsD265.DiffExpGene.anno.txt

source_name: Unelongated culms of 20-day-old  seedlings

value: mir156defghi mutant


title: Unelongated culm of 20-day-old mir156abckl seedlings [D183]

description:
mir156abckl-base (D183)
NIPvsD183.DiffExpGene.anno.txt

value: mir156abckl mutant

value: Unelongated culms of 20-day-old  seedlings


title: Unelongated culm of 20-day-old wild-type seedlings

description: NIP-base


title: DGM-00036_tr (array)

value: nonsmoker

value: M


title: DGM-00041_tr (array)

value: Afr


title: DGM-00041_lg (array)

value: large airway epithelium brushing


title: DGM-10632_M0_sm (array)


title: mm_control_miRNA_rep2

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.8
Adapter trimming: cutadapt 1.18
Alignment: sRNAbench version 08_31_2017
Differentially expressed miRNA analysis: DESeq2 with R version 3.4.3
Genome_build: miRBase 22.1 mature microRNAs
Supplementary_files_format_and_content: miRNA sense mapped results txt files include reads mapped to mature miRNA from sense strand summarized by sRNAbench for each Sample.

organism: Mus musculus

extract_protocol:
The circulating miRNA extraction from three Ccm3/Pdcd10+/- and the three wild types was performed using the miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany).
TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) for mouse BMEC samples and with Illumina small RNA-Seq kits (Illumina, San Diego, California, USA) for miRNA.

tag: strain background

tag: strain

value: wild type littermates

value: 12 to 14 weeks

tag: tissue/cell type

value: serum

tag: molecule subtype

value: miRNA


title: mm_ccm3-chronic_rep5

data_processing:
Raw sequencing QC assessement: FastQC v0.11.5 and FastQC v0.11.7
Alignment: STAR_2.5.3a and STAR_2.6.0c
Post alignement QC assessment: RSeQC and Picard tools with version: 2.9.0-1-gf5b9f50-SNAPSHOT and 2.18.7-SNAPSHOT
Gene transcripts assembly: featureCounts with Rsubread 1.22.1 and Rsubread 1.28.1
Differentially expressed genes analysis: DESeq2 with R version 3.4.3
Genome_build: UCSC human genome model: GENCODE GRCm38 V13 and V17 at ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M13/ and ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17 respectively
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

extract_protocol:
RNAs from the acute and chronic in vivo NVUs were extracted using an RNA isolation kit (RNeasy® Micro Kit, Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using commercially low-input strand specific RNA-Seq kits (Clontech, California, USA) for mouse NVU specimens.

tag: condition

value: cerebral cavernous malformation

value: neurovascular unit (NVUs)


title: mm_ccm3-chronic_control_rep2

value: Cre negative; Ccm3/Pdcd10fl/fl

value: contol vessels


title: mm_ccm3_miRNA_rep1

value: Pdcd10 haploinsufficient


title: mm_ccm3_miRNA_rep2


title: mm_ccm3-chronic_rep4


title: mm_ccm3-chronic_control_rep4


title: mm_control_miRNA_rep1


title: mm_ccm3-chronic_rep3


title: mm_ccm3-chronic_control_rep1


title: mm_control_miRNA_rep3


title: mm_ccm3_miRNA_rep3


title: mm_ccm3-chronic_rep1


title: mm_ccm3-acute_control_rep6


title: mm_ccm3-acute_control_rep5


title: mm_ccm3-acute_control_rep4


title: mm_ccm3-acute_control_rep3


title: mm_ccm3-acute_control_rep2


title: mm_ccm3-acute_rep6


title: mm_ccm3-acute_control_rep1


title: mm_ccm3-acute_rep5


title: mm_ccm3-acute_rep4


title: mm_ccm3-acute_rep3


title: Ctrl WT 4

city: Iowa City

first: Eric

last: Taylor

state: IA

address: 169 Newton Rd

department: Biochemistry

institute: University of Iowa

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Salzberg et al., Nat Methods, 2015: alignment was done using HISAT2 using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx files containg relative change in expression in tumor samples versus paired normal adjacent samples, ANOVA of the paired sample change in expression, and FPKM

source_name: Liver

extract_protocol:
Liver tissue and tumor tissue were removed, flash frozen on liquid nitorgen, and RNA was harvested using Qiagen miRNeasy Kit (Qiagen 74104).  Sequencing libraries were prepped with 500ng of RNA utilizing Illumina TruSeq straned library prep.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: 24 weeks

tag: genotype


title: Ctrl LivKO 4


title: mm_ccm3-chronic_control_rep3


title: Ctrl LivKO 3


title: mm_ccm3-chronic_rep2


title: Ctrl WT 3


title: M13 Normal-adjacent LivKO


title: M20 Normal-adjacent LivKO


title: M6 Normal-adjacent WT


title: M10 Tumor WT

source_name: Liver tumor

value: Liver tumor


title: MC.SCA1lo.CX3CR1lo.PC#3_RNA-seq

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description:
MC.SCA1lo.CX3CR1lo.PC#3
Peritoneal SCA1lo CX3CR1lo Mast Cell
processed data file: Gene_count_table.csv

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a.
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16).
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Peritoneal Cavity

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

value: 6 weeks old

tag: sorting markers

value: Peritoneal Cavity

value: Mast Cells


title: M10 Normal-adjacent WT


title: M20 Tumor LivKO


title: MC.SCA1lo.CX3CR1lo.PC#2_RNA-seq

description:
MC.SCA1lo.CX3CR1lo.PC#2
Peritoneal SCA1lo CX3CR1lo Mast Cell
processed data file: Gene_count_table.csv

tag: cell type


title: M6 Tumor WT


title: Ctrl WT 1


title: Ctrl WT 2


title: MC.SCA1lo.CX3CR1lo.PC#1_RNA-seq

description:
MC.SCA1lo.CX3CR1lo.PC#1
Peritoneal SCA1lo CX3CR1lo Mast Cell
processed data file: Gene_count_table.csv


title: MC.SCA1lo.CX3CR1hi.PC#3_RNA-seq

description:
MC.SCA1lo.CX3CR1hi.PC#3
Peritoneal SCA1lo CX3CR1hi Mast Cell
processed data file: Gene_count_table.csv


title: M2 Normal-adjacent WT


title: M13 Tumor LivKO


title: Ctrl LivKO 2


title: Ctrl LivKO 1


title: M4 Normal-adjacent WT


title: mm_ccm3-acute_rep1


title: MC.SCA1lo.CX3CR1hi.PC#2_RNA-seq

description:
MC.SCA1lo.CX3CR1hi.PC#2
Peritoneal SCA1lo CX3CR1hi Mast Cell
processed data file: Gene_count_table.csv


title: mm_ccm3-acute_rep2


title: MC.SCA1lo.CX3CR1hi.PC#1_RNA-seq

description:
MC.SCA1lo.CX3CR1hi.PC#1
Peritoneal SCA1lo CX3CR1hi Mast Cell
processed data file: Gene_count_table.csv


title: M2 Tumor WT


title: M4 Tumor WT


title: MC.SCA1hi.CX3CR1lo.PC#3_RNA-seq

description:
MC.SCA1hi.CX3CR1lo.PC#3
Peritoneal SCA1hi CX3CR1lo Mast Cell
processed data file: Gene_count_table.csv


title: MC.SCA1hi.CX3CR1lo.PC#2_RNA-seq

description:
MC.SCA1hi.CX3CR1lo.PC#2
Peritoneal SCA1hi CX3CR1lo Mast Cell
processed data file: Gene_count_table.csv


title: MC.SCA1hi.CX3CR1lo.PC#1_RNA-seq

description:
MC.SCA1hi.CX3CR1lo.PC#1
Peritoneal SCA1hi CX3CR1lo Mast Cell
processed data file: Gene_count_table.csv


title: M11 Tumor LivKO


title: M9 Normal-adjacent LivKO


title: M11 Normal-adjacent LivKO


title: M9 Tumor LivKO


title: MC.Ht#2_RNA-seq

description:
MC.Ht#2
Mast Cell from Heart
processed data file: Gene_count_table.csv

source_name: Heart

value: Heart


title: MC.SCA1hi.CX3CR1hi.PC#1_RNA-seq

description:
MC.SCA1hi.CX3CR1hi.PC#1
Peritoneal SCA1hi CX3CR1hi Mast Cell
processed data file: Gene_count_table.csv


title: Ba.Sp#2_RNA-seq

description:
Ba.Sp#2
Splenic Basophil
processed data file: Gene_count_table.csv

source_name: Spleen

value: Spleen

value: Basophils


title: Lung-Met4

city: Toronto

first: Yuning

middle: Jackie

last: Tang

state: Ontario

address: 686 Bay Street

department: Program in Developmental Biology

country: Canada

institute: Hospital for Sick Children

data_processing:
raw data was processed using the TrimGalore toolkit
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool.
Gene counts were compiled using the HTSeq tool.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

source_name: lung met

extract_protocol:
Freshly digested tumor cells from mouse sarcomas were FACS sorted based on their expression of different flourescent reporters (rosa26-driven GFP, RFP, YFP and CFP).  RNA from the sorted cells were extracted using Norgen Single-Cell RNA purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue origin

value: primary soft tissue sarcoma cells

tag: facs sorted cells from tumors

value: No passage in vitro

value: Mixed background


title: MC5

data_processing:
raw data was processed using the TrimGalore toolkit
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool.
Gene counts were compiled using the HTSeq tool.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample ...

source_name: Metastatic Clone

extract_protocol:
Freshly digested tumor cells from mouse sarcomas were FACS sorted based on their expression of different flourescent reporters.  RNA from the sorted cells were extracted using Norgen Single-Cell RNA purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Eo.Sp#2_RNA-seq

description:
Eo.Sp#2
Splenic Eosinophil
processed data file: Gene_count_table.csv

tag: age

value: CD11b+ SiglecF+ FSC low SSC high CD11c-CD4-CD8-CD19-

value: Eosinophil


title: Ba.Sp#3_RNA-seq

description:
Ba.Sp#3
Splenic Basophil
processed data file: Gene_count_table.csv


title: Lung-Met3


title: MC.SCA1hi.CX3CR1hi.PC#3_RNA-seq

description:
MC.SCA1hi.CX3CR1hi.PC#3
Peritoneal SCA1hi CX3CR1hi Mast Cell
processed data file: Gene_count_table.csv


title: Lung-Met1


title: Ba.Sp#1_RNA-seq

description:
Ba.Sp#1
Splenic Basophil
processed data file: Gene_count_table.csv


title: MC.SCA1hi.CX3CR1hi.PC#2_RNA-seq

description:
MC.SCA1hi.CX3CR1hi.PC#2
Peritoneal SCA1hi CX3CR1hi Mast Cell
processed data file: Gene_count_table.csv


title: Lung-Met5


title: MC.Ht#1_RNA-seq

description:
MC.Ht#1
Mast Cell from Heart
processed data file: Gene_count_table.csv


title: Lung-Met6


title: Eo.PC#2_RNA-seq

description:
Eo.PC#2
Peritoneal Eosinophil
processed data file: Gene_count_table.csv


title: Mo.6C+.Bl#2_RNA-seq

description:
Mo.6C+.Bl#2
Ly6Chi blood Monocytes
processed data file: Gene_count_table.csv

source_name: Blood

value: Blood

value: Monocytes


title: Eo.PC#1_RNA-seq

description:
Eo.PC#1
Peritoneal Eosinophil
processed data file: Gene_count_table.csv


title: Non-MC1

source_name: Non-metastatic subclone


title: Lung-Met2


title: Non-MC8


title: Non-MC9


title: Mo.6C+.Bl#1_RNA-seq

description:
Mo.6C+.Bl#1
Ly6Chi blood Monocytes
processed data file: Gene_count_table.csv


title: Non-MC7


title: Non-MC3


title: Eo.Sp#3_RNA-seq

description:
Eo.Sp#3
Splenic Eosinophil
processed data file: Gene_count_table.csv


title: Mo.6C-.Bl#2_RNA-seq

description:
Mo.6C-.Bl#2
Ly6Clo blood Monocytes
processed data file: Gene_count_table.csv


title: Non-MC4


title: Mo.6C-.Bl#1_RNA-seq

description:
Mo.6C-.Bl#1
Ly6Clo blood Monocytes
processed data file: Gene_count_table.csv


title: Non-MC2


title: MF.PC#1_RNA-seq

description:
MF.PC#1
Peritoneal Small Macrophages
processed data file: Gene_count_table.csv

value: Macrophages


title: Non-MC6


title: Non-MC5


title: MF.AT#2_RNA-seq

description:
MF.AT#2
Inguinal & Perigonadal Adipose Tissue Macrophages
processed data file: Gene_count_table.csv

source_name: Adipose Tissue

value: Adipose Tissue


title: MF.RP.Sp#2_RNA-seq

description:
MF.RP.Sp#2
Red Pulp Macrophages
processed data file: Gene_count_table.csv

value: Mertk+ CD64+ CD11blo F4/80+


title: MC7

source_name: Metastatic subclone


title: MF.AT#1_RNA-seq

description:
MF.AT#1
Inguinal & Perigonadal Adipose Tissue Macrophages
processed data file: Gene_count_table.csv


title: MC6


title: MF.RP.Sp#1_RNA-seq

description:
MF.RP.Sp#1
Red Pulp Macrophages
processed data file: Gene_count_table.csv


title: MF.PC#2_RNA-seq

description:
MF.PC#2
Peritoneal Small Macrophages
processed data file: Gene_count_table.csv


title: MF.microglia.CNS#2_RNA-seq

description:
MF.microglia.CNS#2
Brain Microglia Macrophages
processed data file: Gene_count_table.csv

source_name: Brain

value: Brain


title: MC4


title: MF.microglia.CNS#1_RNA-seq

description:
MF.microglia.CNS#1
Brain Microglia Macrophages
processed data file: Gene_count_table.csv

value: 6 weeks old


title: MC9


title: MC3


title: MC10


title: MC11


title: MF.226+II+480lo.PC#2_RNA-seq

description:
MF.226+II+480lo.PC#2
Peritoneal Large Macrophages
processed data file: Gene_count_table.csv

value: Peritoneal Cavity


title: MC1


title: MC8


title: MF.226+II+480lo.PC#1_RNA-seq

description:
MF.226+II+480lo.PC#1
Peritoneal Large Macrophages
processed data file: Gene_count_table.csv


title: VV_Leptin_1

city: Pittsburgh

first: Greg

last: Delgoffe

address: 5115 Center Ave

institute: University of Pittsburgh

data_processing:
CellRanger
BCL to FASTQ
FASTQ to Counts
Aggregation of Counts
mm10
Supplementary_files_format_and_content: aggregated counts matrix, genes and barcodes

source_name: tumor

growth_protocol: CL24 cells were cultured in full growth media DMEM 10%FBS

extract_protocol:
Tumors were digested, lymphocytes were sorted on CD45 expressing cells and then processes for single cell RNA sequencing
10x Genomics Single Cell 3' v2 Kit

treatment_protocol: mice were treated with virus, single intratumoral injection 2.5x106 PFU

tag: cell line

value: CD45+ lymphoctyes

tag: agent

value: leptin expressing virus


title: VV_Leptin_2


title: VV_Ctrl_1

value: Control vaccinia virus


title: MC2


title: N2 day 14 rep3

first: Yidong

last: Shen

state: Shanghai

address: 320 Yueyang Rd.

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

description:
small RNA
446_S_GGCTAC
Results_miRNA_reported.xlsx, Group1vsGroup14.xlsx, Group7vsGroup14.xlsx, Group14vsGroup21.xlsx

data_processing:
The reads were aligned to the C. elegans reference genome (WBcel215.67) using Tophat.
Aligned reads were then mapped against known microRNA sequences by miRDeep.
Differentially expressed microRNAs were figured out using the R package DESeq.
Genome_build: WBcel215.67

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were synchronized by collecting eggs and transferred to 60 mm plates (20 worms per plate) at L4. Worms were transferred to fresh plates every other day until day 10 to avoid the contamination from progenies, and subsequently monitored every other day. Dead worms and worms undergoing internal hatching, bursting vulva, crawling off the plates, or contamination as well as dead worms were removed from the plates.  Worms were handpicked into TRIzol at indicated ages.

extract_protocol:
Total RNA was extracted using QIAGEN miRNeasy Mini.
Small RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: whole worm

value: wild type

value: day 14 of adulthood


title: N2 day 21 rep3

description:
small RNA
446_T_CTTGTA
Results_miRNA_reported.xlsx, Group1vsGroup21.xlsx, Group7vsGroup21.xlsx, Group14vsGroup21.xlsx

value: day 21 of adulthood


title: N2 day 7 rep3

description:
small RNA
446_R_TAGCTT
Results_miRNA_reported.xlsx, Group1vsGroup7.xlsx, Group7vsGroup14.xlsx, Group7vsGroup21.xlsx

value: day 7 of adulthood


title: Mut_Krox20 rep3

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Basecalls performed using CASAVA version
Data were filtered before mapping. The reads following these criteria are kept : Illumina quality filter passed, global quality threshold above 30, polyN at the end of reads trimmed, read length above 30
RNAseq reads were aligned to the mm10 genome from Ensembl genome assembly using STAR. Reads were aligned as paired-end reads.
Data were filtered after mapping. Unmapped reads and multimapped reads were discarded.
Reads ailgned in the genes were counted using htseq-count
Normalisation and differential analysis were performed using DESeq1.83
Genome_build: mm10
Supplementary_files_format_and_content: Count text files

source_name: Sciatic Nerve

extract_protocol:
Sciatics nerves were dissected at 14 days post natal, and total RNA was harvested using Rneasy Fibrous Tissus ( Qiagen).
Illumina TruSeq RNA Sample Prep Kit  was used with 250 ng of total RNA for the construction of sequencing libraries.

value: Sciatic Nerve

value: post natal day 14

value: Krox20 mutant


title: N2 day 1 rep3

description:
small RNA
446_Q_GATCAG
Results_miRNA_reported.xlsx, Group1vsGroup7.xlsx, Group1vsGroup14.xlsx, Group1vsGroup21.xlsx

value: day 1 of adulthood


title: Mut_Krox20 rep2


title: N2 day 14 rep2

description:
small RNA
446_N_CAGATC
Results_miRNA_reported.xlsx, Group1vsGroup14.xlsx, Group7vsGroup14.xlsx, Group14vsGroup21.xlsx


title: Mut_Krox20 rep1


title: N2 day 1 rep2

description:
small RNA
446_J_ACAGTG
Results_miRNA_reported.xlsx, Group1vsGroup7.xlsx, Group1vsGroup14.xlsx, Group1vsGroup21.xlsx


title: WT rep3


title: N2 day 7 rep2

description:
small RNA
446_L_GCCAAT
Results_miRNA_reported.xlsx, Group1vsGroup7.xlsx, Group7vsGroup14.xlsx, Group7vsGroup21.xlsx


title: VV_Ctrl_2


title: N2 day 1 rep1

description:
small RNA
446_B_ATCACG
Results_miRNA_reported.xlsx, Group1vsGroup7.xlsx, Group1vsGroup14.xlsx, Group1vsGroup21.xlsx


title: WT rep2


title: N2 day 7 rep1

description:
small RNA
446_D_CGATGT
Results_miRNA_reported.xlsx, Group1vsGroup7.xlsx, Group7vsGroup14.xlsx, Group7vsGroup21.xlsx


title: PBS_2

value: PBS


title: N2 day 14 rep1

description:
small RNA
446_F_TGACCA
Results_miRNA_reported.xlsx, Group1vsGroup14.xlsx, Group7vsGroup14.xlsx, Group14vsGroup21.xlsx


title: hNPCs, CVB3-infected hNPC 24hpi

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

country: South Korea

institute: Korea Univ.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Embryonic stem cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: human neural progenitor stem cell(hNPC)

tag: passage

tag: infection

tag: time


title: hNPCs, CVB3-infected hNPC 48hpi


title: hNPCs, CVB3-infected hNPC 4hpi


title: hNPCs, CVB3-infected hNPC 72hpi


title: hNPCs, Mock

value: control


title: PBS_1


title: N2 day 21 rep2

description:
small RNA
446_P_ACTTGA
Results_miRNA_reported.xlsx, Group1vsGroup21.xlsx, Group7vsGroup21.xlsx, Group14vsGroup21.xlsx


title: N2 day 21 rep1

description:
small RNA
446_H_TTAGGC
Results_miRNA_reported.xlsx, Group1vsGroup21.xlsx, Group7vsGroup21.xlsx, Group14vsGroup21.xlsx


title: RNA-seq_Y_BC11_Y2

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: RNA-seq in HSCP-HKs

data_processing:
Fastq files were aligned to the HG19 genome using HiSat2 (version 2.0.4) with default parameters.
Transcripts were quantified and FPKM values were generated using cuffquant and cuffnorm from the cufflinks suite (version 2.2.1) (http://cole-trapnell-lab.github.io/cufflinks/) on the HG19 RefSeq transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file of raw fpkm expression values

source_name: Human primary keratinocytes

growth_protocol: All human cells were purchased from approved commercial suppliers who has obtained the necessary patient consent for skin donation for research purposes. The cells were obtained and handled in compliance with the Swiss Human Research Act. Normal human neonatal epidermal keratinocyte progenitor cells (nHPEKs, Lot #EB1110044 (pooled)) and adult normal human epidermal keratinocyte progenitor cells (aHPEKs Lots #ES1303277, and #MC1511045 (both abdominal)) were purchased from CELLnTEC (Bern, Switzerland) at Passage 2 (P2). HPEKs were expanded until Passage 4 (P4) and pellets of 1x106 cells were cryopreserved in liquid nitrogen for later use. HPEKs were cultured from P4 by seeding at an initial density of 5.3x104 cells/cm² using CnT-Prime media (CELLnTEC, #CnT-PR). When cells reached 70-85% confluency, they were detached from the cell culture dish using Accutase Cell Detachment Solution (CELLnTEC). For serial passaging experiments, aHPEKs were grown and passaged about 13 times. aHPEKs were collected for various assays and were considered as “HSCP-HKs” when fast-dividing (between Passages 7-9) whereas aHPEKs that were slow-dividing (Passages 15-17) were considered as “LSCP-HKs”.

extract_protocol:
RNA was isolated with Qiazol (Invitrogen, Cat# 79306), and purified with the miRNeasy kit (Qiagen, Cat# 217004). The amount of RNA was quantified with the Agilent RNA 6000 Nano Kit (Agilent Technologies, Cat# 5067-1511).
RNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 and sequenced using the Illumina HiSeq2500 platform following the manufacturer’s protocol. Samples were sequenced in paired-end mode to a length of 2x76bp base-pairs. Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files. Read quality was assessed by running FastQC (version 0.10) on the FASTQ files.

value: Human primary keratinocytes

tag: barcode

value: GGCTACAT


title: RNA-seq_O_BC27_O3

description: RNA-seq in LSCP-HKs

value: ATTCCTTT


title: Y_INPUT3

description: Whole cell extract input control from H3K27ac pull downs in HSCP-HKs

library_source: genomic

data_processing:
All paired-end ChIP-seq datasets were aligned using Bowtie2 (version 2.2.8) to build version NCBI37/HG19.
Alignments were performed using all default parameters. We used the MACS version 1.4.2 (Model based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to identify regions of ChIP-seq enrichment over background. A p-value threshold of enrichment of 1e-9 was used for all datasets.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format from MACS output

molecule: genomic DNA

extract_protocol:
For H3K27ac: Approximately 4x106 cells were cross-linked with 10% formaldehyde at room temperature for 15 min. After quenching with 125mM glycine for 6min, cells were washed in ice-cold PBS (plus Protease Inhibitor (PI) Cocktail tablet (Sigma) and 100mM PMSF) and collected by scraping in Nuclei EZ lysis buffer (Sigma, plus PI and 100mM PMSF). Nuclei were collected by centrifugation (500xg for 5min at 4°C). In order to increase nuclei collection, pellets were further re-suspended in a Hypotonic Buffer (10mM HEPES, 10mM KCl, 0.1mM EDTA, 0.1mM EGTA, pH8.0) for 10min in ice followed by NP40 (0.5% v/v) and 20sec vortex at maximum speed. Nuclei were collected by centrifugation (14.000rpm, 4°C, 30sec), washed with Wash Buffer C (with PI) (truChIP Chromatin Shearing Kit, Covaris, Brighton, UK) and re-suspended in Shearing buffer D3 (plus PI and 100mM PMSF) (truChIP Chromatin Shearing Kit, Covaris). Nuclei were vortexed for 3 rounds of 10sec and left 15min in ice before freezing in -80°C for later use. After thawing, 130μl nuclei suspensions were transferred into microTUBE (Covaris) and sonicated using a Covaris E220 (10min: duty cycle 2%, Intensity 5, Cycles per Burst 200). Samples were collected into 1.5ml tubes, centrifuged at 10000xg for 10min at 4°C and supernatants transferred into 2ml tubes. DNA concentrations were calculated after DNA isolation using Qiaquick PCR (Qiagen) using Qubit Nucleic Acid Quantification (Invitrogen). For ChIP a modified protocol of the Magna ChIP A/G (Merck #17-10085) protocol was used. In brief 5μg of mice anti-H3K27ac Ab or IgG were coupled with Protein A/G beads at 4°C for 4h. Coupled Ab-beads were mixed with 5μg of samples and incubated overnight at 4°C with rotation. Ab-beads were washed as per manufacturer’s instructions and protein/DNA complexes eluted in Elution buffer (50mM NaCl and 1%SDS in dH2O) for 4h at 65°C. Reverse cross-linking was performed by adding RNAse for 30min at 37°C and 5mM EDTA, 20mM Tris pH7.5 and 100μg/ml Proteinase for another 1h at 45°C. Supernatants were separated and DNA extracted using the MiniElute PCR purification kit (Qiagen).For BRD4: Frozen cells (9x106) were thawed and fixed with 1% formaldehyde for 15min and quenched with 0.125M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4μg of antibody against BRD4. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75nt reads, single end).

tag: input

value: AGACCTTG


title: RNA-seq_Y_BC10_Y1

description: RNA-seq in HSCP-HKs

value: TAGCTTAT


title: RNA-seq_Y_BC16_Y3

description: RNA-seq in HSCP-HKs

value: CCGTCCCG


title: RNA-seq_O_BC25_O2

description: RNA-seq in LSCP-HKs

value: ACTGATAT


title: Y_INPUT2

value: AGGTTCCT


title: WT rep1

tag: strain

value: wild type


title: RNA-seq_O_BC18_O1

description: RNA-seq in LSCP-HKs

value: GTCCGCAC


title: Y_H3K27ac_2

description: ChIP-seq for H3K27ac in HSCP-HKs

value: CACGATTC


title: Y_INPUT1

value: CAGAGTGA


title: Y_BRD4_2

description: ChIP-seq for BRD4 in HSCP-HKs

value: CCTACAGA


title: Y_H3K27ac_1

description: ChIP-seq for H3K27ac in HSCP-HKs

value: GGATTCAC


title: Y_BRD4_1

description: ChIP-seq for BRD4 in HSCP-HKs

value: GTCCCTTA


title: Y_ATAC_4

description: ATAC-seq in HSCP-HKs

data_processing:
All paired-end ATAC-seq datasets were aligned using Bowtie (version 2.2.8) to build version NCBI37/HG19 with the following parameters: --end-to-end --sensitive --no-unal --no-discordant --mm --met-stderr.
To process aligned ATAC-seq data, we used the RIESLING pipeline (Semenkovich et al., 2016) developed jointly with the Gordon laboratory (https://github.com/GordonLab/riesling-pipeline).  Aligned bams were filtered for low quality reads, duplicate reads were removed, reads were sorted using samtools, mitochondrial reads were removed, and further filtering against the ENCODE blacklist.
Peaks were called using MACS1.4.2 which does not take into account paired end fragment information. A threshold of p-value < 1e-9 was used to call enriched regions.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ATAC data files are in wiggle format

extract_protocol:
ATAC-seq (Assay for Transposase-Accesible Chromatin) was performed as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015). In brief, about 3x105 HPEKs that were seeded in 6-well were washed once with 500μl of PBS (on plate) and detached using Accutase (CELLnTEC). Cells were centrifuged at 500xg and cell pellets placed on ice. Cells were re-suspended in 1ml lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) IGEPAL CA-630, 1mM PMSF and PI cocktail). Cell lysates were split into 2x1.5ml tubes (for an equivalent of 1.5x105 HPEKs per tube). The suspension of nuclei was then centrifuged for 10min at 500xg at 4°C, followed by the addition of 50μl transposition reaction mix (25μl TD buffer, 2.5μl Tn5 transposase and 22.5μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina). Samples were then incubated for tagmentation at 37°C for 30min. The reaction was stopped using 50μl Stop Buffer (30mM EDTA, pH8.0 and 90mM NaCl). DNA was isolated using a MinElute Kit (QIAGEN).
ATAC-seq libraries were subjected to 15 cycles of amplification. The Agencourt AMPure XP PCR purification system (Beckman Coulter) was used for purification of PCR amplicons. Library concentration was measured using Qubit dsDNA HS Assay Kit (Invitrogen #Q32854) according to the manufacturer’s instructions. Library integrity was checked by gel electrophoresis. Fragment size distribution was checked using High-sensitivity DNA chip (Agilent #5067-4626) for 2100 Bioanalyzer. Finally, the ATAC library was sequenced on an Illumina HiSeq2500 using HiSeq v4 Sequencing Kit (2 X 76 cycles) (FC-401-4002) according to the manufacturer’s instructions.

value: TAAGGCGA


title: Y_ATAC_6

description: ATAC-seq in HSCP-HKs


title: Y_ATAC_3

description: ATAC-seq in HSCP-HKs


title: Y_ATAC_1

description: ATAC-seq in HSCP-HKs


title: O_INPUT3

description: Whole cell extract input control from H3K27ac pull downs in LSCP-HKs

value: CGCTGATA


title: O_ATAC_6

description: ATAC-seq in LSCP-HKs

value: Human primary keratinocytes

value: TCCTGAGC


title: O_INPUT2

value: GGTCGTAT


title: O_ATAC_4

description: ATAC-seq in LSCP-HKs


title: O_INPUT1

value: CCTGTCAA


title: O_ATAC_1

description: ATAC-seq in LSCP-HKs


title: O_H3K27ac_3

description: ChIP-seq for H3K27ac in LSCP-HKs

value: TATCGCGA


title: O_H3K27ac_2

description: ChIP-seq for H3K27ac in LSCP-HKs

value: AGTCAGGT


title: O_ATAC_2

description: ATAC-seq in LSCP-HKs


title: O_H3K27ac_1

description: ChIP-seq for H3K27ac in LSCP-HKs

value: ACCAAGCA


title: O_BRD4_1

description: ChIP-seq for BRD4 in LSCP-HKs

value: AGCCCTAA


title: Y_H3K27ac_3

description: ChIP-seq for H3K27ac in HSCP-HKs

value: AGACATGC


title: NSD2_Low_1_4C_SYK

first: Priscillia

last: Lhoumaud

address: 550 first avenue Smilow 307

institute: NYU Langone Health

description: 4C (SYK locus) in NSD2 Low cells replicate 1 of 2

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the hg38 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ATAC-seq and ChIP-seq
Peaks were called using Macs/1.4
rwas counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools. For H3K36me2 spiked-in, Bigwigs were created after normalization with the   spike-in Drosophila read counts.
Genome_build: hg38
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: TKO

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit.
For ATAC-seq,ChIP-seq and HiChIP, sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit. RNA libraries were prepared for sequencing using standard Illumina protocols. Hi-C libraries were prepared as per the Arima kit guidelines.
RNAseq, ChIP-seq, ATAC-seq, Hi-C, HiChIP, 4C

tag: parental cell line

value: multiple myeloma cell line

tag: genotype/variation

value: overexpressed NSD2 allele inactivated


title: NSD2_Low_ATAC-seq-merged

description: ATAC-seq NSD2 Low cells (6 replicates merged)

tag: kit

value: Nextera


title: NSD2_High_2_4C_SYK

description: 4C (SYK locus) in NSD2 Low cells replicate 2 of 2

source_name: NTKO

value: wild type NSD2 allele inactivated


title: NSD2_High_ATAC-seq-merged

description: ATAC-seq NSD2 High cells (6 replicates merged)


title: BRD4_pooledInput

description: Pooled whole cell extract input control from both LSCP-HK and HSCP-HK

value: TGCTGCAA


title: NSD2_High_1_4C_SYK

description: 4C (SYK locus) in NSD2 High cells replicate 1 of 2


title: NSD2_Low_3_CTCF HiChIP

description:
CTCF HiChIP in NSD2 Low cells replicate 3 of 3
HiChIP_LOW_CTCF.bw, tkoCTCF.common.loops.sig.arc.format.txt, TKOCTCF_new.hic, TKO_CTCF_merged_ChIP_peaks.narrowPeak,

tag: chip antibody

value: CTCF (Millipore 07-729)


title: NSD2_Low_2_4C_SYK

tag: cell type


title: DN2

city: NEW YORK

first: John

last: Blenis

address: 413 E 69TH ST FL 13

institute: Weill Cornell Medicine

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: hg38
Supplementary_files_format_and_content: genomic “signal maps” were stored in bigWig files using wigToBigWig (v4)

source_name: breast epithelial cell line

growth_protocol: MCF-10A cells were cultured in DMEM:F12 media supplemented with 5% horse serum, 20 ng/ml EGF, 100 ng/ml cholera toxin, 10 μg/ml insulin, 0.5 mg/ml hydrocortizone and penicillin-streptomycin. Inducible-overexpression of GFP or ERK2 D319N was achieved through lentiviral infection of pInducer20 constructs. Stable cells were maintained with 300 μg/mL G418.

extract_protocol:
The cells were then thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).
Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: Cells were induced with 0.5 μg/mL Doxycycline for 72 hours. Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay.

value: MCF10A cells expressing ERK2 D319N

tag: construct

value: pInducer - Neo resistance

tag: induction duration

value: 3 days - 0.5 μg/mL Doxycycline


title: DN1


title: GFP2

value: MCF10A cells expressing GFP


title: Y_ATAC_2

description: ATAC-seq in HSCP-HKs

value: Human primary keratinocytes

value: TAAGGCGA


title: NSD2_High_3_CTCF HiChIP

description:
CTCF HiChIP in NSD2 Low cells replicate 3 of 3
HiChIP_HIGH_CTCF.bw, ntkoCTCF.common.loops.sig.arc.format.txt, NTKOCTCF_new.hic, NTKO_CTCF_merged_ChIP_peaks.narrowPeak,


title: NSD2_Low_2_CTCF HiChIP

description:
CTCF HiChIP in NSD2 Low cells replicate 2 of 3
HiChIP_LOW_CTCF.bw, tkoCTCF.common.loops.sig.arc.format.txt, TKOCTCF_new.hic, TKO_CTCF_merged_ChIP_peaks.narrowPeak,


title: NSD2_High_2_CTCF HiChIP

description:
CTCF HiChIP in NSD2 Low cells replicate 2 of 3
HiChIP_HIGH_CTCF.bw, ntkoCTCF.common.loops.sig.arc.format.txt, NTKOCTCF_new.hic, NTKO_CTCF_merged_ChIP_peaks.narrowPeak,


title: H3.3_ChIP-seq

description: 30 µg total chromatin was used for ChIP

data_processing:
Reads were aligned to the human genome (hg38) using the BWA algorithm (default settings),  Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
H3 enriched regions were identified using the SICER algorithm at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp (for some analyses 0 bp).
Alternatively, to identify promoter peak regions, the MACS algorithm (v1.4.2) with a cutoff of p-value = 1e-7 was used, followed by intersecting peak regions with promoter regions (-1000 bp to 0 relative to TSS). Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: hg38
Supplementary_files_format_and_content: genomic “signal maps” were stored in bigWig files using wigToBigWig (v4)

source_name: metastatic breast cancer cells

growth_protocol: MDA-MB-231 LM2 clones were obtained from Dr. Massague’s lab and were maintained in high glucose DMEM (Gibco) supplemented with 10% FBS (Sigma-Aldrich) and penicillin-streptomycin (Gibco).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: MDA-MB-231 LM2 cells

tag: antibody amount

value: 6 microgram


title: H3.1/H3.2_ChIP-seq

description: 30 µg total chromatin was used for ChIP

tag: cell line

value: 4 microgram


title: O_BRD4_2

description: ChIP-seq for BRD4 in LSCP-HKs

value: TCGATCGA


title: GFP1


title: NSD2_Low_IgG-ChIPseq

description: IgG control ChIPseq in NSD2 Low cells

value: IgG (Abcam ab37415)


title: NSD2_High_1_Hi-C

description:
Hi-C in NSD2 High cells replicate 1 of 2
NSD2_HIGH_arima.hic, NSD2_HIGH_compartments.bedGraph, NSD2_HIGH_domains.k=001.bed, NSD2_HIGH_filtered_Acompartments.bed, NSD2_HIGH_filtered_Bcompartments.bed

value: multiple myeloma cell line

value: Arima


title: NSD2_High_1_CTCF HiChIP

description:
CTCF HiChIP in NSD2 High cells replicate 1 of 3
HiChIP_HIGH_CTCF.bw, ntkoCTCF.common.loops.sig.arc.format.txt, NTKOCTCF_new.hic, NTKO_CTCF_merged_ChIP_peaks.narrowPeak,

value: Nextera


title: K562_bio-zfp281_input

first: Gabriela

last: Pregernig

state: Massachusetts

address: 1325 Boylston Street, Suite 500

institute: Decibel Therapeutics

data_processing:
Basecalls were performed using standard Illumina software.
Raw single-end reads were aligned to the human genome (hg19) using Bowtie v1.0.0 with parameters -S -n 2 -q -m 1.
Peaks were called using MACS v1.4 with default parameters. Peaks were subsequently filtered using a p-value of 1e-9. Corresponding inputs were used as the controls.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files represent the MACS output files, containing peak coordinates and significance/fold enrichment information.

source_name: hemin induced K562 cell line

growth_protocol: The K562 cells were cultured in Isocove's Modified Dulbecco's Medium (IMDM) with 10% fetal calf serum, 2mM glutamine and 100 U/ml penicillin-streptomycin at 37 degrees celsius, 5% CO2

extract_protocol:
The cells were cross-linked with 1% formaldehyde for 10 mins at room temperature and quenched with 125 mM glycine. The cells were washed in PBS and then lysed in buffer containing 1% to 0.1% SDS. The genomic DNA was sonicated to 200 to 1000 bps and the biotin-protein-DNA complexes ware precipitated with Dynabeads™ M-280 Streptavidin (Thermo Cat# 11205D) at 4°C for 2 hours, followed by washing and de-crosslinking and DNA purification for subsequent analysis
Fragmented IP’ed DNA samples were processed using the Beckman Coulter SPRIworks system to generate libraries. Resulting libraries were sequenced on the HiSeq2000.

treatment_protocol: The cells were differentiated by addition of hemin (50 mM, final conc) to growth medium and cultured for 48 hrs.


title: DEL Hx

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: RNA extracted from NLUCAT CRISPR/Cas9-deleted A549 clones cultured in hypoxia

data_processing:
Reads were aligned to the human genome release hg19 using STAR v2.4.0a with default parameters.
Gene counting with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1" options
Genome_build: hg19
Supplementary_files_format_and_content: tablecount.txt.gz: tab-delimited text file including counts values of each gene in each sample

source_name: Lung Adenocarcinoma

extract_protocol:
Total RNA were extracted in Qiazol and purified using the miRNeasy minikit (Qiagen).
Libraries were generated from 500 ng of total RNAs using TruSeq Stranded Total RNA kit with Ribo-Zero (Illumina) and sequenced on a NextSeq500 sequencer (Illumina) with 2x75bp paired-end chemistry.

tag: cell

value: Lung Adenocarcinoma cell line

tag: rin number

value: NLUCAT CRISPR/Cas9-deleted

tag: culture conditions

value: hypoxia


title: NSD2_High_IgG-ChIPseq

description: IgG control ChIPseq in NSD2 High cells

value: wild type NSD2 allele inactivated


title: NSD2_Low_2_H3K36me2-ChIPseq

description: H3K36me2 ChIPseq in NSD2 Low cells replicate 2 of 2

value: overexpressed NSD2 allele inactivated

value: H3K36me2 (Active motif Cat# 39255)


title: NSD2_Low_1_CTCF HiChIP

description:
CTCF HiChIP in NSD2 Low cells replicate 1 of 3
HiChIP_LOW_CTCF.bw, tkoCTCF.common.loops.sig.arc.format.txt, TKOCTCF_new.hic, TKO_CTCF_merged_ChIP_peaks.narrowPeak,

value: CTCF (Millipore 07-729)


title: NSD2_Low_1_H3K36me2-ChIPseq

description: H3K36me2 ChIPseq in NSD2 Low cells replicate 1 of 2


title: K562_BirA_input


title: K562_bio-zfp148_input


title: K562_bio-zfp148_rep2

description: K562_ZBP89_allreps_mfold10,30_pval1e-5_peaks.xls


title: K562_bio-zfp281_rep2

description: K562_ZBP99_allreps_mfold10,30_pval1e-5_peaks.xls


title: input_DNA

value: none (input)


title: NSD2_High_1_H3K36me2-ChIPseq

description: H3K36me2 ChIPseq in NSD2 High cells replicate 1 of 2

value: parental


title: NSD2_Low_1_Rad21-ChIPseq

description: Rad21 ChIPseq in NSD2 Low cells replicate 1 of 2

value: Rad21 (Abcam ab992)


title: NSD2_High_2_H3K36me2-ChIPseq


title: NSD2_Low_2_Rad21-ChIPseq

description: Rad21 ChIPseq in NSD2 Low cells replicate 2 of 2


title: NSD2_High_2_Rad21-ChIPseq


title: K562_BirA_rep1

description: K562_BirA_allreps_mfold10,30_pval1e-5_peaks.xls


title: K562_BirA_rep2


title: WT Hx

description: RNA extracted from parental A549 clones cultured in hypoxia


title: NSD2_Low_3_H3K27ac-ChIPseq

description: H3K27ac ChIPseq in NSD2 Low cells replicate 3 of 3

value: H3K27ac (Abcam ab4729)


title: IgG_1_ChIPSeq

city: Copenhagen

first: Diego

last: Iglesias-Gato

address: Univesitetsparken 2

country: Denmark

institute: Unoversity of Copenahgen

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with the –m 1 setting, and converted to bed files using samtools view and bamToBed.
For peak-finding, measurements of distances to TSSs, as well as visualization of tracks, superimposed tracks, and heatmaps, data were imported into EaSeq using default settings and an extension of each read from its 5'-end to a total length of 250 bases.
Wig files were generated by importing bam-files in EaSeq (http://easeq.net) and exporting as wig-files using default settings
Genome_build: human genome (hg19)
Supplementary_files_format_and_content: Wig files

source_name: IgG, LNCaP cells

growth_protocol: LNCaP cells were cultured on standard RPMI medium supplemented with L-glutamine and 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and REST-DNA complexes were isolated with antibody.
Libraries were prepared following standard Illumina´s protocols

treatment_protocol: No treatment was applied

value: LNCaP

value: Androgen sensitive prostate cancer cells

value: Rabbit IgG (Millipore)


title: IgG_2_ChIPSeq


title: NSD2_Low_2_H3K27ac-ChIPseq

description: H3K27ac ChIPseq in NSD2 Low cells replicate 2 of 3

value: multiple myeloma cell line


title: REST_2_ChIPSeq

source_name: REST, LNCaP cells

value: anti-REST (17-641, Millipore)


title: K562_bio-zfp148_rep1


title: K562_bio-zfp281_rep1


title: NSD2_High_2_H3K27ac-ChIPseq

description: H3K27ac ChIPseq in NSD2 High cells replicate 2 of 3

value: Nextera


title: NSD2_High_3_H3K27ac-ChIPseq

description: H3K27ac ChIPseq in NSD2 High cells replicate 3 of 3


title: NSD2_High_1_H3K27ac-ChIPseq

description: H3K27ac ChIPseq in NSD2 High cells replicate 1 of 3


title: REST_1_ChIPSeq


title: NSD2_Low_1_H3K27ac-ChIPseq

description: H3K27ac ChIPseq in NSD2 Low cells replicate 1 of 3


title: NSD2_Low_3_CTCF-ChIPseq

description: CTCF ChIPseq in NSD2 Low cells replicate 3 of 3


title: NSD2_Low_1_CTCF-ChIPseq

description: CTCF ChIPseq in NSD2 Low cells replicate 1 of 3


title: NSD2_High_1_Rad21-ChIPseq

description: Rad21 ChIPseq in NSD2 High cells replicate 1 of 2


title: Fra-1_ChIPseq

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: H33M3BBXX_BT549_Fra1_16s006339-1-1_Zhao_lane216s006339

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations
peaks were called using MACS Peak Calling with default setting
PeakAnalyzer_1.4 and HOMER peak analysis software was used to annotate peaks
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated

source_name: BT549 cells

growth_protocol: Cells  were maintained in RPMI 1640 supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei, IgG, Fra-1 and DDX5 complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: ERalpha-negtive breast cancer cells

value: Fra-1 (R-20,sc-605, Santa Cruz)


title: NSD2_High_1_CTCF-ChIPseq

description: CTCF ChIPseq in NSD2 High cells replicate 1 of 3


title: DNA input

description: H33M3BBXX_BT549_Input_16s006345-1-1_Zhao_lane216s006345


title: NSD2_High_2_CTCF-ChIPseq

description: CTCF ChIPseq in NSD2 High cells replicate 2 of 3


title: NSD2_Low_2_CTCF-ChIPseq

description: CTCF ChIPseq in NSD2 Low cells replicate 2 of 3


title: NSD2_High_3_CTCF-ChIPseq

description: CTCF ChIPseq in NSD2 High cells replicate 3 of 3


title: NSD2_Low_4_RNAseq

description: RNAseq in NSD2 Low cells replicate 4 of 5


title: DDX5_ChIPseq

description: H33M3BBXX_BT549_DDX5_16s006340-1-1_Zhao_lane216s006340

value: DDX5 (ab21696, Abcam)


title: NSD2_Low_2_RNAseq

description: RNAseq in NSD2 Low cells replicate 2 of 5


title: IgG_ChIPseq

description: H33M3BBXX_BT549_IgG_16s006338-1-1_Zhao_lane216s006338

value: normal rabbit IgG (sc-2027, Santa Cruz)


title: NSD2_Low_1_RNAseq

description: RNAseq in NSD2 Low cells replicate 1 of 5

value: overexpressed NSD2 allele inactivated


title: NSD2_High_5_RNAseq

description: RNAseq in NSD2 High cells replicate 5 of 5

value: wild type NSD2 allele inactivated


title: 59-672-4-UPPL1541-TA-DNA-WES_ATTGGCT

city: Chapel Hill

first: Benjamin

middle: Garrett

last: Vincent

state: NC

address: Lineberger Comprehensive Cancer Center, CB# 7295 125 Mason Farm Rd. Room 5230E Marsico Hall

department: Department of Microbiology and Immunology UNC-Chapel Hill Immunology Division of Hematology/Oncology

institute: University of North Carolina at Chapel Hill

data_processing:
Library strategy: DNA-seq
Illumina bcl2fastq used to convert BCL to FASTQ format
Tumor mutations were called from WES tumor versus match-normal samples using UNCeqR (https://lbc.unc.edu/~mwilkers/unceqr_dist/). RNA-seq files were  used to quantify read coverage, with filter set for >5x coverage for a predicted mutation to be considered for downstream antigen calling.  As such, RNA-seq data was not run through a quantifier (i.e. RSEM) and expression matrix data were not generated or considered for the analysis.  Matched-normal samples for T11 tumor (BALB/c) have been previously deposited at https://www.ncbi.nlm.nih.gov/sra/?term=SRR3502701.
Translated 8-11mer (class I) or 15mer (class II) peptides were derived across all open reading frames, and then predicted for MHC binding affinity using NetMHCPan2.8 (MHC I; http://www.cbs.dtu.dk/services/NetMHCpan-2.8/) and NetMHCIIPan3.0 (MHC II; http://www.cbs.dtu.dk/services/NetMHCIIpan-3.0/).  Class I minor mismatch antigens were predicted similarly in the P815 model against the BALB/c histocompatible donor.
Predicted binders were filtered by binding affinity <500 nM, generally accepted cutoff for immunogenicity as previously noted, with top epitopes screened for immunogenicity using a vaccine/ELISpot approach.
Genome_build: mm9
Supplementary_files_format_and_content: Excel .xlsx file containing top predicted binding affinity MHC I and II tumor-specific antigens from all models represented in the fastq files.

growth_protocol: P815 tumor samples were collected directly from cell line culture (10e5 cells per sample).  For remaining tumors, mice were injected with tumors and monitored until size reached 100mm3 by caliper measurement. Matched normal samples were collected from tail clippings or liver.

extract_protocol:
RNA was extracted from single cell suspension of tumors using Qiagen RNeasy Mini kit (cat. # 74104), and DNA was extracted from single cell suspensions of tumors and matched-normal tail clippings or livers using Qiagen DNeasy kit (cat. # 69504), all according to manufacturer protocol.
Whole exome and transcriptome library preparation was performed using Agilent SureSelect XT All Exon and Illumina TruSeq Stranded mRNA library preparation kits, respectively.

tag: sample type

value: Matched-normal

tag: injected cell line

tag: tissue

value: Liver and tail


title: DBA2-1-Sp-DNA-WES_ATGCCTAA_S1


title: AS-4

city: Wako

first: Xiaoxi

last: Liu

state: Saitama

address: Hirosawa 2-1

department: Brain Science Institute

institute: RIKEN

description: Biological replicate 4 of 4 AS

hyb_protocol: Amplified and Cy3 labeled RNA were fragmentated and hybridized onto mouse Whole Mouse Genome Microarray 4x44K v2  (Agilent-026655)

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2505B)

data_processing: The raw singal intensities were acquired by Feature Extraction Software 9.5 (Agilent) and analyzed by Limma package (3.30.13) under the R environment. The signal intensities were corrected by backgroundCorrect function of the Limma package and the between arrays normalization was performed by using the quantile method. Differentially expressed genes (DEGs) were ranked using a moderated t-statistic.

source_name: hippocampus, AS, replicate 4

label_protocol: 200 ng of total RNA was used for further procedure including Cy3 labeling with T7 RNA polymerase amplification method according to manufacturer's instruction (Low Input Quick Amp Labeling Kit for one color; Agilent)

extract_protocol: Total RNA from hippocampus was extracted using TRIzol (Life Technologies, Gaithersburg, MD), followed by column purification with DNaseI treatment (Promega, Madison, WI). The quantity and quality of RNA was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

value: brain hippocampus

tag: genotype

value: Angelman Syndrome (AS) model

tag: genetic background

tag: age

value: 3 weeks


title: WT(B6)-3

description: Biological replicate 3 of 4 WT

source_name: hippocampus, WT, replicate 3

value: Wild-type


title: DBA2-2-Sp-DNA-WES_GAATCTGA_S5


title: dLN.IL33

first: Vinod

last: Balachandran

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Libraries were diluted to 10nM and clustered on a NovaSeq600 on a pair end read flow cell and sequenced for 28 cycles on R1 (10x barcode and the UMIs), followed by 8 cycles of I7 Index (sample Index), and 89 bases on R2 (transcript), obtaining about 100M clusters per sample, except for Tumor_No_treatment which was clustered at about 10M.
Primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA).
10x Genomics Cell Ranger Single Cell Software suite v3.0.2 was used to perform sample demultiplexing, alignment (mm10), filtering, UMI counting, single-cell 5’end gene counting and performing quality control using the manufacturer parameter.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed files containing sparse matrices in (MEX) & gzipped TSV files with feature (genes) and barcode sequences of detected cellular barcodes.

source_name: ILC2 cells from tumor draining lymph nodes

growth_protocol: WT C57BL/6J mice were injected orthotopically into the pancreas with 1e6 KPC tumor cells for 10 days

extract_protocol:
Fluorescence activated cell-sorted, purified ILC2 were loaded onto to the 10x Genomics Chromium platform to generate Gel Beads-in-Emulsion (GEM). Samples were incubated at 53 °C for 45 min in a C1000 Touch Thermal cycler to generate polyA cDNA barcoded at the 5’end. GEMs were broken and single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads. The cDNA was amplified for 16 cycles. 50ng of cDNA was enzymatically fragmented, end repaired, A-tailed, subjected to a double-sided size selection with SPRIselect beads and ligated to adaptors provided in the kit.
Single-cell RNA-seq libraries were prepared according to 10X Genomics specifications (Chromium Single Cell V(D)J User Guide PN-1000006), see above.

treatment_protocol: Mice were treated with 500 ug of recombinant IL33 alone or with 250 ug blocking PD1 antibody every other day for 10 days post tumor implantation

tag: strain

value: Tumor draining lymph node (mesenteric)


title: NSD2_High_4_RNAseq

description: RNAseq in NSD2 High cells replicate 4 of 5

tag: parental cell line

tag: genotype/variation


title: dLN.IL33.PD1

tag: cell type


title: NSD2_High_3_RNAseq

description: RNAseq in NSD2 High cells replicate 3 of 5

value: parental


title: NSD2_Low_5_RNAseq

description: RNAseq in NSD2 Low cells replicate 5 of 5

value: multiple myeloma cell line


title: AS-1

description: Biological replicate 1 of 4 AS

source_name: hippocampus, AS, replicate 1


title: Tumor.IL33.PD1

source_name: ILC2 cells from pancreatic tumor

value: Pancreatic tumor


title: WT(B6)-4

description: Biological replicate 4 of 4 WT

source_name: hippocampus, WT, replicate 4


title: AS-3

description: Biological replicate 3 of 4 AS

source_name: hippocampus, AS, replicate 3


title: NSD2_Low_3_RNAseq

description: RNAseq in NSD2 Low cells replicate 3 of 5


title: 57-672-2-UPPL1541-TA-DNA-WES_GCCAAGA


title: 58-672-3-UPPL1541-TA-DNA-WES_GACTAGT


title: Tumor.IL33


title: 56-672-1-UPPL1541-TA-DNA-WES_CACTTCG


title: AS-2

description: Biological replicate 2 of 4 AS

source_name: hippocampus, AS, replicate 2


title: WT(B6)-1

description: Biological replicate 1 of 4 WT

source_name: hippocampus, WT, replicate 1


title: NSD2_High_1_RNAseq

description: RNAseq in NSD2 High cells replicate 1 of 5


title: 160616-170 WAT

city: Innsbruck

first: Carina

middle: Michelle

last: Miggitsch

address: Rennweg 10

department: Immunology

country: Austria

institute: Institute for Biomedical Aging Research

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-16

hyb_protocol: Following fragmentation, 60 µl fragmented biotin labeled amplified cDNA plus Affymetrix Expression 3' Amp Reagent Hyb. Control kit. Incubate arrays in the hybridization oven: 16 hr at 45C on GeneChip MTA 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Program FS001_450. Stain 1 solution: SAPE, Stain 2 solution: AB, Stain 3 solution: Array Holding Buffer.

scan_protocol: GeneChips were scanned using the Gene Titan Microarray Scanner (Affimetrix GeneTitan Hyb. Module for WT array plates), Chip type: HuGene_2.1., Chip Lot#: 4310744.

data_processing: To obtain functional information on fMAT adipocytes, Gene Set Enrichment Analysis (GSEA 3.0) (Broad Institute, http://www.broadinstitute.org/gsea/index.jsp) was done as previously described, which identified gene sets that were statistically significant. GSEA was used to analyse data from fMAT and tsWAT obtained from eight female donors between the ages of 44 and 76 years. Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). To run or use this program you first have to adjust your existing files in specific formats: expression dataset file (res, gct, pcl, or txt), phenotype labels file (cls), gene sets file (gmx or gmt), chip (array) annotation file (chip). For the expression data set file we used the file: A3353_Annotations_RMA-GENE-FULL. As a start we used the existing gene matrix (from website) h.all.v6.2.symbols.gmt[Hallmarks] provided by the company GSEA and MSigDB to get an overview of different pathways. In a second run we programmed the gene sets (file type .grp) on our own based on the pathways we were interested. The number of permutations was used 1000. In the end we choose the chip: HuGene_2_0_st.chip.

source_name: Healthy female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ng total RNA (Affymetrix® Human Gene ST Array Plate, Affymetrix WT Pico Amp Kit; Model 1,cRNA step; Model 3, Purification Beads; Model 2, cDNA step; Affymetrix). The label consits of the date, when we recieved the human material, an intern donor number and the abbreviation of the adipose tissue (marrow adipose tissue - MAT, subcutaneous white adipose tissue - WAT).

growth_protocol: Femur marrow adipose tissue and subcutaneous white adipose tissue was shipped separately within 24 hours in complete RPMI medium (RPMI 1640 supplemented with 10% FCS, 100 U/mL penicillin, and 100 μg/mL streptomycin; Invitrogen).

extract_protocol: Bone marrow biopsies were fragmented, washed once with complete RPMI medium (RPMI 1640 supplemented with 10% FCS, 100 U/mL penicillin, and 100 μg/mL streptomycin; Invitrogen) and treated with purified collagenase (CLSPA, Worthington Biochemical; 20 U/mL in complete RPMI medium) for 1 h at 37°C. After centrifugation for 10 minutes at 150 g with low break and before ficoll purification, adipocytes formed a floating layer on the top of the medium which was carefully transferred into a fresh 15 ml tube. BM biopsies were then centrifuged and BMMCs purified by density gradient centrifugation (Ficoll-Hypaque). Subcutaneous fat tissue was placed into a petri dish and reduced into small fragments of approximately 1 mm with a scissor. Small fragments were transferred into a 15 ml Falcon and filled with PBS + 2% FCS to 14 ml. For digestion 200 µl of collagenase (Worthington CLSPA #L5005273; Stock 1000 U/ml; Final concentration 200 U Collagenase) was added and incubated for 1 h at 37°C. The digested suspension was passed through a 100 µM cell strainer and afterwards collected in a 15 ml tube. BM and subcutaneous adipocytes were treated the same. Both 15 ml tubes containing adipocytes were centrifuged at 150 g for 10 min and afterwards, adipocytes were isolated by flotation. Informed consent for test and publication was given and documented from each patient. RNA was isolated from purified bone marrow and subcutaneous adipocytes using the RNeasy Lipid Tissue Mini Kit (Qiagen) including the reagent Qiazol according to the manufactures’ protocol.

treatment_protocol: No treatment were used.

tag: gender

value: female

tag: age (years)


title: Tumor.vehicle

city: New York


title: 160616-169 WAT

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-14


title: NSD2_High_2_RNAseq

description: RNAseq in NSD2 High cells replicate 2 of 5

source_name: NTKO


title: WT(B6)-2

description: Biological replicate 2 of 4 WT

source_name: hippocampus, WT, replicate 2


title: 160616-170 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-15

value: femur marrow adipose tissue


title: 54-621-1-BBN963-TA-DNA-WES_GAATCTG


title: ASD-subject-70Ji

first: Stephen

middle: W

last: Scherer

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

data_processing:
Data quality was assessed using FastQC v.0.11.5
Trimmed reads were screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.10.0
RSeQC package v.2.6.2 was used to assess read distribution, positional read duplication and confirm strandedness of alignments.
Raw trimmed reads were aligned to the reference genome hg19 using STAR v.2.6.0
STAR alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2
In the filtered data set were retained only genes whose reads per kilobase of expressed transcript per million reads of library (RPKM) values were 2 in at least 2 samples.
The method used for normalizing the data was TMM, implemented by the calcNormFactors(y) function.
The 3.1.0 ggplot2 package was used to plot a heat map, and the RPKM values of genes were log2 transformed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: induced pluripotent stem cells (iPSCs)

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen)
rRNA-depletion
RNA library preparation was done following Illumina TruSeq Stranded total RNA library preparation protocol

value: induced pluripotent stem cells (iPSCs)

tag: passages

tag: microdeletion

tag: subject

value: ASD subject


title: Paternal control-68Hii

value: control subject(paternal)


title: 53-670-4-MB49-TA-DNA-WES_ATGCCTA


title: 51-670-2-MB49-TA-DNA-WES_AAGGACA


title: HiC_KA48h_rep1

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

description:
Paired-end
processed data file:
HiC_KA48h_q30.hic

data_processing:
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10. Only reads with mapq > 30 and mapping to nuclear chromosomes were used for the posterior analysis. Data was processed with the extensive use of custom scripts, and Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010) and DeepTools v3.1.0 (Ramirez et al., 2016). RNA-seq data: Reads were aligned with HISAT2 v2.1.0 (Kim et al., 2015). ATAC-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). Duplicated reads were removed with Picardtools and only paired reads were used for the posterior analysis. ChIP-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). HiC data: Hi-C datasets were processed using the Juicer pipeline (Durand et al., 2016) to align reads, filter duplicates, perform matrix normalizations, and obtain the eigenvector. Reads with a mapping quality >= 30 and binned at 25 kb were used in all downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files from whole genome alignments normalized to RPM (read per million sequenced reads).

source_name: Hippocampal excitatory neurons

growth_protocol: Mice were maintained and bred under standard conditions, consistent with Spanish and European regulations and approved by the Institutional Animal Care and Use Committee.

extract_protocol:
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. TRAP immunoprecipitation followed the original protocol by (Heiman et al., 2014) with small changes. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells, in case NE condition nuclei were stained against FOS. Extensive description of protocols indicated in Supplemental Experimental Procedures.
For riboRNA and nuRNA, extraction was re-suspended in RLT buffer for purification with RNeasy Micro kit (Qiagen 74004). Truseq libraries were prepared from ribo-depleted total RNA in the case of nuRNA-seq and from polyA-selected mRNA in the case of riboRNA-seq. ATAC-seq experiments were conducted as the original protocol (Buenrostro et al., 2013), libraries were purified with MinElute PCR purification kit (Qiagen 28004). ChIP-seq was conducted as previously described (Lopez-Atalaya et al., 2013) using the anti-H3K4me3 (Millipore 07-473), anti-CBP (sc583x) and anti-RNAPII (sc901x). In situ Hi-C were conducted as the original protocol (Rao et al., 2014), libraries were prepared with TruSeq.

treatment_protocol: Mice received intragastric administration of tamoxifen when they were ~2 month-old, and we wait 4 weeks before experimentation. For the induction of SE by Kainic Acid (KA), 25 mg/kg was injected intraperitoneally. For the blocking of transcription by Triptolide (TPL) a concentration of 0.8 mg/kg was injected intraperitoneally per mice 2 h before the injection of KA or Saline. For novelty exposure (NE), individually housed mice received 3-4 days of 5 min handling before exposing them to a novel environment during 1h.

value: Adult Forebrain (hippocampus)

value: 3-6 month

value: male


title: HiC_KA48h_rep2


title: ASD-subject-70C

address: 686 Bay Street


title: ASD-subject-70Jii


title: HiC_Sal_rep2

description:
Paired-end
processed data file:
HIC_KA0h_q30.hic


title: HiC_KA1h_rep2

description:
Paired-end
processed data file:
HiC_KA1h_q30.hic


title: HiC_KA1h_rep1


title: 50-670-1-MB49-TA-DNA-WES_GATAGAC

value: Matched-normal

value: Liver and tail


title: Paternal control-68E


title: Paternal control-68Hi


title: 55-621-2-BBN963-TA-DNA-WES_AACGTGA


title: 46-672-4-UPPL1541-cdTu-DNA-WES_GAGCTGA

value: Tumor


title: HiC_Sal_rep1


title: 52-670-3-MB49-TA-DNA-WES_GACAGTG


title: A549 Nx

data_processing:
Reads were first filtered to remove SOLiD adaptors, SOLiD barcodes and rRNAs reads.
Alignment was performed within Lifescope 2.5.1 software RNAseq pipeline using default parameters.
Raw sequence reads were counts and rpkm was calculated by Lifescope 2.5.1
Genome_build: hg19
Supplementary_files_format_and_content: tablecount.txt.gz: tab-delimited text files include conts, RPKM values of genes

source_name: Lung Adenocarcinoma

extract_protocol:
Total RNA were extracted in Qiazol and purified using the miRNeasy minikit (Qiagen).
Total RNA were depleted from ribosomal RNA with the Ribozero kit (epicenter). RNA libraries were generated with the NEB next small library prep set for SOLID.

tag: cell

value: Lung Adenocarcinoma cell line

value: normoxic


title: 240516-165 WAT

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-12


title: Unrelated control-50B

value: control subject(unrelated)


title: 160616-169 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-13


title: 240516-164 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-09


title: 45-672-3-UPPL1541-cdTu-DNA-WES_AGCAGGA


title: 240516-165 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-11


title: 240516-164 WAT

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-10


title: 44-672-2-UPPL1541-cdTu-DNA-WES_GATGAAT


title: 190516-163 WAT

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-08


title: LNCaP_MDV_24h_RNAseq rep2

city: Durham

first: Zhong

last: Chen

address: 905 S. LaSalle Street

institute: Duke University

description:
Biological replicate 2
LNCaP_MDV_24h_gene.read.counts

data_processing:
RNA-seq process: The RNA-seq data was aligned by TopHat 2.0. Reads were mapped to the reference genome build (hg19). Read counts were calculated with Partek. The reads count in exon regions was used to estimate the expression level of the genes.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include read counts of all genes for each Sample.

molecule: polyA RNA

source_name: prostate cancer cells

growth_protocol: The prostate cancer cell line LNCaP was cultured in the RPMI complete medium (10% FBS).

extract_protocol:
For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. After two rounds of processes, the  mRNA was recovered for library generation.
For RNA-seq, the library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina HiSeq 2500 at the OSUCCC sequencing core.

treatment_protocol: For all experiments, cells were maintained in phenol red-free RPMI medium with 5-10% charcoal-stripped FBS for 3 days before treatment. Then cells were treated with vehicle, DHT and MDV for indicated time.

tag: cell line

value: prostate cancer cell line LNCaP

tag: disease state

value: Prostate adenocarcinoma

tag: treatment

value: MDV

tag: time


title: 43-672-1-UPPL1541-cdTu-DNA-WES_ATTGGCT

tag: sample type

tag: injected cell line

tag: tissue


title: LNCaP_MDV_24h_RNAseq rep1

description:
Biological replicate 1
LNCaP_MDV_24h_gene.read.counts


title: 190516-163 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-07

value: female


title: 9-672-3-UPPL1541-cdTu-RNA-RNS_ATTCAGA-ATAGAGG

data_processing:
Illumina bcl2fastq used to convert BCL to FASTQ format
Tumor mutations were called from WES tumor versus match-normal samples using UNCeqR (https://lbc.unc.edu/~mwilkers/unceqr_dist/). RNA-seq files were  used to quantify read coverage, with filter set for >5x coverage for a predicted mutation to be considered for downstream antigen calling.  As such, RNA-seq data was not run through a quantifier (i.e. RSEM) and expression matrix data were not generated or considered for the analysis.  Matched-normal samples for T11 tumor (BALB/c) have been previously deposited at https://www.ncbi.nlm.nih.gov/sra/?term=SRR3502701.
Translated 8-11mer (class I) or 15mer (class II) peptides were derived across all open reading frames, and then predicted for MHC binding affinity using NetMHCPan2.8 (MHC I; http://www.cbs.dtu.dk/services/NetMHCpan-2.8/) and NetMHCIIPan3.0 (MHC II; http://www.cbs.dtu.dk/services/NetMHCIIpan-3.0/).  Class I minor mismatch antigens were predicted similarly in the P815 model against the BALB/c histocompatible donor.
Predicted binders were filtered by binding affinity <500 nM, generally accepted cutoff for immunogenicity as previously noted, with top epitopes screened for immunogenicity using a vaccine/ELISpot approach.
Genome_build: mm9
Supplementary_files_format_and_content: Excel .xlsx file containing top predicted binding affinity MHC I and II tumor-specific antigens from all models represented in the fastq files.


title: LNCaP_MDV_4h_RNAseq rep2

description:
Biological replicate 2
LNCaP_MDV_4h_gene.read.counts


title: LNCaP_MDV_4h_RNAseq rep1

description:
Biological replicate 1
LNCaP_MDV_4h_gene.read.counts


title: LNCaP_DHT_24h_RNAseq rep2

description:
Biological replicate 2
LNCaP_DHT_24h_gene.read.counts

value: DHT


title: 8-672-2-UPPL1541-cdTu-RNA-RNS_ATTCAGA-TATAGCC


title: 7-672-1-UPPL1541-cdTu-RNA-RNS_GAGATTC-GTACTGA


title: LNCaP_DHT_24h_RNAseq rep1

description:
Biological replicate 1
LNCaP_DHT_24h_gene.read.counts


title: LNCaP_DHT_4h_RNAseq rep2

description:
Biological replicate 2
LNCaP_DHT_4h_gene.read.counts


title: 180516-160 WAT

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-06


title: LNCaP_DHT_4h_RNAseq rep1

description:
Biological replicate 1
LNCaP_DHT_4h_gene.read.counts


title: CP-EX-358-T11_Serody_p2_AAGGTACA_S3


title: 180516-160 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-05

value: femur marrow adipose tissue


title: LNCaP_Vehicle_RNAseq rep4

description:
Biological replicate 4
LNCaP_Vehicle_gene.read.counts

value: Vehicle


title: 110416-149 WAT

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-02


title: A549 Hx2

description: RNA extracted from LUAD A549 cells cultured in hypoxia (replicate 2)

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and differential analysis using Limma package in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen)

value: Lung

tag: rin number

tag: culture conditions

value: hypoxia


title: tumor


title: 020516-156 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-03


title: 020516-156 WAT

description:
Gene expression data from subcutaneous white adipose tissue of the thigh harvested from a female donor
A3353-04


title: 110416-149 MAT

description:
Gene expression data from femur marrow adipose tissue harvested from a female donor
A3353-01


title: A549 Hx1

description: RNA extracted from LUAD A549 cells cultured in hypoxia (replicate 1)


title: P815-CL-CL-DNA-WES_AACGTGAT_S2

value: Cell line


title: A549 Nx1

description: RNA extracted from LUAD A549 cells cultured in normoxia (replicate 1)

value: normoxia


title: RCC4 cells treated with siRNA targeting TAZ (WWTR1) and erastin_3

first: Jen-Tsan

last: Chi

address: 101 Science Drive

hyb_protocol: cDNA was amplified using Ambion MessageAmp™ Premier RNA Amplification Kit (Life Technologies) from 200ng total RNA, hybridized to GeneChip U133A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were analyzed with Expression Console and normalized by the RMA (Robust Multi-Array)

source_name: Human RCC4 cells with TAZ silenced by siRNA and erastin

label_protocol: not provided

growth_protocol: Renal cell carcinoma cell line, RCC4 cells, were cultured in DMEM (Thermo-11995) plus 10% heat-inactivated FBS (Hyclone #SH30070.03HI) in humidified incubator, 37°C with 5% CO2

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Renal cell carcinoma cell line, RCC4 cells, were treated with siRNA control, non-targeting (siNT) or siRNA targeting TAZ, also known as WWTR1 (siTAZ) for two days. Later, the cells were treated with either vehicle (DMSO) or 1 µM erastin for 7 hours.

value: clear cell renal carcinoma cell line

value: low TAZ and erastin treatment


title: 10-672-4-UPPL1541-cdTu-RNA-RNS_ATTCAGA-CCTATCC

value: Tumor


title: LNCaP_Vehicle_RNAseq rep3

description:
Biological replicate 3
LNCaP_Vehicle_gene.read.counts


title: DEL3 Hx

description: RNA extracted from NLUCAT1 CRISPR/Cas9-deleted A549 clones cultured in hypoxia (replicate 3)

source_name: DEL3 Hx

tag: genotype/variation

value: NLUCAT1 CRISPR/Cas9-deleted


title: RCC4 cells treated with siRNA targeting TAZ (WWTR1) and erastin_2

tag: cell type


title: LNCaP_Vehicle_RNAseq rep2

description:
Biological replicate 2
LNCaP_Vehicle_gene.read.counts


title: P815-3-T-DNA-WES_GCCAAGAC_S3


title: DEL3 Nx

description: RNA extracted from NLUCAT1 CRISPR/Cas9-deleted A549 clones cultured in normoxia (replicate 3)

source_name: DEL3 Nx


title: RCC4 cells treated with siRNA targeting TAZ (WWTR1) and erastin_1


title: P815-2-T-DNA-WES_CACTTCGA_S4


title: A549 Nx2

description: RNA extracted from LUAD A549 cells cultured in normoxia (replicate 2)


title: DGM-10632_SAE-ALI_S57_L007 (RNA-Seq)

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

institute: Weill Cornell Medical College

description: immortalized basal cells cultured from small airway epithelium sample

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text file includes the RefSeq unique ID with gene ID and location, gene ID  and the FPKM values for all samples

source_name: small airway epithlium basal cells

growth_protocol: Pure populations of nonsmoker amall airway basal cells (BC) were obtained and characterized using detailed protocols as previously described (PMID:1572528). Primary BC were maintained in Bronchial Epithelial Growth Media (BEGM, Lonza, Walkersville, MD) and passaged by seeding at a cell density of 3000 cells/cm2 in BEGM with fresh media changed every 2 days .

extract_protocol:
Total RNA from nonsmoker small airway epithelium and harvested basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500.  HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

treatment_protocol: Passage 1 small airway BC cells from the selected donor were immortalized using retrovirus-mediated expression of human telomerase reverse transcriptase (hTERT) with a puromycin resistance selection marker, in a similar fashion we previously used to generate the BCi-NS1.1 immortalize large airway basal cell line (PMID:24298994).

tag: smoking status

value: nonsmoker

value: small airway epithlium basal cells

value: air-liquid interface culture (passage 57 at day 28)


title: P815-CL-CL-RNA-RNS_ATCACG


title: P815-3-T-RNA-RNS_CGATGT


title: RCC4 cells treated with siRNA targeting TAZ (WWTR1) and DMSO_2

source_name: Human RCC4 cells with TAZ silenced by siRNA and DMSO

value: low TAZ


title: DGM-10632_SAE-BC_S55_L007 (RNA-Seq)

value: control (passage 55)


title: P815-2-T-RNA-RNS_TTAGGC


title: LNCaP_Vehicle_RNAseq rep1

description:
Biological replicate 1
LNCaP_Vehicle_gene.read.counts

value: prostate cancer cell line LNCaP

value: Prostate adenocarcinoma


title: A549 Hx

value: Lung Adenocarcinoma cell line


title: Plus36h_Rep3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with vehicle 36h
GeneCounts.xlsx

data_processing:
RNA-Seq sequencing reads were aligned to hg19 genome using Tophat v2.0.11 using parameters "--library-type fr-firststrand" and using known transcripts annotation from ensembl gene verion 72
Number of reads counts on exons were summarised using featureCounts function available in rsubread R package.
Genome_build: hg19
Supplementary_files_format_and_content: reads counts on genes

source_name: +4OHT + Vehicle 36h

growth_protocol: IMR90 ER:RAS cells were grown in DMEM, 10% FBS, for 6 days and media change was performed at day 3

extract_protocol:
Cells were scraped and homogenised in TRIzol® RNA isolation reagent, mixed with Chloroform in a 5:1 ratio, centrifuged at 15,000 rpm for 30 min and after successful phase separation, the top clear RNA-containing phase was purified using the RNAeasy® Mini Kit (Qiagen)
Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

treatment_protocol: To induce RAS expression and senescence, cells were treated with 100nM 4OHT

value: IMR90 ER:RAS

tag: imr90 passage

tag: days after 4oht induction

value: 6 + treatment time


title: DEL2 Nx

description: RNA extracted from NLUCAT1 CRISPR/Cas9-deleted A549 clones cultured in normoxia (replicate 2)

source_name: DEL2 Nx

value: Lung


title: 40-670-4-MB49-cdTu-DNA-WES_CACTTCG


title: DEL2 Hx

description: RNA extracted from NLUCAT1 CRISPR/Cas9-deleted A549 clones cultured in hypoxia (replicate 2)

source_name: DEL2 Hx

value: hypoxia


title: RCC4 cells treated with siRNA targeting TAZ (WWTR1) and DMSO_3


title: Plus36h_Rep2


title: RCC4 cells treated with siRNA control and erastin_3

source_name: Human RCC4 cells with non-targeting siRNA control and erastin

value: erastin treatment


title: RCC4 cells treated with siRNA control and erastin_1

value: clear cell renal carcinoma cell line


title: Plus36h_Rep1


title: RCC4 cells treated with siRNA targeting TAZ (WWTR1) and DMSO_1


title: WT3 Hx

description: RNA extracted from parental A549 cells cultured in hypoxia (replicate 3)

source_name: WT3 Hx

value: wild type


title: Plus36hPlusC_Rep3

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with vehicle 36h and Caspase inhibitor
GeneCounts.xlsx

source_name: +4OHT + Vehicle 36h + Casp. Inh O/N


title: WT2 Hx

description: RNA extracted from parental A549 cells cultured in hypoxia (replicate 2)

source_name: WT2 Hx


title: 39-670-3-MB49-cdTu-DNA-WES_AACGTGA

value: Tumor


title: 38-670-2-MB49-cdTu-DNA-WES_GAATCTG


title: RCC4 cells treated with siRNA control and erastin_2


title: WT2 Nx

description: RNA extracted from parental A549 cells cultured in normoxia (replicate 2)

source_name: WT2 Nx

value: normoxia


title: 37-670-1-MB49-cdTu-DNA-WES_ATGCCTA


title: Plus36hPlusC_Rep2


title: WT3 Nx

description: RNA extracted from parental A549 cells cultured in normoxia (replicate 3)

source_name: WT3 Nx


title: RCC4 cells treated with siRNA control and DMSO_3

source_name: Human RCC4 cells with non-targeting siRNA control and DMSO

value: control


title: 4-670-4-MB49-cdTu-RNA-RNS_GAGATTC-AGGCGAA


title: RCC4 cells treated with siRNA control and DMSO_2


title: RCC4 cells treated with siRNA control and DMSO_1


title: Plus36hPlusC_Rep1


title: DEL1 Nx

description: RNA extracted from NLUCAT1 CRISPR/Cas9-deleted A549 clones cultured in normoxia (replicate 1)

source_name: DEL1 Nx

value: NLUCAT1 CRISPR/Cas9-deleted


title: WT1 Hx

description: RNA extracted from parental A549 cells cultured in hypoxia (replicate 1)

source_name: WT1 Hx


title: 3-670-3-MB49-cdTu-RNA-RNS_GAGATTC-GGCTCTG


title: 2-670-2-MB49-cdTu-RNA-RNS_GAGATTC-CCTATCC


title: HUCPVC-male-P12-biological rep2

city: Medicine Hat

first: Lorena

last: Braid

state: Alberta

address: PO Box 21053, Crescent Heights PO

institute: Aurora BioSolutions Inc.

hyb_protocol: The total amount of cRNA for the hybridization reaction was 20 µg. Arrays were hybridized for 16 hours at 45°C, 60 RPM in a GeneChip™ Hybridization Oven 640 (Affymetrix, Waltham, MA).

scan_protocol: Chips were scanned using a GeneChip™ 3000 7G Scanner (Affymetrix, Waltham, MA) and the resulting probe array images subjected to grid alignment and fluorescence intensity review in AGCC Viewer. fluidics protocol: Program FS450_0002 was used with GeneChip™ Fluidics Station 450 (Affymetrix, Waltham, MA).

data_processing: The data were analyzed using R/Bioconductor packages, including simpleaffy for .CEL file upload and Affymetrix-recommended quality assessment, and gcrma for GCRMA pre-processing.

label: 3' IVT Biotin

source_name: male HUCPVCs at end of P12

label_protocol: RNA was amplified and labeled using GeneChip™ 3’ IVT Plus kits (Affymetrix, Waltham, MA) following the manufacturer’s instructions with the following modification: 200 ng of RNA was used for the cDNA synthesis.

growth_protocol:
cell culture protocol: HUCPVCs were thawed according to TRT’s proprietary standard operating procedures and expanded in Mesenchymal Stem Cell Growth Media – Chemically Defined™ (MSCGM-CD™; Lonza, Walkersville, MD). Culture vessels were coated with fibronectin (Corning, Corning, NY) at 0.75 µg/cm2 diluted in 0.133 ml/cm2 in Dulbecco’s phosphate buffered saline without calcium or magnesium (DPBS -/-, ThermoFisher Scientific, Waltham, MA) prior to cell seeding into a culture vessel at a density of 1333 cells/cm2. At 70-80% confluence, culture media was removed and cells were washed with DPBS. DPBS wash was removed, and cells enzymatically detached using TrypLE™ Select (ThermoFisher Scientific, Waltham, MA). Once cells were dissociated, an equal volume of MSCGM-CD was added to the suspension and cells were counted with a Millipore Scepter cell counter using 60 µm probes (Millipore, Billerica, MA). Cells were centrifuged at 149 x g for 5 minutes. Supernatant was removed, and the cell pellet was suspended in fresh MSCGM-CD™. An appropriate volume of cells was seeded into new culture vessels at a density of 1333 cells/cm2.
population doubling level calculation: PDL = 3.32 (logXe – logXb) + S  where Xe is the final cell count, Xb is the initial cell count, and S is the PDL at the start of the culture incubation

extract_protocol:
RNA sample collection protocol: The cell suspension was pelleted by centrifugation at 149 x g for 5 minutes. Supernatant was removed, and the cells suspended in 0.5 ml of RNAprotect® Cell reagent (Qiagen, Germantown, MD) and stored at -80⁰C.
Qiagen RNeasy® Plus Mini Kits (Qiagen, Germantown, MD) were used to extract RNA according to manufacturer’s recommendations.  20 µl of 2 M dithiothreitol (DTT) was added per ml of kit buffer (RLT buffer) and 600 µl RLT buffer was used for each sample.  RNA quality (260/280 absorption ratio of 1.8-2.1) and concentration was assessed in 96 well plates using a BioTek Synergy HT microplate reader (BioTek Instruments Inc., Winooski, VT) and  Gen5 2.05 software accounting for path length correction.

tag: donor population name

tag: donor sex

value: M

tag: passage number

tag: experimental start date batch

tag: chip run batch

tag: overall batch

tag: population doubling level


title: Plus16h_Rep2

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with vehicle 16h
GeneCounts.xlsx

source_name: +4OHT + Vehicle 16h

tag: cell line


title: 1-670-1-MB49-cdTu-RNA-RNS_GAGATTC-ATAGAGG

tag: sample type

tag: injected cell line


title: Plus16h_Rep1


title: Ouabain36h_Rep3

description:
mRNA expression profile of senescent IMR90 ER:RAS treated with Ouabain 36h
GeneCounts.xlsx

source_name: +4OHT + Ouabain 36h


title: 42-621-2-BBN963-cdTu-DNA-WES_GACTAGT

tag: tissue


title: LB10-0489S

description: RNA extracted from normal lung tissue of patient

tag: histology

value: LUAD

tag: gender

value: Male

tag: age

value: Normal

tag: tumor stage

tag: recurrence

tag: vital status


title: HUCPVC-male-P11-biological rep2

source_name: male HUCPVCs at end of P11

tag: donor population name


title: DEL1 Hx

description: RNA extracted from NLUCAT1 CRISPR/Cas9-deleted A549 clones cultured in hypoxia (replicate 1)

source_name: DEL1 Hx

tag: rin number

tag: genotype/variation

tag: culture conditions


title: Plus16h_Rep3

tag: imr90 passage

tag: days after 4oht induction


title: 41-621-1-BBN963-cdTu-DNA-WES_GCCAAGA


title: 6-621-2-BBN963-cdTu-RNA-RNS_GAGATTC-CAGGACG


title: HUCPVC-male-P10-biological rep2

source_name: male HUCPVCs at end of P10

tag: donor sex

tag: passage number

tag: experimental start date batch

tag: chip run batch

tag: overall batch

tag: population doubling level


title: Ouabain36h_Rep1

tag: cell line


title: LB06-0610L

description: RNA extracted from Lung Adenocarcinoma (LUAD) patient

tag: tissue

tag: histology

tag: gender

tag: age

tag: sample type

value: IA

value: No

value: Alive