title: WT1_ProB

city: Cincinnati

first: Ramesh

middle: Chandra

last: Nayak

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

description:
Ovation RNA-seq System v2 (NuGEN)
WT B-cell progenitors isolated from chimaric mice at 2 months post secondary transplantation, Exp#1

data_processing:
FASTQ sequence files were aligned to the mouse genome mm10 using TopHat (BowTie 2), and the abundance of gene expression was evaluated using Cufflinks.
To identify differentially expressed genes using default parameters moderated t-test, raw p-value cut-off of 0.05, and an expression cut-off of 1.2-fold using AltAnlayze v2.1.0 (developed at Cincinnati Children's Hospital Medical Center) using database EnsMart72  . The Gene ontology pathway analyses and heatmaps were generated using Altanalyze v2.1.0 software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with cufflinks output

source_name: WT B-cell progenitors

growth_protocol: At around 2 months post secondary transplantation WT chimeric mice developed B-ALL symptoms characterized by head and neck tumors, hind limb paralyses, massive eggress of B cell precursors into peripheral blood. The sick and moribund mice at this stage were euthanized with carbon dioxide and cervcal dislocation. aPKC deficient (DKO) chimeric mice 2 months post tranplantation were did not show any such symptoms, and euthanized with carbon dioxide and cervical dislocation. BM cell from both the WT and DKO chimeric mice were obtained by crushing the tibiae, femurs and pelvis bones, and low density bone marrow (LDBM) cells were isolated by using ficoll gradient separation (Histopaque-1083, Sigma-Aldrich). LDBM cells were stained with CD45.2-FITC, B220-APC-Cy7, CD11b-PE, CD3e-PE, IgM-APC, CD43-PE-Cy7. Antibody treatment was carried out on ice. Leukemic B cell precursors (CD45.2+ CD11b-CD3e-B220+IgM-CD43+) were sorted at purity using a FACSAreaII cell sorter (BD Biosciences)

extract_protocol:
50,000 BCR-ABL+ B cell precursors were isolated from the BM of WT and aPKC DKO chimeric secondary recipients using FACSAreaII cell sorter. Cells were washed with phsphate buffered saline, and lyzed in RLT solution (QIAGEN RNAeasy Mini Kit, Cat#74104), and processed as per manufacturer's instruction. Total RNA was isolated using the column provided by the manufacturer. RNA samples from three independent samples from each WT and aPKC DKO group in a similar manner to ensure reproducibility and allow statistical analyses. RNA quality and quantity were evaluated using Agilent Bioanalyzer, and then processed for retro-transcription, linear amplification and cDNA library generation.
RNA Seq libraries were generated using Illumina Nextera XT DNA Sample Preparation kit and analyzed using paired-end 75 nucleotide sequencing on one HiSeq 2500 (Illumina).

tag: genetic background

value: Scl-tTA-TRE;p210-BCR-ABL;Mx1 Cre; WT

value: bone marrow


title: WT3_ProB

status: Public on Oct 10 2018

type: SRA

state: Ohio

country: USA

institute: Cincinnati Children's Hospital Medical Center

description:
Ovation RNA-seq System v2 (NuGEN)
WT B-cell progenitors isolated from chimaric mice at 2 months post secondary transplantation, Exp#3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: tissue

tag: cell type


title: DKO1_ProB

description:
Ovation RNA-seq System v2 (NuGEN)
aPKC DKO B-cell progenitors isolated from chimaric mice at 2 months post secondary transplantation, Exp#1

source_name: aPKC DKO B-cell progenitors


title: BERG: 31488

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: breed

value: Bergamasco

value: whole blood


title: ES-2 siC rep3

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
DE_ES2_C_vs_IMP1_all.csv
DE_ES2_C_vs_SRF_all.csv

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

organism: Homo sapiens

source_name: ovarian cancer derived cell line

growth_protocol: ES-2 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
1µg of total RNA served as input for rRNA depletion using RiboCop v1.2 (Lexogen). NEBNext Ultra Directional RNA Library kit (NEB) was used for library generation. Sequencing was performed on the Illumina NextSeq 500 platform

treatment_protocol: 72 hours upon transfection cells were harvested for RNA extraction.

tag: cell line

tag: sirna

value: Control siRNA

tag: passages

value: harvested 72h upon transfection


title: WT2_ProB

description:
Ovation RNA-seq System v2 (NuGEN)
WT B-cell progenitors isolated from chimaric mice at 2 months post secondary transplantation, Exp#2


title: NEAP: 31478

value: Neapolitan Mastiff


title: BERG: 31487


title: MARM: 31471

value: Maremma


title: NEAP: 31474


title: NEAP: 31475


title: MARM: 31470


title: DKO2_ProB

description:
Ovation RNA-seq System v2 (NuGEN)
aPKC DKO B-cell progenitors isolated from chimaric mice at 2 months post secondary transplantation, Exp#2


title: H8A_medCor2

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description: Single cell transcriptome from E18.5 mouse medial neocortex

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the mouse genome (build mm10 from UCSC Genome Browser) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: sample name, gene ID, and log2(FPKM) values for each single cell

source_name: medial neocortex

growth_protocol: Mice were maintained in pathogen-free conditions at the animal facility of the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany. All experiments were performed in accordance with German animal welfare legislation and were overseen by the Institutional Animal Welfare Officer. Timed-pregnant C57BL/6J females (E18.5) were used.

extract_protocol:
Single cell isolation and cDNA generation using Fluidigm C1 platform with reagents provided by Fluidigm as well as the SMARTer v4 Ultra Low RNA kit for Illumina (Clontech)
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

treatment_protocol: Medial neocortices from 8 embryonic mice were microdissected under a stereomicroscope and pooled to generate a single cell suspension using the Miltenyi Neural Tissue Dissociation kit according to the manufacturer’s instructions.

tag: strain

tag: developmental stage

tag: Sex

value: female

value: microdissected medial neocortex


title: DKO4_ProB

description:
Ovation RNA-seq System v2 (NuGEN)
aPKC DKO B-cell progenitors isolated from chimaric mice at 2 months post secondary transplantation, Exp#3


title: SC_Cfp1_IP

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

library_source: genomic

data_processing:
ChIP-seq raw reads were aligned to mouse mm9 genome using Bowtie2 (v2.2.9).
SAMtools (v1.2) was used for the data arrangement.
ChIP-seq peaks were called using the following MACS2 (v2.1.0) parameters: -B --nomodel -f BAM -g mm -p 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: The bedGraph files were generated using MACS2

source_name: mouse spermatocytes

growth_protocol: Mouse spermatocytes were freshly isolated from P21 mouse testes.

extract_protocol:
testes were harvested from anesthetized C57BL/6 mice and mechanically dissociated. Seminiferous tubules were removed, minced, and incubated Krebs-Ringer bicarbonate media (EKRB) containing 0.5mg/ml collagenase at 33°C for 1 hour. After removal of extra non-germ cells, dissociated seminiferous tubules were further digested with EKRB containing 0.5mg/ml trypsin and 1µg/ml DNase I at 33°C for 15 min. After washing and centrifugation, cell pellets were resuspended in EKRB containing 1µg/ml DNase I and 0.5% (w/v) BSA. After centrifugation, cells were resuspended in EKRB/0.5% BSA and passed through a cell strainer. Spermatocytes were then isolated using a method of sedimentation velocity at unit gravity at 5°C. Cells suspended in EKRB/0.5% BSA were loaded onto a sedimentation chamber and flow was applied (10ml/min).
ChIP-Seq libraries were produced using Truseq ChIP Sample kit (Illumina) according to manufacturer’s instruction.

tag: age

value: Testes

value: Spermatocytes

tag: chip antibody

value: Cfp1 (BETHYL, A303-161A)


title: H6A_medCor2


title: MARM: 31468


title: MARM: 31466


title: MARM: 31467


title: H5A_medCor2


title: H4A_medCor2


title: NEAP: 31477


title: MARM: 31465


title: H3A_medCor2


title: MARM: 31464


title: SC_Input


title: NEAP: 31479


title: MARM: 31461


title: MARM: 31463


title: NEAP: 31476


title: H2A_medCor2


title: MARM: 31462


title: H12B_medCor2


title: H1A_medCor2


title: MARM: 31460


title: MARM: 31459


title: G8B_medCor2


title: H10A_medCor2


title: G7A_medCor2


title: MARM: 31458


title: G8A_medCor2


title: G5B_medCor2


title: MARM: 31457


title: MANN: 31456

value: Mannara's Dog


title: MANN: 31455


title: G4B_medCor2


title: G5A_medCor2


title: G3B_medCor2


title: MANN: 31451


title: G3A_medCor2


title: MANN: 31454


title: MANN: 31450


title: G2B_medCor2


title: MANN: 31448


title: G2A_medCor2


title: G1A_medCor2


title: MANN: 31447


title: MANN: 31445


title: G12B_medCor2


title: MANN: 31441


title: F9A_medCor2


title: G11A_medCor2


title: MANN: 31443


title: G11B_medCor2


title: F8B_medCor2


title: LAGO: 31440

value: Lagotto Romagnolo


title: LAGO: 31439


title: F8A_medCor2


title: LAGO: 31438


title: F7A_medCor2


title: LAGO: 31436


title: F4A_medCor2


title: F5A_medCor2


title: LAGO: 31433


title: LAGO: 31435


title: MANN: 31446


title: F3A_medCor2


title: F3B_medCor2


title: MANN: 31444


title: LAGO: 31432


title: G10B_medCor2


title: F1A_medCor2


title: LAGO: 31431


title: LAGO: 31429


title: LAGO: 31427


title: F12A_medCor2


title: F10B_medCor2


title: LAGO: 31428


title: E8B_medCor2


title: E9A_medCor2


title: E8A_medCor2


title: F6A_medCor2


title: LAGO: 31425


title: LAGO: 31422


title: F11A_medCor2


title: LAGO: 31437


title: F2A_medCor2


title: LAGO: 31421


title: LAGO: 31424


title: E7B_medCor2


title: LAGO: 31426


title: E5A_medCor2


title: ITGY: 31419

value: Italian Greyhound


title: E4A_medCor2


title: E3A_medCor2


title: E2A_medCor2


title: ITGY: 31414


title: E11B_medCor2


title: ITGY: 31415


title: ITGY: 31412


title: ITGY: 31411


title: ITGY: 31413


title: ITGY: 31410


title: ITGY: 31409


title: D9B_medCor2


title: E10A_medCor2


title: E11A_medCor2


title: D8A_medCor2


title: ITGY: 31406


title: D9A_medCor2


title: E6A_medCor2


title: ITGY: 31407


title: ITGY: 31403


title: ITGY: 31404


title: D7A_medCor2


title: D6A_medCor2


title: ITGY: 31405


title: D4B_medCor2


title: LAGO: 31420


title: D5B_medCor2


title: CIRN: 31394

value: Cirneco dell'Etna


title: CIRN: 31393


title: D4A_medCor2


title: CIRN: 31392


title: D2B_medCor2


title: D3B_medCor2


title: D2A_medCor2


title: D12A_medCor2


title: D12B_medCor2


title: CIRN: 31389


title: ITGY: 31408


title: CIRN: 31386


title: CIRN: 31385


title: CIRN: 31387


title: C8B_medCor2


title: CASD: 31382

value: Central Asian Sheepdog


title: CIRN: 31384


title: C5A_medCor2


title: C6B_medCor2


title: CASD: 31381


title: CAUC: 31380

value: Caucasian Shepherd


title: C4B_medCor2


title: C4A_medCor2


title: C5B_medCor2


title: CAUC: 31379


title: C3A_medCor2


title: CAUC: 31376


title: C2B_medCor2


title: CAUC: 31374


title: CIRN: 31390


title: CAUC: 31373


title: LUPO: 31372

value: Lupo Italiano


title: D11A_medCor2


title: C11A_medCor2


title: C11B_medCor2


title: LUPO: 31368

value: whole blood


title: LUPO: 31369


title: B9A_medCor2


title: LUPO: 31365


title: LUPO: 31363


title: B5A_medCor2


title: B5B_medCor2


title: B6B_medCor2


title: B7A_medCor2


title: B3A_medCor2


title: LUPO: 31366


title: LUPO: 31360


title: LUPO: 31364


title: LUPO: 31358


title: LUPO: 31359


title: B1A_medCor2


title: B2A_medCor2


title: B12A_medCor2


title: B4A_medCor2


title: LUPO: 31362


title: A8B_medCor2


title: C12A_medCor2


title: LUPO: 31357


title: LUPO: 31356


title: A8A_medCor2


title: A7A_medCor2


title: LUPO: 31354


title: LUPO: 31355


title: A6A_medCor2


title: A5B_medCor2


title: LUPO: 31361


title: LUPO: 31353


title: LUPO: 31352


title: A5A_medCor2


title: LUPO: 31350


title: LUPO: 31351


title: A4A_medCor2


title: LUPO: 31349


title: A12A_medCor2


title: LUPO: 31347


title: CANE: 31344

value: Cane Corso


title: LUPO: 31346


title: A4B_medCor2


title: A3A_medCor2


title: CANE: 31342


title: A11A_medCor2


title: LUPO: 31348


title: A1A_medCor2


title: A11B_medCor2


title: A10A_medCor2


title: H9B_medCor1


title: CANE: 31338


title: H8A_medCor1


title: H7B_medCor1


title: CANE: 31333


title: CANE: 31336


title: H4B_medCor1


title: H6B_medCor1


title: CANE: 31332


title: CANE: 31331


title: H3B_medCor1


title: H4A_medCor1


title: CANE: 31330


title: BRAC: 31327

value: Bracco Italiano


title: H1B_medCor1


title: BRAC: 31326


title: H11B_medCor1


title: G9B_medCor1


title: H10A_medCor1


title: CANE: 31328


title: BRAC: 31323


title: CANE: 31337


title: BRAC: 31322


title: G8B_medCor1


title: G9A_medCor1


title: BRAC: 31321


title: CANE: 31329


title: G8A_medCor1


title: BRAC: 31320


title: BRAC: 31324


title: BRAC: 31319


title: BOLO: 31318

value: Bolognese


title: G4A_medCor1


title: BRAC: 31325


title: BOLO: 31317


title: BOLO: 31316


title: G3B_medCor1


title: H3A_medCor1


title: BOLO: 31315


title: BOLO: 31314


title: G3A_medCor1


title: G2A_medCor1


title: G7B_medCor1


title: BOLO: 31311


title: BOLO: 31312


title: G1B_medCor1


title: Control14

type: RNA

city: New York

first: Emma

last: Guttman

state: New York

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mt. SInai

description:
control skin sample
N21

hyb_protocol: The labeled target was fragmented and hybridized to probe arrays, using Encore Biotin Module from NuGen (San Carlos, Calif).

scan_protocol: The chips were washed, stained with streptavidin-phycoerythrin, and scanned (HP GeneArray Scanner; Hewlett-Packard Company, Palo Alto, Calif) On each chip, the human housekeeping genes β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) served as controls. Suite 5.0 software normalized the expression level values using these controls.

data_processing:
Affymetrix CEL files for the HGU133Plus2.0 chips were scrutinized for spatial artifacts using the Harshlight package. Classic microarray quality control was obtained by the Bioconductor’s array Quality Metrics package.
Expression measures obtained using GCRMA algorithm (using GCRMA package from R package/Bioconductor). To follow normality assumptions required by most statistical methods used, the expressions were log2-transformed

label: biotin

source_name: control skin sample

label_protocol: DNA was removed with on-column DNAse digestion by the Qiagen RNAse-free DNAse Set. Total RNA (50 ng) was reverse transcribed and amplified with Ovation Whole Blood Solution from NuGen (San Carlos, Calif).

extract_protocol: Total RNA was extracted by using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, Calif), and DNA was removed with the Qiagen RNAse-free DNAse Set.

value: skin

tag: diagnosis

value: Normal

tag: phenotype


title: BOLO: 31310


title: Control11

description:
control skin sample
N13


title: Control13

description:
control skin sample
N18


title: BOLO: 31309


title: BOLO: 31307


title: BOLO: 31306


title: BOLO: 31308


title: G12B_medCor1

value: female

value: microdissected medial neocortex


title: G12A_medCor1


title: G11B_medCor1


title: BOLO: 31303


title: G10B_medCor1


title: BOLO: 31302


title: BOLO: 31313


title: BOLO: 31304


title: Control8

description:
control skin sample
N8


title: Control9

description:
control skin sample
N11


title: Control7

description:
control skin sample
N5


title: Control12

description:
control skin sample
N17


title: BOLO: 31300


title: G10A_medCor1


title: Control6

description:
control skin sample
182-ACS


title: F9B_medCor1


title: Control5

description:
control skin sample
140-ACS


title: BOLO: 31305


title: Control10

description:
control skin sample
N12


title: Control4

description:
control skin sample
135-ACS


title: F7A_medCor1


title: F7B_medCor1


title: F8A_medCor1


title: F8B_medCor1


title: F6B_medCor1


title: Control3

description:
control skin sample
134-ACS


title: F6A_medCor1


title: Control2

description:
control skin sample
133-ACS


title: F2A_medCor1


title: F1B_medCor1


title: F4B_medCor1


title: F10A_medCor1


title: F12A_medCor1


title: E9B_medCor1


title: E8B_medCor1


title: E8A_medCor1


title: E7B_medCor1


title: Control1

description:
control skin sample
090-CB CS


title: E7A_medCor1


title: E6A_medCor1


title: Ich_LI2

description:
ichthyosis LI skin sample
012-ARCI

source_name: ichthyosis LI skin sample

value: Ichthyosis

value: Lamellar


title: F10B_medCor1


title: Ich_LI4

description:
ichthyosis LI skin sample
020-ARCI


title: Ich_LI5

description:
ichthyosis LI skin sample
022-LI

value: LI


title: Ich_EI5

description:
ichthyosis EI skin sample
019-EI

source_name: ichthyosis EI skin sample

value: Epidermolytic


title: Ich_NS3

description:
ichthyosis NS skin sample
MM-14

source_name: ichthyosis NS skin sample

value: Netherton


title: E5B_medCor1


title: Ich_LI6

description:
ichthyosis LI skin sample
CMH135.14_IC-PI


title: Ich_CIE6

description:
ichthyosis LI skin sample
026-CIE

value: CIE


title: Ich_CIE3

description:
ichthyosis CIE skin sample
009-ARCI

source_name: ichthyosis CIE skin sample


title: Ich_CIE2

description:
ichthyosis CIE skin sample
007-ARCI

value: CIE - very mild - CerS


title: Ich_EI3

description:
ichthyosis EI skin sample
008-EI


title: Ich_LI3

description:
ichthyosis LI skin sample
017-ARCI


title: Ich_CIE5

description:
ichthyosis CIE skin sample
018-ARCI


title: E5A_medCor1


title: Ich_EI4

description:
ichthyosis EI skin sample
014-EI


title: E4B_medCor1


title: E6B_medCor1


title: Ich_LI1

description:
ichthyosis LI skin sample
005-ARCI


title: Rho_KO_S1P_1

city: SAN DIEGO

first: Olivia

last: Yu

state: California

address: 9420 Athena Cir, La Jolla

institute: LJI

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human hg19 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: hg19
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: Rho knock out treated with S1P

extract_protocol:
1. Rinse cell monolayer with ice cold PBS once. Lyse cells directly in a culture dish by adding 1 ml of TRIZOL Reagent per 3.5 cm diameter dish and scraping with cell scraper. Pass the cell lysate several times through a pipette. Vortex thoroughly. The amount of TRIZOL reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present. An insufficient amount of TRIZOL Reagent may result in DNA contamination of the isolated RNA.
2. Add 0.2 ml of chloroform per 1 ml of TRIZOL Reagent. Cap sample tubes securely. Vortex samples vigorously for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 4C. Following centrifugation, the mixture separates into lower red, phenolchloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. Transfer upper aqueous phase carefully without disturbing the interphase into fresh tube.
3. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15C for 10 minutes and centrifuge at not more than 12,000 x g for 10 minutes at 4C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
4. Remove the supernatant completely. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIZOL Reagent used for the initial homogenization. Mix the samples by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 4C. Repeat above washing procedure once. Remove all leftover ethanol.
5. Air-dry or vacuum dry RNA pellet for 5-10 minutes. Do not dry the RNA pellet by centrifuge under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip.
https://support.illumina.com/content/dam/illumina-support/documents/myillumina/f5f619d3-2c4c-489b-80a3-e0414baa4e89/truseq_dna_sampleprep_guide_15026486_c.pdf

value: human glioblastoma cell line (1321N1)

value: Rho KO

tag: treatment


title: E4A_medCor1


title: Rho_KO_S1P_2


title: Ich_NS2

description:
ichthyosis NS skin sample
010-NS


title: Ich_CIE4

description:
ichthyosis CIE skin sample
013-ARCI


title: E3B_medCor1


title: MRTFA_KO_S1P_3

source_name: MRTFA knock out treated with S1P

value: MRTFA KO


title: E1A_medCor1


title: Ich_NS1

description:
ichthyosis NS skin sample
004-ARCI


title: E12A_medCor1


title: E11A_medCor1


title: MRTFA_KO_S1P_2


title: MRTFA_KO_S1P_1


title: Ich_EI2

description:
ichthyosis EI skin sample
006-EI


title: Ich_EI1

description:
ichthyosis EI skin sample
001-EI


title: MRTFA_KO_untreated_2

source_name: MRTFA knock out Untreated

value: Untreated


title: E10A_medCor1


title: MRTFA_KO_untreated_1


title: Ich_CIE1

description:
ichthyosis CIE skin sample
003-ARCI


title: D9B_medCor1


title: E12B_medCor1


title: D9A_medCor1


title: YAP_KO_S1P_3

source_name: YAP knock out treated with S1P

value: YAP KO


title: EKOD2_S

city: Beijing

first: Zeming

last: Zhang

address: 38 Xueyuan Rd , Haidian District,Beijing,China

country: China

institute: Institude of Systems Biomedicine

data_processing:
RNA sequencing libraries were sequenced on an Illumina HiSeq X Ten platform.
Illumina Casava1.8 software used for basecalling.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 83) using HISAT2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample

source_name: Spleen

extract_protocol:
Spleen were thrown into Trizol reagent followed by vortexing to exract total RNA. NEBNext Ultra RNA Library Prep Kit for Illumina was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

value: 10 weeks old

tag: time

value: day 2


title: YAP_KO_S1P_2


title: D8B_medCor1

value: female


title: EKOD0_S

value: day 0


title: D7B_medCor1

value: microdissected medial neocortex


title: D7A_medCor1


title: YAP_KO_S1P_1


title: WTD2_S

value: wild type


title: MRTFA_KO_untreated_3


title: YAP_KO_untreated_3

source_name: YAP knock out Untreated


title: E10B_medCor1


title: WTD0_S


title: YAP_KO_untreated_2


title: D6B_medCor1


title: EKOD2_BM

data_processing:
RNA sequencing libraries were sequenced on an Illumina HiSeq X Ten platform.
Illumina Casava1.8 software used for basecalling.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 83) using TopHat2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample

source_name: Bone marrow

extract_protocol:
Bone marrow tissues were resuspended by Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow


title: YAP_KO_untreated_1


title: D6A_medCor1


title: EKOD0_BM


title: D5A_medCor1


title: WTD2_BM


title: D4B_medCor1


title: WTD0_BM


title: WT_S1P_2

source_name: Wild type treated with S1P


title: WT_S1P_1


title: Lentiviruses expressing PC2 rep3

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: Lentiviruses expressing PC2

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: knee joints

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: An OA mouse model was generated as previously described. Briefly, anterior cruciate ligament transection (ACLT) was performed on male C57BL/6 mice aged 8 weeks. For the ACLT surgery, after opening the joint capsule, the ACL was transected with microscissors under a surgical micro-scope. One week after surgery, lentiviruses expressing Luc, PC2 were injected into the articular cavity. Eight weeks after lentivirus injection, the mice were euthanized and the joints were collected for RNA extraction. The RNA samples of one treatment group were mixed and three technical repeats were performed for RNA-seq.

value: knee joints

value: Lentiviruses expressing PC2


title: WT_untreated_3

source_name: Wild type Untreated


city: Zibo

first: Peiqing

last: Zhao

address: 54# Gongqingtuan Road

department: Center of Translational Medicine

institute: Zibo Central Hospital

description:
Gene expression data from HeLa cells transfected with control vector
E4384-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeView. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HeLa cell line transfected with control vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Hela cells were cultured in DMEM for 24h, and then transfected with lentiviral vetors

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HeLa cells were transfected with TIPE1 or control vector

value: HeLa

tag: transfection

value: control


title: D3A_medCor1

source_name: medial neocortex


title: D2B_medCor1


title: Lentiviruses expressing PC2 rep2

description: Lentiviruses expressing PC2


title: D2A_medCor1


title: Lentiviruses expressing PC2 rep1

description: Lentiviruses expressing PC2


title: WT_untreated_1

value: human glioblastoma cell line (1321N1)

tag: genotype


title: D1B_medCor1

tag: tissue


title: Lentiviruses expressing Luc_rep3

description: Lentiviruses expressing Luc

value: Lentiviruses expressing Luc


title: Lentiviruses expressing Luc_rep2

description: Lentiviruses expressing Luc


title: D12A_medCor1


title: day2

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

description: cell sorted through magnetic beads separation then by flow cytometry

data_processing:
Single cell RNA-seq data were processed using Cell Ranger v1.3.1, which provides a data matrix for all genes and all cells
Genome_build: hg19
Supplementary_files_format_and_content: hdf5 matrx file that contains the UMIs of all genes and all cells

source_name: Umbilical Cord blood

extract_protocol:
Viable cell suspensions of VPA treated hematopoietic stem cells at various time points were isolated and characterized using standard DAPI staining to determine viability. The bulk cellular suspensions were then characterized to determine cell density using a C-Chip DHC-N01 disposable hemocytometer.  A mixture of 5μl of 0.04% trypan blue (BioRad) and 5μl of the single cell suspension was loaded unto the hemocytometer and examined at 10X magnification, using the Invitrogen Evos FL Cell Imaging System-digital inverted microscope prior to loading on the 10X Genomics Chromium platform for cDNA generation.  The Chromium system was used as a microfluidic platform for 3’ gene expression profiling of approximately 1528 to 4921 individual cells per Illumina HiSeq 2500 lane.  Prior to sequencing, the high diversity barcoding was conducted using standard manufacturer’s protocol to separately index each cell’s mRNA transcriptome using unique 3’-end tags using gel emulsion chemistry. Illumina paired-end sequencing libraries were then generated and sequenced from the fragments and the barcodes were leveraged to for differential expression analyses.
Reverse-transcription was performed in the emulsion and cDNA was amplified before library construction (see Zheng et al., 2017 PMID: 28091601). Quality control and quantification of the amplified cDNA were assessed using the High-Sensitivity DNA Bioanalyzer kit. Library quality control and quantification were evaluated.
GEM Drop-Seq, Chromium™ Single Cell 3’ Library & Gel Bead Kit v1

tag: cell type

value: CD34+ Hematopoietic stem cell

tag: culture condition

value: stemline Media (sigma)

tag: cytokine cocktail

value: Thrombopoietin(100ng/ml), FLT-3(100ng/ml), IL-3(50ng/ml), SCF(150ng/ml)

tag: valproic acid 1mm stimulation


title: HeLa cells transfected with TIPE1

description:
Gene expression data from HeLa cells transfected with TIPE1
E4385-1

source_name: HeLa cells transfected with TIPE1

tag: cell line

value: TIPE1 lentiviral vector


title: WT_S1P_3


title: D10B_medCor1

tag: strain


title: D10A_medCor1

tag: developmental stage


title: Non surgery rep3

description: Non surgery

value: Non surgery


title: C9B_medCor1

tag: Sex


title: day4_vpa_set1

description:
cell sorted through flow cytometry
featureCounts.txt

data_processing:
The RNA-seq fastq files were aligned with STAR v2.5.1b with the human genome gencode annotation release 24
featureCounts v1.5.0-p1 is used to summarize the reads for all genes and samples
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file including the counts of reads for each samples

extract_protocol:
Cultured Cells were harvested and CD34+ were sorted through flow cytometry. Total RNA are harvested using the Rneasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols with Ribozero depletion


title: day4_vpa_set2


title: Non surgery rep2

description: Non surgery


title: day4_vpa_set3


title: C9A_medCor1


title: C8B_medCor1


title: day4_ctrl_set3


title: WT_untreated_2

value: Untreated


title: Non surgery rep1

description: Non surgery


title: Rbf replicate 3

city: Chicago

first: Majd

middle: Maher

last: Ariss

state: IL

address: 900 S Ashland Ave rm. 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description:
single cell RNA
Single cell RNA-seq was performed using Drop-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against Drosophila melanogaster genome version BDGP6 (From Ensembl) and corresponding gene modle is extracted from Ensembl version 90.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Genome_build: BDGP6
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell

organism: Drosophila melanogaster

source_name: Third instar eye discs

extract_protocol:
Third instar eye discs from WT and rbf120a mutants were dissociated into single cells using a combination of Trypsin and Collagenase. We then performed Drop-seq on the single cell suspension
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)
single cell RNA-seq

value: eye disc

value: wandering third instar larvae

tag: genotypes


title: day0

description: cell sorted through magnetic beads separation then by FACS sorting


title: Rbf replicate 2


title: C8A_medCor1

value: female

value: microdissected medial neocortex


title: C7B_medCor1


title: Lentiviruses expressing Luc_rep1

description: Lentiviruses expressing Luc


title: day2_vpa_set2


title: WT replicate 11

value: WT


title: Rbf replicate 1


title: C5B_medCor1


title: C6B_medCor1


title: WT replicate 9


title: WT replicate 10


title: day2_vpa_set1


title: day2_ctrl_set3


title: day4_ctrl_set1


title: day2_ctrl_set2


title: WT replicate 8


title: day4_ctrl_set2


title: C7A_medCor1


title: day2_vpa_set3


title: day2_ctrl_set1


title: WT replicate 7


title: C3A_medCor1


title: C3B_medCor1


title: day0_set3

description:
cell sorted through magnetic beads separation then by flow cytometry
featureCounts.txt


title: WT replicate 6


title: day0_set2

description:
cell sorted through magnetic beads separation then by FACS sorting
featureCounts.txt


title: Ich_LI7

description:
ichthyosis LI skin sample
NUTC 346.14

source_name: ichthyosis LI skin sample

value: skin

value: Ichthyosis

value: Lamellar

tag: age


title: WT replicate 4


title: C1B_medCor1


title: C2A_medCor1


title: WT replicate 5


title: day0_set1


title: WT replicate 3


title: C1A_medCor1


title: SetD5Wt_RNA_polyA_rep5

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
RNA-Seq. Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR .Mapped data were analyzed with HOMER's "analyzeRepeats.pl" function with options -raw -condenseGenes and -count exons. Differential expression was performed using Homer's getDiffExpression.pl function, which uses DESeq2.
DiffOutput_SetD5Neurons.csv

data_processing:
All data were aligned to the mm10 assembly of the mouse genome, and all subsequent data analysis was performed using HOMER, and detailed instructions for analysis can be found at http://homer.salk.edu/homer/ . Mapped data were analyzed with HOMER's "analyzeRepeats.pl" function with options -raw -condenseGenes and -count exons. Differential expression was performed using Homer's getDiffExpression.pl function, which uses DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: DiffOutput file contains DESeq2 output for comapring WT to SetD5 +/- neurons. Table include calculated fold changes and adjusted p-values, as well as rlog normalized expression vaues of each gene for each sample.

molecule: polyA RNA

source_name: CD24+ CD45- neuronal cells  isolated from E18.5 mouse fetuses

extract_protocol:
Primary cortical neurons from E18.5 fetuses were extracted as described previously (Beaudoin 2012). Once in single cell suspension, they were stained with pan-neuronal marker CD24 and hematopoietic marker CD45 and sorted by fluorescence-activated cell sorting. Cells were frozen in 2× DTBB buffer (1 M Tris·HCl, 8 M LiCl, 0.5 M EDTA, 1% lithium dodecyl sulfate, and 0.1% Triton X100) + 5mM DTT and stored at -80°C prior to library preparation.
PolyA RNA was first selected from total RNA using magnetic oligo(dT)25 Dynabeads (Life Technologies) and multiple washes with 2× DTBB buffer (1 M Tris·HCl, 8 M LiCl, 0.5 M EDTA, 1% lithium dodecyl sulfate, and 0.1% Triton X100). Poly A enriched mRNA was fragmented in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primer (Invitrogen), 0.5 µL of Oligo dT primer (Invitrogen), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.2 µL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacturer’s instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 µL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a Hi-Seq 4000 (Illumina) using single-end 75bp reads.

value: CD24+ CD45- neuronal cells

value: wild type


title: C12B_medCor1


title: C11B_medCor1


title: WT replicate 2


title: SetD5Wt_RNA_polyA_rep4


title: WT replicate 1


title: SetD5Wt_RNA_polyA_rep3


title: B9B_medCor1


title: NTC

city: Umeå

first: Aman

last: Zare

state: Västerbotten

address: University Hospital, buildings 6 K and 6 L

department: Molecular Biology

country: Sweden

institute: Umeå university

data_processing:
Reads were merged using FLASH (1.2.11) and trimmed using Trimmomatic (0.36)
Reads were mapped against database (Green genes for 16S) using pick_open_reference_otus.py script from Qiime. (-r reference_seqs.fas_97)
Singletons were filtered using filter_otus_from_otu_table.py script from Qiime.
summarize taxa using summarize_taxa_through_plots.py script from Qiime
Rarefaction using alpha_rarefaction.py script from Qiime
Betadiversity using beta_diversity_through_plots.py script from Qiime (-e 10000)
Genome_build: The greengenes database (gg_13_5)
Supplementary_files_format_and_content: tab-delimited OTU table

organism: synthetic construct

source_name: blank

extract_protocol:
The DNA was isolated with phenol/chloroform extraction followed by ethanol precipitation
16S V3-V4 Metagenomic Sequencing Library Preparation guide (15044223B, Illumina) - Exception: 30 cycles of the amplicon PCR using  2.5µl of the extracted DNA as template

tag: feces source

tag: fly samples grow on this media

tag: temperature


title: SetD5Wt_RNA_polyA_rep2


title: genomic DNA from plasma cells (PCs) of PCL-046 at diagnosis

city: Rionero in Vulture, PZ

first: Giovanni

last: Calice

address: Via Padre Pio, 1

country: Italy

institute: IRCCS - CROB Centro di Riferimento Oncologico della Basilicata

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium HumanMethylation450 BeadChip array

scan_protocol: Arrays were scanned using Illumina HiScanSQ system, following standard recommended Illumina scanner setting

data_processing:
Illumina Infinium Human Methylation 450K raw data were imported to R/Bioconductor environment (https://www.r-project.org/,https://www.bioconductor.org/) for quality control. For graphic representation the methylation levels were expressed in terms of  Beta (β) value, that is the ratio between Methylated signal and the Methylated/Unmethylated signals sum (M / (M+U+offset)) (Du P. et al., BMC bioinformatics 2010). M-values were computed as log2 (Methylated/Unmethylated signals) and used for differential methylation analysis. Methylation probes with a detection p-value <0.05 were considered and the data were normalized by SWAN method (Maksimovic J. et al., Genome biology 2012), using minfi package (Aryee MJ., et al., Bioinformatics. 2014). Probes not associated to CpGs, measuring single nucleotide polymorphisms (SNPs) or localized on X and Y chromosomes were discarded.
The non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: highly purified PCs from a pPCL patient

label_protocol: Infinium HD Methylation Assay protocol

extract_protocol: DNA samples were extracted by the use a commercially available kit (Wizard Genomic DNA Purification kit, Promega) according to manufacturer’s protocol

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: subject id

value: bone marrow plasma cells

tag: pc dyscrasia

value: Primary plasma cell leukemia (pPCL)

tag: translocation

value: no main IgH-trx


title: genomic DNA from plasma cells (PCs) of PCL-043 at diagnosis

tag: tissue


title: BMSCs from 4 month HFD-fed rat  rep3

first: XIN

last: FU

address: 33 Ba-Da-Chu Road

department: Research Center

institute: Plastic Surgery Hospital (Institute), Peking Union Medical College & Chinese Academy of Medical Sciences

description: Gene expression data from BMSCs isolated from rat on a HFD for 4 month

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the  Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The BMSCs from rats were isolated by direct whole bone marrow plating and subsequent passage. Cells were cultured in BMSC growth medium consisting of low glucose dulbecco’s modified eagles medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 μg/ml streptomycin. Cells were maintained in atmosphere of 5% CO2 and 95% humidity. Colonies were observed after 4-6 days and reached 80% to 90% confluence in about 12-14 days, followed by regular passage every 3-4 days.

treatment_protocol: At 3 passages, BMSCs were detached from the plate with TryPLE (Life Technologies). After centrifuge, the supernanat was removed and cells pellets were rinsed with PBS and then resuspended in the Trizol solution (GibcoBRL).

tag: passage number

value: Passage 3

value: bone marrow

tag: cell type

value: Mesenchymal stem cells (MSCs)

value: 4 months


title: Ez-29-20d-IV

city: Pittsburgh

middle: R

last: Kennerdell

state: PA

address: 100 Technology Drive

department: Aging Institute

institute: University of Pittsburgh

data_processing:
Real-Time Analysis version 2.4.11 (Illumina, San Diego, CA) was used for base-calling and quality scoring.
The pooled libraries were sequenced on two sequencing runs of a Nextseq 500 (Illumina, San Diego, CA). The two runs are provided separately as "a" files and "b" files.  For each sample, we provide two raw demultiplexed fastq files and two processed data files to account for the multiple sequencing runs. In our analysis we combined the two runs using the collapseReplicates function in the DESeq2 package (Love, et al., PMID 25516281). Reads were mapped to the Drosophila genome dm6 (dmel_r6.15, Hoskins, et al., PMID 25589440) using STAR (version 2.5.2a, Dobin, et al., PMID 23104886) using the default parameters.
Mapped reads were summarized at the gene level using the htseq-count of the python package htseq (version 0.8.0), Anders, et al., (PMID 25260700), using transcript models obtained from the Flybase dmel_r6.15 gtf file (ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.15_FB2017_02/gtf/), while using exons as the feature type.
Genome_build: dm6
Supplementary_files_format_and_content: Processed data files are outputs from htseq-count.  A tab-delimited text file indicating the gene (first column) followed by the number of reads uniquely mapping to the corresponding gene for the given sample (second column). Each run was mapped and assigned separately, such that there are two fastq files and two htseq-count files for each sample.

source_name: brain

growth_protocol: The E(z) alleles E(z)[731] and E(z)[61] were backcrossed 5 generations into a w[1118] background (Bloomington stock 5905, FlyBaseID: FBst0005905), and matching w[1118] flies were used as controls. Flies were aged to 3 days or 20 days on standard molasses medium.

extract_protocol:
Flies were anesthetized using CO2, and then decapitated, followed by brain dissection. The brains of >21 male flies were dissected, carefully removing attached eye and trachael tissue in cold PBS. The PBS was then removed, and the remaining brains were ground in Trizol (Thermo Fisher Scientific, Waltham, MA) using a pellet pestle and frozen at -80 degrees C. Total RNA was purified from dissected brains using the Trizol protocol according to the manufacturer. Total RNA was cleaned of residual DNA using DNA-free (Invitrogen, Carlsbad, CA).  DNA-free reactions were then further purified using Rneasy columns (Qiagen, Germantown, MD) and RNA was eluted in DEPC-treated water. Purified total RNA was evaluated on a Bioanalyzer (Agilent, Santa Clara, CA). Total RNA was quantified using Qubit (Thermo Fisher Scientific, Waltham, MA).
Approximately 95-200 ng of total RNA was used for each library. RNA libraries were prepared for sequencing using TruSeq mRNA High Throughput Library Prep Kit according to the kit manual (Illumina, San Diego, CA).  Individual libraries were quantified with KAPA Library quant kit and pooled accordingly (KAPA Biosystems, Boston, MA). Before loading, the pooled library was quantified with Qubit (Thermo Fisher Scientific, Waltham, MA) and diluted accordingly. Libraries were sequenced in two runs of a Nextseq 500. Data from the two runs are provided separately as "a" files and "b" files.

treatment_protocol: Animals were cultivated and aged at either 25 degrees Celsius or 29 degrees Celsius as indicated.

value: E(z) mutations in BL5905 (FBst0005905) background

value: brain

tag: cultivation temperature

tag: genotype


title: SetD5Wt_RNA_polyA_rep1


title: B8B_medCor1

value: female


title: genomic DNA from plasma cells (PCs) of PCL-028 at diagnosis


title: B9A_medCor1

value: microdissected medial neocortex


title: BMSCs from 4 month HFD-fed rat  rep2

source_name: BMSCs isolated from rat on a HFD for 4 month


title: Ez-29-20d-III


title: Ez-29-20d-I


title: genomic DNA from plasma cells (PCs) of PCL-027 at diagnosis


title: Ez-29-20d-II


title: genomic DNA from plasma cells (PCs) of PCL-029 at diagnosis


title: SetD5Het_RNA_polyA_rep4

value: SetD5 Het


title: B5A_medCor1


title: Ez-25-20d-III


title: BMSCs from 4 month HFD-fed rat  rep1


title: genomic DNA from plasma cells (PCs) of PCL-038 at diagnosis


title: genomic DNA from plasma cells (PCs) of PCL-026 at diagnosis


title: B5B_medCor1


title: Ez-29-20d-V


title: B7A_medCor1


title: B3B_medCor1


title: Ez-25-20d-II


title: SetD5Het_RNA_polyA_rep1


title: BMSCs from 4 month ND-fed rat  rep3

description: Gene expression data from BMSCs isolated from rat on a ND for 4 month


title: B2B_medCor1


title: genomic DNA from plasma cells (PCs) of PCL-023 at diagnosis


title: Ez-25-20d-I


title: genomic DNA from plasma cells (PCs) of PCL-021 at diagnosis


title: genomic DNA from plasma cells (PCs) of PCL-020 at diagnosis


title: genomic DNA from plasma cells (PCs) of PCL-035 at diagnosis


title: w-29-20d-V


title: BMSCs from 4 month ND-fed rat  rep1

source_name: BMSCs isolated from rat on a ND for 4 month


title: genomic DNA from plasma cells (PCs) of PCL-004 at diagnosis


title: C4A_medCor1


title: B2A_medCor1


title: SetD5Het_RNA_polyA_rep2


title: w-29-20d-III


title: B1A_medCor1


title: B1B_medCor1


title: SetD5Het_RNA_polyA_rep3


title: BMSCs from 2 month HFD-fed rat  rep3

description: Gene expression data from BMSCs isolated from rat on a HFD for 2 month

value: 2 months


title: w-29-20d-IV


title: BMSCs from 4 month ND-fed rat  rep2


title: genomic DNA from plasma cells (PCs) of PCL-014 at diagnosis


title: SetD5Het_scRNASeq_rep1

description: scRNA-Seq generated using 10x genomics Single Cell 3’ Reagent Kits V2. Approximately 2500 cells per sample were sequened to a depth o 50,000 reads per cell. Data were aggregated using Cell Ranger software.

data_processing:
Data was mapped to the mouse mm10 genome and aggregated using Cell Ranger V2.1 (10X Genomics). Data was filtered, processed, and analyzed using the Seurat R toolkit version 2.3.0 for single cell genomics. Initial pre-processing thresholds were set to include genes detected in at least 3 cells and cells with at least 200 genes. Additional pre-processing was performed after plotting distributions of number of genes (nGenes), number of unique molecular identifiers (nUMI), and percent mitochondrial transcripts (percent.mito) per cell. The following thresholds were then applied: nGene > 600 and < 5000, nUMI > 500 and < 15000, and percent.mito < 0.06. A total of 6562 cells passed these thresholds and were used for downstream analyses. Data was then normalized using the NormalizeData function with parameters normalization.method = "LogNormalize",  scale.factor = 10000.  Variable genes were identified with the FindVariableGenes function with parameters mean.function = ExpMean, dispersion.function = LogVMR, x.low.cutoff = 0.0125, x.high.cutoff = 3, y.cutoff = 0.5, which identified 1548 variable genes. Data was then scaled using the ScaleData function, with the “vars.to.regress” argument including nUMI and percent.mito to remove these unwanted sources of variation. A total of 100 principal components were calculated from these variable genes using the function RunPCA. Selection of significant PCs to include in further analyses was determined using the JackStraw method with the num.replicate parameter set to 200, along with visualization of each PC using the PCHeatmap function. 61 total PCs with p < 1e-5 were included. Clusters were then identified using the FindClusters function with arguments reduction.type = "pca", dims.use = sigPCs, resolution = 0.6, which identified 14 clusters of cells. Quality control of clusters and samples was performed by plotting nGene and nUMI, which confirmed no major differences based on these parameters. The TSNEPlot function was used to generate t-SNE plots to visualize data by cluster and by sample of origin. Marker genes for each cluster was determined using the FindAllMarkers function with parameters only.pos = TRUE, min.pct = 0.25, and thresh.use = 0.25. Based on these marker genes, clusters 0, 1, 3, 4, 5, and 8 were selected for further analysis. A heatmap of the top 20 marker genes from these clusters was generated with function “DoHeatmap” with max.cells.per.ident set to 100. To identify genes with significantly different gene expression due to genotype within each cluster, the FindMarkers function was used arguments  min.pct = 0.1, logfc.threshold = 0.25, test.use = “MAST”. Data were converted from natural log to log2 fold change values prior to plotting, and X- and Y-linked transcripts were excluded from plots.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing gene expression for each cell. Column names indicate sample_barcode for single cell

extract_protocol:
Primary cortical neurons from E18.5 fetuses were extracted as described previously (Beaudoin 2012). Once in single cell suspension, they were stained with pan-neuronal marker CD24 and hematopoietic marker CD45 and sorted by fluorescence-activated cell sorting.
Single cell suspensions were loaded onto the 10X Genomics Chromium Controller instrument to generate single cell GEMs, targeting 5000 cells per sample. GEM-RT and library construction were performed following the 10X Genomics Protocol (Single Cell 3’ Reagent Kits V2). Library fragment size distributions was determined using an Agilent Bioanalyzer High Sensitivity chip, and library DNA concentrations were determined using a Qubit 2.0 Fluorometer (Invitrogen). Libraries were sequenced to a depth of approximately 50,000 paired end reads per cell using an Illumina HiSeq4000.

tag: 10x indices


title: SetD5Wt_scRNASeq_rep2

tag: strain


title: SetD5Het_scRNASeq_rep2


title: BMSCs from 2 month HFD-fed rat  rep2

source_name: BMSCs isolated from rat on a HFD for 2 month


title: genomic DNA from plasma cells (PCs) of PCL-019 at diagnosis


title: BMSCs from 2 month HFD-fed rat  rep1


title: SetD5Wt_scRNASeq_rep1


title: BMSCs from 2 month ND-fed rat  rep3

description: Gene expression data from BMSCs isolated from rat on a ND for 2 month


title: SetD5Het_RNA_polyA_rep5


title: w-29-20d-II


title: BMSCs from 2 month ND-fed rat  rep2

source_name: BMSCs isolated from rat on a ND for 2 month


title: w-29-20d-I


title: B10B_medCor1

description: Single cell transcriptome from E18.5 mouse medial neocortex

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the mouse genome (build mm10 from UCSC Genome Browser) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: sample name, gene ID, and log2(FPKM) values for each single cell

tag: developmental stage


title: B12A_medCor1

tag: Sex


title: B11B_medCor1


title: w-25-3d-I


title: IR1_UT_3

city: Beer Sheva

first: Jonathan

last: Zorea

address: Ben Gurion blvd

country: Israel

institute: Ben Gurion University

data_processing:
The function calcNormFactors () in the edgeR package has been used for normalization between samples in the quality controlled data
a negative binomial generalized linear model has been fitted, with gene-wise dispersions estimated using the Cox-Reid profile-adjusted likelihood method. Then, a likelihood ratio test has been employed to check differential expression (McCarthy et al., 2012). The dispersion estimation, model fitting and testing have been implemented using the functions estimateDisp(), glmFit () and glmLRT(), respectively, in the edgeR package
To interpret the testing results in a biological context, gene ontology (GO) enrichment analysis and KEGG pathway enrichment analysis have been employed as downstream procedures, using the functions goana () and kegga(), respectively, in the edgeR package
Genome_build: hg18
Supplementary_files_format_and_content: xlsx file contained the logFC for each gene.

extract_protocol:
RNA extracted following the Purelink RNA mini kit protocol (CAT. 12183018A, INVITROGEN)
500ng of total RNA were fragmented followed by reverse transcription and second strand cDNA synthesis. The DS-cDNA was subjected to end repair, A base addition, adapter ligation and PCR amplification to create libraries

tag: cell line

tag: type


title: w-25-3d-III

tag: age


title: w-25-20d-I


title: B10A_medCor1

extract_protocol:
Single cell isolation and cDNA generation using Fluidigm C1 platform with reagents provided by Fluidigm as well as the SMARTer v4 Ultra Low RNA kit for Illumina (Clontech)
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.


title: A9A_medCor1


title: A8B_medCor1


title: BMSCs from 1 month HFD-fed rat  rep2

description: Gene expression data from BMSCs isolated from rat on a HFD for 1 month

value: 1 month


title: A8A_medCor1


title: w-25-3d-II


title: w-25-20d-II


title: LPS03

city: Shanghai

first: Xiang

address: 320 Yue Yang Road

institute: Institute of Neuroscience, Chinese Academy of Sciences

data_processing:
The sequencing data were was processed with the 10X Cell Ranger v2.1.
Genome_build: mm10
Supplementary_files_format_and_content:  csv files contain per-gene, per-cell expression and were created using cellranger mat2csv

extract_protocol:
Single cells were captured and lysed on the 10x Chromium Controller instrument (10x Genomics).
Standard 10x Genomics scRNA-seq library construction protocol was used to construct the library

treatment_protocol: Mice were treated with saline or 10 mg/kg LPS for two hours.

value: post natal day 14

tag: treated with

value: 10 mg/kg LPS (i.p. injection)  for 2 hours

value: Hippocampus


title: A9B_medCor1


title: B12B_medCor1


title: BMSCs from 1 month HFD-fed rat  rep3

source_name: BMSCs isolated from rat on a HFD for 1 month


title: LPS02


title: IR1_UT_2


title: A7B_medCor1


title: IR1_UT_1


title: w-25-20d-III


title: A6A_medCor1


title: LPS01


title: BMSCs from 1 month ND-fed rat  rep2

description: Gene expression data from BMSCs isolated from rat on a ND for 1 month


title: BMSCs from 1 month ND-fed rat  rep1

source_name: BMSCs isolated from rat on a ND for 1 month


title: BMSCs from 1 month HFD-fed rat  rep1


title: IP_UT_3


title: BMSCs from 1 month ND-fed rat  rep3


title: A5B_medCor1


title: SA03

value: Saline (i.p. injection) for 2 hours


title: BMSCs from 2 month ND-fed rat  rep1


title: IP_UT_2


title: SA02


title: SA01


title: F2-25-25 rep4

data_processing:
SortMeRNA version 1.9 was used to filter out rRNA
Trimmomatic version 0.32 was used to remove adapter sequences and trim reads using SLIDINGWINDOW:5:20 MINLEN:50 and the TruSeq3-PE-2.fa adapter file
STAR_2.4.0f1 was used to map the reads against the reference genome; parameters: --outSAMstrandField intronMotif   --outSAMmapqUnique 254   --outFilterMultimapNmax 100   --alignIntronMax 11000   --chimSegmentMin 1
HTSeq 0.6.1 was used to count the reads per gene
edgeR was used for normalisation and differential expression
Genome_build: dm4
Supplementary_files_format_and_content: TPM values in txt format

source_name: whole fly

growth_protocol: Flies were cultivated in bottles with potato mash-yeast-agar medium in a humidified incubator at 18 or 25 °C on a 12/12 light cycle.

extract_protocol:
20 adult males (0-16 h) from both F1 and F2 for all temperatures and all combinations were collected. The RNA was isolated with TRI Reagent according to the manufacturer’s instructions (Thermo Fisher), treated with Baseline-Zero DNase (Epicentre) for 15 minutes at 37°C and purified with RNeasy MinElute Cleanup Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: generation

tag: f2 germ-line source

tag: f2 microbiome source

tag: temperature


title: A4B_medCor1

tag: tissue


title: F2-25-25 rep3


title: IP_UT_1


title: F2-25-25 rep1


title: F2-25-25 rep2


title: A2A_medCor1


title: A2B_medCor1


title: A3A_medCor1


title: A12A_medCor1


title: A4A_medCor1


title: Stress, PPI, 4, FC

city: Aurora

first: Richard

middle: A

last: Radcliffe

state: CO

address: 12850 E Montview Blvd., Room V20-3124

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

data_processing:
Reads were mapped back to the reference genome (mm10) using the STAR algorithm.
Whole gene quantification was determined using HTSeq.
HTSeq output was filtered using the RPLG method (Reads Per Length of Gene) as follows: RPLG = (reads * 151) / gene length. Genes with a median RPLG greater than 1 in any of the four treatment groups were retained for further analysis.
Raw reads were normalized, quantified, and tested fror differential expression (DE) using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include normalized and quantified DESeq2 output

source_name: frontal cortex

extract_protocol:
Total RNA was isolated using the RNeasy Total RNA Isolation Kit (Qiagen Inc., Valencia, CA) and quantified using the Qubit Fluorometer (Life Technologies, Carlsbad, CA). RNA was enriched for the poly-adenylated (polyA) fraction with the use of oligo(dT) magnetic beads.
Bar-coded libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Mice were subjected to three days of either control or stress environment. Sixty minutes after each session, mice recived an injection (ip) of either vehicle or esomeprazole (2 g/kg). Mice were sacrificed and tisuue collected 12 hours after the last drug treatment.

value: postnatal day 63-91

value: frontal cortex

tag: stress

value: Stress

tag: drug tx

value: esomeprazole, 2 mg/kg, ip


title: Stress, PPI, 6, FC


title: F2-25-18 rep4


title: Stress, PPI, 5, FC


title: Stress, PPI, 3, FC


title: Stress, PPI, 2, FC


title: Stress, PPI, 1, FC


title: A11A_medCor1

address: Deutscher Pl. 6

institute: Max Planck Institute for Evolutionary Anthropology

source_name: medial neocortex


title: Stress, vehicle, 6, FC

value: vehicle


title: F2-25-18 rep2


title: Stress, vehicle, 5, FC


title: A11B_medCor1


title: A10B_medCor1


title: A5A_medCor1


title: F2-25-18 rep1


title: Stress, vehicle, 4, FC


title: F2-18-25 rep4


title: F2-18-25 rep3


title: ESC_ZFP296KO2_RNAseq_rep2

city: Zürich

first: Ino

last: Karemaker

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Biological replicate 2

data_processing:
Reads were mapped onto the reference mouse genome mm9 using hisat2
Count tables were generated using HTSeq
Differential gene expression was analysed with the DESeq2 R package
Genome_build: mm9
Supplementary_files_format_and_content: Txt files contain counts

source_name: Embryonic stem cells

extract_protocol:
Total RNA was extracted with an RNeasy Mini Kit (Qiagen)
Libraries were prepared for Illumina sequencing using 5 ng of ChIP material with a Kapa Hyper Prep Kit (Kapa Biosystems), according to the manufacturer’s instructions, but with an additional incubation with USER enzyme (NEB) before library amplification to digest the second cDNA strand

value: Embryonic stem cells

tag: cell type

value: ZFP296 CRISPR KO clone 2 R1 ESCs


title: ESC_ZFP296KO2_RNAseq_rep1

description: Biological replicate 1


title: F2-18-25 rep1


title: Stress, vehicle, 3, FC


title: Stress, vehicle, 2, FC


title: F2-25-18 rep3


title: F2-18-25 rep2


title: ESC_WT_RNAseq_rep2

description: Biological replicate 2

value: WT R1 ESCs


title: F2-18-18 rep3


title: Non-stress, PPI, 5, FC

value: Non-stress


title: ESC_ZFP296KO7_spikein_H3K27ac_input

data_processing:
Reads were mapped onto the reference mouse genome mm9 (NCBI build 37), using the Burrows-Wheeler Alignment tool allowing one mismatch
Mapped reads were filtered for quality and duplicates were removed, using samtools
Peak-calling was performed with the MACS 2.0 tool against a reference input sample from the same cell line
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain called peaks

extract_protocol: Libraries were prepared for Illumina sequencing using 5 ng of ChIP material with a Kapa Hyper Prep Kit (Kapa Biosystems), according to the manufacturer’s instructions

tag: chip antibody

value: ZFP296 CRISPR KO clone 7 R1 ESCs

tag: culture conditions

value: Serum/LIF +2i


title: ESC_ZFP296KO7_spikein_TFs_input


title: Stress, vehicle, 1, FC

tag: strain


title: F2-18-18 rep4


title: F2-18-18 rep2


title: Non-stress, PPI, 6, FC


title: F1-25 rep4


title: ESC_WT_RNAseq_rep1

description: Biological replicate 1


title: Non-stress, PPI, 3, FC


title: F1-25 rep3


title: ESC_ZFP296KO7_spikein_SIN3A

value: SIN3A (Abcam, ab3479)


title: F2-18-18 rep1


title: ESC_ZFP296KO7_spikein_H3K27ac

value: H3K27ac (Diagenode, A1723-0041d)


title: Non-stress, PPI, 2, FC


title: ESC_ZFP296KO7_spikein_CHD4

value: CHD4 (Abcam, ab70469)


title: ESC_ZFP296KO7_spikein_MBD3

value: MBD3 (Bethyl, A302-528A)


title: F1-25 rep2


title: pancancer_ENT + CTLA4 + aHer2 H2

city: Baltimore

first: Evanthia

middle: Theodosiou

last: Roussos Torres

address: 1650 Orleans Street, CRB1 4M

department: Oncology

institute: Johns Hopkins University

description:
Please note, title describes what each tumor was treated with prior to tumpr isolation entinotat-ENT, anti-PD1-PD1, anti-CTLA4-CTLA4, vehicle-PBS+ methylcellulose
Tumors were excised and digested into single cell suspension following 3 full weeks of treatment with drug

hyb_protocol: Followed NanoString nCounter XT gene expression assay protocol. Briefly, hybridization buffer was mixed with the nCounter Myeloid Innate Immunity Panel reporter codeset to prepare a master mix. Master mix, sample and Rnase-fee water was combined with nCounter Myeloid Innate Immunity Panel Capture codeset. Samples were then incubated for 18 h at 65 deg C.

scan_protocol: Raw counts of mRNA hybridized to oligos were counted using the NanoString nCounter instrument.

data_processing: Data from the NanoString nCounter system was normalized to the internal positive controls and housekeeping genes using the recommended settings in the nSolver 4.0 software normalization module (NanoString Technologies). Normalized data was exported and differential expression analysis was performed using a linear model method with the limma package (40) for the R programming language. To identify pathways which were differentially expressed in each treatment, the gage package was used to test for differentially expressed KEGG pathways. Pathways of interest were visualized using the pathview package.

label: Capture probe-3'biotin, Reporter probe-5' barcode signal

source_name: Whole breast tumor, 3 week treated

growth_protocol: The neu-N model is a syngeneic model whereby NT2.5 cells that were derived from a spontaneous mammary tumor are implanted via injection of 5 x 10^4 cells into the mammary fat pad of 7-8 week old female neu-N mice . NT2.5 cells were cultured from frozen stocks and passaged twice before injection. Tumors were allowed to seed for 3 days prior to initiating treatment with various drug combinations as described below . Untreated mice developed palpable tumors within 1 week.

extract_protocol: To obtain single-cell suspensions from breast tumors, tumors were harvested, weighed, diced, and then dissociated using a tumor dissociation kit (Miltenyi Biotec, cat. 130-096-730) and the OctoDissociator (Miltenyi Biotec) per the manufacturers instructions. The 37C_m_TDK_2 program was used to dissociate tumors per the manufacturer’s instructions. Samples were filtered using a 40 µm cell strainer and red blood cells were lysed using ACK lysis buffer (Quality Biological, cat. 118-156-721). The resulting single-cell suspensions were used for  subsequent isolation of specific immune cell types.

treatment_protocol: The ENT dosing solution (5 mg/kg) was made by suspending solid ENT (generously provided by Syndax Pharmaceuticals) in 0.5% methylcellulose via sonication and given by oral gavage daily for three weeks. To imitate oral gavage in control groups, 0.5% methylcellulose was given to vehicle mice as well as mice receiving only antibody therapy during the three weeks of ENT dosing. Mice received anti-PD-1 and/or anti-CTLA-4 twice a week for three weeks. All studies in neu-N model were performed with and without an anti-HER2 antibody to mimic treatment with and without trastuzumab. Anti-HER2 antibody was given once a week for three weeks. Dosage of antibodies was as follows: anti–PD-1, 100 µg/mouse via intraperitoneal injection (i.p.); anti–CTLA-4, 100 µg/mouse i.p.; anti-HER2, 100 µg/mouse i.p. Monoclonal antibodies were obtained from BioXcell [anti–PD-1 (clone RPM1-14), anti–CTLA-4 (clone 9H-10), and anti-HER2 (clone 7.16.4)] and all were diluted to 0.5 mg/mL in PBS. Isotypes were used to treat vehicle mice and were also obtained from BioXcell [anti–PD-1 isotype: rat IgG2a (clone 2A3); anti–CTLA-4 isotype: polyclonal Syrian Hamster IgG; anti-HER2 isotype: mouse IgG2a (clone C1.18.4)]. All isotype antibodies were also diluted to 0.5 mg/mL in PBS.

tag: gender

value: female

value: FVB-Neu-N

value: Syngeneically transplanted whole breast tumor


title: Non-stress, vehicle, 6, FC

value: postnatal day 63-91

value: frontal cortex


title: ESC_ZFP296KO27_spikein_H3K27ac_input

value: ZFP296 CRISPR KO clone 27 R1 ESCs


title: Non-stress, PPI, 1, FC

value: esomeprazole, 2 mg/kg, ip


title: Non-stress, vehicle, 5, FC

value: vehicle


title: ESC_ZFP296KO27_spikein_TFs_input

value: Embryonic stem cells


title: F1-18 rep4


title: pancancer_ENT + CTLA4 + aHer2 H1

label_protocol: Followed NanoString nCounter XT gene expression assay protocol. Briefly, hybridization buffer was mixed with the nCounter Myeloid Innate Immunity Panel reporter codeset to prepare a master mix. Master mix, sample and Rnase-fee water was combined with nCounter Myeloid Innate Immunity Panel Capture codeset. Samples were then incubated for 18 h at 65 deg C.


title: ESC_ZFP296KO27_spikein_SIN3A


title: F1-18 rep3


title: pancancer_ENT + PD1 P2


title: Non-stress, vehicle, 4, FC


title: ESC_ZFP296KO27_spikein_H3K27ac


title: F1-18 rep2


title: pancancer_ENT + PD1 + CTLA 4 A2


title: pancancer_ENT + PD1 + CTLA 4 A1


title: Non-stress, PPI, 4, FC


title: Non-stress, vehicle, 2, FC


title: Stress, PPI, 6, HPC

source_name: hippocampus

value: hippocampus

value: Stress


title: F1-25 rep1


title: ESC_WT_spikein_H3K27ac_input

value: WT R1 ESCs


title: Stress, PPI, 4, HPC


title: Stress, PPI, 5, HPC


title: pancancer_ENT + PD1 P1


title: ESC_WT_spikein_H3K27ac

value: Serum/LIF +2i


title: Non-stress, vehicle, 3, FC

value: Non-stress


title: pancancer_ENT + PD1 + CTLA4 5


title: pancancer_ENT + CTLA4 5


title: Stress, PPI, 3, HPC


title: ESC_WT_spikein_SIN3A

value: SIN3A (Abcam, ab3479)


title: pancancer_ENT + CTLA4 C2


title: Stress, PPI, 2, HPC


title: ESC_WT_spikein_TFs_input


title: ESC_ZFP296KO27_spikein_CHD4

value: CHD4 (Abcam, ab70469)


title: pancancer_ENT + PD1 6


title: F1-18 rep1


title: Non-stress, vehicle, 1, FC


title: ESC_ZFP296KO27_spikein_MBD3

value: MBD3 (Bethyl, A302-528A)


title: Stress, PPI, 1, HPC


title: Stress, vehicle, 6, HPC


title: ESC_WT_spikein_CHD4


title: pancancer_ENT + PD1 5

value: female


title: pancancer_ENT + PD1 + CTLA4 6

value: FVB-Neu-N


title: ESC_WT_SIN3A


title: pancancer_ENT + PD1 (P2)

value: Syngeneically transplanted whole breast tumor


title: pancancer_ENT + CTLA4 6


title: 16S.ME.D.25.25

description:
16S rRNA
OTU table

organism: Bacteria

source_name: fly food + feces

tag: feces source

tag: fly samples grow on this media


title: Stress, vehicle, 5, HPC

value: postnatal day 63-91


title: 16S.ME.C.25.25

description:
16S rRNA
OTU table


title: NPC_WT_H3K27me3

source_name: Neural progenitor cells

value: Neural progenitor cells

value: WT R1 ESC-derived NPCs

value: NPC medium


title: Stress, vehicle, 4, HPC

value: vehicle


title: 16S.ME.B.25.25

description:
16S rRNA
OTU table


title: Stress, vehicle, 3, HPC


title: ESC_WT_spikein_MBD3

value: Embryonic stem cells


title: NPC_WT_H3K27ac

value: H3K27ac (Diagenode, A1723-0041d)


title: 16S.ME.A.25.25

description:
16S rRNA
OTU table


title: pancancer_ENT (E4)


title: NPC_WT_H3K4me3


title: Stress, vehicle, 2, HPC

value: hippocampus

value: Stress


title: 16S.ME.D.25.18

description:
16S rRNA
OTU table


title: NPC_WT_H3K4me1

value: H3K4me1 (Diagenode, A1863-001P)


title: Stress, vehicle, 1, HPC


title: pancancer_ENT + CTLA 4 C1


title: 16S.ME.C.25.18

description:
16S rRNA
OTU table


title: pancancer_ENT (E3)


title: Non-stress, PPI, 6, HPC

value: Non-stress

value: esomeprazole, 2 mg/kg, ip


title: Non-stress, PPI, 5, HPC


title: 16S.ME.B.25.18

description:
16S rRNA
OTU table


title: pancancer_ENT (E2)


title: ESC_ZFP296BAC_GFP

value: GFP (Abcam, ab290)

value: ZFP296-BAC R1 ESCs

value: Serum/LIF +2i


title: 16S.ME.A.25.18

description:
16S rRNA
OTU table


title: pancancer_Vehicle (V3)

value: female

value: FVB-Neu-N


title: ESC_WT_H3K27ac

value: WT R1 ESCs


title: ESC_WT_H3K4me3


title: pancancer_Vehicle (V2)

value: Syngeneically transplanted whole breast tumor


title: Non-stress, PPI, 4, HPC

value: postnatal day 63-91


title: pancancer_ENT + PD1 (P1)


title: Non-stress, PPI, 3, HPC


title: 16S.ME.D.18.25

description:
16S rRNA
OTU table


title: 16S.ME.C.18.25

description:
16S rRNA
OTU table


title: NPC_WT_input

value: Neural progenitor cells

value: WT R1 ESC-derived NPCs

value: NPC medium


title: pancancer_Vehicle (V5)


title: ESC_WT_H3K4me1

value: Embryonic stem cells


title: 16S.ME.B.18.25

description:
16S rRNA
OTU table


title: ESC_WT_input


title: pancancer_Vehicle (V1)


title: 16S.ME.A.18.25

description:
16S rRNA
OTU table


title: ESC_WT_H3K27me3


title: Non-stress, vehicle, 4, HPC

value: hippocampus

value: vehicle


title: Vehicle V2

description:
Please note, title describes what each tumor was treated with prior to cell isolation entinotat-ENT, anti-PD1-PD1, anti-CTLA4-CTLA4, vehicle-PBS+ methylcellulose
G-MDSCs were extracted from tumors following 3 full weeks of treatment with drug

source_name: G-MDSCs, 3 week treated, breast tumor

extract_protocol: G-MDSCs were isolated from single-cell suspensions from tumors following tumor dissociation using Miltenyi Biotec’s Myeloid-Derived Suppressor Cell Isolation Kit (cat. 130-094-538) according to the manufacturer’s protocol. RNA was extracted from whole tumors or G-MDSCs isolated from tumors using the Qiagen RNeasy extraction kit (cat. 74104). Using a NanoDrop ND-1000, RNA quality and quantity were determined (samples with A260/280 < 1.8 were excluded). Gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies). The NanoString PanCancer Immune CodeSet (cat. XT-CSO-MIP1-12) was used to perform the nCounter Gene Expression Assay for whole tumor samples, whereas the Mouse Myeloid CodeSet (cat. XT-CSO-MII2-12) was used to perform nCounter Gene Expression Assay for isolated G-MDSCs. Quantification of target mRNA in each sample was performed by detection within the nCounter Digital Analyzer. Ly6G+ cells were positively selected to isolate G-MDSCs from Ly6G- M-MDSCs and were passed through LS columns (Miltenyi Biotec, cat. 130-042-401) twice to increase purity. Eluted G-MDSCs were then used for downstream assays described below.

value: G-MDSCs isolated from syngeneically transplanted breast tumor


title: 16S.ME.C.18.18

description:
16S rRNA
OTU table


title: Non-stress, vehicle, 6, HPC

value: Non-stress


title: Vehicle V1


title: Non-stress, vehicle, 5, HPC


title: Vehicle 3


title: ENT + PD1 + CTLA4 4


title: ENT + PD1 + CTLA4 2


title: Non-stress, vehicle, 2, HPC


title: 16S.ME.A.18.18

description:
16S rRNA
OTU table


title: ENT + PD1 + CTLA4 3


title: pancancer_ENT (E1)


title: Non-stress, PPI, 2, HPC

value: esomeprazole, 2 mg/kg, ip


title: Non-stress, vehicle, 1, HPC


title: ENT + CTLA4 4


title: Non-stress, PPI, 1, HPC


title: 16S.MF.C.25.25

description:
16S rRNA
OTU table

source_name: fly food


title: 16S.ME.D.18.18

description:
16S rRNA
OTU table


title: ENT + CTLA4 1


title: 16S.MF.B.25.25

description:
16S rRNA
OTU table


title: 16S.ME.B.18.18

description:
16S rRNA
OTU table


title: 16S.MF.A.25.25

description:
16S rRNA
OTU table


title: Non-stress, vehicle, 3, HPC


title: ENT + PD1 4


title: ENT + CTLA4 2


title: ENT + CTLA4 3


title: 16S.MF.D.25.25

description:
16S rRNA
OTU table


title: 16S.MF.C.25.18

description:
16S rRNA
OTU table


title: 16S.MF.B.25.18

description:
16S rRNA
OTU table


title: 16S.MF.A.25.18

description:
16S rRNA
OTU table


title: ASZ_RasV12, RasV12_CBD_rep2

city: Stanford

first: Francois

last: Kuonen

address: 269 Campus Drive CCSR 2145

department: Dermatology

institute: Stanford University

description:
NH7_8_vs_NH5_6_diff_exp.xlsx
NH8

data_processing:
Alignment was run using tophat. RPKM values were called using cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each condition (2 biological replicates), log2 (fold change) and p-value

source_name: ASZ_RasV12, CBD

extract_protocol:
RNA samples were obtained from adherent cells using RNeasy kit from QIAGEN according to manufacturer's instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: BCC cell line (ASZ)

value: basal cell carcinoma

tag: genotype

tag: agent

value: CBD


title: ASZ, CBD_rep1

description:
NH3_4_vs_NH1_2_diff_exp.xlsx
NH3

source_name: ASZ, CBD

value: WT


title: ASZ_RasV12, RasV12_DMSO_rep2

description:
NH7_8_vs_NH5_6_diff_exp.xlsx
NH6

source_name: ASZ_RasV12, DMSO

value: DMSO


title: ASZ_RasV12, RasV12_CBD_rep1

description:
NH7_8_vs_NH5_6_diff_exp.xlsx
NH7


title: ENT + PD1 3

value: female

value: FVB-Neu-N


title: ASZ_RasV12, RasV12_DMSO_rep1

description:
NH7_8_vs_NH5_6_diff_exp.xlsx
NH5


title: ASZ, CBD_rep2

description:
NH3_4_vs_NH1_2_diff_exp.xlsx
NH4


title: ENT + PD1 2


title: ASZ, DMSO_rep1

description:
NH3_4_vs_NH1_2_diff_exp.xlsx
NH1

source_name: ASZ, DMSO


title: 16S.MF.D.18.25

description:
16S rRNA
OTU table


title: ASZ, DMSO_rep2

description:
NH3_4_vs_NH1_2_diff_exp.xlsx
NH2


title: ENT + PD1 1


title: ENT 4


title: 16S.MF.D.25.18

description:
16S rRNA
OTU table


title: 16S.MF.C.18.25

description:
16S rRNA
OTU table


title: ENT 3


title: NFAT5_KO_4

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: murine aortic smooth muscle cell from mouse 4 + Ad-Cre

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Mouse MoGene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: vascular smooth muscle cell (VSMC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: murine aortic VSMCs were cultured in DMEM +15% FCS and propagated 1:3

extract_protocol: RNA was extracted from VSMCs by utilizing the Qiagen mini RNA extraction kit  following man. instr.

treatment_protocol: VSMCs were exposed to adenovirus for 18 hours and incubated for further 48 hours before RNA extraction

value: vascular smooth muscle cell (VSMC)

tag: phenotype


title: 16S.MF.B.18.25

description:
16S rRNA
OTU table


title: NPC_WT_MBD3

value: Neural progenitor cells

value: MBD3 (Bethyl, A302-528A)


title: ESC_WT_CHD4_rep1

value: CHD4 (Abcam, ab70469)

value: WT R1 ESCs

value: Serum/LIF +2i


title: 16S.MF.B.18.18

description:
16S rRNA
OTU table


title: ENT 1


title: 16S.MF.C.18.18

description:
16S rRNA
OTU table


title: NPC_WT_CHD4

value: WT R1 ESC-derived NPCs

value: NPC medium


title: Vehicle 4

value: G-MDSCs isolated from syngeneically transplanted breast tumor


title: 16S.MF.A.18.18

description:
16S rRNA
OTU table


title: 16S.MF.D.18.18

description:
16S rRNA
OTU table


title: ESC_WT_CHD4_rep2

value: Embryonic stem cells


title: ENT 2


title: ENT + PD1 + CTLA4 1


title: ESC_WT_MBD3_rep1


title: ESC_WT_MBD3_rep2


title: Vehicle 2


title: tdp1_J2-2 (re-analysis)

status: Public on Oct 09 2018

city: boulder

first: marko

last: melnick

address: 1725 pleasant st

department: Integrative Physiology

institute: University of Colorado at Boulder

description:
OK803-J2
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt

data_processing:
Trim fastq files using Trimmomatic=0.36. Options were set to ILLUMINACLIP:adaptertrim1ALL.fa:2:30:10.
Align files with STAR-2.5.2b. Reads were aligned with star with the following commands. --runMode alignReads --outSJfilterCountUniqueMin 3 2 2 2 --outSJfilterCountTotalMin 5 3 3 3 --outSJfilterIntronMaxVsReadN 10 20 40 --alignIntronMin 10 --alignIntronMax 5000
Count reads with Rsubread v1.28.1 with options set to allowMultiOverlap = TRUE, strandSpecific = set to 1 or 2 for sense and antisense.
Differential expression with v1.20.0. J2 enrichment processed with commands. dds = DESeq(dds, test=``LRT", reduced= ~ assay + condition, parallel = TRUE)
Genome_build: WS258
Supplementary_files_format_and_content: Normalized Rsubread sense and antisense counts for heat shock worm samples

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Hermaphrodites from each strain were kept at 16◦C on Nematode Growth Media (NGM) seeded with Escherichia coli strain OP50

extract_protocol:
Total RNA was extracted from worms using TRIzol (Invitrogen #15596026) extraction. Chloroform was used to solubilize proteins and TURBO DNase (Invitrogen) was used to remove DNA. For total RNA libraries, 5 μg of RNA was ran through a RiboZero column (Epicenter, #R2C1046) to remove ribosomal RNA. 20 μl of Protein A magnetic beads (Dynabeads, Invitrogen) were washed, blocked, and bound by antibody at a ratio of 10 μl/IP for anti-J2. Tubes were rocked at 15°C for 2 h (anti-J2 IPs). The supernatant was removed, beads were washed, and immunoprecipitated RNA was removed from beads by TRIzol extraction. DNA was removed from immunoprecipitated RNA using TURBO DNase (Invitrogen) and dissolved in nuclease-free water.
Total RNA Libraries were created according to the Illumina TruSeq kits (RS-122-2001). RNA recovered by immunoprecipitation with the J2 antibody (three biologically independent lysates) of young adult worms as well as input material (as a loading control) was converted into strand-specific total RNA libraries using V2 Scriptseq (Epicenter #SSV21106) kits following manufacturer's instructions, except reverse transcription was done with SuperScript III (Invitrogen #18080-044) using incrementally increasing temperatures from 42 to 59°C to allow for transcription though structured RNAs. rRNA was not removed from J2-IP RNA samples.

treatment_protocol: Heat stress treatment was performed in an air incubator set to 35◦C for 3 hours.

value: tdp-1 deletion

tag: developmental stage

value: L4/Day 1 Adults

tag: rip antibody

value: J2 antibody (English & Scientific Consulting Lot:J2-1102 and J2-1103)


title: tdp1_J2-3 (re-analysis)

description:
OK8O3-J2-3
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt


title: Vehicle 1


title: 16S.MF.A.18.25

description:
16S rRNA
OTU table

tag: temperature


title: tdp1_input (re-analysis)

description:
OK803_INPUT
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt


title: N2_J2-3 (re-analysis)

description:
N2-J2-3
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt

value: N2 (wild type)


title: N2_J2-2 (re-analysis)

description:
N2-J2-2
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt


title: ctrl_1

description: murine aortic smooth muscle cell from mouse 1 + Ad-PL

tag: tissue

value: Control


title: ctrl_2

description: murine aortic smooth muscle cell from mouse 2 + Ad-PL


title: N2_J2-1 (re-analysis)

description:
N2-J2-1
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt


title: NFAT5_KO_1

description: murine aortic smooth muscle cell from mouse 1 + Ad-Cre


title: ctrl_3

description: murine aortic smooth muscle cell from mouse 3 + Ad-PL


title: ctrl_4

description: murine aortic smooth muscle cell from mouse 4 + Ad-PL


title: N2_input (re-analysis)

description:
N2_INPUT
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt


title: NFAT5_KO_2

description: murine aortic smooth muscle cell from mouse 2 + Ad-Cre


title: HS Input

description:
N2HS_INP
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt

tag: treatment

value: Heat shock 35◦C for 3 hours


title: HS J2 B

description:
N2HS_J2B
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt


title: HS J2 A

description:
N2HS_J2A
Rsubread_sense.txt
Rsubread_antisense.txt
Rsubread_sense_normalized_rRNA.txt
Rsubread_antisense_normalized_rRNA.txt


title: NFAT5_KO_3

description: murine aortic smooth muscle cell from mouse 3 + Ad-Cre


title: heart Kdm3a-Tg TAC rep2  (#18)

city: Dalals

first: zhi-ping

last: liu

state: TX

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

description: SAMPLE 6

hyb_protocol: Biotin labeled cRNA are hybridized with Illumina MouseWG-6 Beadchips using Illumina standard protocol

scan_protocol: The beadchips are scanned using Illumina HiScanSQ scanner

data_processing: The data is analyzed using Illumina GenomeStudio V2011.1 software

source_name: left ventricle TAC

label_protocol: Sample labeling was performed using Illumina TotalPrep RNA Amplification kit by following manufacturers protocol. Briefly, 500ng total RNA was reverse transcribed to cDNA, followed by transcribing into cRNA with biotin labled dNTP.

growth_protocol: Male c57/BL6 mice were housed at 12h light/12h dark cycle under standard condition.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) by following manufacturer's protocol, followed by clean-up and DNase I treatment with Ambion kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: six to eight weeks old male mice were put to sham or TAC surgery. Heart samples were harvested at 3 weeks later. Heart were rinsed quickly, left ventricles were sliced out and snap frozen in liquid nitrogen, then move to -80C to store until total RNA was extracted.

tag: strain background

tag: genotype/variation

tag: age

value: adult

tag: Sex

value: male

value: heart left ventricle


title: heart WT TAC rep1

value: wild type


title: A498_cisplatin_3000nM_6h

city: Rockville

first: Anne

last: Monks

state: MD

address: 9609 Medical Center Dr

department: Developmental Therapeutics Program

institute: National Cancer Institute

description: gene expression data from A498 treated with 3000nM cisplatin for 6h

hyb_protocol: Biotin labeled antisense cRNA (4 µg per sample) was hybridized to Affymetrix GeneChip HT Human Genome U133A 96-Array plates overnight

scan_protocol: Plates were washed, stained, then scanned on an Affymetrix GeneTitan HT array plate scanner

data_processing: Data were collected using Affymetrix AGCC software.  Initial data quality control was performed using percent present calls generated by Affymetrix Quality Reporter software. Samples failing QC were repeated (R2)

source_name: human tumor cell line A498

label_protocol: Samples (96-well format, 1 µg each) were labeled using Affymetrix (Cleveland OH) HT One-Cycle Eukaryotic Labeling Kit on Biomek FX Target Prep Express system following manufacturer’s suggested protocols

growth_protocol: All cell lines were cultured in RPMI-1640 media with 10% FBS and L-Glutamine and incubated at 37oC, 5%CO2.

extract_protocol: Total RNA was isolated using the Qiagen Rneasy mini kit, quantitated by measuring absorbance at A260, quality of RNA was determined on a Caliper LabChip GX all samples used had an RQS>7.5

treatment_protocol: All drugs were dissolved in DMSO, diluted to their appropriate concentrations in culture media and added to the cells pre-plated for 24h (DMSO final concentration of 0.25%) , and incubated for the indicated times

tag: group

value: member of the NCI-60 cell line panel

value: Renal


title: A498_cisplatin_0nM_2h

description: gene expression data from A498 treated with 0nM cisplatin for 2h


title: A498_cisplatin_0nM_6h

description: gene expression data from A498 treated with 0nM cisplatin for 6h


title: A498_cisplatin_3000nM_24h

description: gene expression data from A498 treated with 3000nM cisplatin for 24h


title: A498_cisplatin_0nM_24h

description: gene expression data from A498 treated with 0nM cisplatin for 24h


title: heart WT Sham

source_name: left ventricle sham


title: A498_cisplatin_15000nM_2h

description: gene expression data from A498 treated with 15000nM cisplatin for 2h


title: heart Kdm3a-Tg TAC rep1 (#446)

description: SAMPLE 5


title: heart WT Sham (#444)

description: SAMPLE 1


title: A498_cisplatin_15000nM_24h

description: gene expression data from A498 treated with 15000nM cisplatin for 24h


title: A498_cisplatin_15000nM_6h

description: gene expression data from A498 treated with 15000nM cisplatin for 6h


title: UO-31_bortezomib_100nM_2h

description: gene expression data from UO-31 treated with 100nM bortezomib for 2h

source_name: human tumor cell line UO-31


title: UO-31_bortezomib_100nM_24h

description: gene expression data from UO-31 treated with 100nM bortezomib for 24h


title: UO-31_bortezomib_100nM_6h

description: gene expression data from UO-31 treated with 100nM bortezomib for 6h


title: UO-31_bortezomib_10nM_2h

description: gene expression data from UO-31 treated with 10nM bortezomib for 2h


title: UO-31_bortezomib_10nM_6h

description: gene expression data from UO-31 treated with 10nM bortezomib for 6h


title: heart Kdm3a-KO Sham


title: heart Kdm3a-KO TAC rep2


title: heart WT TAC rep2


title: heart Kdm3a-Tg Sham (#454)

description: SAMPLE 4


title: heart WT TAC rep1 (#445)

description: SAMPLE 2


title: UO-31_bortezomib_0nM_24h

description: gene expression data from UO-31 treated with 0nM bortezomib for 24h


title: UO-31_bortezomib_0nM_2h

description: gene expression data from UO-31 treated with 0nM bortezomib for 2h


title: UACC-62_bortezomib_10nM_24h

description: gene expression data from UACC-62 treated with 10nM bortezomib for 24h

source_name: human tumor cell line UACC-62

value: Melanoma


title: heart Kdm3a-KO TAC rep1


title: heart WT TAC rep2 (#17)

description: SAMPLE 3


title: UACC-62_bortezomib_100nM_6h

description: gene expression data from UACC-62 treated with 100nM bortezomib for 6h


title: UACC-62_bortezomib_10nM_2h

description: gene expression data from UACC-62 treated with 10nM bortezomib for 2h


title: UACC-62_bortezomib_100nM_2h

description: gene expression data from UACC-62 treated with 100nM bortezomib for 2h


title: UACC-62_bortezomib_0nM_24h

description: gene expression data from UACC-62 treated with 0nM bortezomib for 24h


title: UACC-62_bortezomib_0nM_2h

description: gene expression data from UACC-62 treated with 0nM bortezomib for 2h


title: U251_bortezomib_10nM_6h

description: gene expression data from U251 treated with 10nM bortezomib for 6h

source_name: human tumor cell line U251

value: CNS


title: UACC-62_bortezomib_0nM_6h

description: gene expression data from UACC-62 treated with 0nM bortezomib for 6h


title: UACC-62_bortezomib_10nM_6h

description: gene expression data from UACC-62 treated with 10nM bortezomib for 6h


title: UACC-257_bortezomib_100nM_6h

description: gene expression data from UACC-257 treated with 100nM bortezomib for 6h

source_name: human tumor cell line UACC-257


title: UACC-257_bortezomib_10nM_2h

description: gene expression data from UACC-257 treated with 10nM bortezomib for 2h


title: U251_bortezomib_10nM_24h

description: gene expression data from U251 treated with 10nM bortezomib for 24h


title: UACC-257_bortezomib_0nM_2h

description: gene expression data from UACC-257 treated with 0nM bortezomib for 2h


title: UACC-257_bortezomib_100nM_24h

description: gene expression data from UACC-257 treated with 100nM bortezomib for 24h


title: U251_bortezomib_100nM_2h

description: gene expression data from U251 treated with 100nM bortezomib for 2h


title: U251_bortezomib_10nM_2h

description: gene expression data from U251 treated with 10nM bortezomib for 2h


title: UACC-257_bortezomib_10nM_24h

description: gene expression data from UACC-257 treated with 10nM bortezomib for 24h


title: UACC-62_bortezomib_100nM_24h

description: gene expression data from UACC-62 treated with 100nM bortezomib for 24h


title: UACC-257_bortezomib_0nM_6h

description: gene expression data from UACC-257 treated with 0nM bortezomib for 6h


title: UACC-257_bortezomib_10nM_6h

description: gene expression data from UACC-257 treated with 10nM bortezomib for 6h


title: UO-31_bortezomib_10nM_24h

description: gene expression data from UO-31 treated with 10nM bortezomib for 24h


title: U251_bortezomib_100nM_24h

description: gene expression data from U251 treated with 100nM bortezomib for 24h


title: UACC-257_bortezomib_0nM_24h

description: gene expression data from UACC-257 treated with 0nM bortezomib for 24h


title: U251_bortezomib_100nM_6h

description: gene expression data from U251 treated with 100nM bortezomib for 6h


title: U251_bortezomib_0nM_6h

description: gene expression data from U251 treated with 0nM bortezomib for 6h


title: UACC-257_bortezomib_100nM_2h

description: gene expression data from UACC-257 treated with 100nM bortezomib for 2h


title: U251_bortezomib_0nM_2h

description: gene expression data from U251 treated with 0nM bortezomib for 2h