title: NBT_S288CdU_YPD_R8

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

description:
pTpA_random_design_tiling_etc_YPD_expression.txt.gz
pTpA_random_design_tiling_etc_sequence_IDs.txt

data_processing:
The paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints. The scaffold library instead used 16)+/-10) bp of overlap. This was not required for the Native80 and NBT/designed libraries
Promoters were aligned to themselves using Bowtie2 to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster. The scaffold library was aligned to the designed scaffold sequences, yielding a cluster of sequences derived from each scaffold, which were then subclustered based on the random 80-mer contained within using CD-HIT.  The Native80 and NBT/designed libraries were aligned to the promoter sequences we ordered using Bowtie2.
Mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP).  Note that Abf1TATA sorting bin 16 (R4) was accidentally pooled with part of bin 11 (R9) and so was left out of all analyses and the processed data.
Genome_build: R64
Supplementary_files_format_and_content: compressed text files containing promoter sequences and their corresponding expression levels

organism: Saccharomyces cerevisiae

source_name: Promoter library

growth_protocol: Libraries were transformed into yeast (strain S288C deltaUra3 for Native80 and NBT/designed, and Y8205 for the others) using the lithium acetate method, starting with 1L of yeast harvested at an OD of 0.3-0.4 , ensuring a complexity of at least 1E8 was achieved for random libraries (with the exception of the high-quality pTpA library where a dilution series was performed to achieve the desired complexity). The yeast were then grown in SD-Ura for two days, diluting the media by 1:4 three times during this period.  Media was then changed to YPD, growing for at least 5 generations prior to cell sorting. For YPGly and YPGal experiments, the same pTpA transformation was used and the culture was grown for at least 8 generations (due to the change in carbon source). In the final 10 hours of growth prior to cell sorting, the cultures were allowed to grow continuously in log phase, never achieving an OD above 0.6, by diluting in fresh media.  All cultures were grown in a shaker incubator, at 30C and approximately 250 RPM.

extract_protocol:
Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins (except for scaffold library, where bins were approximarely proportional to the expression variance within the bin), done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SC-Ura (supplemented with 1% Gal for Gal sort) and grown for 2-3 days, shaking at 30C.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center. The scaffold library was sequenced with 300 cycle kits in two reads of 190 and 110 bases. The second replicate of the Native80 library was sequenced with a 300 cycle kit.

treatment_protocol: Prior to sort, yeast were spun down, washed once in ice-cold PBS, and then suspended in ice-cold PBS and kept on ice until cell sorting.

tag: media

value: YPD

tag: libraryid

value: NBT/designed


title: NBT_S288CdU_YPD_R9

status: Public on Aug 20 2019

type: SRA

city: Cambridge

state: MA

country: USA

library_source: genomic

molecule: genomic DNA

tag: strain


title: NBT_S288CdU_YPD_R7


title: NBT_S288CdU_YPD_R4


title: NBT_S288CdU_YPD_R6


title: NBT_S288CdU_YPD_R5


title: H4R3_rep1

city: Chengdu

first: xiaomeng

last: liu

address: No.55,Section 4,South Renmin Road

country: Colombia

institute: Sichuan Cancer Hospital & Institute, Sichuan Cancer Center

description:
H4R3merge_inputmerge_q0.01_peaks.txt
s1

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Whole or any subsets of adaptor sequences were trimmed at 3'- end of the reads.
Clean reads were aligned to refference genome (hg19) using BWA.
Duplication reads were removed by MACS(v2) software.
Unique mapped and non-duplication reads were used to call peaks by MACS(v2) software
Genome_build: hg19
Supplementary_files_format_and_content: peak.txt files include the peaks called by MACS(v2)
Supplementary_files_format_and_content: bedgraph files include the information of modification enrichment which could be visualised in IGV software.

organism: Homo sapiens

source_name: mesenchymal stem cell

growth_protocol: rimary hMSCs were purchased from ScienCell Research Laboratories (Carlsbad, CA, USA). Cells at passage 3 from 3 independent donors were used for the assays. Proliferation media (DMEM; 10% fetal bovine serum; 1% penicillin/streptomycin) and osteogenic media [Proliferation media containing 100 nM dexamethasone (Sigma-Aldrich, St. Louis, MO, USA), 0.2 mM ascorbic acid (Sigma-Aldrich), and 10 mM β-glycerophosphate (Sigma-Aldrich)] were used for cell culture and osteogenic induction respectively.

extract_protocol: Briefly, cells were cross-linked with 1% formaldehyde, resuspended in lysis buffer (1% SDS, 10 mM EDTA, and 50 mM Tris-HCl [pH 8.0]) on ice for 3 min, and fragmented by sonication in RIPA ChIP buffer (0.5 mM EGTA, 140 mM NaCl, 10 mM Tris-HCl, pH 7.5, 1% TritonX-100, 0.01% SDS, 1 mM EDTA and protease inhibitor). The samples were then incubated overnight with Protein A/G-beads bound with antibodies [PRMT3 (Abcam, Cambridge, UK), H4R3me2a (Active Motif, Carlsbad, CA), H3 (Cell Signaling)]. After the crosslinking was reversed, immune complexes containing DNA were purified and eluted. The precipitated DNA for sequencing, including H4R3me2a and PRMT3, were constructed into libraries with NEBNext DNA Library Prep Reagent Set for Illumina (NEB) as described by the manufacturer.

tag: cell type

value: mesenchymal stem cell

tag: chip antibody

value: H4R3me2a (Active Motif, Carlsbad, CA)


title: 422075-POST

city: St. Louis

first: Britt

middle: Juul

last: Andersen

state: MO

address: 4444 Forest Park Blvd.

institute: Washington University

library_source: transcriptomic

data_processing:
Reads were mapped to protein coding genes using HISAT2 (version 2.0.5)
FeatureCounts was used to count reads per gene
DESeq2 was used to generate normalized read counts, and to identify differentially expressed genes between the different comparison groups; AEs vs. no AEs and pre vs. post-treatment
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Excel file with fragment count data, DESeq normalized expression data, FPKMs, and DESeq results for all 38 samples.

molecule: total RNA

source_name: Buffy coat

extract_protocol:
Blood was collected in EDTA tubes, and centrifuged. The buffy coat was collected and added to RNAlater. Total RNA was extracted from buffy coat samples using Qiagen RNeasy kits with an added homogenization step and on-column DNase digestion. The Illumina TruSeq Stranded Total RNA LT Sample Prep Kit (Cat#RS-122-2301) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Buffy coat

tag: adverse event

tag: pre or post treatment

value: Post

tag: age

tag: Sex

value: Male

tag: village

tag: microfilaria/ml

tag: treatment arm

value: ALB


title: 422075-PRE

value: Pre


title: 412423-POST


title: 422091-PRE

value: IVM/ALB


title: NBT_S288CdU_YPD_R2


title: NBT_S288CdU_YPD_R18


title: NBT_S288CdU_YPD_R19


title: NBT_S288CdU_YPD_R3


title: 422091-POST


title: 412423-PRE


title: 422078-POST

value: Moderate

value: IVM/DEC/ALB


title: 422078-PRE


title: 422077-POST


title: NBT_S288CdU_YPD_R17


title: NBT_S288CdU_YPD_R16


title: 422077-PRE


title: H4R3_rep2

description:
H4R3merge_inputmerge_q0.01_peaks.txt
s2


title: NBT_S288CdU_YPD_R15


title: 422089-POST

value: Female


title: NBT_S288CdU_YPD_R14


title: 422076-POST


title: NBT_S288CdU_YPD_R11


title: NBT_S288CdU_YPD_R10


title: 422076-PRE


title: NBT_S288CdU_YPD_R13


title: 422089-PRE


title: NBT_S288CdU_YPD_R12


title: 422144-POST


title: B-T3

city: Taichung

first: Chien Chih

last: Lee

address: 2 Yuh-Der Road

country: Taiwan

institute: China Medical University Hospital

data_processing:
Illumina Pipeline v1.5+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using MapSplice 2.2.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, the number of reads falling in the exons were counted and normalized by the size of the exon and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include exon sites, raw_counts, and RPKM values for each Sample

source_name: Huh7 cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina mRNA-seq sample kit (Cat# RS-930-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.1 mM BS008 for 24 hrs

tag: cell line

value: Hepatocellular carcinoma cell line Huh7

tag: passages

tag: treatment


title: 422144-PRE


title: Yeast_YPD_WT_BULK

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

data_processing:
bcl2fastq to generate FASTQ
Cellranger count v2.1.1 to generate count matrix
Genome_build: Saccharomyces_cerevisiae R64
Supplementary_files_format_and_content: [TSV] tab-separated value file with an index column

source_name: Yeast grown in YPD

extract_protocol:
TRIZOL extraction
Addition of sample barcodes and UMIs during RT. Whole transcriptome amplification by PCR. Nextera XT tagmentation.

tag: growth condition

tag: genotype

value: FY4/FY5 Wild-type


title: SNU449TimeZero

city: Singapore

first: Yu

last: Wang

address: 11 Hospital Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description:
SNU449 GECKOv2 cells at the start of the screen.
PCR amplicon from genomic DNA.
PCR Amplicon Seq
Barcode: AATGCGTT
Processed data file: Count.txt

data_processing:
Demultiplexed raw reads were provided by sequencing vendor.
20bases gRNA reads were trimmed using Partek Flow.
We used MAGECK algorithm to identify and rank a list of candidate targets significantly depleted in the End Point sample.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Count.txt: Tab-delimited text file includes normalized counts for each Sample.

source_name: SNU449, time zero, genomic DNA amplicon

growth_protocol: HCCLM3 and SNU449 were grown in Dulbecco's modified Eagle's medium (DMEM) with 4.5 g/L high glucose, 15mM HEPES buffer and 10% fetal calf serum in a humidified incubator at 37 ºC with 5% CO2.

extract_protocol:
Genomic DNA were extracted using E.Z.N.A.® HP Tissue DNA Maxi Kit (OMEGA bio-tek, USA).
The integrated gRNA region was PCR amplified using Q5® High-Fidelity DNA Polymerase (NEB, USA) with V2 adaptor primers. Illumina compatible libraries were generated using F8N forward primer and sample specific barcoded reverse primers.

treatment_protocol: 100 million HCCLM3 and SNU449 cells were transduced with the lentiviral particles containing a genome-wide set of gRNAs at an MOI of 0.2 to ensure a single copy integration per cell in >95% of the population and over 100X coverage of the library. The transduced cells were selected with 4 µg/ml puromycin for stable integration. The resultant GECKO-ready cells were harvested at Time Zero and End Point after the cells were expanded for 10 population doublings under normal growth conditions.

value: Hepatocellular carcinoma (HCC) cell line

tag: time

value: Time Zero


title: HCCLM3EndPoint

description:
HCCLM3 GECKOv2 cells at the end of the screen.
PCR amplicon from genomic DNA.
PCR Amplicon Seq
Barcode: TGGTAACG
Processed data file: Count.txt

source_name: HCCLM3, end point, genomic DNA amplicon

value: End Point


title: B-C3

value: Cells were treated with 0.1% DMSO for 24 hours


title: SNU449EndPoint

description:
SNU449 GECKOv2 cells at the end of the screen.
PCR amplicon from genomic DNA.
PCR Amplicon Seq
Barcode: CCATTGTT
Processed data file: Count.txt

source_name: SNU449, end point, genomic DNA amplicon


title: 422102-PRE


title: 422102-POST


title: 422098-POST


title: HCCLM3TimeZero

description:
HCCLM3 GECKOv2 cells at the start of the screen.
PCR amplicon from genomic DNA.
PCR Amplicon Seq
Barcode: GATCGTGT
Processed data file: Count.txt

source_name: HCCLM3, time zero, genomic DNA amplicon


title: 422098-PRE


title: 412468-PRE


title: 412468-POST


title: 412473-PRE


title: GECKOv2library

description:
GECKOv2 library.
PCR amplicon from plasmid library.
PCR Amplicon Seq
Barcode: CTCTACTT
Processed data file: Count.txt

molecule: other

source_name: GECKOv2 library plasmids

tag: sample type

value: Genome-wide set of gRNAs


title: 412464-PRE


title: 422060-POST

value: Mild


title: 422060-PRE

value: Buffy coat


title: 422082-POST

value: Post


title: MDA-MB-231 tumorigenic cells curcumin and 2 Gy of photon dose - replicate3

type: RNA

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description: Biological replicate 3 of 6

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

source_name: Human tumorigenic MDA-MB-231 BC cell line

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Respective untreated cell lines, were used as a control. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated cells was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: Non tumorigenic (MCF10A) and tumorigenic breast (MCF7 and MDA-MB-231) immortalized cell lines were collected after 24 hours post curcumin and radiation treatments.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: curcumin and exposed to 2 Gy of photon beam

tag: harvest time post treatment

value: 24 hours

tag: original tissue

value: breast

value: exposed to 2 Gy of photon beam


title: MDA-MB-231 tumorigenic cells curcumin and 2 Gy of photon dose - replicate5

description: Biological replicate 5 of 6


title: 412464-POST

tag: tissue

value: Male


title: MDA-MB-231 tumorigenic cells curcumin and 2 Gy of photon dose - replicate6

description: Biological replicate 6 of 6


title: 422082-PRE

tag: adverse event

value: Moderate

value: Pre

value: IVM/DEC/ALB


title: MDA-MB-231 tumorigenic cells curcumin and 2 Gy of photon dose - replicate4

description: Biological replicate 4 of 6


title: 412412-PRE

tag: pre or post treatment


title: 412473-POST

tag: age


title: MDA-MB-231 tumorigenic cells curcumin and 2 Gy of photon dose - replicate1

description: Biological replicate 1 of 6


title: 412411-POST

tag: Sex

value: IVM/ALB


title: MCF7 tumorigenic cells curcumin and 2 Gy of photon dose - replicate3

description: Biological replicate 3 of 6

source_name: Human tumorigenic MCF7 BC cell line


title: 412411-PRE

tag: village


title: MDA-MB-231 tumorigenic cells curcumin and 2 Gy of photon dose - replicate2

description: Biological replicate 2 of 6


title: 412412-POST

tag: microfilaria/ml


title: MCF7 tumorigenic cells curcumin and 2 Gy of photon dose - replicate6

description: Biological replicate 6 of 6


title: MCF7 tumorigenic cells curcumin and 2 Gy of photon dose - replicate2

description: Biological replicate 2 of 6


title: MCF7 tumorigenic cells curcumin and 2 Gy of photon dose - replicate4

description: Biological replicate 4 of 6


title: 422134-POST

tag: treatment arm


title: 412457-POST


title: MCF10A non tumorigenic cells curcumin and 2 Gy of photon dose - replicate4

description: Biological replicate 4 of 6

source_name: Human non-tumorigenic breast epithelial MCF10A cell line

tag: cell line


title: MCF7 tumorigenic cells curcumin and 2 Gy of photon dose - replicate5

description: Biological replicate 5 of 6


title: MCF7 tumorigenic cells curcumin and 2 Gy of photon dose - replicate1

description: Biological replicate 1 of 6


title: WT 8DAF rep1

city: Manhattan

first: Timothy

last: Durrett

state: KS

address: 1711 Claflin Road

department: Biochemistry and Molecular Biophysics

institute: Kansas State University

description: RNA-Seq data dgat1-1.txt

data_processing:
Raw fastq files were imported into CLC genomics workbench v7.5.1 platform using Illumina import. Reads were imported as paired reads, and reads which fail the quality score based on Illumina pipeline 1.8 and later were removed.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis genome assembly (Araport 11)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
To identify differentially expressed genes, the EDGE test (empirical analysis of differentially expressed genes) was used which is included in CLC genomics workbench. This test implements the “Exact test” for two-group comparisons. This test assumes that all samples have negative binomial distribution and accounts for the biological variability of replicates.
Paramteres used for EDGE test to identify differentially expressed (DE) genes: fold change greater than 2-fold , p value <=0.05 and only those genes were seleced which had RPKM value equal or higher than 0.1
Genome_build: Araport 11
Supplementary_files_format_and_content: Excel spreadsheet files include RPKM values for each sample

organism: Arabidopsis thaliana

source_name: Early seed development

growth_protocol: Dry seeds were cold stratified for two days at 4˚C before growing on soil mixture (4:2:1 mixture of Metromix Professional Growing Mix: vermiculite: perlite) in growth chambers at 23 ˚C under long-day conditions (16 h light / 8 h dark)

extract_protocol:
Total RNA was extracted from the pooled seeds of 30-40 siliques using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s instructions, followed by additional purification with sodium citrate to improve RNA quality. We obtained total RNA yields in the range of 1-3ug for ~50mg seeds. Using an Agilent Bioanalyzer, we confirmed that the RNA Integrity Number (RIN) for all samples was greater than 9.
Total RNA (500 ng) was sequenced at the Genomics Core at the University of Kansas Medical Center. The mRNA fraction was enriched with oligo dT capture, sized, reverse transcribed into cDNA and ligated with the appropriate indexed adaptors using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina). Following Agilent Bioanalyzer QC of the library preparation and library quantification using the Roche Lightcycler96 with KAPA SYBR Fast Universal qPCR kit (KAPA Biosystems), the RNA-Seq libraries were adjusted to a 4nM concentration and pooled for multiplexed sequencing. Libraries were denatured and based on qPCR results, diluted to the appropriate concentration, followed by clonal clustering onto the sequencing flow cell using the TruSeq Paired-End (PE) Cluster Kit v3-cBot-HS (Illumina). The clonal clustering procedure was automated using the Illumina cBOT Cluster Station. The clustered flow cell was sequenced on an Illumina HiSeq 2500 Sequencing System using the TruSeq SBS Kit v3-HS (Illumina) to obtain 100bp pair-end reads, which were trimmed and quality assessed before assembly against the Arabidopsis reference genome (Araport 11) using CLC genomics workbench (v 7.5.1).

treatment_protocol: To isolate seeds at different developmental stages, emerging flowers were tagged with the cotton thread at specific time intervals. Whole siliques were flash frozen in liquid nitrogen and stored at -80 ˚C. Seed harvesting from siliques was done on dry ice

tag: development stage

value: 8 days after flowering (DAF)

value: WT

tag: background ecotype

value: Columbia

value: Seed


title: MCF10A non tumorigenic cells curcumin and 2 Gy of photon dose - replicate5

description: Biological replicate 5 of 6

tag: treatment


title: 412457-PRE


title: MCF10A non tumorigenic cells curcumin and 2 Gy of photon dose - replicate3

description: Biological replicate 3 of 6


title: 422134-PRE


title: MCF10A non tumorigenic cells curcumin and 2 Gy of photon dose - replicate6

description: Biological replicate 6 of 6


title: MCF10A non tumorigenic cells curcumin and 2 Gy of photon dose - replicate1

description: Biological replicate 1 of 6


title: C3HF2_arsenite_non-tumor_3

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Ver 2.0Microarrays (G4858A) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

growth_protocol: Pregnant C3H/HeN mice (F0) were purchased from CLEA Japan and given free access to a standard diet (CA-1; CLEA Japan) and tap water (control mice) or tap water containing 85 ppm sodium arsenite (Sigma) from day 8 to 18 of gestation.  Throughout the experiments, arsenite was only given to F0 pregnant mice and not to F1 or F2 mice.  F1 male and female mice were mated at 10 weeks of age.  The resulting F2 males were reared until arround 74 weeks of age and used for the assessment.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

tag: f0 exposure

value: arsenite

tag: normal or tumor

value: non-tumor

tag: gender

value: male

value: 74 weeks


title: C3HF2_arsenite_tumor_3

value: tumor


title: C3HF2_arsenite_tumor_1


title: C3HF2_arsenite_normal_3

value: normal


title: MCF10A non tumorigenic cells curcumin and 2 Gy of photon dose - replicate2

description: Biological replicate 2 of 6

value: curcumin and exposed to 2 Gy of photon beam

tag: harvest time post treatment

value: 24 hours

tag: original tissue

value: breast


title: C3HF2_arsenite_normal_2


title: C3HF2_arsenite_non-tumor_2


title: C3HF2_arsenite_tumor_2


title: C3HF2_arsenite_normal_1


title: Treatment_E2

city: San Diego

first: Shicheng

last: Guo

state: CA

address: 8730 Costa Verde

institute: MCRI, SHSCI, GHH, UCSD

description: The array images were analyzed using Feature Extraction software (version 10.7.1.1, Agilent Technologies Inc., Santa Clara, CA, USA), and the raw data were obtained and basically analyzed with Genespring. The raw data were initially normalized with the quantile algorithm. The probes that at least in one out of two conditions had flags in “P” were chosen for further data analysis. Differentially expressed genes or lncRNAs were identified through fold change, as well as the calculated P value through t-test. The threshold set for upregulated and downregulated genes was a fold change ≥2.0 and a P ≤ 0.05.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

source_name: FLS_LLDT-8 for 24hrs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were isolated by enzymatic digestion of synovial tissues obtained from RA patients undergoing total joint replacement surgery. Tissues were minced into 1 x 1 x 1 mm pieces and treated for 2 h with 2-4 mg/ml of collagenase (Serva, GERMANY) in DMEM at 37°C in 5% CO2. Dissociated cells were then centrifuged at 500 × g, re-suspended in DMEM supplemented with 10% FCS (Gibco, USA), and plated in 75 cm2 flasks. The cultures were kept at 37°C in 5% CO2 and the culture medium was replaced every 2-3 days. When cells approached confluence, they were passed after diluting 1:3 with fresh medium and re-cultured until used. The purity of the cells was verified by flow cytometric analysis. The FLS, from passages 4, were seeded in 6-well plates.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: LLDT-8 (Shanghai Pharma, Shanghai) was dissolved with 2%DMSO and diluted with DMEM to 100nm/ml and the FLS cells in treatment group were cultured with previous DMEM while the FLS in control group were cultured with pure DMEM for 24 hours. Then all the FLS cells were cultured in DMEM including 10ng/ml TNFA and 10ng/ml IL-17 (PeproTech USA) for 12 hours. Finally, cells were collected and totally RNA were extracted with 1ml Trizol (GE, USA).

tag: subject status

value: rheumatoid arthritis (RA) patient

value: Female

tag: tissue

value: synovial biopsy

tag: cell type

value: Huamn rheumatoid arthritis fibroblast-like synoviocytes cell (FLS)

tag: treated with

value: LLDT-8 for 24hrs


title: C3HF2_arsenite_non-tumor_1

tag: age


title: Control_D1

data_processing: The array images were analyzed using Feature Extraction software (version 10.7.1.1, Agilent Technologies Inc., Santa Clara, CA, USA), and the raw data were obtained and basically analyzed with Genespring. The raw data were initially normalized with the quantile algorithm. The probes that at least in one out of two conditions had flags in “P” were chosen for further data analysis. Differentially expressed genes or lncRNAs were identified through fold change, as well as the calculated P value through t-test. The threshold set for upregulated and downregulated genes was a fold change ≥2.0 and a P ≤ 0.05.

source_name: FLS_DMEM for 24hrs

value: DMEM for 24hrs


title: Control_E1


title: Treatment_B2


title: Treatment_A2


title: Control_B1


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #1 on day 38, bio rep1

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #1 on day 38, biological rep1
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 38 after injection

hyb_protocol: Fragmented and biotin-labeled cDNA at a concentration of 25 ng/ul or 2.25 ug total was hybridized to the Mouse Gene 2.1 ST peg plate. The Mouse Gene 2.1 ST peg plate was hybridized, washed, stained and scanned using the Affymetrix GeneTitan MC instrument. The default method for the Mouse Gene 2.1 peg plate was used on the GeneTitan. The hybridization time for the expression plates was 17 hours and the temperature was 48 C.

scan_protocol: The Mouse Gene 2.1 ST peg plate was scanned using the Affymetrix GeneTitan MC instrument.

data_processing: The data were analyzed using Affymetrix Expression Console and the algorithm used was RMA (with background adjustment, quantile normalization and summarization).

label: biotin

label_protocol: The biotin-labeled cDNA was prepared from 250 ng of total RNA using the Ambion WT Expression Kit and Affymetrix WT Terminal Labeling Kit.

growth_protocol: Cells were grown using standard tissue culture until 60-80% confluent at which point RNA was isolated.

extract_protocol: Total RNA was extracted from the cells using the Quick RNA MiniPrep Zymo Research Kit (Genesee scientific).

treatment_protocol: No cell lines were exposed to any type of treatment.

value: balb/c


title: HKc/DR, SIX1 siR2, Replicate 4

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: Gene expression of HKc/DR cells transfected with anti-SIX1 siRNA-2 duplexes.

hyb_protocol: Amplified and labeled samples were hybridized to GeneChip HuGene 2.0 ST Arrays (Affymetrix) for 16 h at 45°C using a GeneChip Hybridization Oven 640 and a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). Hybridized arrays were washed and stained using GeneChip Fluidics Stations 450 (Affymetrix) according to the manufacturer’s protocol.

scan_protocol: Chip arrays were scanned using a GeneChip Scanner 3000 7G system and computer workstation equipped with GeneChip Command Console 4.0 software (Affymetrix).

data_processing: Scanner-generated probe cell intensity (CEL) files were imported into Expression Console Software (Affymetrix) and processed at the gene-level using Affymetrix’s HuGene-2_0-st library file and the Robust Multichip Analysis (RMA) algorithm to generate CHP files. After confirming good data quality within Expression Console, CHP files containing log2 expression signals for each probe were imported into Transcriptome Analysis Console (TAC) Software version 3.0.0.466 (Affymetrix) to analyze cell type specific transcriptional responses using one-way, between-subject, analysis of variance.

label: Biotin

source_name: Pre-malignant, differentiation-resistant, HPV16-immortalized human keratinocytes (HKc/DR) transfected with anti-SIX1 siRNA-2 duplexes.

label_protocol: Total RNA samples (100 ng) were amplified, fragmented and biotinylated using GeneChip WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) according to manufacturer's protocol. Amplified fragment size distribution was assessed before and after the fragmentation step using an Agilent’s 2100 Bioanalyzer.

growth_protocol: Cells were maintained in keratinocyte medium supplemented with epidermal growth factor (EGF), bovine pituitary extract (BPE) , 5% fetal bovine serum and 1 mM calcium chloride (DR medium) in a humidified atmosphere of 5% CO2 at 37° C.

extract_protocol: Total RNA was isolated from cells using Qiagen’s RNeasy Plus Micro Kit according to the manufacturer’s protocol. RNA was quantified using a NanoDrop 2000c spectrophotometer and integrity was monitored with an Agilent 2100 Bioanalyzer (RIN 9.5-10.0).

treatment_protocol: Cells were seeded in 6-well plates, grown to 70% confluency and transfected with anti-SIX1 or anti-GFP siRNA (control) siRNA duplexes (90 pmol per well) using Lipofectamine RNAiMAX (Invitrogen) following the manufacturer’s instructions. Cells were incubated for 48 h before harvesting them.

tag: transfected with

value: anti-SIX1 siRNA-2


title: Treatment_D2


title: Treatment_C2

value: Male


title: Control_C1


title: C3HF2_control_non-tumor_3

value: control

value: non-tumor


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 43, bio rep3 (from sample 'AxLN Lung Mets2-6wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 43, biological rep3 (belonging to sample type 'AxLN Lung Mets2-6wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 43 after injection


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 43, bio rep2 (from sample 'AxLN Lung Mets2-6wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 43, biological rep2 (belonging to sample type 'AxLN Lung Mets2-6wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 43 after injection


title: HKc/DR, SIX1 siR2, Replicate 1


title: C3HF2_control_non-tumor_2

value: male

value: 74 weeks


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #1 on day 38, bio rep2

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #1 on day 38, biological rep2
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 38 after injection


title: Control_A1


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #1 on day 38, bio rep3

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #1 on day 38, biological rep3
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 38 after injection


title: HKc/DR, SIX1 siR2, Replicate 3


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 43, bio rep1 (from sample 'AxLN Lung Mets2-6wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 43, biological rep1 (belonging to sample type 'AxLN Lung Mets2-6wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 43 after injection


title: C3HF2_control_non-tumor_1


title: HKc/DR, SIX1 siR2, Replicate 2


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #5 on day 14, bio rep3, removed

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #5 on day 14, biological rep3, removed
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 14 after injection


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #2 on day 14, bio rep3

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #2 on day 14, biological rep3
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 14 after injection


title: HKc/DR, SIX1 siR1, Replicate 4

description: Gene expression of HKc/DR cells transfected with anti-SIX1 siRNA-1 duplexes.

source_name: Pre-malignant, differentiation-resistant, HPV16-immortalized human keratinocytes (HKc/DR) transfected with anti-SIX1 siRNA-1 duplexes.

value: anti-SIX1 siRNA-1


title: 48h_5Fu_M231_3

city: Adelaide

first: David

middle: L.

last: Adelson

state: South Australia

address: University of Adelaide

department: Molecular and biomedical science

country: Australia

institute: University of Adelaide

description:
unstranded paired-end RNA-seq
M231_5fu_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Trim_galore (v0.3.7, Babraham Bioinformatics) was used to trim adaptors and low-quality sequences in raw reads with parameters:  --stringency 5 --paired. Then trimmed reads were aligned to reference genome (hg19, UCSC) using STAR (v2.5.3a) with parameters: --outSAMstrandField intronMotif --outSAMattributes All --outFilterMismatchNmax 10 --seedSearchStartLmax 30
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg19, UCSC
Supplementary_files_format_and_content: Tab delimited matrix showing raw counts of refGenes

source_name: total RNAs, cell line

growth_protocol: Human epidermoid carcinoma cell line A431 and huaman adenocarcinoma cell line were purchased from ATCC (CRL-1555™ for A431 and HTB-26™ for MDA-MB-231, VA, USA) and were cultured in DMEM medium (Thermo Fisher Scientifc, MA, USA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientifc, MA, USA) at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
RNA libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Massachusetts, USA) according to the manufacturer's protocol.

treatment_protocol: Drug treatments were designed as follows: CKI  (1.0 mg/mL), doxorubicin (1 ng/ml and 5 mg/ml) and  5-Fu (10 ug/ml )

tag: agent

tag: tumor type

value: adenocarcinoma


title: 4T1-mCherry-rLuc cells from AxLN tumor #2 on day 14, bio rep3 (from sample 'Axillary LN-2wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #2 on day 14, biological rep3 (belonging to sample type 'Axillary LN-2wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 14 after injection


title: HKc/DR, SIX1 siR1, Replicate 2

tag: cell line


title: HKc/DR, SIX1 siR1, Replicate 3


title: HKc/DR, SIX1 siR1, Replicate 1


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #2 on day 14, bio rep1

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #2 on day 14, biological rep1
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 14 after injection


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #2 on day 14, bio rep2

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #2 on day 14, biological rep2
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 14 after injection


title: 48h_5Fu_M231_2

description:
unstranded paired-end RNA-seq
M231_5fu_2


title: 4T1-mCherry-rLuc cells from AxLN tumor #2 on day 14, bio rep1 (from sample 'Axillary LN-2wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #2 on day 14, biological rep1 (belonging to sample type 'Axillary LN-2wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 14 after injection


title: HKc/DR, CONTROL, Replicate 4

description: Gene expression of HKc/DR cells transfected with control, anti-GFP siRNA duplexes.

source_name: Pre-malignant, differentiation-resistant, HPV16-immortalized human keratinocytes (HKc/DR) transfected with control, anti-GFP siRNA duplexes.

value: anti-GFP siRNA


title: 4T1-mCherry-rLuc cells from AxLN tumor #2 on day 7, bio rep3 (from sample 'Axillary LN2-1wk')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #2 on day 7, biological rep3 (belonging to sample type 'Axillary LN2-1wk')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 7 after injection


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #5 on day 14, bio rep2, removed

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #5 on day 14, biological rep2, removed
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 14 after injection


title: HKc/DR, CONTROL, Replicate 3


title: 48h_CKI+5Fu_M231_3

description:
unstranded paired-end RNA-seq
M231_5_C_3


title: 48h_CKI+5Fu_M231_2

description:
unstranded paired-end RNA-seq
M231_5_C_2


title: 48h_CKI+5Fu_M231_1

description:
unstranded paired-end RNA-seq
M231_5_C_1


title: 48h_5Fu_M231_1

description:
unstranded paired-end RNA-seq
M231_5fu_1


title: 48h_CKI_1/20_M231_3

description:
unstranded paired-end RNA-seq
M231_C1_20_3


title: 48h_CKI_1/20_M231_1

description:
unstranded paired-end RNA-seq
M231_C1_20_1


title: 48h_vehicle_control_A431_3

description:
unstranded paired-end RNA-seq
A431_VC_3

value: epidermoid carcinoma


title: 48h_CKI_1/20_M231_2

description:
unstranded paired-end RNA-seq
M231_C1_20_2


title: 48h_untreated_M231_3

description:
unstranded paired-end RNA-seq
M231_M3


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #5 on day 14, bio rep1, removed

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #5 on day 14, biological rep1, removed
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 14 after injection


title: HKc/DR, CONTROL, Replicate 2


title: HKc/DR, CONTROL, Replicate 1


title: 48h_untreated_M231_2

description:
unstranded paired-end RNA-seq
M231_M2


title: 48h_vehicle_control_A431_1

description:
unstranded paired-end RNA-seq
A431_VC_1


title: 4T1-GFP-fLuc cells from MFP tumor #1 on day 28, plate 2, bio rep2 (from sample 'Breast Tumor1-4wks')

description:
4T1-GFP-fLuc cells isolated from MFP tumor #1 on day 28, plate 2, biological rep2 (belonging to sample type 'Breast Tumor1-4wks')
Gene expression data from 4T1-GFP-fLuc (murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase) that were injected into mammary fat pad and then isolated on day 28 after injection


title: 4T1-mCherry-rLuc cells from AxLN tumor #2 on day 14, bio rep2 (from sample 'Axillary LN-2wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #2 on day 14, biological rep2 (belonging to sample type 'Axillary LN-2wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 14 after injection


title: 4T1-mCherry-rLuc cells from AxLN tumor #2 on day 7, bio rep2 (from sample 'Axillary LN2-1wk')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #2 on day 7, biological rep2 (belonging to sample type 'Axillary LN2-1wk')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 7 after injection


title: 4T1-mCherry-rLuc, murine breast cancer cells, plate 2, bio rep2

description:
4T1-mCherry-rLuc, murine breast cancer cells, plate 2, biological rep2
Gene expression data from 4T1-mCherry-rLuc, murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase


title: 4T1-mCherry-rLuc cells from AxLN tumor #2 on day 7, bio rep1 (from sample 'Axillary LN2-1wk')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #2 on day 7, biological rep1 (belonging to sample type 'Axillary LN2-1wk')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 7 after injection


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 36, bio rep3 (from sample 'AxLN Lung Mets1-6wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 36, biological rep3 (belonging to sample type 'AxLN Lung Mets1-6wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 36 after injection


title: 4T1-GFP/fLuc, murine breast cancer cells, plate 2, bio rep2

description:
4T1-GFP/fLuc, murine breast cancer cells, plate 2, biological rep2
Gene expression data from 4T1-GFP/fLuc, murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase


title: 48h_CKI+Doxorubicin_A431_3

description:
unstranded paired-end RNA-seq
A431_C_D_3

value: CKI+Doxorubicin


title: 4T1-GFP-fLuc cells from MFP tumor #1 on day 28, plate 2, bio rep1 (from sample 'Breast Tumor1-4wks')

description:
4T1-GFP-fLuc cells isolated from MFP tumor #1 on day 28, plate 2, biological rep1 (belonging to sample type 'Breast Tumor1-4wks')
Gene expression data from 4T1-GFP-fLuc (murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase) that were injected into mammary fat pad and then isolated on day 28 after injection


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 36, bio rep2 (from sample 'AxLN Lung Mets1-6wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 36, biological rep2 (belonging to sample type 'AxLN Lung Mets1-6wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 36 after injection


title: 48h_vehicle_control_A431_2

description:
unstranded paired-end RNA-seq
A431_VC_2


title: 4T1-GFP/fLuc, murine breast cancer cells, plate 2, bio rep1

description:
4T1-GFP/fLuc, murine breast cancer cells, plate 2, biological rep1
Gene expression data from 4T1-GFP/fLuc, murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase


title: 48h_CKI+Doxorubicin_A431_2

description:
unstranded paired-end RNA-seq
A431_C_D_2


title: 48h_untreated_M231_1

description:
unstranded paired-end RNA-seq
M231_M1


title: 48h_Doxorubicin_A431_3

description:
unstranded paired-end RNA-seq
A431_Doxo_3

value: Doxorubicin


title: 48h_CKI_1/20_A431_3

description:
unstranded paired-end RNA-seq
A431_C_1_20_3


title: 48h_Doxorubicin_A431_1

description:
unstranded paired-end RNA-seq
A431_Doxo_1


title: 4T1-mCherry-rLuc, murine breast cancer cells, plate 2, bio rep1

description:
4T1-mCherry-rLuc, murine breast cancer cells, plate 2, biological rep1
Gene expression data from 4T1-mCherry-rLuc, murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase


title: 48h_CKI_1/20_A431_2

description:
unstranded paired-end RNA-seq
A431_C_1_20_2


title: 48h_CKI_1/20_A431_1

description:
unstranded paired-end RNA-seq
A431_C_1_20_1


title: 48h_CKI+Doxorubicin_A431_1

description:
unstranded paired-end RNA-seq
A431_C_D_1


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 36, bio rep1 (from sample 'AxLN Lung Mets1-6wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 36, biological rep1 (belonging to sample type 'AxLN Lung Mets1-6wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 36 after injection


title: 48h_untreated_A431_1

description:
unstranded paired-end RNA-seq
A431_M1


title: 4T1-GFP-fLuc cells from MFP tumor #2 on day 28, bio rep3 (from sample 'Breast Tumor2-4wks')

description:
4T1-GFP-fLuc cells isolated from MFP tumor #2 on day 28, biological rep3 (belonging to sample type 'Breast Tumor2-4wks')
Gene expression data from 4T1-GFP-fLuc (murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase) that were injected into mammary fat pad and then isolated on day 28 after injection


title: 48h_untreated_A431_2

description:
unstranded paired-end RNA-seq
A431_M2


title: 48h_untreated_A431_3

description:
unstranded paired-end RNA-seq
A431_M3


title: 48h_Baituling_1/10_3

description: unstranded paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
The adaptors and low-quality sequences in raw reads were trimmed with Trim_galore (v0.3.7, Babraham Bioinformatics) using parameters: --stringency 5 --paired. STAR (v2.5.3a) was used to align reads to reference genome (hg19, UCSC) with parameters: --outSAMstrandField intronMotif --outSAMattributes All --outFilterMismatchNmax 10 --seedSearchStartLmax 30
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg19, UCSC
Supplementary_files_format_and_content: Tab delimited matrix showing raw counts of refGenes

growth_protocol: Human adenocarcinoma cell line were purchased from ATCC ( HTB-26™ , VA, USA) and were cultured in DMEM medium (Thermo Fisher Scientifc, MA, USA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientifc, MA, USA) at 37°C with 5% CO2.

treatment_protocol: Drug treatments were designed as follows: CKI  (2.0 mg/mL), Kushen injection (same ratio with CKI) and  Baituling injection (same ratio with CKI )

value: Baituling injection


title: 4T1-GFP-fLuc cells from MFP tumor #2 on day 28, bio rep1 (from sample 'Breast Tumor2-4wks')

description:
4T1-GFP-fLuc cells isolated from MFP tumor #2 on day 28, biological rep1 (belonging to sample type 'Breast Tumor2-4wks')
Gene expression data from 4T1-GFP-fLuc (murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase) that were injected into mammary fat pad and then isolated on day 28 after injection


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #1 on day 14, bio rep2

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #1 on day 14, biological rep2
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 14 after injection


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #1 on day 14, bio rep3

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #1 on day 14, biological rep3
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 14 after injection


title: 48h_Baituling_1/10_2

description: unstranded paired-end RNA-seq


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 14, bio rep3 (from sample 'AxLN Lung Mets-2wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 14, biological rep3 (belonging to sample type 'AxLN Lung Mets-2wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 14 after injection


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 14, bio rep1 (from sample 'AxLN Lung Mets-2wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 14, biological rep1 (belonging to sample type 'AxLN Lung Mets-2wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 14 after injection


title: 4T1-GFP-fLuc cells from MFP tumor #2 on day 28, bio rep2 (from sample 'Breast Tumor2-4wks')

description:
4T1-GFP-fLuc cells isolated from MFP tumor #2 on day 28, biological rep2 (belonging to sample type 'Breast Tumor2-4wks')
Gene expression data from 4T1-GFP-fLuc (murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase) that were injected into mammary fat pad and then isolated on day 28 after injection


title: 4T1-mCherry-rLuc cells from AxLN-derived lung metastasis #1 on day 14, bio rep2 (from sample 'AxLN Lung Mets-2wks')

description:
4T1-mCherry-rLuc cells isolated from AxLN-derived lung metastasis #1 on day 14, biological rep2 (belonging to sample type 'AxLN Lung Mets-2wks')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from a lung metastasis on day 14 after injection


title: 48h_Doxorubicin_A431_2

description:
unstranded paired-end RNA-seq
A431_Doxo_2


title: 4T1-mCherry-rLuc cells from AxLN tumor #1 on day 14, bio rep1, removed

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #1 on day 14, biological rep1, removed
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 14 after injection


title: 4T1-mCherry-rLuc cells from AxLN tumor #1 on day 14, bio rep3, removed

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #1 on day 14, biological rep3, removed
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 14 after injection


title: 4T1-mCherry-rLuc cells from AxLN tumor #1 on day 7, bio rep3 (from sample 'Axillary LN1-1wk')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #1 on day 7, biological rep3 (belonging to sample type 'Axillary LN1-1wk')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 7 after injection


title: 4T1-mCherry-rLuc cells from AxLN tumor #1 on day 14, bio rep2, removed

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #1 on day 14, biological rep2, removed
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 14 after injection


title: 4T1 breast cancer cells from tail vein-derived lung metastasis #1 on day 14, bio rep1

description:
4T1 breast cancer cells isolated from tail vein-derived lung metastasis #1 on day 14, biological rep1
Gene expression data from 4T1 breast cancer cells that were injected into tail vein and then isolated from lung metastasis on day 14 after injection


title: 48h_Baituling_1/10_1

description: unstranded paired-end RNA-seq


title: 48h_Kushen_1/10_2

description: unstranded paired-end RNA-seq

value: Kushen injection


title: 48h_Kushen_1/10_1

description: unstranded paired-end RNA-seq


title: 48h_CKI_1/10_3

description: unstranded paired-end RNA-seq

value: CKI


title: 4T1-mCherry-rLuc cells from AxLN tumor #1 on day 7, bio rep2 (from sample 'Axillary LN1-1wk')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #1 on day 7, biological rep2 (belonging to sample type 'Axillary LN1-1wk')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 7 after injection


title: 48h_CKI_1/10_1

description: unstranded paired-end RNA-seq


title: 4T1-GFP-fLuc cells from MFP tumor #1 on day 28, bio rep2, removed

description:
4T1-GFP-fLuc cells isolated from MFP tumor #1 on day 28, biological rep2, removed
Gene expression data from 4T1-GFP-fLuc (murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase) that were injected into mammary fat pad and then isolated on day 28 after injection

source_name: 4T1-GFP-fLuc cells isolated from MFP tumor on day 28


title: 4T1-mCherry-rLuc, murine breast cancer cells, bio rep2

description:
4T1-mCherry-rLuc, murine breast cancer cells, biological rep2
Gene expression data from 4T1-mCherry-rLuc, murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase


title: 4T1-mCherry-rLuc cells from AxLN tumor #1 on day 7, bio rep1 (from sample 'Axillary LN1-1wk')

description:
4T1-mCherry-rLuc cells isolated from AxLN tumor #1 on day 7, biological rep1 (belonging to sample type 'Axillary LN1-1wk')
Gene expression data from 4T1-mCherry-rLuc (murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase) that were injected into axillary lymph nodes and then isolated from the lymph node tumor on day 7 after injection


title: 4T1-GFP-fLuc cells from MFP tumor #1 on day 28, bio rep1 (from sample 'Breast Tumor1-4wks')

description:
4T1-GFP-fLuc cells isolated from MFP tumor #1 on day 28, biological rep1 (belonging to sample type 'Breast Tumor1-4wks')
Gene expression data from 4T1-GFP-fLuc (murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase) that were injected into mammary fat pad and then isolated on day 28 after injection


title: HeLa NBT rep1_RNASeq

city: Shanghai

first: ZhaoQing

last: Zheng

address: 1200, CaiLun Rd

country: China

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
We mapped RNA-seq reads to transcriptome (Ensembl, release 72) using the software TopHat (v1.4.1).
Cuffdiff (v2.2.0) was used to calculate RNA-seq based gene expression levels using the FPKM metric (fragments per kilobase of exon per million fragments mapped).
We also used Cuffdiff to identify 2350 differentially expressed genes between control and NBT samples using the cutoff of Cuffdiff FDR<5%, an extra filter of p-value≤0.01 from two-sided t-test on FPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample ...

source_name: cervical cancer cells

extract_protocol:
After NBT treatment,cells were collected and RNA was harvested using Trizol reagent.Total RNA samples having RIN > 8 were subjected to library generation using TruSeq mRNA library Kit (Illumina) and sequenced on a HiSeqX PE150
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human cervix carcinoma

value: HeLa

value: cervical

value: NBT


title: HeLa NBT rep3_RNASeq


title: HeLa NBT rep2_RNASeq


title: Both rep 1

city: Toronto

first: Steven

middle: M

last: Chan

state: Ontario

address: 101 College Street, Room 8-354

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
The sequencing data is in FASTQ format generated using bcl2fastq2 v2.17. The quality of the data is assessed using FastQC v.0.11.2.
Fastq files were aligned to UCSC hg19, downloaded from http://support.illumina.com/sequencing/sequencing_software/igenome.html
Reads were trimed using Trim Galore v1.8 and aligned to the reference genome using Tophat v.2.0.11.
Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2 (HTSeq, http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
EdgeR(v3.2.4) function 'rpkm' was to compute rpkm values for each gene in each sample.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

source_name: MOLM13-R2 AML cell line

growth_protocol: MOLM13-R2 cells were grown in RPMI 1640 medium with 10% FBS and 2mM Gluta-Plus.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).
Libraries were prepared using NEBNExt Ultra Directional RNA library prep kit as per manufacturer's instructions

treatment_protocol: Cells were treated with DMSO (vehicle control), venetoclax alone (500 nM), tedizolid alone (5 uM), or combination of the two drugs for 4 days.

value: venetoclax (500 nM) + tedizolid (5 uM)


title: HeLa DMSO rep3_RNASeq

value: DMSO


title: Venetoclax rep 2

value: venetoclax (500 nM)


title: Both rep 2


title: Tedizolid rep 2

value: tedizolid (5 uM)


title: HeLa DMSO rep2_RNASeq


title: Venetoclax rep 1


title: Tedizolid rep 1


title: 4T1-mCherry-rLuc, murine breast cancer cells, bio rep1

description:
4T1-mCherry-rLuc, murine breast cancer cells, biological rep1
Gene expression data from 4T1-mCherry-rLuc, murine breast cancer cells labeled with mCherry fluorescent reporter and renilla luciferase

value: balb/c


title: 48h_Kushen_1/10_3

description: unstranded paired-end RNA-seq

value: adenocarcinoma


title: 4T1-GFP/fLuc, murine breast cancer cells, bio rep1

description:
4T1-GFP/fLuc, murine breast cancer cells, biological rep1
Gene expression data from 4T1-GFP/fLuc, murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase


title: HeLa DMSO rep1_RNASeq


title: DMSO rep 2


title: 48h_CKI_1/10_2

description: unstranded paired-end RNA-seq


title: corrected Pt_hiPSCs

city: seoul

first: Hyun-Seob

address: 71 Daehak-ro, Jongno-gu

department: Biomedical research institute

country: South Korea

institute: Seoul national University Hospital

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  UCSC transcript using Transcriptome with novel splices
Fragments Per Kilobase of exon per Million (FPKM) were performed using cufflinks.
Genome_build: UCSC (hg19)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: iPSCs

growth_protocol: iPSC-derived NSCs were grown on fibronectin coated- with normal neural stem cell medium with basic FGF supplementation.

extract_protocol:
total RNA were isolated from hiPSCs using Trizol reagent. Lexogen SENSE mRNA Library Preparation Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSC derived neural stem cell

tag: genotype

value: corrected LIN28A R192R


title: DMSO rep 1

tag: treatment


title: D1471202G_MDCF3_Treatment

type: protein

first: Jeanette

last: Gehrig

state: Missouri

address: 4515 McKinley

institute: Washington University School of Medicine

hyb_protocol: Following the manufacturer’s protocol and utilizing SOMAmer reagents immobilized on streptavidin beads, proteins from plasma samples were tagged with NHS-biotin reagent, captured as a SOMAmer reagent/protein complex, cleaved, denatured, eluted and hybridized to a custom Agilent DNA microarray. Additional details can be found at http://www.tandfonline.com/doi/abs/10.1586/erm.10.89 and Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

scan_protocol: Microarrays were scanned with an Agilent SureScan scanner at 5 um resolution, and the Cy3 fluorescence readout was quantified. Additional information can be found in Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

data_processing: Raw signal values were processed using Somalogic's SOMAscan standardization procedures, including hybridization normalization, plate scaling, median scaling, and final somamer calibration as described in http://www.tandfonline.com/doi/abs/10.1586/erm.10.89.

molecule: protein

source_name: non-fasted plasma

extract_protocol: Non-fasting venous blood was collected into EDTA-coated tubes, spun, separated into plasma, aliquoted and snap-frozen at -80C until sample processing.

treatment_protocol: Non-fasting plasma collected in EDTA-coated tubes

tag: group

value: Male

tag: wlz

tag: waz

tag: laz


title: D1470202G_MDCF3_Treatment

label_protocol: Following the manufacturer’s protocol and utilizing SOMAmer reagents immobilized on streptavidin beads, proteins from plasma samples were tagged with NHS-biotin reagent, captured as a SOMAmer reagent/protein complex, cleaved, denatured, eluted and hybridized to a custom Agilent DNA microarray. Additional details can be found at http://www.tandfonline.com/doi/abs/10.1586/erm.10.89 and Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

tag: gender


title: D1471201G_MDCF3_Baseline


title: D1470201G_MDCF3_Baseline


title: 4T1-GFP/fLuc, murine breast cancer cells, bio rep2

description:
4T1-GFP/fLuc, murine breast cancer cells, biological rep2
Gene expression data from 4T1-GFP/fLuc, murine breast cancer cells labeled with Green Fluorescent Protein and firefly luciferase

tag: strain


title: Huh7_control_ACTTGAA

city: Amsterdam

first: Cun

address: Plesmanlaan 121,

department: Division of Molecular Carcinogenesis

country: Netherlands

institute: The Netherlands Cancer Institute

description:
polyA+ stranded RNA Library prep from sample
4953_8_Huh7_control_ACTTGAA

data_processing:
The reads were sequenced using a stranded RNA protocol
The reads that are of low complexity or repetitive sequences are filtered
The reads are mapped to the transcriptome.  Reads that do not map to the transcriptome are used for a whole genome mapping in the last step.
Samples are aligned with HiSat2. settings: --min-intronlen 20 --max-intronlen 500000 --rna-strandness F  -k 5 --minins 0 --maxins 500 --fr --new-summary
Steps performed: link, count, QCstrandness, eset
Read counts are determined.Count parameters    Count library type stranded: true  Icount (based on HTSeq-count) GTF version: Homo_sapiens.GRCh38.87.gtf    mode -> union: If a read is mapped to a region with overlapping genes, this read will be dismissed. However, when stranded RNA sequencing has been performed, the read can be used there is an overlap of 2 genes which are in opposite direction.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

molecule: polyA RNA

growth_protocol: Cells were cultured in DMEM with 10% FBS, glutamine and penicillin/streptomycin (Gibco®) at 37 °C / 5% CO2.

extract_protocol:
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hep3B and Huh7 cells are treated with THZ531 for 24 hours. SNU449 cells are treated with THZ531 for 48 hours.

value: liver cancer cell line

value: none (control)


title: SNU449_500nM_GTTTCGG

description:
polyA+ stranded RNA Library prep from sample
4953_13_SNU449_500nM_GTTTCGG

value: 500nM THZ531 for 48 hrs


title: Huh7_250nM_GATCAGA

description:
polyA+ stranded RNA Library prep from sample
4953_9_Huh7_250nM_GATCAGA

value: 250nM THZ531 for 48 hrs


title: Hep3B_250nM_ATCACGA

description:
polyA+ stranded RNA Library prep from sample
4953_6_Hep3B_250nM_ATCACGA


title: Hep3B_control_GTGAAAC

description:
polyA+ stranded RNA Library prep from sample
4953_5_Hep3B_control_GTGAAAC


title: D1455202G_MDCF3_Treatment

value: Female


title: D1454202G_MDCF3_Treatment


title: D1455201G_MDCF3_Baseline


title: D1458201G_MDCF3_Baseline


title: Huh7_500nM_TAGCTTA

description:
polyA+ stranded RNA Library prep from sample
4953_10_Huh7_500nM_TAGCTTA


title: D1451202G_MDCF3_Treatment


title: Pt_hiPSCs

value: LIN28A R192G heterozygous


title: SNU449_control_GGCTACA

description:
polyA+ stranded RNA Library prep from sample
4953_11_SNU449_control_GGCTACA


title: R0821

city: Cincinnati

first: Zhenhua

last: Luo

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The RNA-seq reads were aligned to the human genome (GRCh37/hg19) using TopHat (version 2.1.0)
Transcript quantifications were performed by Cufflinks v2.2.1
Transcript abundances were normalized in reads per kilobase of exon per million mapped reads (RPKM) for single end RNA-seq and fragments per kilobase of exon per million mapped reads (FPKM) for paired end RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM or FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated from liver biopsies using the miRNeasy Kit (QIAGEN). RNA purity was assessed using the Agilent 2100 Bioanalyzer. Total RNA was converted to cDNA using High-Capacity cDNA Reverse Transcrition Kit (ABI).
The cDNA was then used for Illumina sequencing library preparation by TruSeq Stranded mRNA Library Prep Kit. DNA fragments were further end repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls and adapters were ligated for single end or paired end sequencing on Illumina HiSeq 2500.

tag: disease state

value: Biliary Atresia

value: Liver


title: R0526

tag: tissue


title: R0421


title: D1444202G_MDCF3_Treatment


title: D1451201G_MDCF3_Baseline


title: D1437201G_MDCF3_Baseline


title: D1437202G_MDCF3_Treatment


title: SNU449_250nM_GTGGCCT

description:
polyA+ stranded RNA Library prep from sample
4953_12_SNU449_250nM_GTGGCCT

tag: cell type


title: D1458202G_MDCF3_Treatment


title: R0103


title: Hep3B_500nM_TTAGGCA

description:
polyA+ stranded RNA Library prep from sample
4953_7_Hep3B_500nM_TTAGGCA


title: R0039


title: D1454201G_MDCF3_Baseline


title: P2078


title: P1099


title: D1444201G_MDCF3_Baseline


title: P1078


title: D1436201G_MDCF3_Baseline


title: P0935


title: P0919


title: D1432201G_MDCF3_Baseline


title: D1432202G_MDCF3_Treatment


title: P0833


title: D1429202G_MDCF3_Treatment


title: D1428202G_MDCF3_Treatment


title: D1429201G_MDCF3_Baseline


title: D1428201G_MDCF3_Baseline


title: P0514


title: D1422201G_MDCF3_Baseline


title: D1422202G_MDCF3_Treatment


title: D1420202G_MDCF3_Treatment


title: N0781


title: D1436202G_MDCF3_Treatment


title: N0736


title: human HEK293T H3K4me3 - 96

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

description: scACT-seq

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Read in the raw fastq files are separated into 96 files correponding to the 96 pairs of cell barcode. The 96 pairs of barcodes are shown in the file named barcode_96.txt. A read is considered to belong to one of the barcode if the beginning of correpsonding read1 or read 2 contain the same pair of barcodes in theleft and right column respectively.  After separting each set of fastq files into 96 set of files, the 34bp starting from 5' is trimmed and the remainging reads are mapped to human genome using bowtie2.
Since 18 nuclei is sorted for each well, we removed doublets and the top 14 ranked barcodes are considered to be cells. The doublets and the number of 14 were calculated based on the collision rate the same as in the reference (Science. 2015 May 22; 348(6237): 910–914. ) . With requiring the qualified cells have reads more than 500, 1246 single cells are obtained. On the other hand, Using the publsihed HEK293T DNase-seq data, we identified 15756 DHS (as shown in the file called peaks_15756_HEK293T.txt). For each cell, we  calculated the reads that were located within the DHS. Finally, we obtained a read count file for the single cells, in which the 1246 columns referred to single cells, and the 15756 rows refer to 15756 DHS regions.
Genome_build: hg18
Supplementary_files_format_and_content: barcode_96.txt: 2column.  The left column refer to barcode on read 1 starting from the 5' end while The right column refer to barcode on read 1 starting from the 5' end
Supplementary_files_format_and_content: peaks_15756_HEK293T.txt: the first column is chromsome, 2nd column is the start of DHS, 3rd column is the end of DHS
Supplementary_files_format_and_content: scH3K4me3_1246_cells_counts_at_293T.txt: This file contain the read count data of single cells. Each column refer a single cell and each row refer to a DHS, resulting in a matrix of 15756 x 1246. Each element in the matrix represent the number of reads from the single cell located within the DHS.

extract_protocol:
HEK293T cells were washed with PBS and permeabilized using a 10 min incubation on ice in 500 mL of complex formation buffer per ~1 million cells. After permeabilization, all subsequent centrifugations of cells were performed using the following procedure: 1 min spin at 250 *g, rotate tubes 180°, repeat spin, leave ~10 mL of solution in the tube when removing buffer. Pelleted cells were washed once with 500 mL of complex formation buffer and suspended in another 500 mL of buffer. Aliquots of 1,000 cell equivalents were transferred volumetrically to clean microcentrifuge tubes and adjusted to 50 mL total volume using complex formation buffer. 5 mL of antibody-bound PA-Tnp complex was added to each 50 mL cell aliquot and incubated at room temperature for 60 min to allow chromatin binding. Unbound complex was removed using three washes performed as follows: pellet and suspend cells in 500 mL of wash buffer (50 mM Tris pH 8.0, 150 mM NaCl, 0.1% Triton X-100), rotate tube for 8 min at room temperature, repeat. Pelleted cells were rinsed with 500 mL of rinse buffer (50 mM Tris pH 8.0, 50 mM NaCl, 0.1% Triton X-100). The rinse buffer was removed and 90 mL of reaction buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM MgCl2, 0.1% Triton X-100) was added to the pelleted cells for a total volume of ~100 mL. The tubes were incubated for 30 min at 37 °C to allow transposition to occur. The reaction was terminated by addition of 4 mL of 0.5 M EDTA, 2 mL of 10% SDS, and 1 mL of 20 mg/mL Proteinase K followed by a 60 min incubation at 65 °C.
DNA was purified using phenol-chloroform-isopentanol extraction and ethanol precipitation. The DNA pellet was suspended in 10 mL of 10 mM Tris pH 8.0. PCR reactions for library preparation were performed by adding the following to the 10 mL DNA sample: 25 mL of Phusion High-fidelity PCR Master Mix (NEB catalog # M0531S), 1 mL of 5¢ library index barcode, 1 mL of 3¢ library index barcode, and 13 mL of nuclease-free water. Amplification was performed using an initial step of 72 °C for 5 min followed by 15 cycles of: 98 °C for 10 s, 65 °C for 30 s, 72 °C for 15 s, and a final extension step of 72 °C for 5 min. The PCR products were analyzed using agarose gel electrophoresis. Fragments of the desired size were excised and purified using a QIAquick Gel Extraction kit (Qiagen cat # 28506).
scACT-seq

tag: cell lines


title: D1413202G_MDCF3_Treatment

city: St. Louis

tag: age


title: D1420201G_MDCF3_Baseline


title: P2012


title: N0546


title: P0945


title: P0978


title: D1413201G_MDCF3_Baseline


title: human HEK293T H3K4me3 - 95

description: scACT-seq


title: human HEK293T H3K4me3 - 93

description: scACT-seq


title: human HEK293T H3K4me3 - 94

description: scACT-seq


title: N0537


title: N0167


title: human HEK293T H3K4me3 - 90

description: scACT-seq


title: human HEK293T H3K4me3 - 88

description: scACT-seq


title: human HEK293T H3K4me3 - 89

description: scACT-seq


title: human HEK293T H3K4me3 - 92

description: scACT-seq


title: human HEK293T H3K4me3 - 91

description: scACT-seq


title: human HEK293T H3K4me3 - 87

description: scACT-seq


title: N0140


title: D1401201G_MDCF3_Baseline


title: human HEK293T H3K4me3 - 84

description: scACT-seq


title: L0214


title: human HEK293T H3K4me3 - 86

description: scACT-seq


title: N0107


title: Ctrl43182G_Healthy

value: Healthy


title: Ctrl43242G_Healthy


title: Ctrl42922G_Healthy


title: human HEK293T H3K4me3 - 85

description: scACT-seq


title: L0162


title: human HEK293T H3K4me3 - 82

description: scACT-seq


title: human HEK293T H3K4me3 - 83

description: scACT-seq


title: Ctrl42682G_Healthy


title: human HEK293T H3K4me3 - 81

description: scACT-seq


title: Ctrl42522G_Healthy


title: human HEK293T H3K4me3 - 80

description: scACT-seq


title: human HEK293T H3K4me3 - 79

description: scACT-seq


title: 70650


title: 70638


title: D1401202G_MDCF3_Treatment


title: human HEK293T H3K4me3 - 78

description: scACT-seq


title: human HEK293T H3K4me3 - 77

description: scACT-seq


title: human HEK293T H3K4me3 - 76

description: scACT-seq


title: 70616


title: Ctrl42222G_Healthy


title: human HEK293T H3K4me3 - 75

description: scACT-seq


title: human HEK293T H3K4me3 - 74

description: scACT-seq


title: human HEK293T H3K4me3 - 73

description: scACT-seq


title: Ctrl42182G_Healthy


title: Ctrl42022G_Healthy


title: 61171


title: human HEK293T H3K4me3 - 71

description: scACT-seq


title: human HEK293T H3K4me3 - 70

description: scACT-seq


title: human HEK293T H3K4me3 - 69

description: scACT-seq


title: Ctrl41882G_Healthy


title: 61182


title: 61104


title: human HEK293T H3K4me3 - 68

description: scACT-seq


title: human HEK293T H3K4me3 - 67

description: scACT-seq


title: 61096


title: Ctrl41682G_Healthy


title: Ctrl41722G_Healthy


title: human HEK293T H3K4me3 - 65

description: scACT-seq


title: human HEK293T H3K4me3 - 64

description: scACT-seq


title: Ctrl41442G_Healthy


title: human HEK293T H3K4me3 - 66

description: scACT-seq


title: human HEK293T H3K4me3 - 63

description: scACT-seq


title: 61085


title: 61041


title: 61193


title: Ctrl41222G_Healthy


title: human HEK293T H3K4me3 - 72

description: scACT-seq


title: human HEK293T H3K4me3 - 61

description: scACT-seq


title: human HEK293T H3K4me3 - 62

description: scACT-seq


title: Ctrl40942G_Healthy


title: 61007


title: human HEK293T H3K4me3 - 60

description: scACT-seq


title: human HEK293T H3K4me3 - 58

description: scACT-seq


title: human HEK293T H3K4me3 - 59

description: scACT-seq


title: human HEK293T H3K4me3 - 57

description: scACT-seq


title: 41270


title: human HEK293T H3K4me3 - 55

description: scACT-seq


title: human HEK293T H3K4me3 - 54

description: scACT-seq


title: 41195


title: Ctrl40842G_Healthy


title: Ctrl41042G_Healthy


title: human HEK293T H3K4me3 - 56

description: scACT-seq


title: human HEK293T H3K4me3 - 53

description: scACT-seq


title: human HEK293T H3K4me3 - 51

description: scACT-seq


title: Ctrl40722G_Healthy


title: Ctrl40642G_Healthy


title: human HEK293T H3K4me3 - 50

description: scACT-seq


title: Ctrl40442G_Healthy


title: 41087


title: 30825


title: human HEK293T H3K4me3 - 52

description: scACT-seq


title: 61029


title: human HEK293T H3K4me3 - 49

description: scACT-seq


title: Ctrl40142G_Healthy


title: human HEK293T H3K4me3 - 48

description: scACT-seq


title: human HEK293T H3K4me3 - 47

description: scACT-seq


title: 30795


title: C1372202G_MDCF2_Treatment


title: human HEK293T H3K4me3 - 44

description: scACT-seq


title: human HEK293T H3K4me3 - 46

description: scACT-seq


title: human HEK293T H3K4me3 - 45

description: scACT-seq


title: 30728


title: human HEK293T H3K4me3 - 43

description: scACT-seq


title: human HEK293T H3K4me3 - 42

description: scACT-seq


title: 40976


title: C1367202G_MDCF2_Treatment


title: Ctrl40242G_Healthy


title: C1372201G_MDCF2_Baseline


title: human HEK293T H3K4me3 - 41

description: scACT-seq


title: human HEK293T H3K4me3 - 39

description: scACT-seq


title: human HEK293T H3K4me3 - 40

description: scACT-seq


title: human HEK293T H3K4me3 - 38

description: scACT-seq


title: human HEK293T H3K4me3 - 37

description: scACT-seq


title: C1367201G_MDCF2_Baseline


title: C1365202G_MDCF2_Treatment


title: 20741


title: 30706


title: 20718


title: human HEK293T H3K4me3 - 36

description: scACT-seq


title: 30665


title: human HEK293T H3K4me3 - 35

description: scACT-seq


title: human HEK293T H3K4me3 - 34

description: scACT-seq


title: 20699


title: C1360202G_MDCF2_Treatment


title: human HEK293T H3K4me3 - 33

description: scACT-seq


title: 10496


title: human HEK293T H3K4me3 - 31

description: scACT-seq


title: C1360201G_MDCF2_Baseline


title: human HEK293T H3K4me3 - 30

description: scACT-seq


title: C1365201G_MDCF2_Baseline


title: human HEK293T H3K4me3 - 32

description: scACT-seq


title: C1359202G_MDCF2_Treatment


title: UC9612

value: Normal


title: human HEK293T H3K4me3 - 29

description: scACT-seq


title: human HEK293T H3K4me3 - 27

description: scACT-seq


title: UC9101


title: human HEK293T H3K4me3 - 28

description: scACT-seq


title: human HEK293T H3K4me3 - 26

description: scACT-seq


title: C1359201G_MDCF2_Baseline


title: UC9035


title: human HEK293T H3K4me3 - 25

description: scACT-seq


title: C1356202G_MDCF2_Treatment


title: human HEK293T H3K4me3 - 24

description: scACT-seq


title: UC9023


title: human HEK293T H3K4me3 - 22

description: scACT-seq


title: human HEK293T H3K4me3 - 21

description: scACT-seq


title: human HEK293T H3K4me3 - 20

description: scACT-seq


title: UC9011


title: human HEK293T H3K4me3 - 23

description: scACT-seq


title: 20688


title: C1349201G_MDCF2_Baseline


title: C1356201G_MDCF2_Baseline


title: human HEK293T H3K4me3 - 19

description: scACT-seq


title: human HEK293T H3K4me3 - 18

description: scACT-seq


title: human HEK293T H3K4me3 - 17

description: scACT-seq


title: human HEK293T H3K4me3 - 16

description: scACT-seq


title: human HEK293T H3K4me3 - 15

description: scACT-seq


title: C1343202G_MDCF2_Treatment


title: R-0693


title: UC8926


title: human HEK293T H3K4me3 - 14

description: scACT-seq


title: C1349202G_MDCF2_Treatment


title: human HEK293T H3K4me3 - 13

description: scACT-seq


title: C1339202G_MDCF2_Treatment


title: C1343201G_MDCF2_Baseline


title: human HEK293T H3K4me3 - 12

description: scACT-seq


title: P-0451


title: human HEK293T H3K4me3 - 10

description: scACT-seq


title: human HEK293T H3K4me3 - 9

description: scACT-seq


title: human HEK293T H3K4me3 - 11

description: scACT-seq


title: L_0173


title: human HEK293T H3K4me3 - 7

description: scACT-seq


title: human HEK293T H3K4me3 - 8

description: scACT-seq


title: C1339201G_MDCF2_Baseline


title: UC9009


title: human HEK293T H3K4me3 - 6

description: scACT-seq


title: Cint22


title: Cint9


title: C1325202G_MDCF2_Treatment


title: human HEK293T H3K4me3 - 5

description: scACT-seq


title: C1326201G_MDCF2_Baseline


title: human HEK293T H3K4me3 - 4

description: scACT-seq


title: C1325201G_MDCF2_Baseline


title: Cint21


title: ND1 virus-infected stroke, rep 2

city: University Park

first: Gong

last: Chen

state: PA

address: Old Main

institute: Penn State University

data_processing:
quality check using FastQC v0.11.3
reads were aligned to GRCm38 using HISAT2 version 2.0.4
counts summarized using featureCounts v1.5.1 (count) or StringTie v1.3.4 (RPKM)
differential analysis by DESeq2 v1.16.1
Supplementary_files_format_and_content: a txt file containing read count from all samples generated by featureCounts

source_name: ND1 virus-infected stroke, rep 2

extract_protocol:
total RNA were extracted according to protocols accompanying with Macherey-Nagel NucleoSpin RNA kit, then sent to sequencing center for polyA enrichment
libraries were constructed using KAPA RNA kit at UCLA Technology Center for Genomics & Bioinformatics

tag: injury

value: stroke


title: ND1 virus-infected stroke, rep 1

source_name: ND1 virus-infected stroke, rep 1

tag: agent


title: human HEK293T H3K4me3 - 3

description: scACT-seq


title: R_0016


title: Cint19


title: control virus-infected stroke, rep 2

source_name: control virus-infected stroke, rep 2

value: GFP


title: human HEK293T H3K4me3 - 2

description: scACT-seq


title: C1326202G_MDCF2_Treatment


title: C1324202G_MDCF2_Treatment


title: human HEK293T H3K4me3 - 1

description: scACT-seq


title: C1324201G_MDCF2_Baseline


title: Cint18


title: control virus-infected stroke, rep 1

source_name: control virus-infected stroke, rep 1


title: CB-ATO CD8SP sample 2

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

description:
Mature T cell population generated in ATOs from T cell differentiation of human cord blood hematopoietic stem cells
GCAMhsExp.GEO.txt

data_processing:
The STAR ultrafast universal RNA-seq aligner v2.5.2b (Dobin et al., 2013) was used to generate the genome index and perform paired-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCh38 primary assembly) and the exon/intron structure of known gene models (Gencode v26 basic genome annotation).
Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Only protein-coding, long-noncoding, anti-sense and T-cell receptor genes in the Gencode v26 annotation were considered (98% of total counts on average). Independent filtering was applied as follows: genes with less than one count per sample on average, count outliers or low mappability were filtered out for downstream analysis
Counts were normalized per-sample in units of FPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCh38 primary assembly
Supplementary_files_format_and_content: Tab delimited. Table of per-gene and per-sample expression estimates in units of FPKMs

source_name: human cord blood

growth_protocol:
Cord blood ATOs were generated as previously described (Seet et al, 2017, Protocol exchange). MS5-hDLL1  cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“RB27”) composed of RPMI 1640 (Corning, Manassas, VA), 4% B27 supplement (ThermoFisher Scientific, Grand Island, NY), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY), 5 ng/ml rhFLT3L and 5 ng/ml rhIL-7 (Peprotech, Rocky Hill, NJ). RB27 was made fresh weekly. 1.5x105 MS5-hDLL1 cells were combined with 5x103 purified CD34+CD3- cells per ATO in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml RB27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh RB27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer. Flow cytometry cell sorting of CB-ATO derived SP8 T cell population used the following surface phenotypes: CD8 single positive (CD8SP; TCRαβ+CD3+CD8α+CD4-CD45RA+)
The hESC line H1 (WiCell, Madison, WI) was maintained on Matrigel coated plates (growth factor reduced, no phenol red; BD Biosciences, San Jose, CA), and cultured in mTESR medium (Stem Cell Technologies, Vancouver, BC).  PSC-ATOs were generated using purified hEMPs and followed a two-step procedure including a hematopoietic induction phase and a T-cell differentiation phase.  MS5-hDLL4 cells were harvested by trypsinization and resuspended in hematopoietic induction medium composed of EGM2 (Lonza Ref CC-4176) supplemented with ROCK inhibitor Y-27632 dihydrochloride (10uM) (Tocris Bioscience, Cat. 1254) and TGF-βRI inhibitor SB-431542 (“SB blocker”) (10 uM) (Tocris Bioscience, Cat. 1614). 5x105 MS5-hDLL4 cells were combined with 0.5-1x104 purified hEMP per PSC-ATO in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Multiple (up to 12) PSC-ATO cell volumes were prepared per tube. Supernatants were carefully removed and the cell pellet was resuspended by brief vortexing, and resuspended in hematopoietic induction medium at a volume of 6 µl per PSC-ATO. 6 µl of cells were plated as PSC-ATOs on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) (up to 2 PSC-ATOs per insert were plated) and placed in 6-well plates containing 1 ml hematopoietic induction medium per well. Medium was changed completely every 2-3 days for 1 weekM with medium composed of EGM2 with SB blocker (10uM). At day 7, medium was change to EGM2 + SB blocker (10uM) with the hematopoietic cytokines TPO 5ng/ml (Peprotech, Cat. 300-18), FLT3L 5ng/ml (Peprotech, Cat. 300-19), and SCF 50ng/ml (Peprotech, Cat. 300-07). This medium was changed every 2-3 days for an additional 7 days. At day 14, T cell differentiation was induced by changing the medium to “RB27” (described above) supplemented with 10 ng/ml SCF, 5 ng/ml FLT3L, and 5 ng/ml IL-7 (Peprotech, Cat. 200-07). Medium was changed completely every 3-4 days. PSC-ATO cells were harvested by adding MACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer. Flow cytometry cell sorting of ESC-ATO derived  double positive cell population used the following surface phenotypes: DP; CD4+CD8+CD3-. Cord blood ATOs were generated as previously described (Seet et al, 2017, Protocol exchange). MS5-hDLL1  cells were harvested by trypsinization and resuspended in serum free ATO culture medium (“RB27”) composed of RPMI 1640 (Corning, Manassas, VA), 4% B27 supplement (ThermoFisher Scientific, Grand Island, NY), 30 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, St. Louis, MO) reconstituted in PBS, 1% penicillin/streptomycin (Gemini Bio-Products, West Sacramento, CA), 1% Glutamax (ThermoFisher Scientific, Grand Island, NY), 5 ng/ml rhFLT3L and 5 ng/ml rhIL-7 (Peprotech, Rocky Hill, NJ). RB27 was made fresh weekly. 1.5x105 MS5-hDLL1 cells were combined with 5x103 purified CD34+CD3- cells per ATO in 1.5 ml Eppendorf tubes and centrifuged at 300 g for 5 min at 4˚C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended by brief vortexing. ATOs were plated on a 0.4 µm Millicell transwell insert (EMD Millipore, Billerica, MA; Cat. PICM0RG50) placed in a 6-well plate containing 1 ml RB27 per well. Medium was changed completely every 3-4 days by aspiration from around the cell insert followed by replacement with 1 ml with fresh RB27/cytokines. ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the ATO by pipetting with a 1 ml “P1000” pipet, followed by passage through a 50 µm nylon strainer. Flow cytometry cell sorting of CB-ATO derived double positive cell population used the following surface phenotypes: DP; CD4+CD8+CD3-. Postnatal human thymi were obtained under IRB exemption as discarded waste from patients undergoing cardiac surgery at Children’s Hospital Los Angeles (CHLA). Thymic fragments were finely dissected in RPMI and disrupted by pipetting to release thymocytes into suspension, followed by passage through a 70 µm nylon strainer. Cells were analyzed fresh on the same or following day. Flow cytometry cell sorting of thymic SP4 T cell population used the following surface phenotypes: CD4 single positive (CD4SP; TCRαβ+CD3+CD8+CD4-CD45RA+).

extract_protocol:
All samples were extracted using miRNeasy Micro Kit (Qiagen).
1.5ng of total RNA was input to generate sequencing libraries with SMARTer Stranded Total RNA-Seq (Pico) Kit (Clonetech, Cat. 635005).

treatment_protocol: The freshly sorted CB-ATO derived SP8 population was pelleted for RNA extraction

tag: phenotype

value: CD4- CD8+ CD3+ TCRab+ CD45RA+


title: Cint10


title: Cint1


title: Cint11


title: no stroke healthy mouse, rep 1

source_name: no stroke healthy mouse, rep 1

value: no injury

value: no virus


title: CB-ATO CD8SP sample 1