title: ATRi (ATR kinase inhibitor AZD6738) - late

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

data_processing:
Library strategy: repli-seq
Raw Repli-seq reads were trimmed and filtered for quality using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were aligned using bowtie2 (Langmead B & Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357-359.) against GRCh38(hg38).  13(5):819-839.).
Genome-wide replication timing (RT) profiles were constructed, scaled and pooled for analysis as previously described (Marchal C, et al. (2018) Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nat Protoc
Briefly, Log2 ratios of early versus late read counts were calculated for 50kb non-overlapping windows, Loess smoothed at 300kb windows.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph Genome-wide replication timing (RT) profiles:  Log2 ratios of early versus late read counts were calculated for 50kb non-overlapping windows, Loess smoothed at 300kb windows.

source_name: U2OS cells

growth_protocol: RPMI supplemented with 10% FBS and pen/strep.

extract_protocol:
cells were fixed with EtOH, stained with PI, sorted into "early" and "late" S-phase based on DNA content, genomic DNA was extracted, sonicated, BrdU-labeled fragments were immunoprecipitated with an antibody
NEBNext kit (NEB#7370S) was used according to manufacturer's instructions. BrdU IP was performed after the end processing step and before indexing.

treatment_protocol: U2OS cells were treated with DMSO or 5uM AZD6738 for 30 minutes before labelling of the ongoing replication with 10uM BrdU.

tag: time point

value: late

value: U2OS cells

tag: cell type

value: osteosarcoma

value: treated with 5uM AZD6738


title: ATRi (ATR kinase inhibitor AZD6738) - early

status: Public on Jul 26 2019

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: early

tag: cell line

tag: treatment


title: CAP600 H3K4me3_rep2

city: Goyang-si

first: sung bin

last: park

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

department: Department of Life Science

country: South Korea

institute: Dongguk University-Seoul

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
peaks were called using macs version 1.4
Genome_build: hg19
Supplementary_files_format_and_content: peak files with quantitative data, tag density files

source_name: CAP600 H3K4me3

growth_protocol: A breast cancer cell line MCF-7 was purchased from the American Type Culture Collection (ATCC) (Manassas, VA, USA) and cultured in RPMI-1640 medium (Gibco, Los Angeles, CA, USA) supplemented with 10% FBS (Gibco) and 2% Penicillin and Streptomycin (Gibco) maintained at 37 °C in 5% CO2

extract_protocol:
DNA was extracted using DNA Prep. Kit
construction of library was performed using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

treatment_protocol: The CAP device, a type of mesh - DBD (Dielectric Barrier Discharge), was manufactured at the Plasma Bioscience Research Center (Kwangwoon University, Korea). CAP was treated onto the cell in culture media for 600 sec at 0.12 kV, using argon gas flow of 1.5 L/min, with operation frequency 12.89 kHz.

value: Mammary epithelial cell line

value: Cold atmospheric plasma (CAP)

tag: chip antibody

value: Histone H3K4me3 Polyclonal Antibody

tag: chip antibody vendor

value: Signalway Antibody

tag: chip antibody cat. #


title: control - late

value: treated with DMSO


title: 172D_550_wb 33

type: RNA

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

description: raw data file: 2013-10-02_19723172_550PMT_5um_0532.txt, Array D (blocks 25-32)

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon GenePix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split in to eighteen subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 10240 features on each microarray by subtracting the median local background from the median local foreground for each spot. Visually flagged spots were removed prior to averaging and normalizing. The 95th percentile of the negative control spots was also calculated for each array. The spot intensities and 95th percentile of negative controls (TPT95) were transformed by taking the log (base 2) of each value. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The mean probe intensities for each of the probes on each array were then determined by averaging the triplicate spot intensities. Spots that have an average saturated signal were removed prior to normalization. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the non-saturated human probes above threshold in all samples. The log2-transformed spot intensities for all features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays.

label: Oyster-550 fluorescent dye

molecule: total RNA

organism: Mus musculus

source_name: Month 6 40ug MWCNT

label_protocol: The total RNA was DNase digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitious viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus.

extract_protocol: Total RNA was isolated from mouse blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol.

treatment_protocol: Each component consisted of 8 mice per exposure group (dispersion media [DM, negative control]; 1, 10, 40, or 80 μg MWCNT; 120 μg crocidolite asbestos [positive control]) to be sacrificed at 1, 6 or 12 months post-exposure, for a total of 144 mice.

tag: strain/background

tag: gender

value: Male

tag: tissue

value: Blood

value: 40ug MWCNT

tag: time

value: Month 6


title: 171C_550_wb 384

description: raw data file: 2013-10-02_19723171_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 1 80ug MWCNT

value: 80ug MWCNT

value: Month 1


title: control - early


title: 171B_550_wb 49

description: raw data file: 2013-10-02_19723171_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1 40ug MWCNT


title: 171D_550_wb 92

description: raw data file: 2013-10-02_19723171_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 12 120ug crocidolite

value: 120ug crocidolite

value: Month 12


title: 170A_550R_wb 50

description: raw data file: 2013-10-02_19723170_550PMT_5um_redip__0532.txt, Array A (blocks 1-8)


title: 170C_550_wb 376

description: raw data file: 2013-10-02_19723170_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 6 10ug MWCNT

value: 10ug MWCNT


title: 169D_550_wb 362

description: raw data file: 2013-10-02_19723169_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 12 40ug MWCNT


title: SDS_del7q_plus7_R3

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

library_source: transcriptomic

data_processing:
Illumina HiSeq 2500 software used for basecalling for 50 base paired-end sequencing  to a depth of 20-30M reads/sample.
Quality control tests for the sequenced reads  were performed using the FASTQC v0.11.5 software (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads were aligned to the GRCh37/hg19 human genes by using Tophat2 v2.1.1 with standard parameters. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2.1 and the SARTools  pipelines.
Gene level reads and gene level expression estimated as log2(1+FPKM) (Fragments Per Kilobase of transcript per Million mapped reads) scores were computed using the Feature Counts method implemented in the Bioconductor v3.5  RSubread v1.5.3 package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene level counts values for each sample.

source_name: IPSCs with engineered del(7q) and spontaneous acquisition of chr9

growth_protocol: iPSC generation:  Cryopreserved bone marrow mononuclear cells were cultured in StemPro-34 SFM media (Gibco) with 1% nonessential amino acids (NEAA, Gibco), 1 mM L-glutamine (Gibco) and 0.1mM mercaptoethanol (Gibco) and supplemented with 100 ng/mL stem cell factor (SCF), 100ng/mL Flt3 ligand (Flt3L), 100 ng/mL thrombopoietin (TPO) and 20 ng/mL IL-3 for 24 - 48hrs. Viral transduction with the excisable lentiviral vector CMV-fSV2A expressing OCT4, KLF4, c-MYC and SOX2, reprogramming, selection of colonies with hPSC morphology and Cre-mediated vector excision were done as previously described (31).  Characterization of pluripotency by flow cytometry and teratoma formation assay was conducted as previously described (7).  Patient samples were obtained with informed consent under protocols approved by an Institutional Review Board at Fred Hutchinson Cancer Research Center, Seattle Children’s Hospital, and Boston Children’s Hospital.  Cell Culture: Culture of human iPSCs on MEFs (MMC-treated, Applied Stem Cell, Inc) or in feeder-free conditions using matrigel (Gibco) was done as previously described (7).  Human 293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 10% fetal bovine serum (FBS).  Cells were treated with 1µM SD208 (Sigma) or 0.6µg/mL AVID200 (Formation Biologics) for 2 – 4 hrs at 37˚C in the tissue culture incubator prior to harvest.

extract_protocol:
Total RNA was isolated following manufacturer’s instructions for RNeasy Plus Mini Kit (Qiagen). RNA quality was verified on an Agilent 22-TapeStation for a RIN >8.
RNA libraries  were prepared for sequencing using standard Illumina protocols at the Fred Hutchinson Cancer Research Center Genomic core.

treatment_protocol: AAV-mediated gene targeting and selection of clones with 7q deletions.  The AAV targeting vector was previously described (7). Puromycin-resistant colonies were selected and southern blot verification was conducted as previously described (7). Transduction with a Cre-expressing integrase-deficient lentiviral vector was done as previously described (7).  Ganciclovir (Sigma) selection was performed at concentration of 150µM for 14 days.

value: iPSCs

tag: sds status

value: SDS del(7q)+7


title: 169B_550_wb 310

description: raw data file: 2013-10-02_19723169_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 6, 1ug MWCNT

value: 1ug MWCNT


title: 171A_550_wb 116

description: raw data file: 2013-10-02_19723171_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 1 DM

value: DM


title: MDA-MB-231 cells_RCF treated with 9Gy of IR dose rep6

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description: Biological replicate 6 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: MDA-MB-231 cells_RCF treated with 9Gy of IR dose (7days)

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. Untreated MDA-MB-231 cell line was used as a control for MDA-MB-231 cells exposed to 9-23Gy. MDA-MB-231 9Gy treated cells collected 24h post irradiation, were used as control for RCF samples. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from control samples was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: MDA-MB-231 breast cancer cell lines were collected after 24 hours post treatments. RCF samples were collected after 7days post 9Gy of IR treatment.

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

value: breast cancer

value: treated with 9Gy of IR dose (7days)

source_name: MDA-MB-231 breast cancer cell line exposed to 9Gy of IR treatment collected 24h post irradiation


title: SDS_del7q_plus7_R2

source_name: IPSCs with engineered del(7q) and spontaneous acquisition of chr8


title: 168D_550_wb 43

description: raw data file: 2013-10-01_19723168_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 6, 120ug crocidolite


title: MDA-MB-231 cells_RCF treated with 9Gy of IR dose rep3

description: Biological replicate 3 of 6

value: exposed to 9Gy of IR treatment collected 24h post irradiation


title: MDA-MB-231 cells_RCF treated with 9Gy of IR dose rep4

description: Biological replicate 4 of 6


title: MDA-MB-231 cells_RCF treated with 9Gy of IR dose rep5

description: Biological replicate 5 of 6


title: 168C_550_wb 399

description: raw data file: 2013-10-01_19723168_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 6, 80ug MWCNT


title: 170B_550_wb 238

description: raw data file: 2013-10-02_19723170_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1 120ug crocidolite


title: 170D_550_wb 5

description: raw data file: 2013-10-02_19723170_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 12 1ug MWCNT


title: MDA-MB-231 cells_RCF treated with 9Gy of IR dose rep2

description: Biological replicate 2 of 6


title: SDS R3

source_name: iPSCs from two SDS patients with  c.258+2T>C SBDS mutations

value: SDS


title: 42A

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg38 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each  gencode V22 gene.

source_name: ACR_Kidney Allograft Biopsy

growth_protocol: Biopsy tissue immersed in RNAlater and stored in -80C.

extract_protocol:
Total RNA isolated using miRNeasy mini kit (QIAGEN)
TruSeq sample preparation kit v2 (ILLUMINA)

tag: subject status

value: dult kidney transplant recipient

tag: diagnosis

value: Acute Cellular Rejection (ACR)

value: Kidney Allograft Biopsy


title: SDS_del7q_plus7_R1

source_name: IPSCs with engineered del(7q) and spontaneous acquisition of chr7


title: SDS R2


title: 169A_550_wb 402

description: raw data file: 2013-10-02_19723169_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 12, 10ug MWCNT

value: Male

value: Blood


title: 168B_550_wb 404

description: raw data file: 2013-10-01_19723168_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1, 40ug MWCNT

value: 40ug MWCNT

value: Month 1


title: 169C_550_wb 76

description: raw data file: 2013-10-02_19723169_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 1, DM


title: SDS R1


title: SDS_del7q_R3

data_processing:
iPSC generation.  Cryopreserved bone marrow mononuclear cells were cultured in StemPro-34 SFM media (Gibco) with 1% nonessential amino acids (NEAA, Gibco), 1 mM L-glutamine (Gibco) and 0.1mM mercaptoethanol (Gibco) and supplemented with 100 ng/mL stem cell factor (SCF), 100ng/mL Flt3 ligand (Flt3L), 100 ng/mL thrombopoietin (TPO) and 20 ng/mL IL-3 for 24 - 48hrs. Viral transduction with the excisable lentiviral vector CMV-fSV2A expressing OCT4, KLF4, c-MYC and SOX2, reprogramming, selection of colonies with hPSC morphology and Cre-mediated vector excision were done as previously described (31).  Characterization of pluripotency by flow cytometry and teratoma formation assay was conducted as previously described (7).  Patient samples were obtained with informed consent under protocols approved by an Institutional Review Board at Fred Hutchinson Cancer Research Center, Seattle Children’s Hospital, and Boston Children’s Hospital.  Cell Culture.  Culture of human iPSCs on MEFs (MMC-treated, Applied Stem Cell, Inc) or in feeder-free conditions using matrigel (Gibco) was done as previously described (7).  Human 293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 10% fetal bovine serum (FBS).  Cells were treated with 1µM SD208 (Sigma) or 0.6µg/mL AVID200 (Formation Biologics) for 2 – 4 hrs at 37˚C in the tissue culture incubator prior to harvest.   AAV-mediated gene targeting and selection of clones with 7q deletions.  The AAV targeting vector was previously described (7). Puromycin-resistant colonies were selected and southern blot verification was conducted as previously described (7). Transduction with a Cre-expressing integrase-deficient lentiviral vector was done as previously described (7).  Ganciclovir (Sigma) selection was performed at concentration of 150µM for 14 days.  RNA was isolated following manufacturer’s instructions for RNeasy Plus Mini Kit (Qiagen).  RNA quality was verified on an Agilent 22- TapeStation for a RIN >8.  Library prep, quality control and sequencing with Illlumina HiSeq 2500 platform at the Fred Hutchinson Cancer Research Center Genomic core.
Quality control tests for the sequenced reads  were performed using the FASTQC v0.11.5 software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Tophat2 v2.1.1. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2.1 and the SARTools  pipelines.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene level counts values for each sample.

source_name: IPSCs with engineered del(7q)

value: SDS del(7q)


title: SDS_del7q_R2


title: 168A_550_wb 67

description: raw data file: 2013-10-01_19723168_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: 165D_550_wb 8

description: raw data file: 2013-10-01_19723165_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: 120ug crocidolite

value: Month 6


title: 166A_550_wb 288

description: raw data file: 2013-10-01_19723166_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 10ug MWCNT

value: Month 12


title: 167A_550_wb 174

description: raw data file: 2013-10-01_19723167_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 80ug MWCNT


title: 164D_550_wb 95

description: raw data file: 2013-10-01_19723164_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 1, 1ug MWCNT

value: 1ug MWCNT


title: 164C_550_wb 243

description: raw data file: 2013-10-01_19723164_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: 166D_550_wb 409

description: raw data file: 2013-10-01_19723166_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 12, 40ug MWCNT


title: 167B_550_wb 111

description: raw data file: 2013-10-01_19723167_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1, 120ug crocidolite


title: SDS_R3

value: iPSCs


title: 164B_550_wb 218

description: raw data file: 2013-10-01_19723164_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: 167D_550_wb 178

description: raw data file: 2013-10-01_19723167_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 6, 1ug MWCNT


title: 167C_550_wb 366

description: raw data file: 2013-10-01_19723167_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: 163D_550_wb 254

description: raw data file: 2013-10-01_19723163_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 164A_550_wb 355

description: raw data file: 2013-10-01_19723164_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 12, 80ug MWCNT


title: 166B_550_wb 34

description: raw data file: 2013-10-01_19723166_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: 163C_550_wb 327

description: raw data file: 2013-10-01_19723163_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 12, DM

value: DM


title: 166C_550_wb 343

description: raw data file: 2013-10-01_19723166_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 6, DM


title: MDA-MB-231 cells_RCF treated with 9Gy of IR dose rep1

description: Biological replicate 1 of 6

source_name: MDA-MB-231 cells_RCF treated with 9Gy of IR dose (7days)

value: breast cancer

value: treated with 9Gy of IR dose (7days)

source_name: MDA-MB-231 breast cancer cell line exposed to 9Gy of IR treatment collected 24h post irradiation


title: SDS_R2

value: SDS


title: MDA-MB-231 cells treated with 23 Gy of IR dose rep2

description:
Biological replicate 2 of 6
identical to GSM3032685

source_name: MDA-MB-231 cells treated with 23 Gy of IR dose (24 hours)

source_name: MDA-MB-231 breast cancer cell line not exposed to IR treatments

value: not exposed to IR treatments


title: MDA-MB-231 cells treated with 23 Gy of IR dose rep6

description:
Biological replicate 6 of 6
identical to GSM3032689

value: treated with 23 Gy of IR dose (24 hours)


title: SDS_del7q_R1


title: MDA-MB-231 cells treated with 23 Gy of IR dose rep5

description:
Biological replicate 5 of 6
identical to GSM3032688


title: MDA-MB-231 cells treated with 23 Gy of IR dose rep4

description:
Biological replicate 4 of 6
identical to GSM3032687


title: MDA-MB-231 cells treated with 23 Gy of IR dose rep3

description:
Biological replicate 3 of 6
identical to GSM3032686


title: MDA-MB-231 cells treated with 9 Gy of IR dose rep6

description:
Biological replicate 6 of 6
identical to GSM2916583

source_name: MDA-MB-231 cells treated with 9 Gy of IR dose (24 hours)

value: treated with 9 Gy of IR dose (24 hours)


title: MDA-MB-231 cells treated with 9 Gy of IR dose rep4

description:
Biological replicate 4 of 6
identical to GSM2916581


title: 163B_550_wb 403

description: raw data file: 2013-10-01_19723163_550PMT_5um_0532.txt, Array B (blocks 9-16)

value: Male

value: Blood


title: SDS_R1

source_name: iPSCs from two SDS patients with  c.258+2T>C SBDS mutations


title: MDA-MB-231 cells treated with 23 Gy of IR dose rep1

description:
Biological replicate 1 of 6
identical to GSM3032684


title: 163A_550_wb 205

description: raw data file: 2013-10-01_19723163_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 12, 10ug MWCNT


title: 162B_550_wb 240

description: raw data file: 2013-09-27_19723162_550PMT_5um_0532.txt, Array B (blocks 9-16)

value: 40ug MWCNT


title: 162A_550_wb 217

description: raw data file: 2013-09-27_19723162_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: Month 1


title: 162C_550_wb 275

description: raw data file: 2013-09-27_19723162_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: 17A

source_name: ACR_Kidney Allograft Biopsy

value: dult kidney transplant recipient

value: Acute Cellular Rejection (ACR)

value: Kidney Allograft Biopsy


title: 161D_550_wb 340

description: raw data file: 2013-09-27_19723161_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: gcn5_15_II

city: NEWARK

first: Neeraj

last: Chauhan

state: New Jersey

address: 225 Warren Street

department: Department of Microbiology, Biochemistry & Molecular Genetics

institute: NJMS-PHRI

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
The adapters were trimmed by using Trimmomatic with default parameters (Bolger, Lohse, & Usadel, 2014).
The reads were then mapped to C. albicans genome using tophat2 (Kim et al., 2013).
In this analysis we used C_albicans_SC5314_A22 genome and transcriptome downloaded from Candida Genome Database (Skrzypek et al., 2017).
The reads were counted using summarizeOverlaps function from the GenomicAlignments R package (Lawrence et al., 2013).
Genome_build: Differential gene expression analysis were performed using DESeq2 R package (Love, Anders, & Huber, 2014).
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
Supplementary_files_format_and_content: raw counts of sequencing reads

organism: Candida albicans

source_name: fungal cells

extract_protocol:
RNA was isolated using Trizol and glass bead lysis after which RNA was precipitated and DNase treated followed by a column purification step. 5μg DNase-treated total RNA was subjected to mRNA purification using Dynabeads mRNA purification kit (Invitrogen). Remaining rRNA contamination was checked in the bioanalyzer using Agilent RNA 6000 Pico kit (Agilent). Purified mRNA was subjected to fragmentation using the NEBNext® Magnesium RNA Fragmentation Module (New England Biolabs) and purified with RNeasy Plus Mini kit (Qiagen). Then, first-strand cDNA was synthesized with 50 ng/μl random hexamer primers using SuperScript ® III First-Strand Synthesis System for RT-PCR (Invitrogen). dNTPs were eliminated by purifying with MiniQuickSpin DNA Columns and subjected to second strand cDNA synthesis followed by clean-up with Minielute Reaction cleanup kit (Qiagen). cDNA concentration was measured using Quant-iT Picogreen dsDNA Reagents (Invitrogen) in a NanoDrop Fluorospectrophotometer ND-3300 (Thermo Fisher).
Library preparation was done using the KAPA DNA Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions.

tag: genotype

value: gcn5 delta/delta

tag: agent

value: Caspofungin 10 ng/ml

tag: time point (minutes)


title: gcn5_0_III

value: untreated


title: 162D_550R_wb 417

description: raw data file: 2013-09-27_19723162_550PMT_5um_redip_0532.txt, Array D (blocks 25-32)

source_name: Month 12, 120ug crocidolite

value: 120ug crocidolite

value: Month 12


title: wt_45_III

value: wild-type


title: MDA-MB-231 cells treated with 9 Gy of IR dose rep5

description:
Biological replicate 5 of 6
identical to GSM2916582

value: breast cancer


title: 161C_550_wb 161

description: raw data file: 2013-09-27_19723161_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: 10ug MWCNT


title: 161B_550_wb 337

description: raw data file: 2013-09-27_19723161_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: wt_15_III


title: SNAI1_2_2

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

country: China

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: H1 cell line

growth_protocol: H1 cells with or without SNAI1 deletion were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days.

extract_protocol:
H1 drived cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: H1 after SNAI1 deletion samples collected at day 2 after hematopoietic differentiation.


title: WT-2

value: H1 samples collected at day 2 after hematopoietic differentiation.


title: SNAI1_2_1


title: MDA-MB-231 cells treated with 9 Gy of IR dose rep2

description:
Biological replicate 2 of 6
identical to GSM2916579

value: treated with 9 Gy of IR dose (24 hours)

value: not exposed to IR treatments


title: gcn5_45_II


title: wt_0_III


title: 161A_550_wb 200

description: raw data file: 2013-09-27_19723161_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: Male

value: Blood

value: 80ug MWCNT


title: MDA-MB-231 cells treated with 9 Gy of IR dose rep1

description:
Biological replicate 1 of 6
identical to GSM2916578


title: 160B_550_wb 101

description: raw data file: 2013-09-27_19723160_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1, 1ug MWCNT

value: 1ug MWCNT

value: Month 1


title: 160D_550_wb 214

description: raw data file: 2013-09-27_19723160_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 12, 40ug MWCNT

value: 40ug MWCNT


title: 160A_550_wb 98

description: raw data file: 2013-09-27_19723160_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: SNAI1_1_1


title: 160C_550_wb 314

description: raw data file: 2013-09-27_19723160_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: DM


title: SNAI1_1_2


title: gcn5_0_II

value: gcn5 delta/delta

value: untreated


title: IWP2-2

growth_protocol: H1 cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) with or without IWP2 treatment for 2 days and then colected for RNAseq.

value: H1 samples collected at day 2 after IWP2 treatment of hematopoietic differentiation.


title: 159C_550_wb 72

description: raw data file: 2013-09-27_19723159_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: Month 12


title: 159D_550_wb 168

description: raw data file: 2013-09-27_19723159_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: 120ug crocidolite


title: wt_45_II

value: wild-type

value: Caspofungin 10 ng/ml


title: WT-1

value: H1 samples collected at day 2 after hematopoietic differentiation.


title: IWP2-1


title: 159A_550_wb 265

description: raw data file: 2013-09-27_19723159_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: wt_0_II


title: wt_15_II


title: 158D_550_wb 429

description: raw data file: 2013-09-27_19723158_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 12, 1ug MWCNT


title: gcn5_45_I


title: 158C_550_wb 23

description: raw data file: 2013-09-27_19723158_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: 10ug MWCNT


title: 158A_550_wb 223

description: raw data file: 2013-09-27_19723158_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 12, 80ug MWCNT


title: 158B_550_wb 143

description: raw data file: 2013-09-27_19723158_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: DMSO-1 (IWP2)

value: H1 samples collected at day 2 of hematopoietic differentiation.


title: 157D_550_wb 71

description: raw data file: 2013-09-27_19723157_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: Male


title: DMSO-2 (IWP2)


title: 157C_550_wb 164

description: raw data file: 2013-09-27_19723157_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 12, DM

value: Blood


title: 157B_550_wb 330

description: raw data file: 2013-09-27_19723157_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: gcn5_15_I


title: SB-2

growth_protocol: H1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 3 days. Finally, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) with or without SB431542 treatment for 3 days.

value: H1 samples collected at day 8 after SB431542 treatment of hematopoietic differentiation.


title: gcn5_0_I


title: SB-1


title: 157A_550_wb 333

description: raw data file: 2013-09-27_19723157_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 1, 10ug MWCNT


title: 156D_550_wb 78

description: raw data file: 2013-09-26_19723156_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 156C_550_wb 160

description: raw data file: 2013-09-26_19723156_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: 80ug MWCNT


title: 156B_550_wb 35

description: raw data file: 2013-09-26_19723156_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: wt_15_I


title: 154C_550_wb 312

description: raw data file: 2013-09-26_19723154_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: Month 1


title: 154D_550_wb 298

description: raw data file: 2013-09-26_19723154_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: 1ug MWCNT


title: MDA-MB-231 cells treated with 9 Gy of IR dose rep3

description:
Biological replicate 3 of 6
identical to GSM2916580

value: breast cancer

value: treated with 9 Gy of IR dose (24 hours)

value: not exposed to IR treatments


title: wt_0_I

value: untreated


title: DMSO-1

value: H1 samples collected at day 8 of hematopoietic differentiation.


title: CD43-3

growth_protocol: H1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 6 days.

value: H1 derived CD43+ cells collected at day 8 after hematopoietic differentiation


title: DMSO-2


title: CD43-2


title: 154B_550_wb 41

description: raw data file: 2013-09-26_19723154_550PMT_5um_0532.txt, Array B (blocks 9-16)

value: 120ug crocidolite

value: Month 12


title: 154A_550_wb 36

description: raw data file: 2013-09-26_19723154_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: 153C_550_wb 2

description: raw data file: 2013-09-26_19723153_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: DM


title: 152C_550_wb 342

description: raw data file: 2013-09-26_19723152_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 1, 80ug MWCNT


title: CD43-1


title: 152B_550_wb 319

description: raw data file: 2013-09-26_19723152_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1, 40ug MWCNT

value: 40ug MWCNT


title: 153A_550_wb 267

description: raw data file: 2013-09-26_19723153_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 10ug MWCNT


title: 152D_550_wb 301

description: raw data file: 2013-09-26_19723152_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 1, 120ug crocidolite

value: Male


title: 152A_550_wb 391

description: raw data file: 2013-09-26_19723152_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 1, DM

value: Blood


title: CD31CD34-3

value: H1 derived CD31+CD34+ cells collected at day 5 after hematopoietic differentiation


title: CD31CD34-2


title: 151D_550_wb 118

description: raw data file: 2013-09-26_19723151_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 156A_550_wb 97

description: raw data file: 2013-09-26_19723156_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: 151C_550_wb 407

description: raw data file: 2013-09-26_19723151_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 6, 10ug MWCNT

value: Month 6


title: wt_45_I

value: wild-type

value: Caspofungin 10 ng/ml


title: 151A_550_wb 315

description: raw data file: 2013-09-26_19723151_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 80ug MWCNT

value: Month 1


title: 151B_550_wb 383

description: raw data file: 2013-09-26_19723151_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: CD31CD34-1


title: APLNR-3

value: H1 derived APLNR+ cells collected from day 2 after hematopoietic differentiation


title: APLNR-2


title: 150D_550_wb 187

description: raw data file: 2013-09-26_19723150_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 150C_550_wb 350

description: raw data file: 2013-09-26_19723150_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: 150B_550_wb 82

description: raw data file: 2013-09-26_19723150_550PMT_5um_0532.txt, Array B (blocks 9-16)

value: 1ug MWCNT


title: 149D_550_wb 184

description: raw data file: 2013-09-25_19723149_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 150A_550_wb 296

description: raw data file: 2013-09-26_19723150_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: APLNR-1


title: 149B_550_wb 345

description: raw data file: 2013-09-25_19723149_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 6, 40ug MWCNT


title: H1-3

value: Undifferentiated H1 cells


title: 148C_550_wb 201

description: raw data file: 2013-09-25_19723148_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: CTL_mix_2

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

description: total RNA

hyb_protocol: Following fragmentation, 3,6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip MouseGene2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 Scanner.

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V18 was used for annotation.

label: biotin

source_name: WT inflammatory blood monocytes

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation PicoV2 protocol from 900 pg total RNA.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (QIAGEN) according to manufacturer's manual.

treatment_protocol: CD4 T cells from peripheral and mesenteric lymph nodes of C57BL/6 Foxp3-GFP mice were purified by using Dynabeads Untouched Mouse CD4 Cells Kit (Invitrogen). Then, CD4 Treg and Tmem cells were flow-cytometry sorted as CD4+ CD8α- TCRβ+ GFP+ for Treg and CD4+ CD8α- TCRβ+ GFP- CD44hi for Tmem using a FACS-ARIA3 flow cytometer.

tag: genotype/variation

value: WT

tag: strain

value: C57BL/6 LyzCre

tag: age

value: 6-8 weeks


title: 149C_550_wb 196

description: raw data file: 2013-09-25_19723149_550PMT_5um_0532.txt, Array C (blocks 17-24)

tag: treatment


title: CTL_mix_1

description: total RNA


title: 148D_550_wb 286

description: raw data file: 2013-09-25_19723148_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: CTL9

description: total RNA


title: CTL3

description: total RNA


title: 148B_550_wb 132

description: raw data file: 2013-09-25_19723148_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 6, 120ug crocidolite

value: 120ug crocidolite


title: 73

description: total RNA

source_name: TRIM33 inflammatory blood monocytes


title: CTL1

description: total RNA


title: 72 bis

description: total RNA


title: 74

description: total RNA


title: CTL2

description: total RNA


title: H1-2


title: 149A_550_wb 123

description: raw data file: 2013-09-25_19723149_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: DM


title: 148A_550_wb 372

description: raw data file: 2013-09-25_19723148_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 6, 80ug MWCNT


title: HAND1_OE-2

source_name: H1 cell line

growth_protocol: H1 with or without HAND1 overexpression were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 2 days.

value: H1 after HAND1-overexpression derived CD31+ cells collected at day 8 after hematopoietic differentiation.


title: 147D_550_wb 85

description: raw data file: 2013-09-25_19723147_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: Male

value: 40ug MWCNT


title: HAND1_OE-1


title: 146D_550_wb 323

description: raw data file: 2013-09-25_19723146_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: Blood


title: 147C_550_wb 411

description: raw data file: 2013-09-25_19723147_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 6, DM

value: Month 6


title: 147B_550_wb 235

description: raw data file: 2013-09-25_19723147_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1, 1ug MWCNT


title: TRIM33_mix_2

description: total RNA


title: 146B_550_wb 281

description: raw data file: 2013-09-25_19723146_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: 146C_550_wb 65

description: raw data file: 2013-09-25_19723146_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: Control-1

value: H1 derived CD31+ cells collected at day 8 after hematopoietic differentiation.


title: 144D_550_wb 197

description: raw data file: 2013-09-25_19723144_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 146A_550_wb 306

description: raw data file: 2013-09-25_19723146_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: H1-1


title: BC1-CD31+CD34+ cells

source_name: BC1 cell line

growth_protocol: BC1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 6 days.

extract_protocol:
BC1 drived cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BC1 derived CD31+CD34+ cells collected at day 5 after hematopoietic differentiation


title: nwgl rep3

city: Shanghai

first: Xiaowei

last: Zhu

address: Jinqi Road No.1000

institute: Shanghai Academy of Agricultural Sciences

data_processing:
The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS(Illumia) according to the manufacturer’s instructions.
Raw data were filtered using inhouse perl scripts available with Biomarker Technologies Co. Ltd. (Biomarker, Beijing, China).
Clean reads were aligned to the cabbage genome (www.ocri-genomics.org/bolbase/index.html) using HISAT 2.
The mapped reads were assembled using the StringTie (V1.3.1) with gffcompare program annotation.
Genes and lncRNAs expression level was estimated by calculating FPKM values using StringTie (v1.3.1).
Genome_build: cabbage genome (www.ocri-genomics.org/bolbase/index.html) verison 1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Brassica oleracea var. capitata

source_name: nwgl_Cabbage leaf

extract_protocol:
Total RNA was extracted from collected leaves of nwgl and WT plants at harvesting stage using RNAprep Pure Plant kit (Polysaccarides & Polyphenolics-rich) (Tiangen, Beijing, China) according to the manufacturer’s instructions.
Six cDNA libraries (three biological replicates per genotype) were constructed using NEBNextUltraTM Directional RNA library Prep kit (NEB, Ipswich, MA, USA) for Illumina (Illumina, San Diego, CA, USA).

value: glossy mutant nwgl

tag: development stage

value: harvesting stage

value: leaf


title: 144C_550_wb 231

description: raw data file: 2013-09-25_19723144_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: 10ug MWCNT


title: 144A_550_wb 274

description: raw data file: 2013-09-25_19723144_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 80ug MWCNT


title: 143C_550_wb 169

description: raw data file: 2013-09-25_19723143_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: 144B_550_wb 412

description: raw data file: 2013-09-25_19723144_550PMT_5um_0532.txt, Array B (blocks 9-16)


title: 143D_550_wb 138

description: raw data file: 2013-09-25_19723143_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: BC1-APLNR+ cells

value: BC1 derived APLNR+ cells collected at day 2 after hematopoietic differentiation


title: 143B_550_wb 347

description: raw data file: 2013-09-25_19723143_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 6, 1ug MWCNT

value: 1ug MWCNT


title: BC1 cells

value: Undifferentiated BC1 cells


title: nwgl rep2


title: 147A_550_wb 135

description: raw data file: 2013-09-25_19723147_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: nwgl rep1


title: Control-2


title: 143A_550_wb 74

description: raw data file: 2013-09-25_19723143_550PMT_5um_0532.txt, Array A (blocks 1-8)


title: WT rep3

source_name: WT_Cabbage leaf

value: wild type


title: TRIM33_mix_1

description: total RNA

value: C57BL/6 LyzCre

value: 6-8 weeks


title: 142D_550_wb 170

description: raw data file: 2013-09-24_19723142_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: Male

value: 120ug crocidolite


title: BC1-CD43+ cells

value: BC1 derived CD43+ cells collected at day 8 after hematopoietic differentiation


title: WT rep2


title: 178

description: total RNA


title: WT rep1


title: S10_KO

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then paired-end reads were mapped to the human genome (hg19, GRCh37) by Tophat 2.0.14 (bowtie v2.2.1.0, samtools v0.1.19.0) allowing 2 mismatches and 1 best hit
Mapped reads were counted in individual refSeq transcript region of each sample using RSeQC v2.6.1.
The R Bioconductor edgeR package was used to normalize raw reads and compare the difference.
Genome_build: hg19
Supplementary_files_format_and_content: metatable includes raw reads and log2 transformed CPM

source_name: iPSC-derived cardiomyocytes

growth_protocol: iPSCs were cultured in Essential 8 media and were subsequently differentiated based on a chemical modulation of Wnt-pathway protocol. Afterwards, cells were kept in cardiomyocyte maintainance medium.

extract_protocol:
RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq Stranded Total RNA Library Prep 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

treatment_protocol: OGFOD1-knockout iPSC-derived cardiomyocytes were generated using a CRISPR/Cas9-system. They were cultured alongside wildype cardiomyocytes for 15 days and subsequenctly harvested for RNA isolation. Wildtype iPSC-derived cardiomyocytes were treated on day 15 after initiation of the differentiation with either dimethyloxalylglycine (1 mM) or vehicle control for 18h.

tag: cell type

value: ND2 induced pluripotent stem cell-derived cardiomyocytes

value: day 15 iPSC-derived cardiomyocytes


title: S9_KO


title: S12_KO


title: 142C_550_wb 142

description: raw data file: 2013-09-24_19723142_550PMT_5um_0532.txt, Array C (blocks 17-24)

tag: strain/background

value: Blood

value: Month 6


title: 142B_550_wb 189

description: raw data file: 2013-09-24_19723142_550PMT_5um_0532.txt, Array B (blocks 9-16)

tag: gender

value: 40ug MWCNT


title: S8_WT_DMOG

description: wild-type


title: 142A_550_wb 133

description: raw data file: 2013-09-24_19723142_550PMT_5um_0532.txt, Array A (blocks 1-8)

tag: tissue

value: DM


title: S7_WT_DMOG

description: wild-type


title: 141B_550_wb 263

description: raw data file: 2013-09-24_19723141_550PMT_5um_0532.txt, Array B (blocks 9-16)

tag: time


title: S11_KO


title: S5_WT_DMOG

description: wild-type


title: S6_WT_DMOG

description: wild-type


title: S4_WT

description: wild-type


title: S3_WT

description: wild-type


title: 141D_550_wb 100

description: raw data file: 2013-09-24_19723141_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 141C_550_wb 185

description: raw data file: 2013-09-24_19723141_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 1, 10ug MWCNT

value: 10ug MWCNT

value: Month 1


title: S2_WT

description: wild-type


title: 139D_550_wb 54

description: raw data file: 2013-09-24_19723139_550PMT_5um_0532.txt, Array D (blocks 25-32)


title: 141A_550_wb 225

description: raw data file: 2013-09-24_19723141_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 80ug MWCNT


title: 139B_550_wb 247

description: raw data file: 2013-09-24_19723139_550PMT_5um_0532.txt, Array B (blocks 9-16)

value: 1ug MWCNT


title: 139C_550_wb 250

description: raw data file: 2013-09-24_19723139_550PMT_5um_0532.txt, Array C (blocks 17-24)


title: S1_WT

description: wild-type


title: 159B_550_wb 152

description: raw data file: 2013-09-27_19723159_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 12, 40ug MWCNT

value: Month 12


title: 3-1-7

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: brain

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: 10-week-old male BALB/c mice (Vital River Laboratories, Beijing, China) were used in this study and the mice were housed in a temperature-controlled room under a 12 hours light/12 hours dark cycle, with free access to food and water ad libitum.

extract_protocol: Total RNA was extracted from the brain regions using TRIzol Reagent. RNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre)

treatment_protocol: The mice were euthanized by cervical dislocation and brains were dissected using stereomicroscope to separate the four experimental brain regions (olfactory bulb, hypothalamus, hippocampus as well as cerebellum) according to mouse brain atlas

value: cerebellum

value: Balb/c

value: 10 weeks


title: 3-1-5

value: hippocampus

value: Male


title: 138D_550_wb 114

description: raw data file: 2013-09-24_19723138_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 1, 120ug crocidolite

value: 120ug crocidolite


title: CAP600 H3K4me3_rep1

source_name: CAP600 H3K4me3

tag: cell line

value: Mammary epithelial cell line

value: Cold atmospheric plasma (CAP)

tag: chip antibody

value: Histone H3K4me3 Polyclonal Antibody

tag: chip antibody vendor

value: Signalway Antibody

tag: chip antibody cat. #


title: No-CAP H3K4me3_rep1

source_name: No-CAP H3K4me3

value: none (control)


title: 3-1-4

value: hypothalamus


title: 139A_550_wb 119

description: raw data file: 2013-09-24_19723139_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: Blood

value: 10ug MWCNT


title: 138C_550_wb 11

description: raw data file: 2013-09-24_19723138_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: 80ug MWCNT

value: Month 6


title: 138B_550_wb 129

description: raw data file: 2013-09-24_19723138_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1, 40ug MWCNT

value: 40ug MWCNT

value: Month 1


title: 138A_550_wb 84

description: raw data file: 2013-09-24_19723138_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: DM


title: d3.homo.r3

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

description: ES cells were split on mitomycin-treated MEFs in ESC medium without LIF. The following day, the ESCs were preplated twice to isolate the ESCs from the mitomycin-treated feeder cells and subsequently  were seeded on the Wnt3a feeders cells in  Endoderm Differentiation Mmedium containing Activin A (12ng/ml), refreshed every day. Cells were collectd 3 days later for FACS isolation.

data_processing:
RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013). Expression of genes in FPKM was calculated with RSEM (Li et al., 2011).
Genome_build: mm10

source_name: endoderm cells

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research)
Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012)

value: Foxa2 knock-in/knock-out (Foxa2-Venus) KO mouse ES cell line

tag: facs sorting markers

value: Venus-positive


title: 137C_550_wb 105

description: raw data file: 2013-09-24_19723137_550PMT_5um_0532.txt, Array C (blocks 17-24)

value: Male


title: 137D_550_wb 7

description: raw data file: 2013-09-24_19723137_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: 1ug MWCNT


title: 2-1-7

value: cerebellum

value: Balb/c

value: 10 weeks


title: 137A_550_wb 121

description: raw data file: 2013-09-24_19723137_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 1, 80ug MWCNT


title: 1-1-7


title: 137B_550_wb 64

description: raw data file: 2013-09-24_19723137_550PMT_5um_0532.txt, Array B (blocks 9-16)

value: 120ug crocidolite


title: 2-1-1

value: olfactory bulb


title: 1-1-4

value: hypothalamus


title: 1-1-5

value: hippocampus


title: 3-1-1


title: 2-1-4


title: 136D_550_wb 102

description: raw data file: 2013-09-24_19723136_550PMT_5um_0532.txt, Array D (blocks 25-32)

value: Blood


title: 1-1-1


title: 136A_550_wb 51

description: raw data file: 2013-09-24_19723136_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 10ug MWCNT


title: 136C_550_wb 216

description: raw data file: 2013-09-24_19723136_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 1, DM


title: d3.het.r3

value: Foxa2 knock-in/knock-out (Foxa2-Venus) control mouse ES cell line


title: Non-metastatic mammary tumor, Biological Rep 1

city: Atlanta

first: Carlos

middle: S.

last: Moreno

state: GA

address: Michael Street

department: Pathology & Laboratory Medicine

institute: Emory University

description:
Tumor without Metastasis
CMO111204-0004_Mouse 3462

hyb_protocol: Standard hybridization protocol for Affymetrix GeneChip® Mouse Gene 2.0 ST Array using GeneChip® Hybridization Wash and Stain Kit.

scan_protocol: GeneChips were scanned on the the  GeneChip®Scanner 3000 7G platform.

data_processing: Signals were normalized by log2 RMA normalization with default parameters in R/bioconductor.

label: Biotin

source_name: Mouse breast

label_protocol: Standard labeling protocol for Affymetrix GeneChip® Mouse Gene 2.0 ST Array using WT Plus Reagent Kit.

extract_protocol: Total RNA was isolated from frozen mouse mammary tissues (normal or tumor) using mirVana RNA isolation kit, and cleaned-up by Qiagen RNeasy mini kit.

treatment_protocol: At six weeks of age, MMTV-Wnt1 transgenic mice and control littermates were placed into group housing with food provided ad lib and a 6% sucrose solution with 200 ug/ml of doxycycline. When the mammary tumor reached the size of 20 mm, the animal was euthanized and the tumor was collected.

value: FVB

value: mammary tumor

tag: metastatic status

value: non-metastatic

value: Female

tag: genotype

tag: age (onset)

value: 306 days

tag: age (sack)

value: 354 days


title: 136B_550_wb 113

description: raw data file: 2013-09-24_19723136_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 1, 1ug MWCNT

value: Male

value: 1ug MWCNT

value: Month 1


title: 2-1-5

tag: strain

value: Balb/c

tag: age

value: 10 weeks


title: Metastatic mammary tumor, Biological Rep 2

description:
Tumor with Metastasis
CMO111204-0008_Mouse 3070

value: metastatic

value: 194 days

value: 281 days


title: Metastatic mammary tumor, Biological Rep 1

description:
Tumor with Metastasis
CMO111204-0007_Mouse 3075

value: 251 days

value: 300 days


title: Metastatic mammary tumor, Biological Rep 3

description:
Tumor with Metastasis
CMO111204-0009_Mouse 3096

value: 242 days

value: 284 days


title: Non-metastatic mammary tumor, Biological Rep 2

description:
Tumor without Metastasis
CMO111204-0005_Mouse 3140

value: FVB

value: mammary tumor

value: 192 days

value: 222 days


title: Normal mammary gland, Biological Rep 3

description:
Control
CMO111204-0003_Mouse 3150

value: mammary

value: Female

value: Wild-type Wnt1

value: No tumor

value: 538 days


title: Non-metastatic mammary tumor, Biological Rep 3

description:
Tumor without Metastasis
CMO111204-0006_Mouse 3040

value: non-metastatic

value: 247 days

value: 298 days


title: Normal mammary gland, Biological Rep 2

description:
Control
CMO111204-0002_Mouse 3076

value: 556 days


title: Normal mammary gland, Biological Rep 1

description:
Control
CMO111204-0001_Mouse 3137

value: 533 days


title: WTHFD18BAT

first: LEI

last: WANG

state: MD

address: Building 8A, Room B1A05 8 Center Dr , MD 20814

data_processing:
Reads were trimmed for adapter sequences using cutadapt v1.16.
Trimmed reads were then aligned to the mouse mm9 genome using hisat v2.1.0
Expression data were analyzed by genomatix genome analyzer.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files include RPKM values for each Sample

source_name: BAT tissue

extract_protocol:
Adipose tissue (iWAT and eWAT) of C57BL/6J mice (males) maintained on HFD for 12 weeks was digested with KRH buffer (2% FFA-free BSA) containing 3.3mg/ml collagenase I via incubation at 37 ℃ for 30-45 min. When the tissue was fully digested, 10 ml of KRH buffer was added to terminate collagenase activity. Cells were then filtered through a 250 μm cell strainer. After 10 min, the floating top layer containing mature adipocytes was collected. Mature adipocytes were washed twice with KRH buffer containing 5 mM EDTA and then used for RNA-seq analysis. Brown adipose tissues (BAT) were isolated and quickly freezed in liquied nitrogen.
Total RNA extracted from mature adipocytes (iWAT and eWAT) and BAT tissue. RNAs with RIN >8 (assessed by the Agilent 2100 Bioanalyzer system) were used to prepare transcriptome libraries using the NEBNext Ultra RNA library prep kit (New England Biolabs).

treatment_protocol: Fed with regular chow

value: wild type

value: BAT adipocytes


title: WTHFD17BAT


title: WTHFD5BAT


title: WTHFD16BAT


title: WTHFD2BAT


title: 2cell HMVEC 24hr #1

description:
2012-06-13_19706201_600PMT_532.txt
Array # (Block ID): A

scan_protocol: The microarrays were scanned on an Axon Genepix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split in to four subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 8816 features on each microarray by subtracting the median local background from the median local foreground for each spot. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The spot intensities and T were transformed by taking the log (base 2) of each value; and all further calculations were performed with the log-transformed values. The spot intensities for the 8760 features associated with an oligonucleotide probe were averaged per probe in order to obtain the mean of the triplicate spots for each probe (i.e. probe intensities). The normalization factor (N) for each microarray was calculated as the 20% trim mean of the average human probes spot intensities above threshold in all samples. The probe intensities were then normalized, by subtracting N from each spot intensity and adding back the grand mean of N across all microarrays. The data was filtered to retain values for the 1718 human microRNA probes on the microarray minus any probes showing an overall saturation of signal.

source_name: HMVEC 2cell 1.2ug/ml MWCNT 24hr

label_protocol: The RNA samples were DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through Nanosep 100K columns (Pall Corporation) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: For monoculture exposures, SAEC and HMVEC were plated directly into 100 mm cell culture dishes (Corning, Tewksbury, MA; growth area: 55 cm2), allowed to form intact barriers for 72 h, serum starved overnight, and exposed directly to MWCNT at a concentration of 1.2 µg/mL in 10 mL of their respective media for either 6 or 24 h. DM for 24 h was used as a negative control. Six biological replicates of each SAEC and HMVEC monoculture exposure condition were collected for microarray analysis. Both SAEC and HMVEC in monoculture have been shown to interact with MWCNT (Pacurari et al. 2012; Snyder-Talkington et al. 2013b).    For coculture exposures, SAEC and HMVEC were allowed to form intact epithelial and endothelial barriers for 72 h, serum starved overnight, and SAEC were exposed to MWCNT at a concentration of 1.2 µg/mL in 10 mL of SAEC media for either 6 or 24 h. DM for 24 h was used as a negative control. HMVEC in the coculture system were not directly exposed to MWCNT, and MWCNT are not apparent in HMVEC transmission electron microscopy preparations following SAEC exposure in coculture (Snyder-Talkington et al. 2013a).Six biological replicates of each SAEC and HMVEC coculture at each exposure condition were collected for microarray analysis. The total number of monoculture and coculture samples for microarray analysis was 72.

extract_protocol: Total RNA was isolated from SAEC and HMVEC using RNAprotect Cell Reagent and an RNeasy Mini Kit from Qiagen according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA concentrations were determined using a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For cell culture exposures, MWCNT were prepared in DM. Transmission electron micrographs of MWCNT dispersed in DM determined that DM promoted significant dispersion of MWCNT. MWCNT were prepared in DM, followed by indirect sonication at 4°C for 5 min (Hielscher ultrasonic processor, UIS259L) at amplitude 100% and cycle 1. Following indirect sonication, the suspension was directly sonicated for 5 min at 5W output and 10% duty cycle (Branson Sonifier 450). The stock solution (0.5 mg/mL) of MWCNT was kept at 4°C and used within 2–3 weeks. Prior to cell culture experiments, the MWCNT stock solution was directly sonicated for 1 min at 5W output and 10% duty cycle.

value: HMVEC

tag: culture

value: coculture


title: ATAC.d2.FVF.Gata.r2

description: ES cells were seeded without feedeers in gelatin-coated plates and grown for 48h in ES standard medium (LIF/serum) supplemented with 40ng/ml doxycycline.

data_processing:
reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

source_name: ES cells

extract_protocol:
ATAC-seq was done as previously described (Buenrostro et al., 2013). Briefly, 50000 FACS sorted cells were washed in 1xPBS, re-suspended in 50 ul of lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40,) and spun at 500g for 10 min at 4 °C to collect nuclei. Nuclei were subsequently re-suspended in 50 µl Transposase reaction containing 25µL 2x tagmentation buffer, 22.5 µl water, 2.5 µl Tn5 Transposase (Illumina Nextera DNA Library Preparation Kit, cat. FC-121-1030). Reactions were incubated for 30 min at 37° C in a thermomixer shaking at 300 rpm and DNA purified using Qiagen PCR clean-up MinElute kit (Qiagen).
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as described (Buenrostro et al., 2013). After 4 cycles libraries were then monitored with qPCR: 5 µl PCR sample in a 15 µl reaction with the same primers. qPCR output was monitored for the ΔRN; 0.25 ΔRN cycle number was used to estimate the number of additional cycles of the PCR reaction needed for the remaining PCR samples. Amplified libraries were purified with the Qiagen PCR clean-up MinElute kit (Qiagen) and size selected for fragments less than 600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.

value: doxycycline (Dox) inducible Foxa2-Venus, Gata4-tBFP ES cell line (T134)

tag: genotype/variation

value: TetON-Foxa2-Venus; TetON-Gata4-tBFP

value: Venus-positive/tBFP-positive

tag: antibody


title: 2cell SAEC 24hr #6

description:
2012-05-25_19706199_650PMT_0532.txt
Array # (Block ID): C

source_name: SAEC 2cell 1.2ug/ml MWCNT 24hr

value: SAEC


title: WTHFD1BAT

tag: cell type


title: ATAC.d2.FVF.Gata.r1


title: 2cell SAEC 24hr #3

description:
2012-05-25_19706196_650PMT_0532.txt
Array # (Block ID): D


title: WTHFD16EWAT

source_name: eWAT adipocytes

value: eWAT adipocytes


title: WTHFD5EWAT


title: WTHFD4EWAT


title: 2cell SAEC 24hr #2

description:
2012-05-25_19706196_650PMT_0532.txt
Array # (Block ID): C


title: WTHFD3EWAT


title: WTHFD1EWAT


title: WTHFD16IWAT

source_name: iWAT adipocytes

value: iWAT adipocytes


title: WTHFD2EWAT


title: WTHFD4IWAT


title: WTHFD3IWAT


title: 2cell SAEC 24hr #1

description:
2012-05-25_19706196_650PMT_0532.txt
Array # (Block ID): B


title: WTHFD5IWAT


title: 2cell SAEC 24hr #5

description:
2012-05-25_19706199_650PMT_0532.txt
Array # (Block ID): B


title: 2cell SAEC 6hr #5

description:
2012-05-25_19706195_650PMT_0532.txt
Array # (Block ID): D

source_name: SAEC 2cell 1.2ug/ml MWCNT 6hr


title: WTHFD1IWAT


title: 2cell SAEC 24hr #4

description:
2012-05-25_19706199_650PMT_0532.txt
Array # (Block ID): A


title: 2cell SAEC 6hr #6

description:
2012-05-25_19706196_650PMT_0532.txt
Array # (Block ID): A


title: WTHFD2IWAT


title: 2cell SAEC 6hr #4

description:
2012-05-25_19706195_650PMT_0532.txt
Array # (Block ID): C


title: 2cell SAEC 6hr #3

description:
2012-05-25_19706195_650PMT_0532.txt
Array # (Block ID): B


title: 2cell SAEC 6hr #2

description:
2012-05-25_19706195_650PMT_0532.txt
Array # (Block ID): A


title: 2cell SAEC No tx #3

description:
2012-05-25_19706192_650PMT_0532.txt
Array # (Block ID): D

source_name: SAEC 2cell DM control


title: 2cell SAEC No tx #5

description:
2012-05-25_19706194_650PMT_0532.txt
Array # (Block ID): B


title: 2cell SAEC 6hr #1

description:
2012-05-25_19706194_650PMT_0532.txt
Array # (Block ID): D


title: 2cell SAEC No tx #2

description:
2012-05-25_19706192_650PMT_0532.txt
Array # (Block ID): C


title: 2cell SAEC No tx #1

description:
2012-05-25_19706192_650PMT_0532.txt
Array # (Block ID): B


title: 2cell HMVEC 6hr #6

description:
2012-05-25_19706192_650PMT_0532.txt
Array # (Block ID): A

source_name: HMVEC 2cell 1.2ug/ml MWCNT 6hr


title: 2cell HMVEC 6hr #5

description:
2012-05-25_19706191_650PMT_0532_rev061512.txt
Array # (Block ID): D


title: 14dp1dTAC_neontal_rep1

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

institute: Medizinische Fakultät Mannheim

data_processing:
Raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using the Trim Galore! wrapper tool
Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star).
Feature counts were determined using R package “Rsubread”. Only genes showing counts greater 5 at least two times across all samples were considered for further analysis (data cleansing).
Gene annotation was done by R package “bioMaRt. Before starting the statistical analysis steps, expression data was log2 transformed and normalized according to 50th percentile).
Differential gene expression was calculated by R package “edgeR”.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated;  log2_TMM data

source_name: regenerative transverse aortic constriction (started at postnatal day P1 after birth), ended at postnatal day 14

growth_protocol: 14 day old neonatal mice hearts

extract_protocol:
Total RNA was isolated from the left ventricule with Qiazol according to the manufacture protocol
The RNA sequencing library was generated from 200ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to manufacture´s protocols. TruSeq SBS Kit v3-HS (50 cycles, single ended run) with an average of 3 x107 reads per RNA sample

treatment_protocol: Transverse aortic constriction (TAC) either on postnatal day 1 or 7

tag: protocol

value: Transverse aortic constriction

tag: tissue

value: heart


title: WT-1

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: brain

extract_protocol:
Cerebral cortex was dissected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage


title: KO-6

value: Cd93 KO


title: 2cell SAEC No tx #6

description:
2012-05-25_19706194_650PMT_0532.txt
Array # (Block ID): C

tag: cell line


title: WT4


title: 7dp7dTAC_neontal_rep3

source_name: non-regenerative stage (started at P7 after birth) transverse aortic constriction, ended at postnatal day 14


title: 14dp1dTAC_neontal_rep3


title: ctr_neonatal_sham_rep3

value: sham


title: KO5


title: ctr_neonatal_sham_rep2


title: 2cell HMVEC 6hr #2

description:
2012-05-24_19706189_650PMT_0532.txt
Array # (Block ID): C


title: 2cell SAEC No tx #4

description:
2012-05-25_19706194_650PMT_redip_0532.txt
Array # (Block ID): A


title: 2cell HMVEC 6hr #1

description:
2012-05-24_19706189_650PMT_0532.txt
Array # (Block ID): B


title: 2cell HMVEC 6hr #3

description:
2012-05-25_19706191_650PMT_0532_rev061512.txt
Array # (Block ID): B


title: 7dp7dTAC_neontal_rep2


title: 7dp7dTAC_neontal_rep1


title: 2cell HMVEC No tx #6

description:
2012-05-24_19706189_650PMT_0532.txt
Array # (Block ID): A

source_name: HMVEC 2cell DM control


title: 2cell HMVEC No tx #3

description:
2012-05-24_19706188_650PMT_0532.txt
Array # (Block ID): B


title: 2cell HMVEC No tx #4

description:
2012-05-24_19706188_650PMT_0532.txt
Array # (Block ID): C


title: 2cell HMVEC No tx #5

description:
2012-05-24_19706188_650PMT_0532.txt
Array # (Block ID): D


title: 14dp1dTAC_neontal_rep2


title: 2cell HMVEC 6hr #4

description:
2012-05-25_19706191_650PMT_0532_rev061512.txt
Array # (Block ID): C


title: ctr_neonatal_sham_rep1


title: 2cell HMVEC 24hr #4

description:
2012-05-24_19706187_650PMT_0532.txt
Array # (Block ID): A


title: 2cell HMVEC 24hr #6

description:
2012-05-24_19706187_650PMT_0532.txt
Array # (Block ID): C


title: 2cell HMVEC No tx #1

description:
2012-05-24_19706187_650PMT_0532.txt
Array # (Block ID): D


title: 2cell HMVEC 24hr #2

description:
2012-05-24_19706186_650PMT_0532.txt
Array # (Block ID): C


title: SAEC 24hr #4

description:
2012-05-24_19706185_650PMT_0532.txt
Array # (Block ID): C

source_name: SAEC 1cell 1.2ug/ml MWCNT 24hr

value: monoculture


title: SAEC 24hr #3

description:
2012-05-24_19706185_650PMT_0532.txt
Array # (Block ID): B


title: SAEC 24hr #2

description:
2012-05-24_19706185_650PMT_redip_0532.txt
Array # (Block ID): A


title: SAEC 24hr #5

description:
2012-05-24_19706185_650PMT_0532.txt
Array # (Block ID): D


title: ATAC.d3F.r2

data_processing:
Reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl.

source_name: mesendoderm cells

growth_protocol: The cells were cultured for few consecutive passages on gelatine and ES medium. On the day of differentiation, mESCs were seeded on 10 cm gelatine coated dishes directly in endoderm differentiation medium (EDM) supplemented with 1 ng/ml of murine Wnt3a and 10 ng/ml of Activin A. Freshly prepared EDM supplemented with Wnt3a and Activin A was added every day. Cells were collected on day0, day3 and day5 for FACS isolation.

extract_protocol:
ATAC-seq was done as previously described (Buenrostro et al., 2013). Briefly, 50000 FACS sorted cells were washed in 1xPBS, re-suspended in 50 ul of lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40,) and spun at 500g for 10 min at 4 °C to collect nuclei. Nuclei were subsequently re-suspended in 50 µl Transposase reaction containing 25µL 2x tagmentation buffer, 22.5 µl water, 2.5 µl Tn5 Transposase (Illumina Nextera DNA Library Preparation Kit, cat. FC-121-1030). Reactions were incubated for 30 min at 37° C in a thermomixer shaking at 300 rpm and DNA purified using Qiagen PCR clean-up MinElute kit (Qiagen).
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as described (Buenrostro et al., 2013). After 4 cycles, libraries were then monitored with qPCR: 5 µl PCR sample in a 15 µl reaction with the same primers. qPCR output was monitored for the ΔRN; 0.25 ΔRN cycle number was used to estimate the number of additional cycles of the PCR reaction needed for the remaining PCR samples. Amplified libraries were purified with the Qiagen PCR clean-up MinElute kit (Qiagen) and size selected for fragments less than 600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.

value: double knock-in (DKI) mouse ES cell line carrying Foxa2-Venus and Sox17-Cherry gene fusions

tag: time point


title: SAEC 6hr #6

description:
2012-05-24_19706184_650PMT_0532.txt
Array # (Block ID): C

source_name: SAEC 1cell 1.2ug/ml MWCNT 6hr


title: ATAC.d3F.homo.r3

source_name: endoderm cells

growth_protocol: ES cells were split on mitomycin-treated MEFs in ESC medium without LIF. The following day, the ESCs were preplated twice to isolate the ESCs from the mitomycin-treated feeder cells and subsequently were seeded on the Wnt3a feeders cells in Endoderm Differentiation Mmedium containing Activin A (12ng/ml), refreshed every day. Cells were collected 3 days later for FACS isolation.

value: Foxa2 knock-in/knock-out (Foxa2-Venus) KO mouse ES cell line

value: Venus-positive


title: SAEC 24hr #6

description:
2012-05-24_19706186_650PMT_0532.txt
Array # (Block ID): A


title: ATAC.d5FS.r1


title: SAEC 6hr #4

description:
2012-05-24_19706184_650PMT_0532.txt
Array # (Block ID): A


title: SAEC 6hr #5

description:
2012-05-24_19706184_650PMT_0532.txt
Array # (Block ID): B


title: SAEC 24hr #1

description:
2012-05-24_19706184_650PMT_0532.txt
Array # (Block ID): D


title: 2cell HMVEC No tx #2

description:
2012-05-24_19706188_650PMT_0532.txt
Array # (Block ID): A


title: SAEC 6hr #3

description:
2012-05-22_19706183_650PMT_0532.txt
Array # (Block ID): D


title: SAEC No tx #5

description:
2012-05-22_19706182_650PMT_0532.txt
Array # (Block ID): D

source_name: SAEC 1cell DM control


title: SAEC 6hr #2

description:
2012-05-22_19706183_650PMT_0532.txt
Array # (Block ID): C


title: SAEC 6hr #1

description:
2012-05-22_19706183_650PMT_0532.txt
Array # (Block ID): B


title: SAEC No tx #6

description:
2012-05-22_19706183_650PMT_0532.txt
Array # (Block ID): A


title: ATAC.d5FS.r2


title: ATAC.d3F.homo.r1


title: 2cell HMVEC 24hr #3

description:
2012-05-24_19706186_650PMT_0532.txt
Array # (Block ID): D

source_name: HMVEC 2cell 1.2ug/ml MWCNT 24hr


title: SAEC No tx #4

description:
2012-05-22_19706182_650PMT_0532.txt
Array # (Block ID): C


title: ATAC.d3F.het.r2

value: Foxa2 knock-in/knock-out (Foxa2-Venus) control mouse ES cell line


title: SAEC No tx #3

description:
2012-05-22_19706182_650PMT_0532.txt
Array # (Block ID): B


title: SAEC No tx #2

description:
2012-05-22_19706182_650PMT_0532.txt
Array # (Block ID): A


title: ATAC.d3F.homo.r2


title: ATAC.d3F.r1


title: ATAC.d0.r2

source_name: ES cells


title: ATAC.d0.r1


title: ATAC.d3F.het.r1


title: ATAC.d2.FVFp.r2

growth_protocol: ES cells were seeded without feeders in gelatin-coated plates and grown for 48h in ES standard medium (LIF/serum) supplemented with 40ng/ml doxycycline.

value: doxycycline (Dox) inducible Foxa2-Venus ES cell line (T119)


title: HMVEC 24hr #6

description:
2012-05-18_19706180_650PMT_0532.txt
Array # (Block ID): C

source_name: HMVEC 1cell 1.2ug/ml MWCNT 24hr

value: HMVEC


title: HMVEC 24hr #5

description:
2012-05-18_19706180_650PMT_redip_0532.txt
Array # (Block ID): B


title: ATAC.d2.FVFn.r2

value: Venus-negative


title: HMVEC 24hr #3

description:
2012-05-18_19706179_650PMT_0532.txt
Array # (Block ID): D


title: HMVEC 24hr #4

description:
2012-05-18_19706180_650PMT_0532.txt
Array # (Block ID): A


title: HMVEC 24hr #2

description:
2012-05-18_19706179_650PMT_0532.txt
Array # (Block ID): C


title: Tec_Gl_Bv_H3

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

data_processing:
Quality control and filtering of raw data was performed using the FastQC and FASTQ Quality Filter (-q 20 –p 75) from FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
According to library preparation kit recommendations, 12 bp segments of raw reads were trimmed out with FASTQ Trimmer from FASTX-toolkit
RNA-seq reads were aligned to NCBI GRCh38 genome (https://support.illumina.com/sequencing/sequencing_software/igenome.html) using HISAT2 aligner (--score-min L,0,-0.5)
Reads corresponding to rRNA and tRNA were removed using split_bam tool from RSeQC package and masked annotation file
Reads aligned to genomic locations were counted using FeatureCounts tool from the Subread package. Differential expression analysis was performed with DESeq2
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: tabular files were generated with featureCounts and contain raw gene counts

molecule: polyA RNA

source_name: HUVEC cultivated on Tec-Gl-Bv

extract_protocol:
For gene expression analysis HUVEC cells from 3 different biological donors were used. HUVEC cells were seeded on surface scaffolds as described above, after 48 hours culture medium was removed, matrices were washed with one change of phosphate buffer and transferred to tubes with 750 μl of TriZol reagent (Life Technology, USA). RNA samples were isolated according to the protocol supplied by the manufacturer. RNA was precipitated with 70% alcohol in the presence of 40 µg glycogen (Thermo Scientific, Lithuania): the precipitate was air dried, dissolved in RNA storage medium (Sigma, Germany) and then dried on a vacuum rotary evaporator.
The libraries were prepared for the sequencing using Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Austria) and were sequenced with Illumina HiSeq3000

treatment_protocol: Umbilical vein was washed with 50 ml of phosphate buffer (PBS), then with 20 ml of collagenase IV buffer (1.5 mM HEPES, 14 mM NaCl, 0.4 mM KCl, 0.12 mM CaCl2, 0.04 mM MgSO4, 0.76 mM D-glucose, pH 7.4), and incubated for 15 min at 37°C with 0.1 % collagenase IV (Gibco, USA) in collagenase IV buffer. After incubation, supernatant with detached cells was collected, vein was additionally washed with 20 ml PBS, both solutions were combined and centrifuged at 800g for 10 minutes to pellet cells. Cells were resuspended and cultivated in IMDM (Gibco, USA) with 10% FBS (Gibco, USA) and antibiotics. The next day adherent cells were carefully washed with IMDM to remove blood cells and further cultivated in fresh IMDM with 10% FBS (passage 0). The cells were passaged with 0.1% solution of collagenase IV once per 3-4 days after 70-80% confluence was achieved. Cells from the 2-nd passage were seeded on the surface of dUV and 3D matrices. To obtain synthetic scaffolds, discs (d = 16 mm) were cut out of matrix specimens and dUV fragments, placed in a 24-well plate and pressed down with polytetrafluoroethylene rings (outer and inner diameters, 16 and 12 mm). Scaffolds in plates were treated with 25 kGy electron beam irradiation using ILU-6 accelerator (INP, Russia). Before seeding with cells scaffolds were pre-incubated with IMDM for 2 hours. HUVEC were seeded onto scaffolds in density of 8×103 cells per each plate well. After 12 hours non-adhered cells were removed, fresh culture medium was added and cells were cultivated for 48 hours. Control cells (TCPS) were cultivated in wells without any matrices.

tag: sample type

value: HUVEC obtained from the third donor cultivated on Tec-Gl-Bv


title: HMVEC 24hr #1

description:
2012-05-18_19706179_650PMT_0532.txt
Array # (Block ID): B


title: ATAC.d3F.het.r3

tag: facs sorting markers


title: HMVEC 6hr #6

description:
2012-05-18_19706179_650PMT_0532.txt
Array # (Block ID): A

source_name: HMVEC 1cell 1.2ug/ml MWCNT 6hr


title: Tec_Gl_Bv_H2

value: HUVEC obtained from the second donor cultivated on Tec-Gl-Bv


title: mouse_3_zone_3

city: Rehovot

first: Shalev

last: Itzkovitz

state: Israel

address: 234 Herzl

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: miRNA expression hepatocytes - mouse 3, zone 3

hyb_protocol: cDNAs were hybridized to according to the Agilent microRNA Hybridization Kit protocol.

scan_protocol: Chips were  scanned using Agilent G2505B array scanner with default parameters.

data_processing: Data were extracted using the Agilent Feature Extraction software with default parameters. miRNAs that were not expressed in at least one zone in all three mice were removed from the analysis. miRNAs that were not annotated as high confidence in miRBase v22 were removed from the analysis. The raw signal for each miRNA (in each chip) was divided by the total signal from all miRNAs in that chip.

source_name: Mouse 3, Zone 3 hepatocytes

label_protocol: Total RNA was labeled with Cy3 during transformation into cDNA using an RNA Agilent miRNA Labeling Kit and Spike Kit.

growth_protocol: Mice were fed ad libitum and were kept in a reverse light-dark cycle

extract_protocol: See associated paper (Ben Moshe et al., Nat. Metab., 2019) for full details. Liver cells from anesthetized mice were dissociated via liberase perfusion. The cell isolate was immuno-labeled for CD73, E-cadherin, CD45, and CD31 and stained with Hoechst and and a viability stain (Zombie Green). The labeled isolate was depeleted of unviable, CD45+ and CD31+ cells and filtered for tetraploid cells. The remaining 4n hepatocytes were sorted based on CD73 and E-cadherin intensities as a proxy of position along the porto-central axis (zone 1 - most pericentral / higher CD73, zone 8 - most periportal / higher E-cadherin). 50,000 cells were sorted for each population (in each mouse). Total RNA was extracted from the hepatocyte pellet using the Direct-zol RNA Mini-prep kit (Zymo Research, USA).

tag: Sex

value: Male

value: 3 months

value: tetraploid hepatocytes


title: mouse_3_zone_8

description: miRNA expression hepatocytes - mouse 3, zone 8

source_name: Mouse 3, Zone 8 hepatocytes


title: SAEC No tx #1

first: Nancy

last: Guo

address: 2816 Health Sciences Center

description:
2012-05-18_19706180_650PMT_0532.txt
Array # (Block ID): D

value: SAEC


title: mouse_3_zone_7

description: miRNA expression hepatocytes - mouse 3, zone 7

source_name: Mouse 3, Zone 7 hepatocytes


title: mouse_3_zone_4

description: miRNA expression hepatocytes - mouse 3, zone 4

source_name: Mouse 3, Zone 4 hepatocytes


title: mouse_3_zone_2

description: miRNA expression hepatocytes - mouse 3, zone 2

source_name: Mouse 3, Zone 2 hepatocytes


title: mouse_3_zone_5

description: miRNA expression hepatocytes - mouse 3, zone 5

source_name: Mouse 3, Zone 5 hepatocytes


title: mouse_3_zone_6

description: miRNA expression hepatocytes - mouse 3, zone 6

source_name: Mouse 3, Zone 6 hepatocytes


title: ATAC.d2.FVFp.r1


title: ATAC.d2.FVFn.r1


title: mouse_3_zone_1

description: miRNA expression hepatocytes - mouse 3, zone 1

source_name: Mouse 3, Zone 1 hepatocytes


title: Tec_Gl_H3

source_name: HUVEC cultivated on Tec-Gl

value: HUVEC obtained from the third donor cultivated on Tec-Gl


title: HMVEC 6hr #5

description:
2012-05-18_19706178_650PMT_0532.txt
Array # (Block ID): D


title: HMVEC 6hr #4

description:
2012-05-18_19706178_650PMT_0532.txt
Array # (Block ID): C


title: mouse_2_zone_8

description: miRNA expression hepatocytes - mouse 2, zone 8

source_name: Mouse 2, Zone 8 hepatocytes


title: HMVEC 6hr #3

description:
2012-05-18_19706178_650PMT_0532.txt
Array # (Block ID): B


title: Tec_Gl_H2

value: HUVEC obtained from the second donor cultivated on Tec-Gl


title: mouse_2_zone_7

description: miRNA expression hepatocytes - mouse 2, zone 7

source_name: Mouse 2, Zone 7 hepatocytes


title: Tec_Gl_H1

value: HUVEC obtained from the first donor cultivated on Tec-Gl


title: HMVEC 6hr #2

description:
2012-05-18_19706178_650PMT_redip_0532.txt
Array # (Block ID): A

value: monoculture


title: Tec_Gl_Bv_H1

value: HUVEC obtained from the first donor cultivated on Tec-Gl-Bv


title: HMVEC 6hr #1

description:
2012-05-18_19706177_650PMT_0532.txt
Array # (Block ID): D


title: mouse_2_zone_5

description: miRNA expression hepatocytes - mouse 2, zone 5

source_name: Mouse 2, Zone 5 hepatocytes


title: Posteriorized embryonic-like sacs

city: Syracuse

first: Yi

last: Zheng

address: 900 S Crouse Ave

department: Biomedical and Chemical Engineering

institute: Syracuse University

data_processing:
Illumina HiSeq 4000 for basecalling
10x Genomics Cell Ranger pipeline (version 3.0.0) for barcoding, alignment, filtering
Rstudio 1.1.156 and Seurat 3.0.0.9 for visualization and analysis
Genome_build: hg19
Supplementary_files_format_and_content: TSV and MTX, generated by Cell Ranger pipeline, including barcodes, features and matrix  RDS, generated using Seurat, including visualization parameters  TXT, README

source_name: Posteriorized embryonic-like sacs

extract_protocol:
Posteriorized embryonic-like sacs (48 hours) within the microfluidic devices, amniotic-like cells derived using transwell and H9 cells were dissociated into single cells by incubating in Accutase for 1 hour. Cells from posteriorized embryonic-like sacs were lysed and barcoded with 10x Chromium Controller Instrument (10x Genomics). Amniotic-like cells derived using transwell and H9 cells were mixed at a 2:1 ratio, before lysed and barcoded with 10x Chromium Controller Instrument.
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Single Cell 3' v2). The libraries were sequenced on Illumina HiSeq 4000 with paired-end sequencing (One sample per flow cell).

value: In-vitro human ESCs


title: Mixture of amniotic-like cells (transwell) and H9 cells


title: Tec_H3

source_name: HUVEC cultivated on Tec

value: HUVEC obtained from the third donor cultivated on Tec


title: HMVEC No tx #6

city: Morgatown

institute: West Virginia University

description:
2012-05-18_19706177_650PMT_redip_0532.txt
Array # (Block ID): C

source_name: HMVEC 1cell DM control


title: Tec_H1

value: HUVEC obtained from the first donor cultivated on Tec


title: H2030-EV

city: lexington

first: ramon

middle: chang

last: sun

state: KY

address: 741 S. Limestone, BBSRB, B177

institute: University of kentucky

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Cutadapt.
Read quality was checked for each sample using FastQC
High-quality reads were then imported into STAR  for alignment into BAM files.
Genome_build: hg38
Supplementary_files_format_and_content: Cufflinks abundance measurements

source_name: ATCC

growth_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before RNA extraction

extract_protocol:
Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: empty vector

value: lung cancer cel line

tag: passage

value: Passage 5


title: H2030-malin-OE


title: H1299-malin-OE


title: H1299-EV


title: Tec_H2

value: HUVEC obtained from the second donor cultivated on Tec


title: A549-malin-OE


title: HMVEC No tx #4

description:
2012-05-18_19706177_650PMT_redip_0532.txt
Array # (Block ID): A

value: HMVEC


title: HMVEC No tx #5

description:
2012-05-18_19706177_650PMT_redip_0532.txt
Array # (Block ID): B


title: mouse_2_zone_4

description: miRNA expression hepatocytes - mouse 2, zone 4

source_name: Mouse 2, Zone 4 hepatocytes

value: Male


title: mouse_2_zone_3

description: miRNA expression hepatocytes - mouse 2, zone 3

source_name: Mouse 2, Zone 3 hepatocytes

value: 3 months


title: A549-EV


title: mouse_2_zone_2

description: miRNA expression hepatocytes - mouse 2, zone 2

source_name: Mouse 2, Zone 2 hepatocytes

value: tetraploid hepatocytes


title: mouse_2_zone_6

description: miRNA expression hepatocytes - mouse 2, zone 6

source_name: Mouse 2, Zone 6 hepatocytes


title: dUV_H2

source_name: HUVEC cultivated on dUV

value: HUVEC obtained from the second donor cultivated on dUV


title: mouse_2_zone_1

description: miRNA expression hepatocytes - mouse 2, zone 1

source_name: Mouse 2, Zone 1 hepatocytes


title: dUV_H3

value: HUVEC obtained from the third donor cultivated on dUV


title: mouse_1_zone_8

description: miRNA expression hepatocytes - mouse 1, zone 8

source_name: Mouse 1, Zone 8 hepatocytes


title: HMVEC No tx #3

description:
2012-05-18_19706176_650PMT_0532.txt
Array # (Block ID): D


title: HMVEC No tx #2

description:
2012-05-18_19706176_650PMT_0532.txt
Array # (Block ID): C


title: HDullest_R2B

city: Cambridge

first: Heather

middle: P

last: Harding

state: Cambridge

address: Hills Road

department: CIMR Clinical Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
CLB_GCN_O16
Histidinol treated_Dullest_sorted_round_2_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls

data_processing:
Library strategy: Amplicon sequencing
Compressed fastq files containing base calls were produced by the sequencing facility.
The MAGECK program (PMID: 25476604 PMCID: PMC4290824) was used for trimming and mapping the reads to the guide library (see supplementary file 'CHO_library_B_GCN Screen_counts.xls' columns A-F for library).
The raw guide counts were adjusted to total counts per sample to equalize between samples.
Genome_build: The genome used to build the guide list was GCF_000223135.1 (CriGri_1.0). Please see the supplementary file 'CHO_library_B_GCN Screen_counts.xls' columns A-F for the sg guide sequences and genes targeted.
Supplementary_files_format_and_content: *.txt: Tab-delimited text files, column A Guide unique ID, column B normalized guide counts.

organism: Cricetulus griseus

source_name: CHO cells

growth_protocol: Cells with a stable ISR reporter (CHOP::GFP) and stable Cas9 expression were infected with lentivirus prepared from pooled sgRNA expression library plasmid and helpers by transfection into HEK293T cells. After selection of the infected cells with puromycin for two weeks the cells were left untreated or treated and then sorted as indicated.

extract_protocol:
Genomic DNA containing the integrated sgRNA viral expression vectors was prepared using the DNAzol method.
Two round of PCR were used to produce barcoded amplicons that were pooled for sequencing. The first round of amplicon used vector directed primers flanking the 20bp sgRNA and the second round added barcodes to the individual samples.

treatment_protocol: Cells were treated with histidinol to inhibit histidinyl-tRNA synthetase at 0.5 mM for 20 hours before collection and replating or sorting for dull cells and then replating. After recovery, some cells were expanded and aliquots saved for DNA prep or an additional round of sorting.

value: CHO

value: Chinese hamster ovary cell line

tag: treatment

value: Histidinol 0.5 mM, 20hr

tag: selection

value: Survival and sort for dullest

tag: round of selection


title: TCPS_H3

source_name: HUVEC cultivated on TCPS

value: HUVEC obtained from the third donor cultivated on TCPS


title: HDullest_R2A

description:
CLB_GCN_O15
Histidinol treated_Dulestl_sorted_round_2_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls


title: TCPS_H2

value: HUVEC obtained from the second donor cultivated on TCPS


title: TCPS_H1

value: HUVEC obtained from the first donor cultivated on TCPS


title: HDull_R2A

description:
CLB_GCN_O13
Histidinol treated_Dull_sorted_round_2_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls

value: Survival and sort for medium dull


title: HDull_R2B

description:
CLB_GCN_O14
Histidinol treated_Dull_sorted_round_2_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls


title: HMVEC No tx #1

description:
2012-05-18_19706176_650PMT_0532.txt
Array # (Block ID): B

value: monoculture