title: FB80_DMSO_sensitive

city: Bonn

first: Sarah

last: Kemski

address: Kurt-Georg-Kiesinger-Allee 3

department: Research

country: Germany

institute: Federal Institute for Drugs and Medical Devices

data_processing:
Basecalls performed using Illumina Miseq system software
Adapter trimming was performed with the program cutadapt.
Reads were aligned to the whole human genome using bowtie2.
DESeq2 was used to calculate the fold change, p-value (Wald test) and adjusted p-value (Benjamini Hochberg Adjustment)
Genome_build: hg19
Supplementary_files_format_and_content: xls file containing miRNA calls

source_name: pirmary human fibroblasts, more reactive to erlotinib incubation, incubated with DMSO

growth_protocol: For the experiments keratinocytes were cultured in EpiLife medium with 1% humen keratinocyte growth supplements, 1% pen/strep and 0.1%  amphotericin B, medium was changed every 2-3 days and cells were passaged when reaching a confluence of 75%. Fibroblasts were cultured in basal fibroblast growth medium 2 with 2% FCS, 5 µg/ml Insulin, 0.001 µg/ml fibroblast growth factor (FGF) and 1 % Pen/Strep. The medium was changed every 2-3 days and cells were passaged when reaching a confluence of 75% every 5-7 days

extract_protocol:
Total miRNA was extracted after treatment with Erlotinib using TriFast. 1 ml TriFast was used for each sample to lyse the cells. Cell lysate was mixed with chloroform and centrifuged. Upper aqueous phase was mixed with isopropanol and centrifuged. Supernatant was discarded and pellets were washed with 75% ethanol and centrifuged. Supernatant was again discarded and RNA pellet was resolved in 50 µl RNase-free water.
RNA sequencing libraries were generated using the NEBNext Mulitplex Small RNA Library Prep Set for Illumina (NEB E7300S) following size selection by running the samples on a 10 % polyacrylamide gel and isolating the 147 bp. Samples were purified using the QIAquick PCR Purification Kit (Qiagen, 28104). Libraries were validated on a High Sensitivity DNA chip using the 2100 Bioanalyzer (Agilent).

treatment_protocol: Cells were starved for 2 h with medium without any supplements. Afterwards cells were incubated with DMSO (0.05%) or Erlotinib (5 µM) for 2h (keratinocytes) or 24h (fibroblasts) and then stimulated with EGF (4 nM) ( Three different conditions: DMSO, DMSO + EGF, Erlotinib + EGF)

tag: cell line

value: pirmary human fibroblasts

value: DMSO

tag: molecule subtype

value: microRNA


title: FB93_EGF_sensitive

status: Public on Apr 30 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: pirmary human fibroblasts, more reactive to erlotinib incubation, incubated with DMSO and EGF

tag: cell type

tag: treatment

value: DMSO + EGF


title: FB80_EGF_sensitive


title: FB93_DMSO_sensitive


title: FB80_Erlotinib_sensitive

source_name: pirmary human fibromlasts, more reactive to erlotinib incubation, incubated with Erlotinib and EGF

value: Erlotinib + DMSO


title: FB93_Erlotinib_sensitive


title: 1577AA_MSCB-149

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse or human genome reference.
Gene quantification was performed using UMI information to correct for amplification biases.
Genome_build: human: GRCh38. Gencode release 26.  Mouse: GRCm38. Gencode release M15.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

molecule: polyA RNA

source_name: pancreas

extract_protocol:
Short-term cultured pancreatic islet cells were isolated from a healthy pancreas donor. The culturing process favor the enrichment of pancreatic islet cells while large eliminating endothelial and immune cell types. Primary bladder epithelial cells were isolated by FACS (CD45-, CD140a-, CD31-, Ter119-) from a healthy mouse.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014). This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes (bases 1 to 6 and 7 to 14, respectively). Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

value: pancreatic islet cell


title: FB79_Erlotinib_sensitive


title: 1577AA_MSCB-148


title: 1577AA_MSCB-147


title: FB79_EGF_sensitive


title: FB79_DMSO_sensitive


title: FB76_Erlotinib_sensitive


title: FB76_EGF_sensitive


title: 1577AA_MSCB-146


title: rad53 G1

city: Madrid

first: Mohammed

last: Al Mamun

state: Madrid

address: Calle Ramiro de Maeztu, 9

department: Cell and Molecular Biology

institute: CIB-CSIC

library_source: genomic

data_processing:
DNA libraries were sequenced on Illumina HiSeq2500 platform using single-end sequencing strategy.
Fastq files were aligned against S288C yeast reference genome using Bowtie 2 version 2.3.5.1
sort and index the resultant bam (converted from sam) files using samtools version 1.9
read coverage were mapped in 100 bp windows using bedtools version 2.29.0
ratios were made between replication time points against corresponding G1s using Repliscope version 1.1.0
Genome_build: S288C
Supplementary_files_format_and_content: bed formatted binwise coverage with score field
Supplementary_files_format_and_content: bigwig files containing ration between replication time points against the G1 sample

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: rad53 G1

growth_protocol: All strains are RAD5+ derivatives from W303 and are listed in Table S1. For 10-fold serial dilution assays cells were grown on YPDA for 48 hours at 30ºC, unless otherwise stated. α-factor was used to a final concentration of 5 µg/ml to arrest cells in G1. Release into S-phase in the presence of HU was performed at the concentrations and for the times indicated in the figures.

extract_protocol: CGS analysis was performed as previously reported (Frattini et al., 2017).

value: treated with αFactor


title: 0002.U2

city: Durban

first: Alex

last: Sigal

state: KwaZulu-Natal

address: 719 Umbilo Road, level 5 K-RITH tower building, Nelson R. Mandela Medical School, Umbilo

country: South Africa

institute: Africa Health Research Institute

description:
Uninfected control MDM
CountMatrix_HR_MtbAggs.txt (read count data file)
metaData_HR_MtbAggs.txt (metadata file)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using the RSEM software package to generate raw read counts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: CountMatrix_HR_MtbAggs.txt: Tab-delimited text file matrix containing raw read counts for each sample.
Supplementary_files_format_and_content: metaData_HR_MtbAggs.txt: Tab-delimited text file matrix containing metadata for each of the processed samples.

source_name: Monocyte derived macrophages (MDM)

extract_protocol:
10000 monocyte derived macrophages (per sample) were sorted by FACS into Trizol reagent and flash frozen in a dry ice and ethanol slurry. RNA for populations was extracted according to protocols described by J Trombetta et al. (John J Trombetta, David Gennert, Diana Lu, Rahul Satija, Alex K Shalek, and Aviv Regev. Preparation of single-cell rna-seq libraries for next generation sequencing. Current protocols in molecular biology, 107(1):4–22, 2014.) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Monocyte-derived macrophages (MDM)

value: Uninfected

tag: donor

tag: batch


title: 0002.U3


title: 0002.U1


title: FB136_EGF_insensitive

source_name: pirmary human fibroblasts, less reactive to erlotinib incubation, incubated with DMSO and EGF


title: FB136_DMSO_insensitive

source_name: pirmary human fibroblasts, less reactive to erlotinib incubation, incubated with DMSO


title: FB76_DMSO_sensitive


title: 1577AA_MSCB-145


title: 0002.SL2

description:
MDM infected with single Mycobacterium tuberculosis bacteria
CountMatrix_HR_MtbAggs.txt (read count data file)
metaData_HR_MtbAggs.txt (metadata file)

value: Mtb Singles Low Infected


title: 0002.SL1


title: FB64_EGF_insensitive


title: FB136_Erlotinib_insensitive

source_name: pirmary human fibromlasts, less reactive to erlotinib incubation, incubated with Erlotinib and EGF


title: FB99_Erlotinib_insensitive


title: FB99_EGF_insensitive


title: FB99_DMSO_insensitive


title: 0002.SL3


title: MUV014-10X

city: Boston

first: Li

last: Jiang

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

country: USA

institute: Dana Farber Cancer Institute

description: Frozen nucleus sample

data_processing:
Illumina bcl2fastq 2.20 is used for demultiplexing
Sequenced reads were mapped to hg38 whole genome using cellranger (3.0.2) and default setting
UMI were calculated using cellranger (3.0.2) and default setting
Genome_build: hg38
Supplementary_files_format_and_content: Three Cell Ranger output files including barcodes, gene names, and count matrix for each sample

source_name: Human ependymoma cells

extract_protocol:
10X protocol
Illumina, Nextera XT Library Prep kit,

tag: tissue type

value: Human ependymoma

tag: age at diagnosis

tag: gender

value: male


title: 1577AA_MSCB-144


title: 0002.SH1

description:
MDM infected with multiple, non-aggregated Mycobacterium tuberculosis bacteria
CountMatrix_HR_MtbAggs.txt (read count data file)
metaData_HR_MtbAggs.txt (metadata file)

value: Mtb Singles High Infected


title: 0002.A3

description:
MDM infected with multiple aggregated Mycobacterium tuberculosis bacteria
CountMatrix_HR_MtbAggs.txt (read count data file)
metaData_HR_MtbAggs.txt (metadata file)

value: Mtb Aggregate Infected


title: 1577AA_MSCB-143


title: 1577AA_MSCB-142


title: HK11_EGF_insensitive

source_name: pirmary human keratinocytes, less reactive to erlotinib incubation, incubated with DMSO and EGF

value: pirmary human keratinocytes


title: FB57_Erlotinib_insensitive


title: 0002.SH3


title: 1577AA_MSCB-141


title: FB64_Erlotinib_insensitive


title: HK12_DMSO_sensitive

source_name: pirmary human keratinocytes, more reactive to erlotinib incubation, incubated with DMSO


title: FB64_DMSO_insensitive


title: 0002.A1


title: 0002.SH2


title: HK10_Erlotinib_sensitive

source_name: pirmary human keratinocytes, more reactive to erlotinib incubation, incubated with Erlotinib and EGF


title: 1577AA_MSCB-136


title: 1577AA_MSCB-140


title: FB57_DMSO_insensitive


title: HK12_Erlotinib_sensitive


title: 0004.U1


title: HK12_EGF_sensitive

source_name: pirmary human keratinocytes, more reactive to erlotinib incubation, incubated with DMSO and EGF


title: 1577AA_MSCB-138


title: HK11_Erlotinib_insensitive

source_name: pirmary human keratinocytes, less reactive to erlotinib incubation, incubated with Erlotinib and EGF


title: HK8_DMSO_sensitive


title: 1577AA_MSCB-139


title: HK8_Erlotinib_sensitive


title: 1577AA_MSCB-131


title: HK7_EGF_sensitive


title: HK11_DMSO_insensitive

source_name: pirmary human keratinocytes, less reactive to erlotinib incubation, incubated with DMSO


title: FB57_EGF_insensitive


title: HK10_EGF_sensitive


title: 0002.A2


title: HK7_Erlotinib_sensitive


title: HK6_EGF_insensitive


title: HK10_DMSO_sensitive


title: 0004.U3


title: HK6_DMSO_insensitive


title: HK5_Erlotinib_sensitive


title: HK9_Erlotinib_insensitive


title: 1577AA_MSCB-135


title: 0004.U2


title: HK9_EGF_insensitive


title: 1577AA_MSCB-134


title: HK9_DMSO_insensitive


title: HK8_EGF_sensitive


title: 0004.SL3


title: 1577AA_MSCB-133


title: 1577AA_MSCB-137


title: 0004.SH2


title: 1577AA_MSCB-128


title: 1577AA_MSCB-132


title: HK5_DMSO_sensitive


title: 0004.SH1


title: HK3_Erlotinib_insensitive


title: 1577AA_MSCB-126


title: HK3_EGF_insensitive


title: 0004.SL2


title: HK7_DMSO_sensitive


title: HK6_Erlotinib_insensitive


title: HK2_Erlotinib_insensitive


title: 1577AA_MSCB-124


title: HK4_Erlotinib_sensitive


title: 1577AA_MSCB-123


title: HK1_Erlotinib_insensitive


title: HK1_EGF_insensitive


title: 0004.SL1


title: 1577AA_MSCB-130


title: 6082.U1


title: 0004.SH3


title: 1577AA_MSCB-129


title: SMS.YM-155_6h

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

data_processing:
The raw SMS reads were filtered for length (≥25 bases) and sequence quality using Helisphere package. The remaining reads were then aligned to the GRCh37/hg19 assembly of the human genome using indexDPgenomic software
Genome_build: GRCh37
Supplementary_files_format_and_content: BED files containing coordinates of aligned SMS reads

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using TRNzol Universal (Tiangen, DP424) and Total RNA kit I (Omega, R6834-02) according to the manufacturer’s protocols and quantified using Qubit 3.0 Fluorometer (Life technologies). Total RNA (5 μg) was treated with 5 U of TURBO DNase (Thermo Fisher Scientific, AM2238) in 1× TURBO DNase buffer (Thermo Fisher Scientific, AM2238) at 37°C for 30 min to remove genomic DNA, and then purified with 2× volumes of VAHTS RNA Clean Beads (Vazyme, N412).
Total RNA samples were used for cDNA synthesis performed with a modified version of the not-so-random hexamer method to avoid synthesis of rRNA. The cDNA samples were polyA−tailed with TdT, blocked and used directly for sequencing on the Helicos/SeqLL SMS platform.

treatment_protocol: For drug treatments, 1.5 million cells were seeded in 3 ml of the medium without antibiotic per well in 6-well plates. After 16 hours, various drugs or DMSO/water controls were added and incubated for 3 or 6 hr. All drugs were obtained from Abmole Bioscience Inc and dissolved in DMSO (with the exception of YM-155 and cytarabine that were dissolved in water). The concentration of DMSO was kept at 0.1% in all treatments.

value: chronic myelogenous leukemia cell line

value: treated with YM-155 for 6 hours


title: SMS.Z-DEVD-FMK_6h

value: treated with Z-DEVD-FMK for 6 hours


title: SMS.Z-DEVD-FMK_3h

value: treated with Z-DEVD-FMK for 3 hours


title: 1577AA_MSCB-120


title: HK5_EGF_sensitive

value: microRNA


title: SMS.Talazoparib_3h

value: treated with Talazoparib for 3 hours


title: 1577AA_MSCB-118


title: 6082.SH3


title: SMS.Tacrolimus_6h

value: treated with Tacrolimus for 6 hours


title: SMS.YM-155_3h

value: treated with YM-155 for 3 hours


title: SMS.Water_3h

value: treated with Water for 3 hours


title: SMS.SN-38_6h

value: treated with SN-38 for 6 hours


title: HK4_EGF_sensitive

value: DMSO + EGF


title: 1577AA_MSCB-127

value: pancreatic islet cell


title: 0004.A2

value: Monocyte-derived macrophages (MDM)


title: HK4_DMSO_sensitive

value: DMSO


title: 0004.A3


title: 0004.A1


title: HK3_DMSO_insensitive


title: 1577AA_MSCB-125


title: 6082.SH2

value: Mtb Singles High Infected


title: HK2_EGF_insensitive


title: 6082.SH1


title: HK2_DMSO_insensitive


title: 6082.U2

value: Uninfected


title: HK1_DMSO_insensitive

value: pirmary human keratinocytes


title: 6082.U3


title: 1577AA_MSCB-115


title: 1577AA_MSCB-122


title: 1577AA_MSCB-121


title: SMS.SC75741_3h

value: chronic myelogenous leukemia cell line

value: treated with SC75741 for 3 hours


title: 6082.A2

value: Mtb Aggregate Infected


title: 6082.SL3

value: Mtb Singles Low Infected


title: 6082.SL2


title: 1577AA_MSCB-119


title: SMS.Talazoparib_6h

value: treated with Talazoparib for 6 hours


title: SMS.Water_6h

value: treated with Water for 6 hours


title: 6082.SL1


title: SMS.Tacrolimus_3h

value: treated with Tacrolimus for 3 hours


title: 1577AA_MSCB-117


title: 1577AA_MSCB-113


title: 6056.U3


title: 1577AA_MSCB-111


title: 1577AA_MSCB-114


title: 6056.U2


title: 1577AA_MSCB-116


title: SMS.SN-38_3h

value: treated with SN-38 for 3 hours


title: SMS.Selumetinib_6h

value: treated with Selumetinib for 6 hours


title: SMS.Selumetinib_3h

value: treated with Selumetinib for 3 hours


title: SMS.SC75741_6h

value: treated with SC75741 for 6 hours


title: 6056.U1


title: SMS.Palbociclib_6h

value: treated with Palbociclib for 6 hours


title: 6056.SL3

value: Monocyte-derived macrophages (MDM)


title: 6056.SL2


title: SMS.Olaparib_3h

value: treated with Olaparib for 3 hours


title: SMS.SC-514_6h

value: treated with SC-514 for 6 hours


title: SMS.Ruxolitinib_6h

value: treated with Ruxolitinib for 6 hours


title: SMS.SC-514_3h

value: treated with SC-514 for 3 hours


title: 6082.A1


title: SMS.Ruxolitinib_3h

value: chronic myelogenous leukemia cell line

value: treated with Ruxolitinib for 3 hours


title: SMS.RI-1_6h

value: treated with RI-1 for 6 hours


title: 1577AA_MSCB-106

value: pancreatic islet cell


title: SMS.NU7441_3h

value: treated with NU7441 for 3 hours


title: 1577AA_MSCB-109


title: 6082.A3

value: Mtb Aggregate Infected


title: SMS.Panobinostat_6h

value: treated with Panobinostat for 6 hours


title: SMS.Panobinostat_3h

value: treated with Panobinostat for 3 hours


title: 1577AA_MSCB-104


title: 1577AA_MSCB-110


title: SMS.Palbociclib_3h

value: treated with Palbociclib for 3 hours


title: SMS.Olaparib_6h

value: treated with Olaparib for 6 hours


title: SMS.MK-2206_6h

value: treated with MK-2206 for 6 hours


title: 6056.A2


title: 1577AA_MSCB-112


title: SMS.RI-1_3h

value: treated with RI-1 for 3 hours


title: SMS.MK-2206_3h

value: treated with MK-2206 for 3 hours


title: SMS.NU7441_6h

value: treated with NU7441 for 6 hours


title: 1577AA_MSCB-107


title: 6056.SH2

value: Monocyte-derived macrophages (MDM)

value: Mtb Singles High Infected


title: SMS.Nifuroxazide_6h

value: treated with Nifuroxazide for 6 hours


title: 1577AA_MSCB-100


title: 1577AA_MSCB-108


title: 6058.U2

value: Uninfected


title: 1577AA_MSCB-099


title: 6056.SH1


title: SMS.Lenalidomide_6h

value: chronic myelogenous leukemia cell line

value: treated with Lenalidomide for 6 hours


title: SMS.Mirin_3h

value: treated with Mirin for 3 hours


title: SMS.Nifuroxazide_3h

value: treated with Nifuroxazide for 3 hours


title: 6058.U1


title: 1577AA_MSCB-102

value: pancreatic islet cell


title: 6056.A3

value: Mtb Aggregate Infected


title: 6056.SL1

value: Mtb Singles Low Infected


title: 1577AA_MSCB-098


title: 1577AA_MSCB-103


title: SMS.Lenalidomide_3h

value: treated with Lenalidomide for 3 hours


title: 6056.A1


title: 1577AA_MSCB-105


title: 1577AA_MSCB-101


title: 6058.U3


title: SMS.KU-60019_6h

value: treated with KU-60019 for 6 hours


title: SMS.Mirin_6h

value: treated with Mirin for 6 hours


title: 1577AA_MSCB-096


title: 6056.SH3


title: NEFA.R4

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
The raw FASTQ files were quality-checked using FastQC (v. 0.11.2). Adapters and quality trimmer and filtering were performed using the Trimmomatic software.
The remaining reads were aligned to the bovine reference genome (Bos taurus ARS-UCD1.2, release 98) with the STAR aligner (v. 2.7) and the read counts estimated at the gene level using featureCounts from the Rsubread package for the R software.
The resulting matrix of read counts was analyzed with the DESeq2 package for the R software. Normalization and filtering were performed through DESeq2 methods.
Genome_build: bosTau9
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample.

organism: Bos taurus

source_name: Ovarian cortical tissue strips

growth_protocol: samples were cultured at 38.5C in 5% CO2 in a humidified chamber. Media supplementation was done at 25% every other day.

extract_protocol:
Total RNA was extracted using TRIzol plus RNA Purification kit and included DNase treatment; RNA was further purified using PureLink Isolation kit as per manufacturer’s instructions.
cDNA libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing following manufacturer's recommendations using UDI-adapter and UMI Second-Strand Synthesis modules (Lexogen). The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA). The libraries were quantified by fluorometry on a Qubit fluorometer (Life Technologies, Carlsbad, CA), and pooled in equimolar ratios. Libraries were sequenced in one lane of the HiSeq 4000 sequencer (Illumina, San Diego, CA) with single-end 100 bp reads.
OTHER - 3'-tag RNAseq

treatment_protocol: Ovarian cortex fragments were cultured with 0.72mM combination of free fatty acids (palmitic acid, stearic acid and oleic acid) for a total of 8 days.

value: High NEFA


title: NEFA.R5


title: 6058.SL2


title: 6058.SL3


title: 1577AA_MSCB-097


title: 1577AA_MSCB-095


title: NEFA.R2


title: 6058.SL1


title: SMS.Imatinib_6h

value: treated with Imatinib for 6 hours


title: CON.R4

value: Control


title: SMS.KU-60019_3h

value: treated with KU-60019 for 3 hours


title: CON.R5


title: 1577AA_MSCB-093


title: SMS.Ibrutinib_6h

value: treated with Ibrutinib for 6 hours


title: 6058.SH3

value: Monocyte-derived macrophages (MDM)

value: Mtb Singles High Infected


title: SMS.Imatinib_3h

value: chronic myelogenous leukemia cell line

value: treated with Imatinib for 3 hours


title: 1577AA_MSCB-092


title: 1577AA_MSCB-091


title: 6058.SH1


title: 6058.A3


title: EOC1129_pOvaR1_RNA1_seq6b

city: Helsinki

first: Elina

middle: A

last: Pietilä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Internal control of EOC1129_pOvaR1_RNA1_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

data_processing:
Read pairs were trimmed using Trimmomatic (version 0.33)
the first 12 and last 5 bases were cropped due to uneven per base sequence content
leading bases with a quality score lower than 20 and any trailing bases with a quality score lower than 30 were removed
the reads were scanned with a 3-base wide sliding window, cutting when the average quality per base dropped below 20
resulting sequences shorter than 20bp were discarded. Trimmed reads were aligned to the reference genome (GRCh38.d1.vd1) using STAR (version 2.5.2b), allowing up to 10 mismatches, and all alignments for a read were output
Genome_build: GRCh38.d1.vd1
Supplementary_files_format_and_content: Matrix table with effective counts

source_name: Tumor tissue from treatment-naïve patient

growth_protocol: Cells were not cultured

extract_protocol:
Total RNA was extracted from fresh patient tissues and ascites-derived cells by using RNeasy kit from QIAGEN (Qiagen, Hilden, Germany) with DNase I treatment. RNA quality and concentration were tested with Bioanalyzer 2100 (Agilent CA, USA). All samples fulfilled the criteria of RNA integrity number (RIN) > 7 and concentration > 50 ng/µl.
Sequencing libraries were constructed in Beijing Genomics Institute (Beijing, China) using a modified protocol similar to the TrueSeq Stranded Total RNA with RiboZeroKit (Illumina Inc.)

treatment_protocol: The post-chemotherapy samples were collected from patients after chemotherapy treatment.

tag: disease state

value: high-grade serous ovarian carcinoma

tag: anatomical location

value: Primary

tag: treatment strategy

value: Neoadjuvant chemotherapy


title: 1577AA_MSCB-090

value: pancreatic islet cell


title: SMS.I-BET151_6h

value: treated with I-BET151 for 6 hours


title: EOC1120_pPer1_RNA1_seq6b

description:
Internal control of EOC1120_pPer1_RNA1_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: Peritoneum

value: Primary debulking surgery


title: EOC891_r1Asc_RNA2_seq6

description: The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

source_name: Ascites-derived cells from post-chemotherapy relapse patient

value: Ascites


title: 6058.SH2


title: PC3: Plasma Cell 3

city: Montpellier

first: Jerome

last: Moreaux

address: 80 Av. Augustin Fliche

department: Biological Hematology

country: France

institute: CHRU Montpellier

data_processing:
RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner. All statistical analyses were performed with the statistics software R and R packages developed by BioConductor project. The expression level of each gene was summarized and normalized using DESeq2 R/Bioconductor package. Differential expression analysis were performed using DESeq2 pipeline. P values were adjusted to control the global FDR across all comparisons with the default option of the DESeq2 package. Genes were considered differentially expressed if they had an adjusted p-value of 0.05 and a fold change of 1.5.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts as provided by DESeq2.

extract_protocol:
RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany) according to manufacture instructions.
The RNA sequencing library preparation was done with 150ng of input RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit. Paired-end RNA-seq were performed with illumina NextSeq sequencing instrument.

tag: tissue

value: plasma cells


title: 6058.A2

value: Mtb Aggregate Infected


title: 1577AA_MSCB-087


title: PC2: Plasma Cell 2


title: SMS.I-BET151_3h

value: treated with I-BET151 for 3 hours


title: SMS.EPZ-6438_6h

value: treated with EPZ-6438 for 6 hours


title: 1577AA_MSCB-086


title: 1577AA_MSCB-089


title: EOC677_rAsc_RNA1_seq6


title: EOC891_r2Asc_RNA2_seq6


title: 1577AA_MSCB-094


title: SMS.Etoposide_6h

value: treated with Etoposide for 6 hours


title: 1577AA_MSCB-088


title: SMS.DMSO_6h

value: treated with DMSO for 6 hours


title: 1577AA_MSCB-084


title: 1577AA_MSCB-083


title: 1577AA_MSCB-082


title: CON.R2

value: Control


title: EOC286_r2Asc_RNA1_seq6


title: prePB3: Preplasmablast 3

value: preplasmablasts


title: SMS.Etoposide_3h

value: chronic myelogenous leukemia cell line

value: treated with Etoposide for 3 hours


title: SMS.Ibrutinib_3h

value: treated with Ibrutinib for 3 hours


title: prePB2: Preplasmablast 2


title: PC1: Plasma Cell 1


title: SMS.EPZ-6438_3h

value: treated with EPZ-6438 for 3 hours


title: 1577AA_MSCB-085

value: pancreatic islet cell


title: EOC783_pOvaR1A_RNA1_seq6

value: high-grade serous ovarian carcinoma

value: Primary


title: EOC783_pOvaL1A_RNA1_seq6

value: Primary debulking surgery


title: PB3: Plasmablast 3

value: plasmablasts


title: 1577AA_MSCB-078


title: EOC677_r3Asc_RNA1_seq6

value: Ascites

value: Neoadjuvant chemotherapy


title: PB2: Plasmablast 2


title: EOC752_rAsc_RNA1_seq6


title: SMS.Cyclophosphamide_3h

value: treated with Cyclophosphamide for 3 hours


title: SMS.DMSO_6h.B2


title: 1577AA_MSCB-077


title: 6058.A1

value: Monocyte-derived macrophages (MDM)

value: Mtb Aggregate Infected


title: EOC554_rAsc_RNA1_seq6


title: EOC752_r2Asc_RNA1_seq6


title: EOC587_pAdnL1_RNA_seq6


title: 1577AA_MSCB-076


title: MBC3: Memory B Cell 3

value: memory B cells


title: EOC87_pPer1B_RNA1_seq6

value: Peritoneum


title: MBC1: Memory B Cell 1


title: SMS.DMSO_3h

value: treated with DMSO for 3 hours


title: 1577AA_MSCB-081


title: EOC891_pOvaR1_RNA_seq6


title: 1577AA_MSCB-080


title: SMS.Cytarabine_6h

value: chronic myelogenous leukemia cell line

value: treated with Cytarabine for 6 hours


title: EOC783_pPer1B_RNA1_seq6


title: prePB1: Preplasmablast 1

value: preplasmablasts


title: SMS.Cytarabine_3h

value: treated with Cytarabine for 3 hours


title: EOC752_pPer_RNA1_seq6


title: 1577AA_MSCB-079

value: pancreatic islet cell


title: 1577AA_MSCB-074


title: HSC4+DAPT 1

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and Trim  Galore software.
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using HISAT2
Transcripts quantification using HTSeq
Gene differential expression using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes counts

source_name: human oral squamous cell carcinoma cell line

extract_protocol:
After treatment, total RNA was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: oral squamous cell carcinoma cell line HSC4

value: DAPT


title: EOC733_pPer1_RNA1_seq6

value: high-grade serous ovarian carcinoma


title: PB1: Plasmablast 1

value: plasmablasts


title: SMS.DMSO_3h.B2


title: 1577AA_MSCB-071

source_name: pancreas


title: SMS.Cyclophosphamide_6h

value: treated with Cyclophosphamide for 6 hours


title: MBC2: Memory B Cell 2


title: HSC4 control 1

value: control


title: EOC3_pPer1_RNA1_seq6

value: Neoadjuvant chemotherapy


title: Rd combination #3

city: Los Angeles

first: Katherine

middle: K

last: Slemmons

state: CA

address: 4650 Sunset Blvd

department: Hematology/Oncology

institute: Children's Hospital Los Angeles

data_processing:
Quality control and adapter trimming were performed using trim_galore (v0.4.2) with default parameters (https://github.com/FelixKrueger/TrimGalore).
Reads were aligned to the GRCh38 reference genome and transcriptome using HISAT2 (v2.1.0)
transcript quantification was performed using feature Counts (v1.5.1)
Differential expression analysis was performed using the ‘DESeq2’ R package (v1.16.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized abundance measurements in DESeq format.

source_name: RD cell line

growth_protocol: The cell lines were cultured in RPMI-1640, 100 units/ml penicillin and 100 μg/ml streptomycin, 2 mM glutamine, and 10% heat inactivated fetal bovine serum at 37ºC in an atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted using the KingFisher (ThermoFisher) per manufacturer’s recommendations.
Transcriptome libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA Library Prep kit following manufacturer’s protocol. Libraries were PCR amplified and paired-end cluster generation was performed using the Illumina’s Nextseq 500 on a High-Output Sequencing Reagent Kit v2 (2 x 75bp). Samples were run in biological triplcates, in 2 cell lines, and compared to the DMSO treated control.

treatment_protocol: SGI-110 was obtained from AdooQ and resuspended in DMSO at 10mM. Dasatinib was obtained from SelleckChem and resuspended in DMSO at 10mM. Cells were treated with DMSO or 0.5µM SGI-110, Dasatinib or both for 5 days.

tag: disease

value: embryonal rhabdomyosarcoma

value: SGI-110 + Dasatinib


title: EOC293_pPer1_RNA1_seq6b

description:
Internal control of EOC293_pPer1_RNA1_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: Primary debulking surgery


title: SMS.10074-G5_6h

value: treated with 10074-G5 for 6 hours


title: HSC4+DAPT 3


title: SMS.CHIR-124_6h

value: treated with CHIR-124 for 6 hours


title: HSC4 control 2


title: 1577AA_MSCB-068


title: Rd combination #2


title: Rd combination #1


title: RD Dasatinib #3

value: Dasatinib


title: 1577AA_MSCB-065


title: 1577AA_MSCB-067


title: SMS.CHIR-124_3h

value: chronic myelogenous leukemia cell line

value: treated with CHIR-124 for 3 hours


title: 1577AA_MSCB-075


title: HSC4+DAPT 2


title: SMS.BML-277_6h

value: treated with BML-277 for 6 hours


title: 1577AA_MSCB-064

value: pancreatic islet cell


title: EOC891_pPer1_RNA_seq6

value: Peritoneum


title: PS13-585-D1-P3

type: genomic

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 11.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval. All data are Log2(Cy5 tumor/Cy3 reference)

source_name: Invasive breast ductal carcinoma

label_protocol: DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes. 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Tumor and reference DNA templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols [22]. All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

growth_protocol: Fresh tumor samples from surgical resectiions of patients with invasive breast ductal carcinoma were flash-frozen and maintaned at -80 degrees C.

extract_protocol: Biopsies were minced in the presence of NST buffer and DAPI according to published protocols (Holley et al, 2012). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Influx cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).

tag: tissue source

value: Lymph node

tag: tissue preparation

value: frozen tissue

tag: flow sort content

value: Human tumor

source_name: Reference pooled 46XX

tag: sample type

value: Normal female genome


title: 1577AA_MSCB-073


title: HSC4 control 3

tag: cell line

value: oral squamous cell carcinoma cell line HSC4

value: control


title: EOC310_pPer1_RNA1_seq6

value: high-grade serous ovarian carcinoma


title: EOC677_pPer1_RNA_seq6

value: Neoadjuvant chemotherapy


title: 1577AA_MSCB-072

tag: cell type


title: SMS.10074-G5_3h

tag: treatment

value: treated with 10074-G5 for 3 hours


title: PS13-585-F1-P3


title: RD SGI-110 #3

value: embryonal rhabdomyosarcoma


title: 1577AA_MSCB-070


title: EOC136_pMes1_RNA1_seq6a

value: Mesentery


title: 1577AA_MSCB-069


title: EOC891_pOme1_RNA_seq6

value: Omentum


title: EOC87_pOme1A_RNA1_seq6


title: EOC783_pOme1A_RNA1_seq6

value: Primary debulking surgery


title: 1577AA_MSCB-066


title: PS13-585-A12-P5

value: Primary tumor


title: EOC883_pAsc1_RNA1_seq6

source_name: Ascites-derived cells from treatment-naïve patient

value: Ascites


title: RD Dasatinib #2

value: Dasatinib


title: RD SGI-110 #1


title: EOC540_p2Ome1_RNA_seq6


title: RD DMSO #3

value: DMSO


title: EOC677_pAsc_RNA1_seq6


title: RD Dasatinib #1


title: 1577AA_MSCB-059

value: pancreatic islet cell


title: EOC568_pMes1_RNA1_seq6b

description:
Internal control of EOC568_pMes1_RNA1_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: SMS.BML-277_3h

value: chronic myelogenous leukemia cell line

value: treated with BML-277 for 3 hours


title: 1577AA_MSCB-058


title: 1577AA_MSCB-057


title: PS13-585-F2-P5

value: Lymph node

value: frozen tissue

value: Human tumor

value: Normal female genome


title: Rh30 combination #1

source_name: Rh30 cell line

value: alveolar rhabdomyosarcoma

value: SGI-110 + Dasatinib


title: EOC677_iOvaR_RNA1_seq6a

description:
Internal control of EOC677_iOvaR_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

source_name: Tumor tissue from post-chemotherapy patient

value: high-grade serous ovarian carcinoma

value: Primary

value: Neoadjuvant chemotherapy


title: Rh30 combination #3


title: 1577AA_MSCB-055


title: Rh30 combination #2


title: EOC389_iOvaR1_RNA1_seq6


title: 1577AA_MSCB-063


title: PS13-585-B2-P3


title: Rh30 Dasatinib #3


title: RD SGI-110 #2

value: embryonal rhabdomyosarcoma


title: 1577AA_MSCB-062


title: PS13-585-B1-P3


title: PS13-585-B3-P3


title: 1577AA_MSCB-061


title: 1577AA_MSCB-053


title: EOC87_iPer1B_RNA_seq6

value: Peritoneum


title: PS13-585-A12-P3

value: Primary tumor


title: PS13-585-A11-P3


title: RD DMSO #2


title: EOC293_pAsc_RNA1_seq6b

description:
Internal control of EOC293_pAsc_RNA1_seq6b and EOC293_pAsc1_RNA1_seq5
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: Ascites

value: Primary debulking surgery


title: Rh30 Dasatinib #1

value: Dasatinib


title: PS13-585-A10-P5


title: RD DMSO #1

value: DMSO


title: EOC1129_pAsc1_RNA1_seq6b

description:
Internal control of EOC1129_pAsc1_RNA1_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: EOC677_iPer_RNA_seq6


title: EOC677_iOvaR_RNA1_seq6b

description:
Internal control of EOC677_iOvaR_RNA1_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: PS13-585-A8-P3


title: 1577AA_MSCB-051

value: pancreatic islet cell


title: 1577AA_MSCB-056


title: EOC87_iOme1A_RNA1_seq6

value: Omentum


title: 1577AA_MSCB-054


title: PS13-585-A11-P5

value: frozen tissue


title: PS13-585-A10-P6

value: Human tumor


title: EOC286_iOva_RNA1_seq6


title: EOC87_iOme1_RNA1_seq6b

description:
Internal control of EOC87_iOme1_RNA1_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: Rh30 SGI-110 #1


title: Rh30 DMSO #3


title: EOC3_iOme2_RNA1_seq6b


title: PS13-585-A7-P3

value: Normal female genome


title: EOC3_iOme2_RNA1_seq6a


title: 1577AA_MSCB-046


title: Rh30 DMSO #1

value: alveolar rhabdomyosarcoma


title: EOC286_iOme_RNA1_seq6


title: Rh30 SGI-110 #3


title: 1577AA_MSCB-052


title: PS13-585-A8-P5


title: PS13-585-A10-P3


title: 1577AA_MSCB-050


title: PS13-585-A9-P3


title: Rh30 SGI-110 #2


title: EOC136_iOme1_RNA1_seq6


title: 1577AA_MSCB-060


title: PS13-585-A4-P5


title: EOC87_iOme1_RNA1_seq6a

description:
Internal control of EOC87_iOme1_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: PS13-585-A4-P3


title: 1577AA_MSCB-044


title: EOC883_iAsc_RNA1_seq6

source_name: Ascites-derived cells from post-chemotherapy patient


title: 1577AA_MSCB-048


title: PS13-585-A6-P3


title: Rh30 Dasatinib #2


title: PS13-585-A3-P5


title: Rh30 DMSO #2


title: 1577AA_MSCB-045


title: 1577AA_MSCB-047


title: Scramble-3

city: Wuhan

first: Yulan

last: Zeng

state: Hubei

address: No.1277 Jiefang Rd, Jianghan District

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
The RNA integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies).
Single-end libraries sequencing with BGISEQ-500 were prepared with the mRNA-seq sample prep kit (DNBSEQ) according to the manufacturer’s specifications.
DNBSEQ data analysis pipeline was then used for sequence analysis. All samples were allocated to lanes and processed in blinded fashion to keep bias to a minimum
The original data of sequencing includes reads with low quality, linker contamination and high content of unknown base N are removed before data analysis to ensure the reliability of the results.
This project used SOAPnuke, a filtering software independently developed by Huada Corporation, to make statistics and trimmomatic to filter. Firstly, readers including connectors are removed. Then the reads with unknown base N content more than 5% are wiped off. Finally, the low-quality reads are removed (we define reads with a mass value of less than 10 and a proportion of more than 20% of the total number of bases in the reads as low-quality reads).
Genome_build: mm8
Supplementary_files_format_and_content: Analysis description: The filtered “Clean Reads” are saved in FASTQ format.After the quality control of the original data, we used Bowtie2 to compare clean reads to the reference gene sequence, and then RSEM was used to calculate the expression levels of genes and transcripts.

growth_protocol: Human lung cancer cell lines (A549)  were purchased from the American Type Culture Collection (ATCC). All cells were cultured in RPMI-1640 medium or DMEM supplemented with 10% FBS and 1% penicillin/streptomycin and incubated at 37°C in a 5% CO2 incubator.

extract_protocol:
A549 cells were transfected with 20 nM doses of siRNAs using Lipofectamine RNAiMAX reagent (Invitrogen) for 48 h. Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard DNASEQ protocols

treatment_protocol: The targeting siRNA sequences in this study were as follows: SiCDK5#1, 5’-GUCGAUGACCAGUUGAAGAtt-3’;SiCDK5#2, 5’-CCACAACAUCCCUGGUGAAtt-3’;SiCDK5#3, 5’-GCAGAACCUUCUGAAGUGUtt-3’, which have been described previously. Indicated siRNAs (P: pool containing equal amounts of three individual CDK5 siRNAs)

tag: tag

value: human lung cancer cell line

tag: genotype/variation

value: transfected with Scramble


title: Peritoneal Macrophages Control 3

city: Santiago

first: Gabriela

last: Tejon

state: Ñuñoa

address: Las Palmeras 3425

department: Sciences

country: Chile

institute: Universidad de Chile

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, used CLC Genomics Workbench software version 7.0.4.
Mapped to Mus musculus GRCm38.p6 whole genome using salmon V0.8.0.
Deseq2 stadistical package was obtained for differential gene expression analysis.
Supplementary_files_format_and_content: Tab-delimited text files include total count values for each Sample.

organism: Mus musculus

source_name: Peritoneal Control Macrophages

extract_protocol:
Peritoneal cells are harvested, then Peritoneal macrophages were selected by cell sorter BD FACSAriaII, and RNA was obteinend usig Trizol reagent. KAPA Stranded mRNA-Seq kit from Illumina platform was used with almost 150 ng of total RNA recovery.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: New Zealand white/BALB/c mice

value: non-lupus-susceptible control

value: Periontel cavity

value: Macrophages

tag: age


title: Peritoneal Macrophages Lupic 3

source_name: Peritoneal Lupic Macrophages

value: New Zealand black/New Zealand white mice


title: PS13-585-A5-P3

value: Primary tumor


title: Peritoneal Macrophages Control 2


title: Scramble-2


title: Peritoneal Macrophages Lupic 1


title: 1577AA_MSCB-043


title: Peritoneal Macrophages Lupic 2


title: 1577AA_MSCB-042


title: Peritoneal Macrophages Control 1


title: SiCDK5-3

value: transfected with CDK5-targeting siRNAs


title: Scramble-1


title: 1577AA_MSCB-040


title: 1577AA_MSCB-039


title: SiCDK5-2


title: 1577AA_MSCB-037


title: 1577AA_MSCB-038


title: SiCDK5-1


title: helaSi4b

source_name: HeLa_NEK2 siRNA#2

growth_protocol: HeLa cells were grown in DMEM medium supplemented with 10% fetal bovine serum and 100 μg/ml penicillin. All of the above cells were cultured at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
HeLa cells were transfected with control or NEK2-targeting siRNAs using Lipofectamine RNAiMAX for 48 h. Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard DNASEQ protocols

treatment_protocol: The targeting siRNA sequences in this study were as follows: NEK2 siRNA#1, 5′-GGATCTGGCTAGTGTAATT-3′ and NEK2 siRNA#2, 5′-GCTAGAATATTAAACCATG-3′, which have been described previously. HeLa  cells were transfected with indicated siRNAs (50 nM) using Lipofectamine RNAiMAX reagent (Invitrogen) according to the manufacturer‘s instructions. Subsequent experiments were performed 48 h post transfection.

value: HeLa

value: cervical cancer cell lines


title: 1577AA_MSCB-036

value: pancreatic islet cell


title: The liver_ squalene_rep4 [L]

type: RNA

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

institute: Universidad de Zaragoza

description: 11-week diet intervention

hyb_protocol: Oligoarray control targets and Hi-RPM Hybridization Buffer were added, and fragmented samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and let hybridize at 65°C for 17 hours. After hybridization, slides were washed sequential with Gene Expression Wash Buffer 2.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7) using a G2505C scanner

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

label: Cyanine 5

source_name: The liver pool 8

label_protocol: 200 ng of total RNA were primed with 0.8 µl of T7 DNA primer mix at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Affinity Script RNase Block Mix and 1 mM nucleotides. Labelled RNA was prepared with 0.24 µl of  Cyanine 3-CTP or Cyanine 5-CTP in presence of 0.21 µl T7 RNA Polymerase Blend and 1 µl of nucleotide mix.

growth_protocol: Apoe-deficient mice on C57BL/6J genetic background were obtained from Charles River (Charles River Laboratories, Barcelona, Spain). To establish groups with similar initial plasma cholesterol, blood samples were taken (after four-hour fasting) from the facial vein.  All animals were housed in sterile filter-top cages in rooms maintained under a 12-h light/12-h dark cycle. All had ad libitum access to food and water and the study protocol was approved by the Ethics Committee for Animal Research of the University of Zaragoza.

extract_protocol: At sacrifice, the livers were immediately removed and frozen in liquid nitrogen. RNA from each liver was isolated using Tri-reagent (AMBION, TX, USA). DNA contaminants were removed by TURBO DNAse treatment using the DNA removal kit from AMBION. RNA was quantified by absorbance at A260/280. The integrity of the 28 S and 18 S ribosomal RNAs was verified by agarose gel electrophoresis and by Bioanalyzer using Eukaryote Total RNA Nano kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Control group mice (n=9) received a purified Western diet containing 0.15% cholesterol and 20% refined palm oil (Gustav Heess, S.L., Barcelona, Spain) and a treatment group (n=10) received the same diet but containing 1% squalene (Sigma, Madrid, Spain), equivalent to a dose of 1 g/ kg mouse assuming a daily intake of 3 g per mouse

tag: genetic background

value: Apoe-deficient on C57BL/6J

tag: diet

value: Western + 1percent squalene

label: Cyanine 3

source_name: The liver pool 4

value: Western


title: 1577AA_MSCB-041


title: helaSi4c


title: The liver_ squalene_rep2 [J]

description: 11-week diet intervention

source_name: The liver pool 2

source_name: The liver pool 6


title: The liver_ squalene_rep1 [I]

description: 11-week diet intervention

source_name: The liver pool 5

source_name: The liver pool 1


title: The liver_ squalene_rep3 [K]

description: 11-week diet intervention

source_name: The liver pool 3

source_name: The liver pool 7


title: 1577AA_MSCB-035

source_name: pancreas


title: 1577AA_MSCB-033


title: helaSi4a


title: PS13-585-A2-P3

source_name: Invasive breast ductal carcinoma

value: frozen tissue

value: Human tumor

source_name: Reference pooled 46XX

value: Normal female genome


title: 1577AA_MSCB-049


title: PS13-1750 -A4-P4


title: PS13-1750 -A8-P4


title: dtec1_24h_1

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Av. Robisco Pais

country: Portugal

institute: Institute for Bioengineering and Biosciences, Instituto Superior Técnico

data_processing:
Sequenced reads were trimmed for adaptor sequence, low-quality base calls using Skewer v0.2.2 with parameters -m pe -l 36 -q 15 -Q 15
Reads were mapped to CBS138 whole genome using TopHat v2.1.1 with parameters -p 12 -g 1 --b2-very-sensitive --library-type fr-firststrand
Reads counts per feature (ORF) were obtained with the htseq-count script from HTSeq (v 0.7.1) using parameters -m union -s reverse -t gene -i Name
Genome_build: CBS138
Supplementary_files_format_and_content: Table with read counts for each feature (ORF)

organism: Nakaseomyces glabratus

source_name: Cell culture

growth_protocol: Cells were grown in SDB (pH 5.6) medium. Planktonic cells were cultured at 30ºC with orbital agitation (250rpm), while biofilm cells were cultured at 30ºC, in square Petri dishes, with orbital agitation (30rpm). Cells were pelleted and frozen at -80ºC until RNA extraction.

extract_protocol:
Ambion Ribopure-Yeast RNA kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: condition

value: 24h of biofilm condition


title: PS13-1750 -A7-P4


title: PS13-1750 -A10-P4


title: PS13-585-A3-P3


title: 1577AA_MSCB-032


title: PS13-1750 -A9-P4


title: PS13-1750 -A6-P4


title: PS13-585-A1-P3


title: 1577AA_MSCB-034


title: dtec1_exp_2

value: planktonic condition


title: 1577AA_MSCB-030


title: The liver_ squalene_rep2 [B]

description: 11-week diet intervention


title: dtec1_24h_2


title: PS13-1750 -A3-P4


title: helaSi2a

source_name: HeLa_NEK2 siRNA#1


title: helaNCb

value: control


title: helaSi2c


title: dtec1_exp_1


title: helaNCc


title: shStau2_rep3

city: Planegg-Martinsried

first: Michael

middle: A.

last: Kiebler

address: Großhaderner Straße 9

department: Department for Cell Biology & Anatomy

institute: Biomedical Center (BMC)

data_processing:
fastq generation incl. demultiplexing and adapter trimming, bcl2fastq v2.19.1.403
alignment and extraction of counts/gene, STAR aligner v2.6.1a_08-27, command: STAR --runThreadN 16 --genomeDir rnor6.0 --readFilesCommand zcat --readFilesIn $FASTQ --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:"$sample" SM:"$sample" CN:MUW_CF PG:STAR --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
Genome_build: Rattus norvegicus genome rnor6.0
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample

organism: Rattus norvegicus

source_name: cultured cortical neurons

growth_protocol: Neurons were cultured in NMEN+B27 for 14 Days

extract_protocol:
RNA was extracted using TRIzol
Sequencing libraries were be prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext  UltraTM II Directional RNA Library Prep Kit for Illumina according to manufacturer's  protocols (New England Biolabs).

treatment_protocol: Neurons were transduced with lentivirus particles for shControl, shPum2 and shStau2 for 4 days

tag: developmental stage

value: 14 days in vitro

value: Stau2 depletion

value: cultured cortical neurons


title: 1577AA_MSCB-031

extract_protocol:
Short-term cultured pancreatic islet cells were isolated from a healthy pancreas donor. The culturing process favor the enrichment of pancreatic islet cells while large eliminating endothelial and immune cell types. Primary bladder epithelial cells were isolated by FACS (CD45-, CD140a-, CD31-, Ter119-) from a healthy mouse.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014). This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes (bases 1 to 6 and 7 to 14, respectively). Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.


title: helaSi2b


title: The liver_ squalene_rep1 [A]

description: 11-week diet intervention


title: shStau2_rep2


title: PS13-1750 -A5-P4

value: Primary tumor


title: HelaNCa


title: shStau2_rep1


title: PS13-9062-F5-P6


title: defg1_24h_2


title: 1577AA_MSCB-028


title: defg1_exp_2


title: PS13-1750 -A1-P4


title: PS13-1750 -A2-P5


title: 1577AA_MSCB-026


title: 1577AA_MSCB-027


title: shPum2_rep2

value: Pum2 depletion


title: PS13-1750 -A2-P4


title: defg1_24h_1


title: 1577AA_MSCB-029


title: shControl_rep3

value: Control


title: Wt_24h_1

value: Wild type


title: shPum2_rep3


title: Wt_24h_2


title: shControl_rep2


title: defg1_exp_1


title: 1577AA_MSCB-025

value: pancreatic islet cell


title: 1577AA_MSCB-023


title: shPum2_rep1


title: Wt_exp_1


title: PS13-9062-F4-P5


title: PS13-9062-F3-P4


title: 1577AA_MSCB-024


title: PS13-9062-F6-P7


title: Wt_exp_2


title: shControl_rep1


title: bATAC-Human_H460_LKB1_Rep1

city: STANFORD

first: Jeffrey

middle: Michael

last: Granja

address: 279 Campus Drive W

department: Genetics

institute: Stanford University

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-Human-Peak-Summarized-Experiment.rds
bATAC-Matrices-Human-chromVAR-Summarized-Experiment.rds

data_processing:
ATAC-seq:
Fastq reads were trimmed using cutadapt and then aligned to the genome with bowtie 2 and then filtered for high quality read paired alignment.
Mitochondrial and picard identified pcr duplicates were then discarded.
Macs2 was then used to identify peak regions that were reproducible across replicate samples and then to create a sample by peak matrix.
Bulk RNA-seq:
Fastq reads were trimmed using cutadapt and then pseudo aligned to the genome with Kallisto.
Counts were then compiled from each sample to build a sample by gene counts matrix.
Single Cell ATAC-seq:
The Cell Ranger ATAC Software Suite (version 1.2.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the Tn5 transposase made cuts
Regions of enriched accessibility, i.e. peaks were identified with MACS2
Barcodes likely associated with whole cells were identified by analyzing the number of fragments (1000) mapped near TSS regions (enriched over background) and a peak-barcode matrix is defined
CRISPR Screen:
Fastq reads were aligned to sgRNA barcodes using casTLE (implementing bowtie).
Counts were then compiled from each sample across both screen halves and normalized.
The counts matrix was then used as input to MaGeCK for downstream analysis.
Genome_build: mm10/hg38
Supplementary_files_format_and_content:
Processed ATAC-seq/scATAC-seq data is provided as an R SummarizedExperiment object. This object contains counts alongth with row and column metadata corresponding to the individual cells and peak/motif/gene chromatin accessibility. Fragments file contain Tn5 corrected cut sites per sample or cell.
Processed RNA-seq data is provided in an xlsx file containing counts/tpm for each sample per gene. Additionally, Kallisto generated transcript abundances per sample are provided.
Processed CRISPR Screen data using casTLE (bowtie) is provided as a counts table for each sgRNA count sample per gene and a table of results from MAGeCK analysis.
*insertion.bw: Sample Bigwig file of chromatin accessibilty
*Fragments.tsv.gz: Sample Fragments Files containing Tn5 cut sites of chromatin accessibility
*chromVAR-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing samples by TF accessibility.
*Peak-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing samples by peak accessibility.
*abundance.tsv: Sample transcript abundances from Kallisto.
bRNA-Matrices-Initial-LKB1-Resoration.xlsx: Matrix excel file containing transcript abundances and counts for each sample with descriptions.
bRNA-Matrices-Mouse-Tumor-Metastases-Matrices.xlsx: Matrix excel file containing transcript abundances and counts for each sample with descriptions.
Save_LKB1_ArchRProject.zip: Saved ArchRProject from ArchR for scATAC-seq mouse data.
*singlecell.csv: 10x Genomics Single Cell QC statistics file.
*fragments.tsv.gz: Sample Fragments Files containing Tn5 cut sites per cell of chromatin accessibility
*chromVAR-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing cells by TF accessibility.
scATAC-LKB1-GeneScoreMatrix-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing cells by gene accessibility.
scATAC-LKB1-PeakMatrix-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing cells by peak accessibility.
Screen-Counts-s1*counts.csv: Counts file from casTLE for each sample of CRISPR screen half 1.
Screen-Counts-s1_s2*counts.csv: Counts file from casTLE for each sample of CRISPR screen half 2. (Repeat of sample from half 1)
Screen-Counts-s2*counts.csv: Counts file from casTLE for each sample of CRISPR screen half 2.
Screen-Matrices-Combined-sgRNA-Counts.tsv: Combined Matrix file of all samples for CRISPR screen.
Screen-Matrices-Mageck-Results-Gene-Summary.txt: Results file from MaGeCK analysis of CRISPR screen data.

source_name: Immortalized cell line

extract_protocol:
50,000 cultured cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the resulting nuclei were then transposed and processed for bulk ATAC-seq (Corces et al. Nature Methods 2017).
Omni-ATAC-seq (Corces et al. Nature Methods 2017,  doi:10.1038/nmeth.4396)

tag: tissue/cell type

value: lung cancer

tag: timepoint of treatment

tag: source

value: human derived (ATCC)

tag: growth media

value: RPMI; 10% FBS; 1% pen-strep


title: 1577AA_MSCB-022

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

address: C. Baldiri Reixac, 4; Barcelona Science Park

institute: Centro Nacional de Análisis Genómico

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse or human genome reference.
Gene quantification was performed using UMI information to correct for amplification biases.
Genome_build: human: GRCh38. Gencode release 26.  Mouse: GRCm38. Gencode release M15.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).


title: bATAC-Human_H460_LKB1_Rep2


title: 1577AA_MSCB-020


title: bATAC-Human_H460_KEAP1_Rep2


title: Sample_16k_PRL_1

city: Bunkyo-ku

first: Takashi

last: Shimizu

country: Japan

institute: University of Tokyo

description: Gene expression data of NRCMs

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the mouse reference genome mm10 with HISAT2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: bigwig

source_name: NRCMs

extract_protocol:
Total RNA was isolated from hears by using a miRNeasy micro Kit (Qiagen) with the DNase digestion step, according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

value: 16k PRL

value: neonate rat cardiomyocytes (NRCMs)


title: Sample_16k_PRL_3

description: Gene expression data of NRCMs


title: Sample_23k_PRL_3

description: Gene expression data of NRCMs

value: 23k PRL


title: Sample_16k_PRL_2

description: Gene expression data of NRCMs


title: 1577AA_MSCB-021


title: Sample_23k_PRL_2

description: Gene expression data of NRCMs


title: 1577AA_MSCB-019


title: 1577AA_MSCB-018


title: bATAC-Human_H460_KEAP1_Rep1


title: 1577AA_MSCB-017


title: bATAC-Human_H460_GFP_Rep2


title: bATAC-Human_H460_GFP_Rep1


title: Sample_23k_PRL_1

description: Gene expression data of NRCMs


title: Sample_LacZ_3

description: Gene expression data of NRCMs


title: 1577AA_MSCB-016


title: bATAC-Human_H358_LKB1_Rep2


title: bATAC-Human_H358_LKB1_Rep1


title: Sample_LacZ_2

description: Gene expression data of NRCMs


title: 1577AA_MSCB-015


title: 1577AA_MSCB-014


title: bATAC-Human_H358_KEAP1_Rep2


title: 1577AA_MSCB-013


title: bATAC-Human_H358_KEAP1_Rep1


title: 1577AA_MSCB-012


title: Sample_LacZ_1

description: Gene expression data of NRCMs


title: 1577AA_MSCB-010


title: bATAC-Human_H358_GFP_Rep1


title: bATAC-Human_H2009_LKB1_Rep2


title: bATAC-Human_H2009_LKB1_Rep1


title: 1577AA_MSCB-008


title: bATAC-Human_H358_GFP_Rep2


title: 1577AA_MSCB-011


title: bATAC-Human_H2009_KEAP1_Rep2


title: 1577AA_MSCB-009


title: 1577AA_MSCB-007


title: 1577AA_MSCB-006


title: 1577AA_MSCB-005


title: bATAC-Human_H2009_KEAP1_Rep1


title: bATAC-Human_H1975_LKB1_Rep2


title: 1577AA_MSCB-003


title: bATAC-Human_H2009_GFP_Rep2


title: bATAC-Human_H1975_KEAP1_Rep2


title: 1577AA_MSCB-002


title: 1577AA_MSCB-001


title: bATAC-Human_H1975_KEAP1_Rep1


title: bATAC-Human_H1975_GFP_Rep2


title: bATAC-Human_H2009_GFP_Rep1


title: Primary hepatocytes, Ad-CREBH3, replicate2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.51.1)

label: biotin

source_name: Mouse primary hepatocytes, 24 hrs after transduction with adenoviruses encoding nuclear CREBH (Ad-CREBH)

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Primary hepatocytes cultured from 8 – 10 w-old male (wildtype) C57BL/6J mice were anesthetized with ketamine and xylazine, and prepared as described in the manuscript. Livers of wildtype mice were perfused with liver perfusion medium (Life Technologies; Carlsbad, CA), for 5 min followed by liver digestion medium (Life Technologies; Carlsbad, CA) for 10 min at 5 mL/min. Primary hepatocytes were then cultured with M199 medium supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum in  60 mm dishes at 1x10^6 cells/dish.

extract_protocol: Total RNA was extracted from cells using TRIzol reagent (Life Technologies, Bleiswijk, The Netherlands) and subsequently purified using the RNeasy Micro kit (Qiagen, Venlo, The Netherlands). RNA integrity was verified with RNA 6000 Nano chips on an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Cells were transduced with adenoviruses encoding green fluorescent protein (Ad-GFP; control) or nuclear CREBH (Ad-nuclear CREBH) at a multiplicity of infection of 100 viral particles/cell. Three 60 mm dish replicates per transduction (Ad-GFP or Ad-nuclear CREBH)  were collected 24 h after adenovirus transduction for microarray analysis.

tag: transduction with adenovirus encoding

value: CREBH (nuclear cyclic AMP-responsive element-binding protein H)


title: Primary hepatocytes, Ad-GFP, replicate1

source_name: Mouse primary hepatocytes, 24 hrs after transduction with adenoviruses encoding green fluorescent protein (Ad-GFP; control)

value: GFP (green fluorescent protein; control)


title: Primary hepatocytes, Ad-CREBH3, replicate3


title: Primary hepatocytes, Ad-GFP, replicate2


title: bATAC-Human_H1975_LKB1_Rep1

tag: cell line


title: bATAC-Human_H1650_LKB1_Rep1


title: Primary hepatocytes, Ad-CREBH3, replicate1


title: SS_09: SOV-senktide embryo senktide300-3

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

institute: Nagoya University

hyb_protocol: For microarray hybridization, 1650 ng of Cy3-labeled cRNA was fragmented and hybridized on a slide of bovine 4 × 44K microarray (Agilent Technologies; 023647) at 65°C for 17 hours.

scan_protocol: Slides were scanned on the Agilent G2505C DNA microarray scanner.

data_processing: Background correction of the Cy3 raw signals was performed using the Agilent Feature Extraction software (version 10.5.1.1). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Embryos from SOV cows

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction. Labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from the endometrial samples using RNeasy Plus Universal Mini kit (Qiagen) according to the manufacturer’s instructions. Total RNA quality and quantity were confirmed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

value: Senktide 300 nmolmin, 2h

tag: tissue

value: Embryos


title: Primary hepatocytes, Ad-GFP, replicate3


title: 1577AA_MSCB-004

tag: cell type


title: SS_07: SOV-senktide embryo senktide300-1

tag: treatment


title: SS_10: SOV-senktide embryo senktide300-4


title: bATAC-Human_H1650_LKB1_Rep2


title: 20AAO: 20_Atrial_Appendage_Old

city: Milwaukee

first: Arshad

last: Jahangir

state: WI

address: 2801 Kinnic Kinnic River Parkway, Suite 777

department: Cardiology

institute: Advocate Aurora Health

hyb_protocol: Labeled cRNA, synthesized and amplified from the double-stranded cDNA template, was fragmented and hybridized onto GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) according to manufacturer’s protocol. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B2 were added along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and BSA to the hybridization buffer. The hybridization mixture was heated at 99°C for 5 min followed by incubation at 45°C for 5 min, before sample was injected into the microarray. Hybridization was carried out at 45°C for 16 hours, mixing on a rotisserie at 60 rpm. After hybridization, solutions were removed and arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Invitrogen Corporation, Carlsbad, CA).

scan_protocol: After washes, probe arrays were scanned using the GeneChip 3000 scanner (Affymetrix, Santa Clara, CA). The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated before hybridization onto the GeneChip® Human Genome U133 Plus 2.0 array by hybridizing onto a test-3 array, and analyzed as a measure of quality control. Intensity values for each probe cell in the arrays were calculated by GeneChip software.

data_processing: Data normalization and analysis was performed using GeneSpring GX 7.3 (Agilent Technologies). Intensity values for each probe cell in the arrays were calculated by GeneChip® software, and flags were assigned to each probe set declaring Present, Marginal, or Absent call (Detection Call Algorithm). Probe cell intensities were used to calculate an average intensity for each set of probe pairs representing a gene. Data analysis and normalization were performed by GeneSpring GX bioinformatics software (Agilent Technologies). Quality control (QC) was performed on the normalized intensity values after excluding the probe sets with absent call in 100% of the arrays. After applied QC filtering to diminish background noise created by low-intensity gene probes, genes were clustered into the two age group conditions (Aged vs Adults). Gene expression profiles was visualized as volcano plots to identify genes significantly upregulated or downregulated in each group. Statistical analysis was performed using the unpaired unequal variance t-test (Welch test). The hierarchical clustering for groups and entities was performed using Euclidean distance metric and Ward’s linkage algorithm.

label: Biotin

source_name: Right Atrial Appendage Aged

label_protocol: Total isolated RNA (100 ng) from each sample was converted to cDNA following instructions provided in the Two-Cycle cDNA synthesis kit and Target Labeling Protocols (Affymetrix, Santa Clara, CA). The obtained cDNA was purified by phase lock gel (Eppendorf, Westbury, NY) with phenol/chloroform extraction and used as a template for the in vitro transcription reaction. Biotinylated cRNA was then synthesized using an RNA transcript labeling reagent (Affymetrix, Santa Clara, CA).

growth_protocol: Within 5–10 min after surgical resection, atrial tissue was snap-frozen in liquid nitrogen, and stored at –80°C until RNA extraction.

extract_protocol: Total RNA was extracted from the whole heart with TRIzol and purified using an affinity resin column (Qiagen RNeasy Mini kit, Germantown, MD) according to manufacturer’s protocol.

treatment_protocol: No treatment was added to samples prior to RNA extraction.

value: Right Atrial Appendage

tag: age group

value: > 65 years old

tag: gender

value: Male


title: SS_05: SOV-senktide embryo senktide30-3

value: Senktide 30 nmolmin, 2h


title: SS_06: SOV-senktide embryo senktide30-4


title: Ghr-0120

city: Buffalo

first: Omer

last: Gokcumen

state: NY

address: 639 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

description: GHR - study cohort

data_processing:
Quality control of the obtained sequences was performed using FastQC. A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 7/2019), and the results of all the samples were reviewed by MultiQC.
Adaptor sequences and low quality bases were discarded by Trimmomatic.
Filtered reads were mapped to mouse transcriptome reference (GRCm38) from Ensembl and quantified using Kallisto. The transcripts were merged into genes with tximport and Ensembl BioMart.
Differential expression analyses were performed by DESeq2, which calculates the fold change of each gene using the Wald test and a correction for multiple hypotheses.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file provided normalized gene expression as well as comparative analysis results from DeSeq2.

source_name: Liver

growth_protocol: To quickly generate a cohort of mice for calorie restriction, d3/d3 males were sent to The Jackson Laboratory for sperm cryopreservation followed by in vitro fertilization of C57BL/6NJ ooyctes and embryo transfer.

extract_protocol:
28 to 34-day-old mice were sacrificed and liver samples were taken and directly put into RNAlater (Thermo Fisher). They were then sent for RNA extraction and sequencing by GENEWIZ.
KAPA Hyperprep

treatment_protocol: The cohorts were kept with their mothers which were fed standard (Ad libitum) diets until 1 weaning (~1month). After weaning, half of the mice were fed 40% calorie restricted chow for another month while the other half were fed Ad Libitum diets. All mice were sacrificed at ~2 months

value: Liver

tag: Sex

value: F

tag: strain


title: Ghr-0148

description: GHR - study cohort

value: M


title: Ghr-0126

description: GHR - study cohort


title: Ghr-0150

description: GHR - study cohort


title: Ghr-0149

description: GHR - study cohort


title: SS_08: SOV-senktide embryo senktide300-2


title: SS_03: SOV-senktide embryo senktide30-1


title: 15AAO: 15_Atrial_Appendage_Old


title: 12AAO: 12_Atrial_Appendage_Old


title: 18AAO: 18_Atrial_Appendage_Old


title: SS_01: SOV-senktide embryo vehicle-1

value: DMSO


title: SS_04: SOV-senktide embryo senktide30-2


title: SS_02: SOV-senktide embryo vehicle-2


title: bATAC-Human_H1975_GFP_Rep1

value: lung cancer

value: human derived (ATCC)


title: Rep2_Pre_sort

city: Shanghai

first: Huabing

last: Li

address: 280 Chongqing South Rd, Building #5-6th floor, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

description:
Rep2.countsummary.txt
Rep2_higVlow.gene_summary.txt

data_processing:
The raw reads were trimmed with fastx_trimmer in FASTX-Toolkit and sgRNA sequences were counted by MAGeCK.
Enriched genes were retrieved with MAGeCK test subcommand.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files including coutsummary

source_name: Raw 264.7 cells

extract_protocol: Genomic DNA were isolated from TNFa-low, TNFa-High and pre-sort cell populations,sgDNA sequences were PCR- amplified and subjected to Illumina sequencing.

value: wildtype


title: Ghr-0094

description: GHR - study cohort


title: bATAC-Human_H1650_KEAP1_Rep2

value: RPMI; 10% FBS; 1% pen-strep


title: 11AAO: 11_Atrial_Appendage_Old


title: bATAC-Human_H1650_GFP_Rep2


title: Ghr-0108

description: GHR - study cohort

value: WT


title: Rep2_TNF_low


title: bATAC-Human_H1650_KEAP1_Rep1


title: Ghr-0093

description: GHR - study cohort


title: 9AAO: 9_Atrial_Appendage_Old


title: Rep1_Pre_sort

description:
Rep1.countsummary.txt
Rep1_higVlow.gene_summary.txt


title: Rep1_TNF_low


title: Ghr-0085

description: GHR - study cohort


title: Ghr-0087

description: GHR - study cohort


title: bATAC-Human_H1437_LKB1_Rep2


title: 10AAO: 10_Atrial_Appendage_Old


title: KO_LPS IP

data_processing:
The reads were mapped to rRNA sequences by using bowtie2 (2.3.5.1)
The unmapped reads of previous step were mapped to GRCm38 genome by using STAR (2.5.0a) with default parameters
The m6A peak regions were identified by custom script (divide each transcript into several 100 nt windows which contain a 50 nt overlap region with adjacent windows, and statistic the significance of normalized fragment count change between IP and input by Poisson distribution. Adjacent windows were merged to one peak)
Genome_build: GRCm38
Supplementary_files_format_and_content: BigWig file contains normalized tracks (strand-specific), BED file contains the genomic coordination of m6A peaks.

extract_protocol:
Total RNAs were isolated from WT_CON, KO_CON, WT_LPS and KO_LPS Raw 264.7 cells, subjected to standard m6A RIP protocol.
10 ng RNA from input and enriched IP RNA samples were used for library preparation with the SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (Clontech) according to the manufacturer’s instructions

value: Raw 264.7 cells

value: LPS

tag: rip antibody

value: Anti-m6A(Millipore ABE572 )


title: Ghr-0082

description: GHR - study cohort

tag: genotype


title: Ghr-0086

description: GHR - study cohort


title: bATAC-Human_H1437_KEAP1_Rep1


title: bATAC-Human_H1437_KEAP1_Rep2


title: bATAC-Human_H1437_LKB1_Rep1


title: 6AAO: 6_Atrial_Appendage_Old


title: Ghr-0079

description: GHR - study cohort


title: Rep2_TNF_high


title: KO_CTL IP

value: CTL


title: WT_LPS IP


title: bATAC-Human_H1650_GFP_Rep1


title: WT_CTL IP


title: bATAC-Human_H1437_GFP_Rep1


title: bATAC-Human_H1437_GFP_Rep2


title: Rep1_TNF_high


title: KO_LPS Input


title: KO_CTL Input


title: Ghr-0074

description: GHR - study cohort


title: Ghr-0081

description: GHR - study cohort


title: bATAC-Human_H1355_LKB1_Rep2


title: 13AAY: 13_Atrial_Appendage_Young

source_name: Right Atrial Appendage from Adults

value: Right Atrial Appendage

value: < 65 years old


title: bATAC-Human_H1355_LKB1_Rep1


title: 8AAO: 8_Atrial_Appendage_Old

value: > 65 years old

value: Female


title: 3AAO: 3_Atrial_Appendage_Old

value: Male


title: Ghr-0077

description: GHR - study cohort

value: Liver

value: AL


title: bATAC-Human_H1355_KEAP1_Rep1


title: 12AAY: 12_Atrial_Appendage_Young


title: 14AAY: 14_Atrial_Appendage_Young


title: 9AAY: 9_Atrial_Appendage_Young


title: 7AAY: 7_Atrial_Appendage_Young


title: 11AAY: 11_Atrial_Appendage_Young


title: Ghr-0072

description: GHR - study cohort

value: F


title: Mettl3 _KO1

data_processing:
FastQC (version 0.11.2) (Andrews.2010) and Skewer (v0.2.2) (Bolger AM, el at. 2014) software were performed for quality control.
STAR (v2.4.2a) (Dobin A, et al. 2013) software were used for sequence alignment.
Expression estimation of gene and transcript was performed by using RSEM (V1.2.29) (Li B, et al. 2011)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
mRNA was extracted from total RNA using magnetic beads with oligo-dT then were fragmented randomly.
Libraries were prepared according to the manufacturer's instructions (Illumina). Briefly, mRNA was extracted from total RNA using magnetic beads with oligo-dT then were fragmented randomly. The first strand of cDNA and the second strand are then synthesized using reverse transcriptase. The reverse transcription product is subjected to terminal repair, followed by addition of an A base at the 3' end. Subsequently, the fragments were ligated with a Illumina universal adapter. After PCR amplified, the ligation products were purified in order to remove the incompletely ligated fragment and the self-ligated adapter. Library sizes were detected using an Agilent 2100 Bioanalyzer and library concentrations were detected using Qubit 2.0. The DNA sequencing was performed according to Illumina's standard protocol.

value: Mettl3 _KO

value: LPS treatment for 6h


title: 3AAY: 3_Atrial_Appendage_Young


title: Ghr-0070

description: GHR - study cohort

value: M


title: Mettl3 _WT2

value: Mettl3 _WT


title: bATAC-Human_H1355_GFP_Rep1

value: lung cancer

value: human derived (ATCC)

value: RPMI; 10% FBS; 1% pen-strep


title: Ghr-0060

description: GHR - study cohort

value: WT


title: WT_LPS Input

value: Raw 264.7 cells

value: wildtype

value: LPS


title: Ghr-0065

description: GHR - study cohort


title: 10AAY: 10_Atrial_Appendage_Young

value: Right Atrial Appendage

value: < 65 years old


title: Mettl3 _KO2


title: Anqa1_IP2

city: Toronto

first: Alejandro

last: Saettone

state: Ontario

address: 686 Bay Street

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
ChIP-seq reads were assessed for quality using fastqc
ChIP-Seq reads were aligned using BWA and SAMtools
Heursitic method: Peak calling from the genetic and intergenic regions were respectively counted and extracted
MACS2 was use for narrow peaks calling
Peaks normalization and Fold enrichment calculations were performed
Genome_build: T_thermophila_June2014_assembly.fasta
Supplementary_files_format_and_content: *_peaks.txt: Text files include peaks generated by MACS2.

organism: Tetrahymena thermophila

source_name: Cells grown in SPP liquid media

growth_protocol: 30C; 100rpm; SPP liquid media

extract_protocol:
Lysates were clarified from sonicated nuclei and RebL1-FZZ and Anqa1-FZZ -histone-DNA complexes were isolated with ANTI-FLAG® M2 Affinity Gel (Sigma)
Illumina's  TruSeq ChIP Sample Preparation Kit (cat# IP-202-1012)

value: B2086 Anqa1-FZZ

value: Vegetative Growth

tag: extraction

value: Immunoprecipitation


title: bATAC-Human_H1355_KEAP1_Rep2


title: Ghr-0064

description: GHR - study cohort

value: Liver

value: AL


title: WT_CTL Input

value: CTL


title: Ghr-0063

description: GHR - study cohort

value: M


title: bATAC-Human_H1355_GFP_Rep2


title: Ghr-0055

description: GHR - study cohort

value: F


title: Anqa1_INPUT2

tag: developmental stage

value: Whole cell extraction


title: 2AAY: 2_Atrial_Appendage_Young

value: Male


title: Anqa1_IP1


title: bATAC-Human_A549_LKB1_Rep1

tag: tissue/cell type

value: lung cancer

value: human derived (ATCC)

value: RPMI; 10% FBS; 1% pen-strep


title: bATAC-Human_A549_LKB1_Rep2

tag: timepoint of treatment


title: 1AAY: 1_Atrial_Appendage_Young

value: Female


title: Ghr-0051

description: GHR - study cohort

value: WT


title: bATAC-Human_A549_KEAP1_Rep1

tag: source


title: RebL1_IP2

value: B2086 RebL1-FZZ


title: Ghr-0048

description: GHR - study cohort


title: RebL1_INPUT2


title: bATAC-Human_A549_GFP_Rep1

tag: growth media


title: RebL1_IP1


title: Mettl3 _WT1

value: Raw 264.7 cells

value: Mettl3 _WT

value: LPS treatment for 6h


title: EOC1129_pOvaR1_RNA1_seq6a

city: Helsinki

first: Elina

last: Pietilä

address: Haartmaninkatu 8

institute: University of Helsinki

description:
Internal control of EOC1129_pOvaR1_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

data_processing:
Read pairs were trimmed using Trimmomatic (version 0.33)
the first 12 and last 5 bases were cropped due to uneven per base sequence content
leading bases with a quality score lower than 20 and any trailing bases with a quality score lower than 30 were removed
the reads were scanned with a 3-base wide sliding window, cutting when the average quality per base dropped below 20
resulting sequences shorter than 20bp were discarded. Trimmed reads were aligned to the reference genome (GRCh38.d1.vd1) using STAR (version 2.5.2b), allowing up to 10 mismatches, and all alignments for a read were output
Genome_build: GRCh38.d1.vd1
Supplementary_files_format_and_content: Matrix table with effective counts

source_name: Tumor tissue from treatment-naïve patient

extract_protocol:
Total RNA was extracted from fresh patient tissues and ascites-derived cells by using RNeasy kit from QIAGEN (Qiagen, Hilden, Germany) with DNase I treatment. RNA quality and concentration were tested with Bioanalyzer 2100 (Agilent CA, USA). All samples fulfilled the criteria of RNA integrity number (RIN) > 7 and concentration > 50 ng/µl.
Sequencing libraries were constructed in Beijing Genomics Institute (Beijing, China) using a modified protocol similar to the TrueSeq Stranded Total RNA with RiboZeroKit (Illumina Inc.)

tag: disease state

value: high-grade serous ovarian carcinoma

tag: anatomical location

value: Primary

tag: treatment strategy

value: Neoadjuvant chemotherapy


title: Anqa1_INPUT1

value: B2086 Anqa1-FZZ

value: Vegetative Growth


title: Ghr-0049

description: GHR - study cohort

tag: tissue

value: Liver

value: AL

value: F


title: Ghr-0053

description: GHR - study cohort

tag: treatment


title: bATAC-Human_A549_KEAP1_Rep2

tag: cell line

value: lung cancer


title: Ghr-0041

description: GHR - study cohort

value: M


title: EOC1030_pOvaR2_RNA1_seq4

value: Primary debulking surgery


title: RebL1_INPUT1

value: Whole cell extraction


title: Ghr-0042

description: GHR - study cohort

value: WT


title: bATAC-Human_A549_GFP_Rep2

value: human derived (ATCC)

value: RPMI; 10% FBS; 1% pen-strep


title: Ghr-0038

description: GHR - study cohort


title: EOC1120_pPer1_RNA2_seq5

value: Peritoneum


title: EOC1030_pOvaR1_RNA1_seq4


title: EOC1129_pPer2_RNA1_seq5


title: Ghr-0036

description: GHR - study cohort


title: Ctrl_NC_rep1

city: Oxford

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: Oxford University

description: siCTRL Replicate 1

hyb_protocol: Standard Illumina hybridization protocol on Illumina HumanHT-12 v4 beadchips

scan_protocol: Standard Illumina scanning protocol on an Illumina iScan Scanner. The Illumina GenomeStudio (v.1.9.0, Illumina Inc.) was used to generate bead files

data_processing: GenomeStudio data were processed in R (v.3.2) (Ihaka and Gentleman, 1996) using Bioconductor (v.3.1) (Gentleman et al., 2004) and the lumi package (v.2.20.2) (Du et al., 2008). Quality controls were carried out using the arrayQualityMetrics package (v.3.24.0) (Kauffmann et al., 2009) taking into account array intensity distributions, distance between arrays and variance mean-dependence. Principal component analysis was used to decide which arrays to process together. Background correction followed by variance stabilizing transform (Lin et al., 2008) and quantile between microarrays normalization were carried out with the lumi package. Data from two independent chips were merged and batch effects were accounted for and corrected using combat (Johnson et al., 2007) as implemented in the sva package (v.3.2) (Leek et al., 2012). From the 47323 probe sets available on the HumanHT12 V4 chip, removal of un-expressed probes resulted in 22839 probesets. A linear model was applied employing the limma package (v.3.24.13) (Ritchie et al., 2015) followed by empirical Bayesian analysis to determine differential expression between not-treated and treated samples. Genes were considered differentially expressed if the adjusted P-value, calculated using the Benjamini–Hochberg method (Benjamini and Hochberg, 1995) in order to minimize false discovery rate, was less than 0.05 and the mean level of expression was greater than 1.5-fold.

source_name: HEK293 T-Rex cells treated with 100 pmol of control siRNA

label_protocol: mRNA samples were processed using the Illumina TotalPrep-96 RNA Amplification Kit followed by the Illumina Whole-Genome Gene Expression Direct Hybridisation Assay

growth_protocol: Flp-In T-REx HEK293 cells, parental or stably expressing full length 3xFLAG-ZMYND8 or 3xFLAG-ZMYND8 N228F mutant, were maintained in DMEM (Lonza), supplemented with 10 % heat-inactivated foetal bovine serum (FBS - Sigma), 100 U/mL penicillin (Gibco), 100 µg/mL streptomycin (Gibco), and 200µg/ml Hygromycin (Invitrogen).

extract_protocol: Cells were washed once with PBS (Cat.#14190-094; Gibco), and total RNA was extracted and prepared using the RNeasy Mini Kit (Cat.#74106; Qiagen) including an on-column DNase I digestion (Cat.#79254; Qiagen), according to the manufacturer’s instructions. The resulting RNA was quantified and quality controlled using a Nanodrop spectrophotometer (model ND1000; Thermo Scientific) and the Agilent RNA 6000 Nano Kit (Cat.#5067-1511, Agilent Technologies).

treatment_protocol: Over-expression of ZMYND8 or N228F mutant: Cells were grown at 37 °C in a humidified cabinet at 5 % CO2. Protein expression was induced by treatment of cells with 1 µg/ml Tetracycline for 24 h  ZMYND8 knock-down experiments were performed by RNA interference using Lipofectamine RNAiMAX reagent (Cat.#13778-150). HEK293 cells were reverse transfected with 100 pmol Stealth siRNAs targeting ZMYND8 (Cat.#HSS119060; Invitrogen) or Stealth Negative Control for 48 hours. After 48 hours, cells were harvested for RNA extraction


title: ZMYND8_KD_rep3

description: siZMYND8 Replicate 3

source_name: HEK293 T-Rex cells treated with 100 pmol of siZMYND8


title: ZMYND8_KD_rep1

description: siZMYND8 Replicate 1


title: N288F_rep2

description: ZMYND8 N228F OE Replicate 2

source_name: ZMYND8 N228F mutant over-expression (24 h 100 nM doxycycline induction)


title: ZMYND8_KD_rep2

description: siZMYND8 Replicate 2


title: Ctrl_NC_rep2

description: siCTRL Replicate 2


title: N288F_rep3

description: ZMYND8 N228F OE Replicate 3


title: Ghr-0034

description: GHR - study cohort


title: Ctrl_NC_rep3

description: siCTRL Replicate 3


title: Ghr-0024

description: GHR - study cohort


title: Ghr-0015

description: GHR - study cohort


title: Ghr-0026

description: GHR - study cohort


title: EOC1120_pPer1_RNA1_seq6a

description:
Internal control of EOC1120_pPer1_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: EOC1032_pPer_RNA1_seq3


title: EOC1129_pOme1_RNA1_seq5

value: Omentum


title: EOC1129_iMes1_RNA1_seq6

value: high-grade serous ovarian carcinoma

value: Mesentery


title: EOC868_rPer_RNA1_seq3

source_name: Tumor tissue from post-chemotherapy patient

value: Neoadjuvant chemotherapy


title: Ghr-0013

description: GHR - study cohort


title: S. venezuelae - pIJLK04_Alderaan_Apr10_180 min_2

city: Jülich

first: Max

last: Hünnefeld

address: Wilhelm-Johnen-Straße

department: Institute for Bio- and Geosciences 1: Biotechnology

institute: Forschungszentrum Jülich

data_processing:
all data processing steps were conducted using CLC genomic workbench V. 20.0.4 software (QIAGEN, Hilden, Germany)
An initial quality check to analyze read quality and sequencing performances was followed by a trimming step to remove read-through adapter sequences, left-over adapter sequences, low quality reads (limit = 0.05) and ambiguous nucleotides.
Mapping and calculation of transcripts per millon (TPM) was conducted using the RNA-seq analysis function with follwing parameters: Mismatch cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.8, Similarity fraction: 0.8, Strand specific: both, Maximum number of hits for a read: 10
Genome_build: NC_018750.1 (Streptomyces venezuelae), MT711975.1 (Phage Alderaan)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample. 1st column is gene name, 2nd column is expression value (TPM).
Supplementary_files_format_and_content: Matrix table with expression data (TPM) for every gene and every sample. 1st column is gene name, 2nd column is gene origin (Alderaan or Svenezuelae), 3rd column is genomic region,  follwing columns – expression (in transcripts per million) for every sample (replicate 1, replicate 2).

organism: Streptomyces venezuelae ATCC 10712

source_name: Bacterial cells

growth_protocol: Pre-cultures of Streptomyces venezuelae ATCC10712 carrying an apramycin-resistant cassette on the plasmid pIJLK04 were inoculated in GYM medium to an inital spore titer of 108 spores/ml  in presence and absence of 10 µg/ml apramycin. After cultivation at 30 °C and 120 rpm for 16 h, main cultures in GYM medium containing the indicated supplements were inoculated with overnight cultures in the same medium to an initial OD450= 0.15. Infection was performed by adding phage Alderaan to an initial phage titer of 107 PFU/ml. Further cultivation was performed at 30 °C and 120 rpm.

extract_protocol:
RNA isolation was performed using the Monarch Total RNA Miniprep Kit (New England Biolabs)
RNA libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on the Illumina NovaSeq 6000 platform.

treatment_protocol: At the indicated time points, 2 OD units of each culture were harvested on ice and cells were stored at - 80 °C until RNA isolation.

tag: phage

value: Alderaan

tag: apramycin-conc

value: 10 µg/ml

tag: time point

value: 180 min


title: S. venezuelae - pIJLK04_Alderaan_Apr10_180 min_1


title: ZMYND8FL_rep3

description: ZMYND8 OE Replicate 3

source_name: ZMYND8 over-expression (24 h 100 nM doxycycline induction)


title: ZMYND8FL_rep2

description: ZMYND8 OE Replicate 2


title: EOC868_rMes_RNA1_seq3


title: EOC160_r1Mes1_RNA1_seq5


title: Ghr-0014

description: GHR - study cohort

value: Liver

value: AL

tag: Sex

tag: strain


title: Ghr-0008

description: GHR - study cohort

tag: genotype


title: S. venezuelae - pIJLK04_Alderaan_Apr0_180 min_2

value: 0 µg/ml


title: EOC742_r4Asc_RNA1_seq6

source_name: Ascites-derived cells from post-chemotherapy relapse patient

value: Ascites


title: S. venezuelae - pIJLK04_Alderaan_Apr0_180 min_1


title: S. venezuelae - pIJLK04_Alderaan_Apr10_90 min_2

value: 90 min


title: Ghr-0023

description: GHR - study cohort

value: F


title: vector_rep3

description: HEK293 T-Rex (vector) Replicate 3

source_name: HEK293 T-Rex (vector)


title: antigen-specific CD8+ T cells Trp2 (Dct) wild-type single cells_day7

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
single cell polyA RNA
scRNAseq_WT_day7

data_processing:
Illumina bcl2fastq (bulk RNAseq) or 10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Read mapping was performed via Hisat2 (Bulk RNAseq) or Cell Ranger count (scRNAseq) using the mouse reference genome (mm10).
Gene level quantification was completed using Subread featureCounts (bulk RNASeq) or Cell Ranger count software.
Raw counts data was imported into R for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized read count values for each sample

source_name: antigen-specific CD8+ T cells

growth_protocol: Trp2/Kb-specific cells were isolated from pre-immune WT and Dct-/- mice using tetramer enrichment followed by fluorescence-activated cell sorting on double tetramer positive cells.

extract_protocol:
Bulk RNAseq (samples 1-6): cells were isolated from three separate cohorts, with each cohort comprising eight WT and eight Dct-/- mice; Qiagen RNEasy Plus Mini Kit was used to extract RNA. Single cell RNA-seq (scRNAseq samples 1 and 2): sorted cells were supplied as input to the 10x Genomics single cell protocol.
Bulk: Clontech StrandedRNA Pico Mammalian workflow was used for library preparation; scRNAseq: Chromium Single Cell Immune Profiling was used for library preparation. Samples were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: antigen-specific CD8+ T cells

value: wildtype

value: spleen

value: mice were treated with TriVax (200 ug Trp2) 7 days prior


title: EOC295_rAsc_RNA_seq6b

description:
Internal control of EOC295_rAsc_RNA_seq6a
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: antigen-specific CD8+ T cells Trp2 (Dct) knockout single cells_day3

description:
single cell polyA RNA
scRNAseq_KO_day3

value: Dct-/-

value: mice were treated with TriVax (200 ug Trp2) 3 days prior


title: ZMYND8FL_rep1

description: ZMYND8 OE Replicate 1


title: S. venezuelae - pIJLK04_Alderaan_Apr0_90 min_2


title: vector_rep2

description: HEK293 T-Rex (vector) Replicate 2


title: N288F_rep1

description: ZMYND8 N228F OE Replicate 1


title: Ghr-0002

description: GHR - study cohort


title: antigen-specific CD8+ T cells Trp2 (Dct) knockout single cells_day7

description:
single cell polyA RNA
scRNAseq_KO_day7


title: S. venezuelae - pIJLK04_Alderaan_Apr10_90 min_1


title: EOC742_r3Asc3_RNA_seq6

value: high-grade serous ovarian carcinoma

value: Primary debulking surgery


title: vector_rep1

description: HEK293 T-Rex (vector) Replicate 1


title: S. venezuelae - pIJLK04_Alderaan_Apr0_90 min_1

value: Alderaan