title: Cauda_2

tag: strain


title: DMSO-1

status: Public on Jul 07 2020

type: SRA

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (hg19 and FANTOM_CAT.lv3_robust.all_lncRNA) (http://genome.ucsc.edu/) using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
HTSeq and DESeq2 were used for expression quantitation and differential expression analysis.
we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5.
Genome_build: hg19 and FANTOM_CAT.lv3_robust.all_lncRNA
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Whole RNA was extracted from 5 million cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
Sequencing libraries were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002)
Illumina TruSeq mRNA, ribodepletion, single End 50 Cycle, strand specific

treatment_protocol: THP-6  cells were lentivirally transduced with shControl, shEts1_3, or shEts1_2. Two days later the cells were selected in 10 ug/ml puromycin. The next day, the cells were harvested.

tag: group

value: DMSO

tag: cell line

value: Transduced THP-6 cells

tag: disease

value: T lymphoblastic leukemia/lymphoma


title: shEts1_2-3


title: Sample28_glucose100%_BHB0mM

city: Honolulu

first: Michael

last: Weichhaus

state: Hawaii

address: 3140 Waialae Avenue

department: Natural Sciences and Mathematics

institute: Chaminade University of Honolulu

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Illumina fastq files were pseudoaligned using "kallisto" (v0.46.1) using their prebuilt indices constructed from Ensembl Homo_sapiens.GRCh38 databases  creating abundance files (attached as processed data files)
Samples were loaded into "R" (version 4.0) using tximport and analyzed using the DESeq2 (version 1.28.1) pipeline.
Differential gene expression was established after shrinking DESeq2 outputs according to the the protocol established by Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Matrix with FPKM of all sample, treatment conditions and genes

source_name: metastatic breast cancer

growth_protocol: Cells were routinely maintained in DMEM with 10% FBS, 2 mM glutamine and 50 ng/ml gentamycin

extract_protocol:
Total RNA was extracted using Qiagen’s RNeasy Mini Kit
TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Cells were treated as indicated with reduced glucose and/or beta-hydroxybutyrate

value: glucose concentration [g/l]:4.5

tag: treatment 2

value: beta hydroxybutyrate [mm]:0


title: PFHxS_47

type: RNA

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Retroperitoneal fat pad, rat exposed to PFHxS

hyb_protocol: RNAs were hybridized to the Rat Clariom S Array (ThermoFischer Scientific).

scan_protocol: Arrays were immediately scanned, and images were analyzed and rigorously quality controlled for hybridization artifacts.

data_processing: The resulting CEL files were processed using the oligo package available performed in R/Bioconductor (Gentleman et al., 2004). Data were then normalized and background corrected using the RMA method with the Brainarray custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (Dai et al., 2005).

label: biotin

organism: Rattus norvegicus

source_name: Retroperitoneal fat pad

label_protocol: Total RNA was amplified and labelled using the Gene Chip WT PLUS Reagent Kit according to the manufacturer’s instructions (ThermoFischer Scientific).

growth_protocol: The animals were housed in a room with controlled environmental conditions with reversed light/dark cycles of 12 hours with light intensity 500 lux starting at 9 PM, humidity 55% 6 5, temperature at 21 +/- 1C and ventilation changing air 10 times per hour. All animals had ad libitum access to standard diet with ALTROMIN 1314 (soy- and alfalfa-free, ALTROMIN GmbH, Lage, Germany) and acidified tap water (to prevent microbial growth) in PSU bottles (84-ACBTO702SU Tecniplast)

extract_protocol: Total RNA was extracted from the left retroperitoneal fat pad using the RNeasy Lipid Tissue Mini kit (Qiagen) including on-column DNase I treatment according to manufacturer’s instructions

treatment_protocol: Retroperitoneal fat pad was placed in RNAlater and stored at -80 °C until preparation for transcriptional analysis

value: Wistar

tag: treatment

value: Exposed to PFHxS

tag: age

value: Adult (13 months old)

tag: tissue

value: Retroperitoneal fat pad

tag: Sex

value: Female


title: Cauda_1

city: Houston

first: Thomas

last: Garcia

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Fastq files were trimmed with Trim Galore!
Trimmed files were aligned to GRCm38 using HISAT2.
Aligned features were quantified using featureCounts.

organism: Mus musculus

source_name: Cauda

extract_protocol:
RNA was extracted using Trizol/chloroform followed by purification using a Rneasy Mini kit from Qiagen with an on-column Dnase treatment.
Libraries were constructed using a KAPA standed mRNA-seq kit.

value: Cauda


title: Seabass_PostStress_T4_R1

city: MONTPELLIER

first: Bruno

last: GUINAND

address: Place E. Bataillon - Campus Triolet

institute: Université de Montpellier

library_source: genomic

data_processing:
Raw sequencing data were trimmed of low quality reads and adapter residues using Trim Galore!. The trimmed reads were then demultiplexed with STACKS.The option disable_rad_check was applied to avoid reads with bisulfite-modified restriction sites to be discarded. The demultiplexed reads were trimmed a second time on both 5’ and 3’ ends with the options --clip_R1 --clip_R2 and --three_prime_clip_R1 --three_prime_clip_R2 to remove introduced methylated cytosines during adapter ligation.
Using the bismark_genome_preparation function of the program bismark (Krieger and Andrews 2011, Bioinformatics, doi: 10.1093/bioinformatics/btr167), a bisulfite converted version of the European sea bass genome was prepared against which the demultiplexed and trimmed reads were mapped
The R package MethylKit was used to determine differential methylation between pre- and post-stress fish. Coverage was normalized across samples. Using Methylkit, differentially methylated CpG sites were determined between pre- and post-stress individuals using logistic regression (30X read depth; nominal q-value: 0.001; 15% methylation threshold)
Genome_build: GCA_000689215.1
Supplementary_files_format_and_content: Txt files providing chromosomes, posotions, strand, percentages cytosine and thymine for each methylated sites

molecule: genomic DNA

organism: Dicentrarchus labrax

growth_protocol: 20 sea bass families were reared separately in open circulation tanks at Nireus S.A. research facilities (Greece). Fish were tagged at ~280 days post-hatch and distributed in 20 tanks; each tank receiving 1 fish from each family (i.e., 20 fish per tank). Throughout the experimental period, the photoperiod was set at 12L:12D, the water temperature and the salinity held constant (18.1 ± 0.2°C and 28 ppt, respectively). Fish were submitted to one acute challenge test per month for three consecutive months, from July to October 2018.

extract_protocol:
Blood from the caudal vessel was collected. Plasma and red blood celles were separated by centrifugation at 2,000g for 10 min. Careful separation of the plasma and RBCs was performed using 200 µl pipettes. RBC extracts were heparinized (heparin sodium; Sigma-Aldrich), transferred in microtubes and conserved at -20°C in 1 ml of RNA later. Genomic DNA was extracted using the Macherey Nagel Nucleo Spin Tissue DNA kit and quantified using a Qubit fluorometer (Qubit dsDNA BR Assay Kit, Q32853, Invitrogen).
EpiGBS approach adapted from van Gurp et al. (2016, Nature Methods doi: 10.1038/nmeth.3763), with main addition of a second restriction enzyme in the protocol. The couple of enzymes retained: MspI/ SfbI. A single libray was prepared: 200 ng of DNA of each sample were digested in a 40 µl reaction, using 0.25 µl MspI (NEB, 20,000 U/ml R0106S), 0.25 µl SbfI-HiFi (NEB 20,000 U/ml R3642L) and 4 µl of 10X cutsmart buffer. The reaction was run overnight at 37°C. Unique forward and reverse adapter combinations allow multiplexing samples in the library. We added forward and reverse adapters in unique combinations (1 µl of adapter, 2.5 µM), 0.5 µl T4 Ligase (NEB, 400,000 U/ml m0202L), 6 µl of 10X T4 ligase buffer and 11.5µl water were added directly to the digested DNA. Adapters were ligated for 3 h at 23°C followed by 10 min of enzyme inactivation at 65°C. After ligation, all samples were pooled and one third of the total volume was used in the following step. The mixture volume was reduced using a Qiaquick PCR purification kit (28104 Qiagen). The resulting product was cleaned a second time to ensure the removal of small fragments and adapter remnants using CleanPCR paramagnetic beads (Proteigene, CPCR-0050) with a ratio of 0.8X [sample : beads]. a nick translation was performed to repair the nick of the DNA at the restriction site and to fully methylate the hemi-methylated adapters. To do so, 19.25 µl of the concentrated and purified ligation pool were used in a 25 µl reaction, including 0.75 µl DNA Polymerase I (E. coli, 10,000 U/ml M0209S), 2.5 µl of 10 mM 5-Methylcytosine dNTP mix (Zymo Research, D1030), and incubated at 15 °C for one hour. The library was then treated with sodium bisulfite using the EZ DNA Methylation Gold Kit (D5005, Zymo Research) following manufacturer instructions to convert unmethylated cytosines to uracil, paying attention to the optimal DNA amount per reaction. After bisulfite conversion, 14 cycles of PCR (95°C for 1 min, 91°C for 10s, 65°C for 15s, 72°C for 10s and a final elongation step at 72°C for 5 min) were performed, followed by a paramagnetic bead clean up with a 0.8X ratio. The library quality was verified on an Agilent 5300 Fragment Analyzer (Santa Clara, USA). It was sequenced (paired-end, 150 bp) on one lane of a SP flow cell on an ILLUMINA NovaSeq 6000.

treatment_protocol: Fish were exposed to high density stress by lowering water levels in the tank to 1/3 of the original volume, followed by chasing of the fish with a net for five minutes and a 30 min waiting period before sampling. This protocol took place in each tank then for each fish individual entering the experiment. It was repeated for 3 consecutive times at 20-21 day intervals (period long enough for fish to recover). An initial blood sampling occurred two weeks prior to the implementation of the stress challenge (T0 label, July 19th, 2018, pre-stress/control group) then at the end of the challenge test (T4 label, October 5th, 2018).

tag: developmental stage

value: juvenile

value: 9 months

value: post-stress

tag: family

value: R

tag: cell type

value: blood red cells


title: shEts1_2-2


title: DMSO-2


title: Ctrl_105

description: Retroperitoneal fat pad, control rat

value: Control


title: Sample9_glucose5%_BHB10mM

value: glucose concentration [g/l]:0.225

value: beta hydroxybutyrate [mm]:10


title: shEts1_2-4

value: Transduced THP-6 cells

value: T lymphoblastic leukemia/lymphoma


title: Sample24_glucose5%_BHB25mM


title: Seabass_PostStress_T4_R14


title: Caput_3

source_name: Caput

value: Caput


title: Sample22_glucose5%_BHB0mM

value: beta hydroxybutyrate [mm]:0


title: Caput_2


title: shEts1_2-1


title: Sample7_glucose100%_BHB0mM

value: glucose concentration [g/l]:4.5


title: shEts1_3-3


title: Ctrl_4

description: Retroperitoneal fat pad, control rat

value: Wistar

value: Adult (13 months old)


title: PFHxS_39

value: Exposed to PFHxS

value: Retroperitoneal fat pad

value: Female


title: Caput_1


title: Sample3_glucose5%_BHB25mM

value: beta hydroxybutyrate [mm]:25


title: shEts1_3-2


title: Ctrl_3

description: Retroperitoneal fat pad, control rat


title: IRF4null_2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw data was demultiplexed into cells and the data mapped to the mouse mm10 genome build using CellRanger v2.1.1.
Biological replicates for WT and IRF4null B cells were aggregated using the CellRanger aggr function with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: UMI transcript counts for each cell (columns) and all detected genes (rows)

molecule: polyA RNA

source_name: B cell

extract_protocol:
Adoptively transferred cells were FACS isolated and resuspended in 1xPBS at 1000 cells/ul for GEM loading.
GEM creation and library preparation was performed according to the 10x recommended protocol.

treatment_protocol: B cells of the indicated genotype were harvested from the spleen 72 hours following LPS innoculation.

value: female

tag: sorting markers

value: Spleen

tag: cd19-cre status

value: Positive

tag: b cell genotype

value: CD19-CRE;Irf4 fl/fl


title: IRF4null_1


title: Sample2_glucose5%_BHB10mM

value: glucose concentration [g/l]:0.225


title: shEts1_3-1


title: Seabass_PostStress_T4_M13

value: juvenile

value: 9 months

value: post-stress

value: M

value: blood red cells


title: Seabass_PostStress_T4_S14

value: S


title: Seabass_PostStress_T4_M19


title: shControl-3

value: shControl

value: Transduced THP-6 cells

value: T lymphoblastic leukemia/lymphoma


title: Sample1_glucose5%_BHB0mM

value: beta hydroxybutyrate [mm]:0


title: Seabass_PostStress_T4_G12

value: G


title: Seabass_PostStress_T4_G10


title: Cor55-1

data_processing:
Fastq files were trimmed with Trim Galore!
Trimmed files were aligned to GRCh38 using HISAT2.
Aligned features were quantified using featureCounts.

source_name: Corpus

value: Corpus

value: 55 year old patient


title: Seabass_PostStress_T4_M18


title: WT_2

value: female

value: Spleen

value: Negative

value: wild-type


title: shControl-2


title: WT_1


title: Ctrl_74

description: Retroperitoneal fat pad, control rat

value: Wistar

value: Control

value: Adult (13 months old)

value: Retroperitoneal fat pad

value: Female


title: Seabass_PostStress_T4_G9

value: juvenile

value: 9 months

value: post-stress

value: blood red cells


title: Cap40-A

value: Caput

value: 40 year old patient


title: shControl-1

value: shControl

value: Transduced THP-6 cells

value: T lymphoblastic leukemia/lymphoma


title: CD65-1

value: Cauda

value: 65 year old patient


title: 2464-RP-60

city: Frederick

first: Patric

last: Schyman

state: Maryland

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description:
Treatment
2464-RP-60-GGACATCA-TACCTGCA_S181

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.2) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Rattus norvegicus transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Genome_build: Rattus norvegicus transcriptome (Rnor_6.0)
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

source_name: High_HgCl2_10 h_kidney

extract_protocol:
Frozen whole kidney samples were powdered in liquid nitrogen, since these organs are histologically heterogeneous. Total RNA was isolated from powdered kidney, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: Sprague-Dawley

tag: treatment/dose

value: High (0.50 mg/kg HgCl2)

tag: duration

value: Kidney


title: Seabass_PostStress_T4_G5

value: G


title: T55-2

source_name: Testis

value: Testis

value: 55 year old patient


title: 2464-RP-59

description:
Treatment
2464-RP-59-GTCATCGT-CCGCTTAA_S180

tag: strain


title: Seabass_PostStress_T4_R3

value: juvenile

value: R


title: Seabass_PostStress_T4_G7

value: 9 months

value: post-stress


title: 2464-RP-57

description:
Treatment
2464-RP-57-CTCGAACA-GCAATTCC_S178


title: Cor65-2

value: Corpus


title: Cor40-1

value: 40 year old patient


title: Seabass_PostStress_T4_T18

value: T

value: blood red cells


title: CD55-2


title: Cd40-2


title: 2464-RP-54

description:
Treatment
2464-RP-54-TACCTGCA-GGACATCA_S175

source_name: High_HgCl2_34 h_kidney


title: 2464-RP-55

description:
Treatment
2464-RP-55-GTCGATTG-AAGACCGT_S176


title: Wild type rep5

city: Cincinnati

first: Gurjit

last: Khurana Hershey

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw reads in fastq format were processed using Computational Suite For Bioinformaticians and Biologists (CSBB-v3.0)
CSBB uses fastqc for quality check and Bowtie2 for mapping
Differential gene expression analysis was carried out with RUVSeq with log2 fold change (FC) ≥1 or ≤−1, P<0.05 and false discovery rate (FDR) ≤5%
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Epidermis

extract_protocol:
Back skin epidermis was separated from dermis with the use of dispase. Tissues were stored in RNAlater. Total RNA was isolated with the RNeasy Microarray Tissue Mini Kit (Qiagen) according to manufactures’ instructions.
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit

value: Mixed background

value: Epidermis

value: 8 week old

tag: genotype

value: wild type


title: Seabass_PostStress_T4_P2

value: P


title: Seabass_PostStress_T4_F2

value: F


title: Seabass_PostStress_T4_R2


title: Seabass_PreStress_T0_G14

value: 6 months

value: pre-stress

value: G


title: Wild type rep4


title: Te40-1

value: Testis


title: Ca65-2

value: Caput

value: 65 year old patient


title: 2464-RP-58

description:
Treatment
2464-RP-58-CAACTCCA-GAATCCGT_S179

value: Sprague-Dawley

value: High (0.50 mg/kg HgCl2)

value: Kidney


title: Seabass_PreStress_T0_F13

value: juvenile


title: 2464-RP-56

description:
Treatment
2464-RP-56-TATGGCAC-TTGCGAGA_S177


title: 2464-RP-53

description:
Treatment
2464-RP-53-CCGCTTAA-GTCATCGT_S174


title: 2464-RP-52

description:
Control
2464-RP-52-GAATCCGT-CAACTCCA_S173

source_name: Vehicle_saline_34 h_kidney

value: Vehicle (1 ml/kg saline)


title: HPB_shETS1_1

description: HPB-ALL cells transduced with shRNA against ETS1 were collected after 5 days of puromycin selection.

hyb_protocol: Following fragmentation, cDNA was hybridized for 20 hr at 48C to Affymetrix Human Genome U133 Plus 2.0 arrays.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing:
Data was analyzed using the affy package implemented in the R-statistical environment. gcRMA was used to estimate log2 transformed expression values for each probe-set.
HPB_shETS1_supplement.xlsx: Supplementary file with gene annotation, which performs a two-sample T-test and computes an average fold-change.

source_name: HPB-ALL cell line

label_protocol: 10 ng of RNA from each sample was amplified using the Ovation PicoSL WTA System (NuGen), labeled by the Encore BiotinIL Module (NuGen).

growth_protocol: HPB-ALL cells were cultured in standard conditions in RPMI 1640 media supplemented with 10% FBS and 1% Penicillin/Streptomycin.

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

treatment_protocol: HPB-ALL cells that were transduced with a plKO-shRNA LUC and shETS1 were collected at 5 days after puromycin selection.

tag: cell line

value: HPB-ALL

tag: shRNA

value: Male


title: K14Kif3a-/- rep5

value: Mixed background

value: Epidermis

value: 8 week old


title: HPB_shLUC_2

description: HPB-ALL cells transduced with shRNA against LUC were collected after 5 days of puromycin selection.

value: shLUC


title: 2464-RP-51

description:
Control
2464-RP-51-GCAATTCC-CTCGAACA_S172


title: Wild type rep3

value: wild type


title: Seabass_PreStress_T0_D18

value: 6 months

value: pre-stress

value: D

value: blood red cells


title: Te52-2

value: Testis

value: 52 year old patient


title: Wild type rep6


title: Seabass_PreStress_T0_R11

value: R


title: HPB_shLUC_1


title: K14Kif3a-/- rep4


title: 2464-RP-49

description:
Treatment
2464-RP-49-AAGACCGT-GTCGATTG_S170

source_name: Low_HgCl2_34 h_kidney

value: Sprague-Dawley

value: Low (0.25 mg/kg HgCl2)

value: Kidney


title: K14Kif3a-/- rep3


title: Sample 26 [WGS]

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Library strategy: shallow whole genome sequencing
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --no-spliced-alignment --rna-strandness RF --dta -k 5
Secondary alignments were filtered out using samtools (v 1.5)
Copy number variatons were analyszed using R/cn.MOPS (v 1.28.0) using chromosome normalization (poisson) excluding sex chromosomes
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including genomic regions, log ratios of read counts and copy number values for each sample

source_name: reference DNA

extract_protocol:
Genomic DNA was extracted using the AllPrep Kit (Quiagen). 10mg of snap-frozen tissue was homogenized in RLT Plus buffer with a Precellys 24 tissue homogenizer (Bertin Instruments) and processed, according to the manufacturer's instructions. Integrity of genomic DNA was testet on an agarose gele.
A total amount of 1.0μg DNA per sample was used as input material for the DNA sample preparations. Sequencing libraries were generated using NEBNext® DNA Library Prep Kit following manufacturer's recommendations and indices were added to each sample. The genomic DNA is randomly fragmented to a size of 350bp by shearing, then DNA fragments were end polished, A-tailed, and ligated with the NEBNext adapter for Illumina sequencing, and further PCR enriched by P5 and indexed P7 oligos. The PCR products were purified (AMPure XP system) and resulted libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified using real-time PCR.

tag: tumor subtype

value: Ctrl

value: reference DNA (Promega)


title: K14Kif3a-/- rep6

value: Mixed background


title: Seabass_PreStress_T0_F10

value: juvenile

tag: treatment

value: F


title: K14Kif3a-/- rep2

value: Epidermis

tag: age

value: 8 week old


title: 2464-RP-48

description:
Treatment
2464-RP-48-TGGTGAAG-CTTACAGC_S169

tag: tissue


title: Seabass_PreStress_T0_P9

value: 6 months

value: P


title: 2464-RP-47

description:
Treatment
2464-RP-47-CCAGTTGA-GACGTCAT_S168


title: Seabass_PreStress_T0_P11

value: pre-stress


title: Wild type rep2

value: wild type


title: Seabass_PreStress_T0_R10

value: blood red cells


title: Sample 25 [WGS]

source_name: non-transformed thyroid tissue

value: NT

value: non-transformed thyroid tissue


title: K14Kif3a-/- rep1


title: Cp55-A

value: Caput

value: 55 year old patient


title: 2464-RP-46

description:
Treatment
2464-RP-46-AAGACACC-GTAACCGA_S167

value: Sprague-Dawley

value: Low (0.25 mg/kg HgCl2)

value: Kidney


title: Sample 24 [WGS]


title: Sample 23 [WGS]


title: 2464-RP-50

description:
Treatment
2464-RP-50-TTGCGAGA-TATGGCAC_S171


title: Seabass_PreStress_T0_R8

value: R


title: Wild type rep1

value: Mixed background


title: 2464-RP-45

description:
Control
2464-RP-45-CAATAGCC-TCTACGCA_S166

value: Vehicle (1 ml/kg saline)


title: Sample 21 [WGS]

source_name: primary thyroid tumor

value: PTC

value: thyroid


title: Placenta, STZ Sample 3

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

description: STZ - 2262

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)
Supplementary_files_format_and_content: Control vs STZ.xlsx reports abundamce measurements

source_name: Placenta (junctional zone)

growth_protocol: [animal protocol] Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age).  Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.

extract_protocol:
Placentation sites were dissected on gestation day 18.5 and junctional zones were isolated. Dissected junctional zone tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzolÒ reagent (Thermo Fisher Scientific, catalog No. 15596018).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility.

treatment_protocol: A single dose of either streptozotocin (STZ; 45 mg/kg of body weight) or vehicle control solution (0.1 M citrate buffer, pH 4.2) was administered via tail vein injection on gd 6.5.

value: Holtzman Sprague-Dawley

tag: gestation day


title: Sample 22 [WGS]


title: 2464-RP-44

description:
Control
2464-RP-44-AGCGAGAT-CCAGTATC_S165


title: Placenta, STZ Sample 2

description: STZ - 2205

value: streptozotocin (STZ; 45 mg/kg of body weight)


title: 2464-RP-43

description:
Control
2464-RP-43-TCCATTGC-TACGGTCT_S164


title: Seabass_PreStress_T0_T19

tag: developmental stage

value: juvenile

value: 6 months

value: pre-stress

value: T


title: Sample 20 [WGS]


title: Sample 19 [WGS]


title: Seabass_PreStress_T0_P3

tag: family

value: P

value: blood red cells


title: Placenta, STZ Sample 1

description: STZ - 2202


title: Sample 18 [WGS]


title: 2464-RP-39

description:
Control
2464-RP-39-TCTACGCA-CAATAGCC_S160

source_name: Vehicle_saline_10 h_kidney


title: Sample 17 [WGS]


title: Placenta, Control Sample 2

description: Control - 2208

value: vehicle control solution (0.1 M citrate buffer, pH 4.2)


title: Placenta, Control Sample 3

description: Control - 2209


title: 2464-RP-42

description:
Treatment
2464-RP-42-CTTACAGC-TGGTGAAG_S163

value: Sprague-Dawley

value: High (0.50 mg/kg HgCl2)


title: Seabass_PreStress_T0_H3

value: H

tag: cell type


title: 2464-RP-41

description:
Treatment
2464-RP-41-GACGTCAT-CCAGTTGA_S162

value: Kidney


title: Seabass_PreStress_T0_P5


title: Sample 16 [WGS]

value: FTC


title: Sample 14 [WGS]


title: Placenta, Control Sample 1

description: Control - 2207


title: 2464-RP-37

description:
Control
2464-RP-37-TACGGTCT-TCCATTGC_S158

value: Vehicle (1 ml/kg saline)


title: Seabass_PreStress_T0_R1

value: R


title: Sample 15 [WGS]

value: thyroid


title: 2464-RP-38

description:
Control
2464-RP-38-CCAGTATC-AGCGAGAT_S159


title: Seabass_PreStress_T0_G8

value: G


title: Seabass_PreStress_T0_S2

value: S


title: Sample 13 [WGS]


title: Sample 12 [WGS]


title: 2464-RP-36

description:
Control
2464-RP-36-GGAATGTC-AGGAACAC_S157


title: Seabass_PreStress_T0_K18

value: juvenile

value: K


title: MCF7_48_3: 48 hours incubation repeat 3

city: Jerusalem

first: Yuval

last: Tabach

address: The Institute For Medical Research-Israel-Canada

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
The pair-end samples were demultiplexed according to "Hashimshoni et al 2016, CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol. 17, 77."
Adapters were trimmed by cutadapt
The reads were mapped to the human genome version GRCh38 using STAR
The reads were counted by HTseq-count
The count matrix was normalized to the size of all the libraries analyzed
Genome_build: GRCh38

source_name: Breast adenocarcinoma cell line

growth_protocol: DMEM supplied with 10% FBS, 1% L-glu and 1% penicillin/streptomycin

extract_protocol:
RNA was extracted from each sample with RNA extraction kit purchased from 5prime
CEL-seq2 protocol

treatment_protocol: 54uM of phenolaTi treated at different time points (according to incubation periods) and than harvest at the same time

value: Breast adenocarcinoma cell line

tag: tag

value: 48 hours incubation with phenolaTi


title: Seabass_PostStress_T4_B5

value: 9 months

value: post-stress

value: B


title: 2464-RP-40

description:
Control
2464-RP-40-GTAACCGA-AAGACACC_S161

value: Sprague-Dawley


title: Seabass_PreStress_T0_C3

value: 6 months

value: pre-stress

value: C

value: blood red cells


title: 2464-RP-35

description:
Treatment
2464-RP-35-GAACGGTT-GGAGGAAT_S156

source_name: Low_HgCl2_10 h_kidney

value: Low (0.25 mg/kg HgCl2)

value: Kidney


title: Sample 11 [WGS]

value: FTC

value: thyroid


title: 2464-RP-34

description:
Treatment
2464-RP-34-AGCTAAGC-GTCGTTAC_S155


title: MCF7_48_1: 48 hours incubation repeat 1


title: 2464-RP-33

description:
Treatment
2464-RP-33-TGGAAGCA-GAGAGTAC_S154


title: MCF7_24_3: 24 hours incubation repeat 3

value: 24 hours incubation with phenolaTi


title: MCF7_24_2: 24 hours incubation repeat 2


title: 2464-RP-32

description:
Treatment
2464-RP-32-CTTGCTAG-TCATCTCC_S153


title: MCF7_24_1: 24 hours incubation repeat 1


title: 2464-RP-31

description:
Treatment
2464-RP-31-CAGTGCTT-TTCCAGGT_S152


title: Medaka Dnmt1 Mut3

city: Freiburg im Breisgau

last: Boehm

address: Stübeweg 51

department: Immunology

institute: MPI-IE Freiburg

data_processing:
Basecalling was performed with Illumina MiSeq Control Software/RTA version 2.6.2.1.
Raw sequencing reads were trimmed with cutadapt version 1.9.1 (Martin, 2011), removing the first two 5'-most nucleotides and Illumina adapter sequences. Base quality trimming was performed using prinseq lite version 0.20.4 .
Bisulfite-specific mapping to bisulfite-converted MEDAKA1.72 genome was performed with Bismark v0.14.6 and Bowtie2 v2.2.8 in non-directional mode allowing for dovetail alignments.
Samtools sorted and indexed bams were used for methylation bias calculation (MethylDackel v0.1.7) and read count extraction in target regions with methylCtools version 0.9.4(Hovestadt et al., 2014), using MAPQ threshold 10, SNP detection, counting one of two overlapping mates, skipping 5 nucleotides from read ends, and zero-padding.
Data postprocessing was performed in R version 3.2.3. Raw methylation values were set to NA for CpG positions with at least 0.25 SNP allelic frequency as well as for positions with aggregate coverage of less than 10 reads. Single CpG methylation values were aggregated per target genomic interval as mean values.
Genome_build: MEDAKA1.72
Supplementary_files_format_and_content: Single CpG as well as mean methylation values in target genomic intervals are summarized in corresponding tab-separated tables for all samples.

organism: Oryzias latipes

source_name: dnmt1 mutant rep3

extract_protocol:
Genomic DNA was extracted from 3 dnmt1+/+ and 3 dnmt1-/- medaka at 18 dpf using DNeasy blood and tissue kit (Qiagen).
150ng of DNA was used for the bisulfite reaction using the EZ DNA methylation kit (Zymo Research) and the bisulfite-treated DNA was recovered in 15ml of elution buffer. 1ml of bisulfite-treated DNA solution was used for 30 cycles of PCR amplification with the indicated bisulfite primers in a reaction volume of 20ml; 1ml of the first PCR reaction was used for a nested PCR reaction with P5 and P7 adaptor-attached bisulfite primers. After the nested PCR reactions, amplicons were purified using PCR purification kit (Qiagen) and qualified and quantified by gel electrophoresis, the High Sensitivity DNA kit (Agilent) for the Agilent Bioanalyzer and the Qubit dsDNA HS assay kit (Invitrogen). The eight amplicons derived from the same original source were mixed at 1ng/ml each and 15ml of the mixture were amplified using P5 and P7 primers attached to barcodes using NEBNext DNA library prep kit (New England Biolabs), following the manufacturer«s protocol. The amplicons were purified using AMPure XP (Beckman Coulter) and qualified and quantified using Bioanalyzer and Qubit dsDNA HS assay kit. Finally, all amplicons were mixed at 1ng/ml each and 5 ml of mixed amplicons were used for sequencing in paired-end 150bp mode on 1 lane of MiSeq Sequencing System (Illlumina).

value: whole embryo

value: cab

tag: surface phenotype


title: HPB_shETS1_2

description: HPB-ALL cells transduced with shRNA against ETS1 were collected after 5 days of puromycin selection.

value: HPB-ALL

tag: Sex

value: Male


title: MCF7_15_3: 15 hours incubation repeat 3

value: Breast adenocarcinoma cell line

value: 15 hours incubation with phenolaTi


title: Seabass_PostStress_T4_E13

value: juvenile

value: 9 months

value: post-stress

value: E


title: Seabass_PostStress_T4_H19

value: H


title: Sample 8 [WGS]

value: ATC


title: Seabass_PostStress_T4_I17

value: I

value: blood red cells


title: Sample 7 [WGS]


title: Sample 9 [WGS]


title: MCF7_15_2: 15 hours incubation repeat 2


title: Medaka Dnmt1 Mut1

source_name: dnmt1 mutant rep1


title: MCF7_48_2: 48 hours incubation repeat 2

value: 48 hours incubation with phenolaTi


title: Seabass_PostStress_T4_C19

value: C


title: Seabass_PostStress_T4_O17

value: O


title: MCF7_15_1: 15 hours incubation repeat 1


title: Sample 10 [WGS]

value: thyroid


title: Seabass_PostStress_T4_O3


title: Sample 6 [WGS]


title: Medaka Dnmt1 Mut2

source_name: dnmt1 mutant rep2

value: whole embryo

value: cab


title: MCF7_6_2: 6 hours incubation repeat 2

value: 6 hours incubation with phenolaTi


title: MCF7_6_3: 6 hours incubation repeat 3

value: Breast adenocarcinoma cell line


title: Sample 3 [WGS]


title: Medaka WT2

source_name: control rep2

value: wt


title: Sample 2 [WGS]


title: Medaka WT3

source_name: control rep3


title: Seabass_PostStress_T4_K10

value: juvenile

value: K


title: Seabass_PostStress_T4_H9

value: 9 months

value: post-stress


title: Seabass_PostStress_T4_H17

value: H


title: Sample 1 [WGS]

value: ATC


title: Medaka WT1

source_name: control rep1


title: MCF7_3_3: 3 hours incubation repeat 3

value: 3 hours incubation with phenolaTi


title: Sample 5 [WGS]


title: Seabass_PostStress_T4_O8

value: blood red cells


title: MCF7_3_2: 3 hours incubation repeat 2


title: Seabass_PostStress_T4_N18

value: N


title: BMDM-STING S365A-DMXAA

city: Dallas

last: Yan

state: TEXAS

address: 6000 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Sample 12

data_processing:
Genes expression level is quantified by a software package called RSEM
Genome_build: mm9
Supplementary_files_format_and_content: The file AllSamples.GeneExpression.FPKM.txt, a expression table for all samples

source_name: Bone marrow

growth_protocol: T cells were stimulated with anti-CD3 (5 ug/ml)and anti-CD28 (5 ug/ml) antibodies in RPMI complete medium; BMDMs were grown in the DMEM complete medium with M-CSF  containing conditional medium from L-929 cells

extract_protocol:
Total RNA was isolated with using the Trizol reagent. Quality was examined using a bioanalizer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO or DMXAA (10 ug/ml) for 16 hours

value: bone marrow derived macrophages

tag: passages

value: STING S365A

value: DMXAA


title: Seabass_PostStress_T4_K4


title: BMDM-STING KO-DMXAA

description: Sample 11

value: STING KO


title: Seabass_PostStress_T4_O6

value: O


title: Seabass_PostStress_T4_J9

value: J


title: Sample 4 [WGS]

value: thyroid


title: BMDM-WT-DMXAA

description: Sample 10

value: WT


title: M9-g_con-female

description: Gene expression data from CTR

hyb_protocol: RNAs were hybridized to the Rat Gene 2.0 ST Array (ThermoFischer Scientific).

scan_protocol: Arrays were immediately scanned, and images were analyzed and rigorously quality controlled for hybridization artefacts.

data_processing: The resulting CEL files were processed using the oligo package available performed in R/Bioconductor (Gentleman et al., 2004). Data were then normalized and background corrected using the RMA method with the Brainarray custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (ragene20strnentrezg.db_22.0.0) (Dai et al., 2005).

source_name: Anogenital region

label_protocol: Total RNA was amplified and labelled using the Gene Chip™ WT PLUS Reagent Kit according to the manufacturer’s instructions (ThermoFischer Scientific).

growth_protocol: Twelve time-mated nulliparous, young adult Sprague Dawley rats with a body weight of approximately 230 g (Taconic, Ejby, Denmark) were supplied at GD3. The day of vaginal plug detection was designated GD1. On GD4, dams were randomized into 2 groups of 6 animals with similar body weight distributions. Animals were housed in pairs until GD17 and thereafter individually. The animals were housed in semi-transparent plastic cages with Tapvei aspen bedding situated in an animal room with controlled environmental conditions: 12h light-dark cycles with light starting at 9 p.m., temperature 22 ± 1°C, humidity 55 ± 5%, 10 air changes per hour. Feed (Altromin Standard diet 1324) and tap water were provided ad libitum in BPA-free bottles (Scanbur 84-ACBT0702SU).

extract_protocol: Total RNA was isolated from the tissue of the anogenital region using RNeasy mini kits, including on-column DNaseI treatment, according to manufacturer’s instructions (Qiagen, Hilden, Germany). The RNA purity and quantity was analysed using the Agilent 2100 Bioanalyzer system and Eukaryote Total RNA Nano assay (Agilent Technologies, Santa Clara, USA) according to manufacturer’s instructions and only samples with a RIN-score >7 was included for further analyses.

treatment_protocol: The test compound used in this study was Finasteride (purity > 98%, CAS No.: 98319-26-7). Corn oil was used as control compound (vehicle) (product number: C8267-2.5L). Both compounds were purchased from Sigma-Aldrich. From GD7-21, dams were weighed daily and dosed by oral gavage with either vehicle control (corn oil) or Finasteride (10 mg/kg bw/day).

value: Anogenital region

value: Sprague Dawley

value: Fetus (GD21)

tag: gender

value: Female

value: Corn oil


title: MCF7_0_3: Untreated cells repeat 3

value: Breast adenocarcinoma cell line

value: Untreated


title: MCF7_6_1: 6 hours incubation repeat 1

value: 6 hours incubation with phenolaTi


title: Seabass_PostStress_T4_E6

value: juvenile

value: 9 months

value: post-stress

value: E

value: blood red cells


title: BMDM-STING S365A-DMSO

description: Sample 9

value: bone marrow derived macrophages

tag: strain

value: STING S365A

value: DMSO


title: MCF7_0_2: Untreated cells repeat 2


title: T cell-STING S365A-DMXAA

description: Sample 6

source_name: Splenic T cells

value: CD3/CD28 antibody activated T cell

tag: genotype

value: DMXAA


title: MCF7_0_1: Untreated cells repeat 1


title: T cell-STING KO-DMXAA

description: Sample 5

value: STING KO


title: Seabass_PostStress_T4_E2


title: Seabass_PreStress_T0_H16

value: 6 months

value: pre-stress

value: H


title: BMDM-WT-DMSO

description: Sample 7

value: WT


title: T cell-WT-DMXAA

description: Sample 4


title: MCF7_3_1: 3 hours incubation repeat 1

value: Breast adenocarcinoma cell line

value: 3 hours incubation with phenolaTi


title: M3-g_con-female

description: Gene expression data from CTR

value: Anogenital region

value: Sprague Dawley

value: Fetus (GD21)

value: Female

value: Corn oil


title: Treated_1

city: Minneapolis

first: Samira

last: Azarin

state: Minnesota

address: 421 Washington Ave SE

department: Chemical Engineering and Materials Science

institute: University of Minnesota Twin Cities

description:
Treated_1_S9
Replicate 1 of OVCAR-3 cells surviving 0.5 uM cisplatin treatment for 24 hours and recovered for 2 weeks

data_processing:
Trimming of low-quality ends and removal of adapter sequences was completed using Trimmomatic
Spliced Transcripts Alignment to a Reference (STAR) was used for mapping of reads to the human reference genome (GRCh38.91)
FPKM values were computed using Cufflinks and normalized to transcripts per million (TPM)
Genome_build: human reference genome (GRCh38.91)
Supplementary_files_format_and_content: Tab delimited file including transcripts per million (TPM) for all genes for each sample

growth_protocol: OVCAR-3 cells were cultured in RPMI 1640 media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific) at 37 C and 5% CO2

extract_protocol:
Total RNA was collected from cells using the RNeasy Mini Kit (Qiagen) and 1 ug total RNA was used to generate libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: *See "description" column of SAMPLES section

tag: cell line

value: Ovarian adenocarcinoma cell line


title: Seabass_PreStress_T0_R19

value: juvenile

value: R

value: blood red cells


title: Treated_2

description:
Treated_2_S10
Replicate 2 of OVCAR-3 cells surviving 0.5 uM cisplatin treatment for 24 hours and recovered for 2 weeks


title: BMDM-STING KO-DMSO

description: Sample 8

value: bone marrow derived macrophages

value: DMSO


title: T cell-STING S365A-DMSO

description: Sample 3

value: CD3/CD28 antibody activated T cell

value: STING S365A


title: Extracted_2

description:
Extract_2_S8
Replicate 2 of OVCAR-3 cells surviving immobilization for 3 days and recovered in standard culture conditions for 2 weeks


title: T cell-STING KO-DMSO

description: Sample 2

value: STING KO


title: Extracted_1

description:
Extract_1_S7
Replicate 1 of OVCAR-3 cells surviving immobilization for 3 days and recovered in standard culture conditions for 2 weeks


title: Seabass_PreStress_T0_L15

value: 6 months

value: pre-stress

value: L


title: M8-d_con-female

description: Gene expression data from CTR

value: Anogenital region


title: M5-d_con-female

description: Gene expression data from CTR

value: Sprague Dawley


title: Seabass_PostStress_T4_L6

value: 9 months

value: post-stress


title: M28-i_exposed-male

description: Gene expression data from CTR

value: Fetus (GD21)

value: Male

value: Finasteride


title: Day 3_2

description:
Day3_2_S6
Replicate 2 of OVCAR-3 cells immobilized in silica gels for 3 days

source_name: OVCAR-3_Day 3

value: Ovarian adenocarcinoma cell line

value: immobilized in silica gels for 3 days


title: M4-e_con-female

description: Gene expression data from CTR

value: Female

value: Corn oil


title: T cell-WT-DMSO

description: Sample 1

value: CD3/CD28 antibody activated T cell

value: WT

value: DMSO


title: M28-f_exposed-male

description: Gene expression data from CTR


title: M4-a_con-female

description: Gene expression data from CTR


title: Control siRNA rep2

city: Beijing

first: Yiman

last: Tang

address: Zhongguancun South street

country: China

institute: Peking University

data_processing:
After filtering, clean reads are mapped to reference using HISAT / Bowtie2 tool.
Gene expression were quantified and normalized using RSEM tool
KEGG pathway enrichment analysis and Gene Ontology analysis of DEGs were subsequently conducted
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: mesenchymal stem cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA sequencing of control and LAP2α deficient cells (each with 2 biological replicates) was performed using BGISEQ-500 sequencing system.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

value: adipose-derived stem cells

value: negative control


title: Day 3_1

description:
Day3_1_S5
Replicate 1 of OVCAR-3 cells immobilized in silica gels for 3 days


title: Day 1_2

description:
Day1_2_S4
Replicate 2 of OVCAR-3 cells immobilized in silica gels for 24 hr

source_name: OVCAR-3_Day 1

value: immobilized in silica gels for 24 hr


title: Control siRNA rep1


title: LAP2α siRNA rep2

value: LAP2-alpha knockdown


title: Day 1_1

description:
Day1_1_S3
Replicate 1 of OVCAR-3 cells immobilized in silica gels for 24 hr


title: Seabass_PreStress_T0_E14

value: juvenile

value: 6 months

value: pre-stress

value: E

value: blood red cells


title: Seabass_PreStress_T0_O13

value: O


title: LAP2α siRNA rep1


title: Seabass_PreStress_T0_J14

value: J


title: Control 1_2

description:
Control_2_S2
Replicate 2 of OVCAR-3 cells in standard culture conditions

value: Ovarian adenocarcinoma cell line

value: standard culture conditions


title: TW2.6-NOG14

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

description:
Sample 11
Experiment 1

data_processing:
Partek Flow  was used for base calling, trimming, filtering of quality <20 and adaptor sequences
Clean reads were aligned to the hg38 and mm10 genomes, respectively
for each sample, hg38.bam and mm10.bam files were subjected to XenofilteR (pmid 30286710)  to remove ambiguous reads
XenofilteR-processed hg38.bam and mm10.bam were subjected to Parktek Flow for gene count quantitation (Partek E/M GRCh38 and mm10, respectively)
abundance measurements (cpm) for each gene in each sample were used to construct the expression matrix (OSCC_CDX_hg38_cpm and OSCC_CDX_mm10_cpm)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Tab-delimited text files include cpm values for each sample.

organism:
Homo sapiens
Mus musculus

source_name: OSCC cell line TW2.6

extract_protocol:
The tumors of xenografts were removed and RNA was extracted using TRIZOL reagent. Illumina TruSeq RNA Sample Prep Kit (for samples 1 to 9) and TruSeq Rapid PE Cluster Kit V2 (for samples 10 and 11) were used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

value: NOG

value: xenograft tumor

tag: day of collection

tag: batch

tag: library preparation

value: TruSeq Rapid PE Cluster Kit V2 (stranded mRNA-seq)

tag: core lab

value: Yang-Ming U, TW


title: M27-h_exposed-male

description: Gene expression data from CTR

tag: tissue

value: Anogenital region

value: Sprague Dawley

value: Fetus (GD21)

value: Male

tag: treatment

value: Finasteride


title: S3-3

city: Cuernavaca

first: Mario

last: Zurita

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: UNAM

data_processing:
After filtering, clean reads are quantify for a quality analysis using FastQC v0.11.7 and MultiQC v1.5.dev0
De novo assembly were performed for each developmental stage using Trinity v2.8.4
For abundance quantification we used kallisto v0.44.4 with a bootstrap of 100 for each developmental stage replica
Supplementary_files_format_and_content: fasta format file include assembly for each developmetal stage
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each developmental stage replica

organism: Anastrepha ludens

source_name: Embryos

growth_protocol: Embryos growth at 25° C in water

extract_protocol:
Embryos were collected, fresh frozen on liquid nitrigen, and RNA was harvested using TRI Reagent reagent.
RNA libraries were prepared for sequencing using estándar Illumina protocols

tag: develop event

value: Gastrulation

tag: time


title: Seabass_PreStress_T0_A17

tag: developmental stage

value: juvenile

tag: age

value: 6 months

value: pre-stress

tag: family

value: A

tag: cell type


title: Seabass_PreStress_T0_I19

value: I

value: blood red cells


title: Seabass_PreStress_T0_K16

value: K


title: cultured cells, reprogrammed (rep2)

city: Milan

last: Barilani

address: Via F. Sforza 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

description:
StemMACS culture medium
hiPSC 2

data_processing:
QuantStudio™ 12K Flex Real-Time PCR Software, normalization to RNU44, RNU48 and U6 rRNA (undetermined targets in at least one sample were not further analyzed)
Matrix normalized worksheet contains data normalized to house-keeping small RNA as reported above, Fold Change worksheet reports MSC/hiPSC values

label: FAM

source_name: human induced pluripotent stem cells from human cord blood mesenchymal stem cells

label_protocol: Commercial kits and protocols from manufacturer (Thermo Fisher Scientific): TaqMan Advanced miRNA cDNA Synthesis Kit and TaqMan OpenArray Real-Time PCR Master Mix

growth_protocol: RNA extraction was performed on samples deriving from 80% confluent cell cultures

extract_protocol: RNA enriched in small RNA from cell samples lysed with QIAzol Lysis Reagent using the miRNeasy Mini Kit and the Rneasy MinElute Cleanup Kit, all from Qiagen

treatment_protocol: Steady state

tag: sample type

value: small RNA


title: Seabass_PreStress_T0_J12

data_processing:
Raw sequencing data were trimmed of low quality reads and adapter residues using Trim Galore!. The trimmed reads were then demultiplexed with STACKS.The option disable_rad_check was applied to avoid reads with bisulfite-modified restriction sites to be discarded. The demultiplexed reads were trimmed a second time on both 5’ and 3’ ends with the options --clip_R1 --clip_R2 and --three_prime_clip_R1 --three_prime_clip_R2 to remove introduced methylated cytosines during adapter ligation.
Using the bismark_genome_preparation function of the program bismark (Krieger and Andrews 2011, Bioinformatics, doi: 10.1093/bioinformatics/btr167), a bisulfite converted version of the European sea bass genome was prepared against which the demultiplexed and trimmed reads were mapped
The R package MethylKit was used to determine differential methylation between pre- and post-stress fish. Coverage was normalized across samples. Using Methylkit, differentially methylated CpG sites were determined between pre- and post-stress individuals using logistic regression (30X read depth; nominal q-value: 0.001; 15% methylation threshold)
Genome_build: GCA_000689215.1
Supplementary_files_format_and_content: Txt files providing chromosomes, posotions, strand, percentages cytosine and thymine for each methylated sites

value: J


title: Venous Angioblasts 77 days post transplant

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

data_processing:
Raw sequencing data (bcl files) were converted to fastq files with Illumina bcl2fastq, version 2.19.1
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Cells with a very small library size (< 1500) and a very high (4X Standard Deviation above Median) mitochondrial genome transcript ratio were removed.  Genes detected (UMI count > 0) in less than three cells were removed.
Normalization by scran R package
Clustering and Gene Expression Analysis by Seurat package
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat scaled gene expression values for filtered cells in CSV text format

source_name: Sorted tdRFP+ HPSC-derived human cells from mouse liver sample

growth_protocol: tdRFP+ hPSCs (HES2 background) were differentiated to CD34+ venous angioblasts via manipulation of VEGF, bFGF, and NOTCH pathways after mesoderm specification.

extract_protocol:
Freshly euthanized mice (<1 min post cervical dislocation) were aseptically prepared allowing 3-5ml of collagenase (0.2%w/v in 20% FCS/PBS) to be perfused in situ via a 26G1/2 needle cannulated portal vein.  Perfused, dissected intact liver was transferred to ice cold HANKS buffer (ThermoFisher, 14175-095) in a 10cm culture plate.  Isolated livers were minced (~2-3mm pieces) with a sterile razor blade, washed twice in hanks buffer by 1 minute settling, and further dissociated for 50 minutes rotating in a 10cm plate at 70RPM (37˚C, 5% CO2, 95% Air) in 24ml liver dissociation solution comprising (66%v/v HANKS buffer, 33%v/v RPMI1640, BSA (0.17%w/v, Proliant), collagenase type 1 (0.3125%w/v, Sigma), DNAse (1U/ml).  Following light trituration by 10ml serological pipette, homogenate was further dissociated for 10 minutes.  Total liver homogenate was filtered (100µm) and centrifuged at 50xg for 5 minutes to pellet hepatocytes and cell clumps.  Supernatant (non-parenchymal fraction) was pelleted (350xg, 5 minutes) and resuspended in ammonium chloride (STEMCELL Technologies, 07850) for 10 minutes on ice to lyse RBCs.  RBC-free NPC was washed three times (90% HANKS buffer, 10% RPMI1640, 0.05% BSA), filtered (40µm) and used for surface marker staining including: anti-CD31-FITC (BD Biosciences, Clone WM59, 15:100), rabbit-anti-LYVE1 (Abcam, Polyclonal, 1:1000), anti-CD32-PeCy7 (Biolegend, Clone FUN-2, 3:100), Donkey-anti-rabbit-APC (FAB fragment, Jackson, 0.5:100), FcR blocking human IgG (Miltenyi, 15:100) in RPMI1640 with 0.5% BSA and 1U/ml DNAse at 1x106 cells/ 100µl.  After antibody staining, cells were washed twice in RPMI1640 with 0.5% BSA and stained with DAPI.  FACS was performed to validate that the sample contained expected DAPI- tdRFP+ CD31+ CD32+ LYVE1+ hPSC-derived LSECs.  Once confirmed, DAPI- (live cells) tdRFP+ (hPSC-derived) cells were purified from the mouse liver cells (tdRFP-).  Sorted cells were washed one time to resupended in PBS for immediate scRNA-seq processing.
10X Genomics Single Cell 3' v2 Reagent Kit

treatment_protocol: A 3 day old NSG pup was irradiated (100cGy) and on day 4 was injected intrahepatically with 1 million day 8 CD34+ venous angioblasts.  77-days later the adult NSG mouse was sacrificed to facilite recovery of hPSC(tdRFP+) cells

tag: host strain

value: NSG mouse (NOD scid gamma mouse)

tag: injected cell type

value: DAPI-, tdRFP+, RBC-lysed Non-Parenchymal Liver Fraction


title: Control 1_1

description:
Control_1_S1
Replicate 1 of OVCAR-3 cells in standard culture conditions

tag: cell line

value: Ovarian adenocarcinoma cell line

value: standard culture conditions


title: cultured cells, reprogrammed (rep1)

description:
StemMACS culture medium
hiPSC 1


title: M22-n_exposed-male

city: Rennes

last: Chalmel

address: 9 avenue du Pr. Léon Bernard

institute: Inserm U1085-Irset

description: Gene expression data from CTR

value: Anogenital region

tag: strain

value: Sprague Dawley

value: Fetus (GD21)

tag: gender


title: M22-i_exposed-male

description: Gene expression data from CTR

value: Male

value: Finasteride


title: cultured cells, unreprogrammed (rep2)

description:
alphaMEM-glutamax 20% FBS culture medium
MSC 2

source_name: human cord blood mesenchymal stem cells


title: S2-3

value: Cellularization

value: 9 to 18 h


title: Seabass_PreStress_T0_B19

extract_protocol:
Blood from the caudal vessel was collected. Plasma and red blood celles were separated by centrifugation at 2,000g for 10 min. Careful separation of the plasma and RBCs was performed using 200 µl pipettes. RBC extracts were heparinized (heparin sodium; Sigma-Aldrich), transferred in microtubes and conserved at -20°C in 1 ml of RNA later. Genomic DNA was extracted using the Macherey Nagel Nucleo Spin Tissue DNA kit and quantified using a Qubit fluorometer (Qubit dsDNA BR Assay Kit, Q32853, Invitrogen).
EpiGBS approach adapted from van Gurp et al. (2016, Nature Methods doi: 10.1038/nmeth.3763), with main addition of a second restriction enzyme in the protocol. The couple of enzymes retained: MspI/ SfbI. A single libray was prepared: 200 ng of DNA of each sample were digested in a 40 µl reaction, using 0.25 µl MspI (NEB, 20,000 U/ml R0106S), 0.25 µl SbfI-HiFi (NEB 20,000 U/ml R3642L) and 4 µl of 10X cutsmart buffer. The reaction was run overnight at 37°C. Unique forward and reverse adapter combinations allow multiplexing samples in the library. We added forward and reverse adapters in unique combinations (1 µl of adapter, 2.5 µM), 0.5 µl T4 Ligase (NEB, 400,000 U/ml m0202L), 6 µl of 10X T4 ligase buffer and 11.5µl water were added directly to the digested DNA. Adapters were ligated for 3 h at 23°C followed by 10 min of enzyme inactivation at 65°C. After ligation, all samples were pooled and one third of the total volume was used in the following step. The mixture volume was reduced using a Qiaquick PCR purification kit (28104 Qiagen). The resulting product was cleaned a second time to ensure the removal of small fragments and adapter remnants using CleanPCR paramagnetic beads (Proteigene, CPCR-0050) with a ratio of 0.8X [sample : beads]. a nick translation was performed to repair the nick of the DNA at the restriction site and to fully methylate the hemi-methylated adapters. To do so, 19.25 µl of the concentrated and purified ligation pool were used in a 25 µl reaction, including 0.75 µl DNA Polymerase I (E. coli, 10,000 U/ml M0209S), 2.5 µl of 10 mM 5-Methylcytosine dNTP mix (Zymo Research, D1030), and incubated at 15 °C for one hour. The library was then treated with sodium bisulfite using the EZ DNA Methylation Gold Kit (D5005, Zymo Research) following manufacturer instructions to convert unmethylated cytosines to uracil, paying attention to the optimal DNA amount per reaction. After bisulfite conversion, 14 cycles of PCR (95°C for 1 min, 91°C for 10s, 65°C for 15s, 72°C for 10s and a final elongation step at 72°C for 5 min) were performed, followed by a paramagnetic bead clean up with a 0.8X ratio. The library quality was verified on an Agilent 5300 Fragment Analyzer (Santa Clara, USA). It was sequenced (paired-end, 150 bp) on one lane of a SP flow cell on an ILLUMINA NovaSeq 6000.

value: juvenile

value: 6 months

value: pre-stress

value: B


title: Seabass_PreStress_T0_O10

value: O

value: blood red cells


title: Seabass_PreStress_T0_E8

value: E


title: Seabass_PreStress_T0_L7

value: L


title: cultured cells, reprogrammed (rep4)

description: StemMACS culture medium

data_processing:
QuantStudio™ 12K Flex Real-Time PCR Software, normalization to Endogenous Control = [GAPDH_Hs99999905_m1  CDKN1A_Hs00355782_m1  GUSB_Hs99999908_m1  B2M_Hs99999907_m1  IPO8_Hs00183533_m1  POLR2A_Hs00172187_m1  G6PD_Hs00166169_m1  PPIA_Hs99999904_m1  TFRC_Hs99999911_m1  ACTB_Hs99999903_m1  CDKN1B_Hs00153277_m1  UBC_Hs00824723_m1  RPLP0_Hs99999902_m1  CASC3_Hs00201226_m1  UBE2D2_Hs00366152_m1  TBP_Hs99999910_m1  HPRT1_Hs99999909_m1  HMBS_Hs00609297_m1  PGK1_Hs99999906_m1  YWHAZ_Hs00237047_m1  HPRT1_Hs01003267_m1] (undetermined targets in at least one sample were not further analyzed)
Matrix normalized worksheet contains data normalized to house-keeping genes as reported above, Fold Change worksheet 1 reports (average of MSC 1 and MSC 2)/(average of hiPSC 1 and hiPSC 2), Fold Change worksheet 2 reports (average of hiPSC 3 and hiPSC 4)/(average of hiPSC 1 and hiPSC 2)

source_name: human induced pluripotent stem cells derived from fibroblasts

label_protocol: Commercial kits and protocols from manufacturer (Thermo Fisher Scientific): SuperScript IV VILO Master Mix for cDNA synthesis and TaqMan OpenArray Real-Time PCR Master Mix

extract_protocol: Total RNA was extracted by standard Trizol protocol

value: hiPSC


title: cultured cells, reprogrammed (rep3)

description: StemMACS culture medium


title: cultured cells, unreprogrammed (rep1)

description:
alphaMEM-glutamax 20% FBS culture medium
MSC 1

value: small RNA


title: M4-j_con-male

description: Gene expression data from CTR

value: Anogenital region

value: Corn oil


title: M6-n_con-male

description: Gene expression data from CTR

value: Sprague Dawley

value: Fetus (GD21)


title: S3-2

value: Gastrulation


title: S2-1

value: Cellularization


title: S3-1


title: OC3-NOG08

description:
Sample 10
Experiment 1

source_name: OSCC cell line OC3

tag: mouse strain

value: NOG

value: xenograft tumor

tag: day of collection

tag: batch

value: TruSeq Rapid PE Cluster Kit V2 (stranded mRNA-seq)

value: Yang-Ming U, TW


title: M5-h_con-male

description: Gene expression data from CTR

tag: tissue

value: Male


title: Seabass_PreStress_T0_T5

value: juvenile

value: 6 months

tag: treatment

value: pre-stress

value: T


title: M8-h_con-male

description: Gene expression data from CTR


title: S2-2

tag: develop event

value: 9 to 18 h


title: 6_day_post_amputation_limb

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

data_processing:
demultiplexed with the mkfastq option of Cell Ranger 2.1.1.
Assignment of barcodes to cells and transcript quantification were performed using Cell Ranger 3.0.2
Genome_build: Custom reference from   PMID  30262634  appended to this submission

organism: Ambystoma mexicanum

source_name: 6 day post amputation limb

extract_protocol:
Single cells
Chromium Single Cell RNAseq kit (v2 Chemistry)

value: adult axolotls

tag: Sex

value: female

tag: tissue/cell type

value: amputated axolotl limbs at 6 DPA


title: 1_day_post_amputation_limb

source_name: 1 day post amputation limb

tag: age

value: amputated axolotl limbs at 1 DPA


title: Seabass_PreStress_T0_H18

city: MONTPELLIER

last: GUINAND

address: Place E. Bataillon - Campus Triolet

institute: Université de Montpellier

tag: developmental stage

tag: family

value: H

value: blood red cells


title: S1-2

value: Syncytium

tag: time

value: 0 to 9 h


title: cultured cells, reprogrammed (rep2)

description: StemMACS culture medium

source_name: human induced pluripotent stem cells derived from cord blood mesenchymal stem cells

tag: cell type

value: hiPSC


title: cultured cells, reprogrammed (rep1)

description: StemMACS culture medium


title: peripheral_leukocytes_macrophages

source_name: peripheral leukocytes and macrophages

value: peripheral leukocytes with presumptive macrophages from the intraperitoneal cavity


title: S1-1


title: Seabass_PreStress_T0_P7

value: P


title: peripheral_leukocytes

source_name: peripheral leukocytes

value: peripheral leukocytes


title: Seabass_PreStress_T0_O3

value: juvenile

value: O


title: cultured cells, gold standard pluripotent stem cells

description: StemMACS culture medium

source_name: human embryonic stem cells

value: hESC


title: cultured cells, unreprogrammed (rep1)

description: alphaMEM-glutamax 20% FBS culture medium

value: MSC


title: Seabass_PreStress_T0_B5

value: 6 months

value: pre-stress

value: B


title: cultured cells, unreprogrammed (rep2)


title: S1-3


title: 2CBS_HiC_rep2

status: Public on Jul 06 2020

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
For PLAC-seq, paired-end reads were first mapped to mm10 reference genome. We modified the original WAPS mapping procedure by replacing the bowtie2 alignment tool with bwa-mem and integrated MAPS feather post-filtering pipeline to resolve the chimeric reads
Hi-C reads were aligned to mm10 using bwa-mem for each read separately and then paired. For chimeric reads, only 5′ end-mapped locations were kept. Duplicated read pairs mapped to the same location were removed to leave only one unique read pair. The output bam files were transformed into juicer file format for visualization in Juicebox. Contact matrices were normalized using the Knight–Ruiz matrix balancing method
Genome_build: mm10
Supplementary_files_format_and_content: juicer hic files that can be visualized in Juicebox and cis-contacts of chr3 of the PLAC-seq data.

source_name: embryonic stem cells

growth_protocol: Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.

extract_protocol: PLAC-seq experiments were performed in biological replicates using MboI, following the protocol described by Fang, R., Yu, M., et al., Cell research 2016(PMID: 27886167). Hi-C experiments were performed in biological replicates using MboI, following the protocol described by Rao et al., Cell 2014 (PMID: 25497547)

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

tag: chip antibody

tag: genotype


title: 2CBS_HiC_rep1

tag: cell line

tag: strain


title: untreated_rep1

city: Vestec

first: Peter

last: Draber

state: Czech Republic

address: Průmyslová 595

department: BIOCEV

country: Czech Republic

institute: First Faculty of Medicine, Charles University

data_processing:
RNA was quantified at the transcript-level using Salmon (0.13.1) (Patro et al, 2017). First, a reference mouse transcriptome from Gencode M21(GRCm38.p6) was created by combining the sequence of protein-coding genes and long non-coding RNAs. Then, the transcriptome was indexed using Salmon index with parameter `–gencode`. Salmon quant was then run for each sample using parameters `–gcBias`, `–validateMappings`, and `–allowDovetail`.
Transcript-level estimates from Salmon were summarized into gene level estimates using tximport (Soneson et al, 2015); all genes with at least 5 reads in at least 1 sample were retained for downstream analysis; with these parameters 15,935 genes were obtained. Differential gene expression analysis was performed using DESeq2 (Love et al, 2014), using independentFiltering and using the Benjamini-Hochberg procedure to adjust p-values. Genes with adjusted p-value less than 0.01 are reported as statistically significant.

source_name: ST2 untreated

growth_protocol: Cells were cultivated in DMEM supplemented with 10% fetal calf serum (FCS) (Gibco), 100 U/ml penicillin (BB Pharma), 100 μg/ml streptomycin (Sigma Aldrich), 40 μg/ml gentamicin (Sandoz).

extract_protocol:
Total RNA was extracted from the cells using RNeasy Mini Kit (Qiagen) with on column DNAse treatment exactly according the manufacturers protocol. The quality and quantity of isolated RNA was evaluated using Nanodrop and TapeStation 2200 (Agilent Technologies). The ensuing RNA sequencing analysis was based on three independent experiments.
For each sample, 1 ug of total RNA (RIN >7.0, rRNA ratio (28S:18S rRNA) >1.0) was sent to Macrogen Inc. for library preparation and sequencing. Briefly, first TruSeq RNA stranded library was generated and then sequencing was performed on the Illumina NovaSeq6000 with 151bp paired-ends configuration, with about 30M reads per sample.

treatment_protocol: For the RNA sequencing experiment, ST2 cells were grown in 6 well plates, washed and stimulated with IL-17 (500 ng/ml) in the presence or absence of MRT67307 (2 μM) in DMEM supplemented with 0.5% FCS.


title: treatment_inhibitor_mrt_rep1

source_name: ST2 treatment_inhibitor_mrt


title: untreated_rep3


title: treatment_mrt_stimulation_il17_rep2

source_name: ST2 treatment_mrt_stimulation_il17


title: treatment_inhibitor_mrt_rep3


title: treatment_inhibitor_mrt_rep2


title: stimulation_il17_rep1

source_name: ST2 stimulation_il17


title: stimulation_il17_rep2


title: treatment_mrt_stimulation_il17_rep3


title: stimulation_il17_rep3


title: HY29

city: Orange

first: Patricia

middle: C

last: Lopes

address: 450 N Center St

department: Biological Sciences

institute: Chapman University

description: readcounts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data filtering: reads containing adapters, reads containing N>0.1% and low quality reads were filtered out
Mapping was done using the STAR software package
Normalized abundance counts were generated using the DESeq2 R package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw (not normalized) readcount values for each sample

source_name: Hypothalamus

extract_protocol:
Brains were removed and flash frozen on dry ice; brain regions were later punched out, placed in Trizol and homogeneized; Total RNA was isolated from the aqueous layer obtained post chloroform extraction, using the Direct-zol RNA Miniprep Plus kit (Zymo, catalogue # R2071) according to manufacturer’s instructions, with the additional DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

value: male

tag: gregariousness

value: high


title: HY26

description: readcounts.txt

value: female


title: HY30

description: readcounts.txt


title: HY28

description: readcounts.txt


title: untreated_rep2


title: treatment_mrt_stimulation_il17_rep1


title: HY27

description: readcounts.txt

value: low


title: 4CBS_HiC_rep2


title: 4CBS_HiC_rep1


title: HY20

description: readcounts.txt


title: HY23

description: readcounts.txt


title: HY19

description: readcounts.txt


title: HY24

description: readcounts.txt


title: HY25

description: readcounts.txt


title: HY16

description: readcounts.txt


title: HY22

description: readcounts.txt


title: HY21

description: readcounts.txt


title: HY15

description: readcounts.txt


title: HY10

description: readcounts.txt


title: HY12

description: readcounts.txt


title: HY2

description: readcounts.txt


title: HY7

description: readcounts.txt


title: Hi26

description: readcounts.txt

source_name: Hippocampus


title: Hi27

description: readcounts.txt


title: HY8

description: readcounts.txt


title: Hi28

description: readcounts.txt


title: HY5

description: readcounts.txt


title: HY11

description: readcounts.txt


title: Hi29

description: readcounts.txt


title: Hi30

description: readcounts.txt


title: HY6

description: readcounts.txt


title: HY13

description: readcounts.txt


title: Hi25

description: readcounts.txt


title: Hi24

description: readcounts.txt


title: HY1

description: readcounts.txt


title: HY4

description: readcounts.txt


title: HY9

description: readcounts.txt


title: HY3

description: readcounts.txt


title: HY17

description: readcounts.txt


title: Hi21

description: readcounts.txt


title: Hi22

description: readcounts.txt


title: Hi23

description: readcounts.txt


title: Hi18

description: readcounts.txt


title: Hi17

description: readcounts.txt


title: Hi16

description: readcounts.txt


title: Hi19

description: readcounts.txt


title: Hi15

description: readcounts.txt


title: Hi12

description: readcounts.txt


title: Hi20

description: readcounts.txt


title: CX30

description: readcounts.txt


title: Hi10

description: readcounts.txt


title: CX27

description: readcounts.txt


title: Hi8

description: readcounts.txt


title: Hi7

description: readcounts.txt


title: Hi11

description: readcounts.txt


title: Hi1

description: readcounts.txt


title: CX29

description: readcounts.txt


title: Hi5

description: readcounts.txt


title: Hi9

description: readcounts.txt


title: Hi6

description: readcounts.txt


title: Hi13

description: readcounts.txt


title: Hi2

description: readcounts.txt


title: CX28

description: readcounts.txt


title: Hi3

description: readcounts.txt


title: Hi4

description: readcounts.txt


title: CX22

description: readcounts.txt


title: CX21

description: readcounts.txt


title: CX20

description: readcounts.txt


title: CX25

description: readcounts.txt


title: CX23

description: readcounts.txt


title: CX18

description: readcounts.txt


title: CX17

description: readcounts.txt


title: CX19

description: readcounts.txt


title: CX16

description: readcounts.txt


title: CX24

description: readcounts.txt


title: CX15

description: readcounts.txt


title: CX12

description: readcounts.txt


title: CX26

description: readcounts.txt


title: CX11

description: readcounts.txt


title: CX9

description: readcounts.txt


title: CX10

description: readcounts.txt


title: CX7

description: readcounts.txt


title: CX8

description: readcounts.txt


title: CX2

description: readcounts.txt


title: CX3

description: readcounts.txt


title: CX6

description: readcounts.txt


title: CX1

description: readcounts.txt


title: CX5

description: readcounts.txt


title: CX4

description: readcounts.txt


title: INY-4_day_30

city: Los Angeles

first: Theodore

middle: S.

last: Nowicki

address: 2-159 Factor Building, 10833 Le Conte Avenue

department: Jonsson Comprehensive Cancer Center

institute: University of California Los Angeles

data_processing:
Complete processing and analysis pipeline can be found at https://github.com/NuttyLogic/Epigenetic-suppression-of-transgenic-TCR-expression-in-ACT
Illumina BCL files files demultiplexed using bcl2fastq2v2.2.0
adapters were trimmed from demultiplexed fastq files using CutAdaptV2.4 using the following parameters; -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --pair-filter=any -m 40
Trimmed fastq files aligned to human reference hg38 using BSBoltV0.1.2 using the following parameters; -BT2-local -BT2-score-min L,160,0 -discord
Duplicated Marked using SamtoolsV1.9 using the following parameters; markdup
Methylation calls made using BSBoltV0.1.2 using the following parameters; -min-qual 25 -min 5
Genome_build: combined hg38 and MSCV

source_name: PBMC

extract_protocol:
AllPrep DNA/RNA isolation kit according to the manufacturer’s instructions (Qiagen)
Genomic DNA isolated from patient PBMC samples was bisulfite converted using the EZ DNA Methylation- Gold Kit (Zymo Research) according to the manufacturer’s instructions.  Libraries were prepared using the NEBNext Ultra II DNA kit (NEB) according to manufacturer instructions with few modifications. Briefly, sonicated DNA was subjected to EndPrep (End Repair and A-tailing), followed by Adapter Ligation using 2.5μL of Illumina TruSeq pre-methylated Adapters (Illumina). Samples were purified using 0.85x NEB Purification Beads and eluted in 15μL of 10mM Tris-HCl, pH 8. Samples were mixed in 16-sample pools and column purified using a DCC-5 (Zymo Research). Elution was performed with 10μL of 60°C 10mM Tris-HCl, pH 8. Each sample pool was subject to hybrid capture with custom biotinylated RNA probes designed to tile the MSCV vector (MyBaits Arbor Bioscience - Human_6K and Human patch2) according to the manufacturer's protocol. Captured DNA was eluted by heating in 20μL of 10mM Tris-HCl  pH 8+0.05% Tween-20. The eluted DNA was then subject to bisulfite conversion using the DNA Methylation  Lightning kit (Zymo Research). Converted DNA was then amplified using xGen Library Amplification Primer  Mix (IDT) and Kapa Uracil+ Ready Mix.

value: M

tag: ethnicity

value: Hispanic

tag: type of cancer

value: Melanoma

tag: active disease sites

value: Lung, lymph nodes, adrenal gland, liver, trachea, brain

tag: Stage

value: IV

tag: evidence of tumor response

value: No

tag: response at end of study

value: PD

tag: progression free survival

tag: overall survival

tag: infusion product

value: no


title: INY-4_day_0

tag: Sex

tag: age

value: yes


title: INY-4_day_70


title: INY-3_day_30

value: F

value: Caucasian

value: Synovial Sarcoma

value: Right popliteal fossa; Lung

value: Yes by PET/CT


title: INY-3_day_0


title: CX13

description: readcounts.txt

value: male


title: F-9_day_70

value: Skin, lymph nodes

tag: days from infusion


title: INY-2_day_70

value: lymph nodes, Liver


title: INY-2_day_30

value: M


title: INY-2_day_0


title: F-9_day_0


title: F-9_day_30


title: F-8_day_70

value: SC, Bone

value: Yes by CT

value: SD


title: INY-3_day_70

value: IV


title: F-8_day_30

value: Melanoma


title: F-7_day_70


title: F-7_day_30


title: F-8_day_0


title: F-7_day_0


title: F-6_day_70

value: Lung, lymph nodes

value: Yes by PE


title: F-3_day_70

value: Lung, Liver

value: no


title: F-6_day_30

value: Caucasian


title: ZC-57

city: Hangzhou

first: Shu

last: Zheng

state: Zhejiang

address: 88 Jiefang Road,

institute: Zhejiang University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: colorectal tumor tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Written informed consent from each patient was obtained. Freshly frozen tissues of primary colorectal tumors in 19 patients with from resectable CRLM (2 patients with T2N0M1 and 17 patients with T3/4N0M0) were obtained from hospital. All tissue samples were collected, immediately snap-frozen in liquid nitrogen, and stored at -80℃ until RNA extraction. Total RNA isolation was performed with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. The RNA concentration was determinate using the NanoDrop-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: Colon

tag: gender

value: Male

tag: disease

value: T3/4N0M0 tissue


title: ZC-27

value: Female

value: T2N0M1 tissue


title: F-3_day_30

value: Yes by PET/CT


title: ZC-49

value: Rectum


title: ZC-41


title: ZC-44


title: ZC-65


title: ZC-63


title: ZC-04


title: ZC-33


title: ZC-21


title: F-6_day_0

value: M

value: yes


title: M3H4

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
After demultiplexing, quality of data was examined using FastQC (v 0.11.7). Illumina and MATQ-seq adapters were removed using cutadapt (v 1.9). Trimmed reads were mapped to salmonella enterica SL1344 genome (NCBI RefSeq accession numbers: NC_016810.1, NC_017718.1, NC_017719.1 and NC_017720.1) using STAR aligner (v 2.5.4b) with default settings. Read counts of each gene was determined using the featurecount program. Afterwards, data was normalized using DESeq2 package and the normalized data was used for PCA analysis. The normalized libraries were subjected to a PCA. The differentially expressed genes between different culture conditions were analyzed using DEseq2.
Genome_build: NC_016810.1, NC_017718.1, NC_017719.1 and NC_017720.1
Supplementary_files_format_and_content: csv file:Read count table for each gene was determined using the HTSeq program

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: bacteria

growth_protocol: Salmonella Typhimurium SL1344 strain (JVS 1574) and Pseudomonas aeruginosa strain PAO1 were grown in 5 ml Lennox broth in a 37°C at 220 rpm, overnight (O/N) and diluted 1:1,000 in a new 250 mL flask, containing 10 mL of LB. The cells were grown at 37°C and 220 rpm until an OD600 of 0.3 was reached indicating mid exponential phase. Stationary phase culture (SPI1) was grown in Lennox broth over night to an OD600 of 2.0.

extract_protocol:
Each well of the 48-well plate was pre-filled with 2.6 µL lysis buffer containing 0.26 µL Lysis buffer (Takara), 0.03 µL RNase Inhibitor (100U/uL, Takara), 0.25 µL DPBS (Gibco) and 0.5 uL Lysozyme (5 Units, Epicentre). The lysis buffer was always prepared freshly and ready plates were kept on ice.
MATQ-seq protocol was performed following the initial report (Sheng, Cao et al. 2017). In brief, RNA was reverse transcribed using Superscript III (Life Technologies). Residual primers were digested with T4 DNA Polymerase (New England Biolabs). In a further step RNase H and RNase If (New England Biolabs) were used for enzymatic RNA digestion. Tdt Terminal Transferase (New England Biolabs) and dCTP were provided for the tailing step. Subsequently second strand was synthesized using GAT21 6N3G MALBAC primer and deepvent exo- DNA polymerase (New England Biolabs). Amplification was performed with a PCR mix including GAT27 PCR primer, and a 24 cycle PCR program. Amplified cDNA was purified using 40 µL of Ampure XP beads (Beckman Coulter) with a 1:1 v/v beads: amplicons. cDNA concentration was measured using Qubit HS Assay (Life Technologies) and fragment size distribution was observed using a high sensitivity DNA kit Bioanalyzer (Agilent). Libraries were prepared using Nextera XT (Illumina) with the minor modifications as described in (Patel, Tirosh et al. 2014). Briefly, an input of 1 ng of cDNA was tagmented using one-quarter of the recommended volumes and a longer fragmentation time (10 min) and resuspended in 15 µL EB (Qiagen).

treatment_protocol: NaCl shock and Anaerobic shock conditions were generated as described in (Kroger, Colgan et al. 2013). For NaCl shock generation, NaCl was added to MEP-bacteria cultures to a final concentration of 0.3 M, followed by 10 minutes continued incubation at 37°C shaking. For anaerobic shock generation, 5 ml of MEP-bacteria cultures were filled in a test-tube, covered with 2 ml of mineral oil and subsequently incubated at 37°C for 30 min without agitation. 2 mL of culture (stationary or stimulated cells) were pelleted, washed twice with 1 mL of Dulbecco's phosphate-buffered saline (DPBS, Gibco) and subjected to a mild-fixation to prevent advert transcriptome changes by replacing DPBS with 1 mL of a 1:1 v/v RNAlater (Thermo Fischer) – DPBS solution.

tag: condition

value: Anaerobic Shock

tag: number of cells


title: M3H6


title: ZC-43


title: ZC-66


title: ZC-17


title: F-3_day_0

tag: ethnicity

value: SD


title: ZC-26


title: M3G6


title: ZC-07


title: ZC-11


title: ZC-64


title: F-1_day_70

tag: type of cancer

value: Melanoma

value: Lung, Stomach, Liver, Pancreas, Peritoneum, Soft tissues

value: PD


title: M3H5


title: ZC-51


title: F-1_day_30

tag: active disease sites


title: M3G5


title: M3G4


title: F-13_day_70

value: Lung, Abdomen, SC

tag: Stage

value: MIIIb


title: F-1_day_0

value: Caucasian

tag: evidence of tumor response


title: F-13_day_30

tag: response at end of study

value: no


title: F-13_day_0

tag: progression free survival


title: ZC-34

value: Colon


title: M3F6


title: F-12_day_30

value: Lung, lymph nodes

value: MIVb

tag: overall survival


title: F-12_day_70

tag: infusion product


title: M3F5


title: F-12_day_0

tag: Sex


title: M3E7


title: M3E5


title: M3E6


title: ESO-6_day_30

tag: age

value: Osteosarcoma

value: Lung

value: IV


title: ESO-5_day_70

value: F

value: Synovial Sarcoma

value: Right popliteal fossa; Lung

value: Yes by PET/CT

value: PR


title: ESO-6_day_0

value: M

value: yes


title: M3D5

value: Anaerobic Shock


title: M3E4


title: ESO-5_day_30


title: M3C6


title: M3C7


title: M3C5


title: ESO-5_day_0


title: M3C4


title: M3F4


title: ESO-6_day_70

value: PD


title: M3B5


title: M3B4


title: ESO-4_day_0

value: Caucasian

value: Left Infraclavicular Mass; Left Pectoralis Mass

value: III


title: M3A5


title: ESO-3_day_0

value: Right Lung; Multiple pulmonary Nodules


title: ESO-4_day_30

value: no


title: M3A3

value: NaCl Shock


title: ESO-3_day_30


title: M3A7


title: M3A6


title: ESO-1_day_70

value: Hispanic

value: Liposarcoma

value: Right Renal Fossa; Liver left Lobe; Hepatic Segment; Peritoneal, Perihepatic Nodule

value: No


title: M3D4


title: ESO-1_day_30

value: IV


title: ESO-1_day_0


title: M3A2


title: 17_SC

organism: Pseudomonas aeruginosa PAO1


title: 18_SC


title: ESO-4_day_70

value: Synovial Sarcoma

value: Yes by PET/CT


title: M3A1


title: M2H11


title: 16_SC


title: M2H10


title: ESO-3_day_70

value: F

value: PR


title: M2H9


title: M2H8


title: M2H5


title: M2H7


title: 12_SC

value: Anaerobic Shock


title: M2H4


title: 10_SC


title: M2H3


title: 6_SC


title: 7_SC


title: 8_SC


title: M2G11


title: M2G10


title: 5_10cells


title: M2G7


title: 3_10cells


title: 15_SC


title: M2G6


title: M2G5


title: 14_SC


title: M2G4


title: 1_10cells


title: 13_SC


title: Plasmid

city: Aarhus

first: Jacob

middle: GIehm

last: Mikkelsen

address: Høegh-Guldbergs Gade 10

department: Biomedicin

country: Denmark

institute: Aarhus University

data_processing:
Library strategy: Targeted deep sequencing of DNA amplicons
MAGeCK v0.5.8 -count, with default parameters
MAGeCK v0.5.8 -test, with default parameters
Genome_build: Mapped to the genome-wide library GeCKO v2 (A+B) from Feng Zhang. (Addgene#1000000049)

organism: unidentified plasmid

source_name: Plasmid DNA

growth_protocol: Cells were kept at 0.3-1x106 cells/mL, cultured in RPMI 10% FBS and 1% P/S

extract_protocol:
Cells were lysed and gDNA was extracted by precipitation  of proteins by NaCl (6M) and subsequent precipitation  of gDNA with isopropanol
A nested PCR approach was used to generate PCR amplicons with sufficient coverage of the lirary. PCR amplicons were processed by end repair, ligated to BGISEQ sequencer compatible adapters, generating DNB-based sequencing libraries without PCR amplification

treatment_protocol: Mock; medium containing human serum, RTX-SEC; medium containing 10 µg/mL rituximab and human serum (14 days), and RTX-REC; medium with 10 µg/mL rituximab increased to 25 µg/mL at day 16 and with repeated re-administration of human serum (21 days)

tag: cell line

tag: cell type


title: 11_SC


title: M2G3


title: M2G2

value: Late Stationary Phase


title: M2F11


title: 9_SC


title: M2G9


title: M2F10


title: M2G8


title: M2F8


title: 4_10cells


title: CCNB1_KD_2

city: Stockholm

first: Erik

last: Sonnhammer

address: Tomtebodavagen 23A

department: Biochemistry & Biophysics

country: Sweden

institute: SciLifeLab/ Stockholm University

data_processing: Data normalized by first averaging technical replicates and then by dividing by spike-in gene. Fold Change calculated via deltaDeltaCt R package using positive and negative experimental controls

source_name: human squamous carcinoma cell line

label_protocol: For FAM, the filter 465/510 gets excitation absorbance ~0.38 and emission intensity ~0.31

growth_protocol: A diverse set of genes is assembled from different pathways and complexes, each interacting to some degree with the oncogene MYC. Each readout gene is perturbed in the human squamous carcinoma cell line A431 via transfection with short interfering RNAs (siRNAs) using the Ambion RNA-Seq Library Construction Kit. In order to minimizing siRNA off target effects, three to four siRNA are used per RNA interference (RNAi), which are then averaged to highlight the effects of the targeted siRNA perturbation. Cells were collected at 72 hours after siRNA knockdown and washed of Phosphate-Buffer Solution (PBS), and lysed using CelluLyser. Cell counts were calculated using the resazurin fluorescence assay. Since no endogenous gene can be assumed to be free of MYC regulation, which is thought to be a universal transcriptional amplifier, a proprietary RNA transcript was added to each sample to act as a reference gene for the quantitative polymerase chain reaction (qPCR) analysis, spiked-in in proportion to the cell count before RNA isolation. Negative controls are included, which siRNA does not map to human genes, as well as an untreated control absent of any siRNA. The cDNA was prepared from the RNA and preamplified in preparation for the high-throughput qPCR screening. Finally, the transcript profiles with respect to the 40 target genes were determined using TaqMan assays on Fluidigm's Biomark platform using 96x96 Dynamic Array integrated fluidic circuits. Raw qPCR output was then processed as a function of the samples’ initial quantity returning a measure of fold change via the experimental controls. Three experimental replicates were made per targeted perturbation and five outlying replicates were discarded due to clear machine read error, thus the dataset is composed of 40 genes (N) and 115 samples. Including all controls, a total of 18432 qPCRs were performed on 192 samples. Two technical replicates were performed to ensure minimal machine error. They generated very similar values up to 25 qPCR cycles.

treatment_protocol: Wells prepared with transfection reagents and RNAi. Transfection proceeded by adding cells to wells and waiting 4 hours. During this time the RNAi sequences go into the cells, and probably start working. Media changed; at this point you should have constant perturbation until RNAi effect diminishes. RNAi diminished, perturbation ends, happening several days after transfection.

tag: sample type

value: second targeted knockdown of CCNB1 via ASX04ZMX


title: 2_10cells


title: CCNB1_KD_1

value: first targeted knockdown of CCNB1 via ASX04ZMX


title: BYSL_MYB_doubleKD

value: BYSL_MYB double knock down


title: M2F7


title: M2F4


title: BYSL_MAX_doubleKD

value: BYSL_MAX double knock down


title: M2F6


title: BYSL_KD_3

value: third targeted knockdown of BYSL via ASX055LN


title: BYSL_KD_2

value: second targeted knockdown of BYSL via ASX055LN


title: M2E10


title: BYSL_KD_1

value: first targeted knockdown of BYSL via ASX055LN


title: BRD4_KD_2

value: second targeted knockdown of BRD4 via ASX051I6


title: BRD4_KD_1

value: first targeted knockdown of BRD4 via ASX051I6


title: M2E8

value: NaCl Shock


title: M2E11


title: M2E9


title: BRD4_KD_3

value: third targeted knockdown of BRD4 via ASX051I6


title: M2E7


title: M2F9


title: BRCA1_STAT5B_doubleKD

value: BRCA1_STAT5B double knock down


title: BRCA1_KD_3

value: third targeted knockdown of BRCA1 via ASX053MG


title: M2E6


title: PT1_ESR1_E2_ChIP_DNA

city: Chicago

first: Serdar

middle: E

last: Bulun

state: Illinois

address: 303 E. Superior, Lurie Research Building

department: Obstetrics and Gynecology

institute: Northwestern University

description: ESR1 ChIP DNA

data_processing:
Libraries were sequenced under 75bp single-end sequencing format. Adapters were trimmed using cutadapt. Sequences were aligned to the hg38 reference genome using Bowtie2. Peak calling and motif analysis were performed using Homer under default settings.
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are peak files from ESR1 ChIP-Seq sample.

source_name: Isolated stromal cells post-hysterectomy

growth_protocol: DMEM/F12 w/ 10% FBS and 1x antibiotic/antimycotic

extract_protocol:
7.5e8 cells (patient number = 1) were used for ChIP-Seq using the SimpleChIP Kit (Cell Signaling Technology, #9005). ESR1 antibody was purchased from Santa Cruz (#sc-543).
Next-generation sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8502) and KAPA Single-Indexed Adapter Kit (KAPA Biosystems, KK8710).

treatment_protocol: 17β-estradiol treatment for 72 hours in in phenol red-free DMEM/F12 media supplemented with 2% charcoal-dextran-stripped FBS, treatment was replenished 3 hours prior to harvesting. E2 treatment: 10 nM 17β-estradiol.

value: Primary endometrial stromal cells

tag: individual

value: Patient 1

tag: antibody target


title: BRCA1_DP2_doubleKD

value: BRCA1_DP2 double knock down


title: BRCA1_KD_2

value: second targeted knockdown of BRCA1 via ASX053MG


title: M2F3

tag: condition

tag: number of cells


title: M2E5


title: PT1_ESR1_ChIP_Input

description: Chromatin input

value: input


title: M2E4


title: BRCA1_KD_1

value: first targeted knockdown of BRCA1 via ASX053MG


title: PT2_E2_siESR1

data_processing:
Libraries were sequenced under 75bp single-end sequencing format. Adapters were trimmed using cutadapt. Trimmed reads were aligned to the hg38 reference genome using Tophat default parameters. Raw count files were generated using HTSeq based on Ensembl Release 75 annotation. Differentially expressed genes were detected using edgeR following the cutoff FDR-adjusted P<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are HTSeq raw count files from each RNA-Seq sample.

extract_protocol:
Confluent cells from 1-6cm plate were collected in RLT Buffer + beta-mercaptoethanol. Total RNA was extracted from using Qiagen RNeasy RNA micro kit (Qiagen, 74004).
Next-generation sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase (Roche, #7962282001).

treatment_protocol: 48 hour siRNA treatment with 16 nM ESR1-targeting siRNA or ON-TARGETplus nontargeting control siRNA (siCTRL)  in phenol red-free DMEM/F12 media supplemented with 10% charcoal-dextran-stripped FBS, followed by 17β-estradiol or vehicle treatment for 72 hours, treatment was replenished 3 hours prior to harvesting. E2 treatment: 10 nM 17β-estradiol; Vehicle treatment: equal volume ethanol.

tag: genotype

value: Patient 2

tag: treatment

value: Estradiol


title: PT2_E2_siCTRL

value: siCTRL


title: PT2_Veh_siESR1

value: Vehicle


title: PT2_Veh_siCTRL


title: BIRC5_ENO1_doubleKD

value: BIRC5_ENO1 double knock down


title: M2D11

value: Anaerobic Shock


title: PT1_E2_siESR1


title: PT1_Veh_siESR1


title: M2E3


title: BIRC5_BRD4_doubleKD

value: BIRC5_BRD4 double knock down


title: M2D10


title: BIRC5_KD_2

value: second targeted knockdown of BIRC5 via ASX04ZH8


title: M2D9

value: NaCl Shock


title: PT1_Veh_siCTRL


title: BIRC5_KD_3

value: third targeted knockdown of BIRC5 via ASX04ZH8


title: BIRC5_KD_1

value: first targeted knockdown of BIRC5 via ASX04ZH8


title: M2D8


title: M2D7


title: BCL2_JUND_doubleKD

value: BCL2_JUND double knock down


title: BCL2_RB1_doubleKD

value: BCL2_RB1 double knock down


title: PT1_E2_siCTRL

value: Primary endometrial stromal cells

value: Patient 1