title: genomic DNA from maternal facing placenta tissue  [S0199]

value: ART

value: malay


title: Mm_E12_5_MS252_166

status: Public on Aug 01 2022

type: SRA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: cDNAs amiplified from 1 ng total RNA extracted from cells using 3'-RNA-seq technology

library_source: transcriptomic

data_processing:
The processing of the 3-prime-sequencing data for calculating the gene-expression levels was performed as described previously (Nakamura et al., 2015).  In brief, all reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences.
The reads of 30-bp or longer were mapped onto a mouse transcript reference, ref_GRCm38.p6, using Tophat v2.0.11/Bowtie2 v2.2.7.  Read counts per gene were calculated using HTSeq v0.9.1 with the default settings.  Read counts were converted to read counts per million mapped reads (RPM) and used for the analysis.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Germ cells from E12.5 fetal ovary (Vasa+)

extract_protocol:
The cells were lysed and the total RNAs were purified using a NucleoSpin RNA XS (Takara Bio, #U0902A) according to the manufacturer’s instructions.  1 ng of total RNAs from each sample was used for the synthesis and amplification of cDNAs.
The cDNA synthesis was performed according to the single-cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., 2015).  The cDNA libraries for Nextseq500 (Illumina) were constructed as described previously (Ishikura et al., 2016).The sequencing was performed on an Illumina Nextseq500/550 platform with a Nextseq500/550 Hiqh output kit (Illumina).

tag: developmental stage

tag: genotype

tag: Sex

value: Female

tag: celltype

value: Germ cells


title: male WT rep3 [MUP19]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

library_source: genomic

data_processing:
Trim Galore v0.6.4 used for read trimming
Bismark v0.22.3 used for read mapping and methylation site extraction
EdgeR v3.32.1 used for DMR analysis
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Compressed methylation coverage report

molecule: genomic DNA

source_name: male WT_liver

extract_protocol:
At twelve weeks of age mice were sacrificed by cardiac puncture and liver samples were taken and snap frozen. Genomic DNA was extracted using the All Prep DNA/RNA Extraction Kit (QIAGEN).
The gDNA was digested with  MspI (Tango Buffer.Thermo Scientific), followed by nucleotide end-repair and A-tailing (Klenow Fragment exo- with dCTPs, dGTPs, and dATPs in Tango Buffer, Thermo Scientific) and heat inactivation.  EM-seq Adaptors (NEB E7165A, New England Biolaps) were ligated to the A-tailed DNA fragments using T4 DNA ligase (HC; Thermo Scientific). Bisulfite conversion was performed using ZYMO EZ-96 DNA Methylation-DirectTM MagPrep Kit.  Bisulfite converted libraries were amplified  Kapa (Uracil+ 2x MasterMix ;Roche) and purified (0.8x SPRIselect; Agencourt, Beckman Coulter).

value: male

value: WT


title: genomic DNA from maternal facing placenta tissue  [S0186]

type: genomic

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
R/Rstudio
Average Beta
The filtered and normalized (preprocessNoob) average Beta values are provided in the EPIC850k-GUSTO-Placenta-BetaNoob-708655Probes-Geo.txt.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: maternal facing side placenta tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Frozen sections of placenta are chipped and crushed in liquid nitrogen on aluminum foil-lined mortar and pestle. Mortar and pestle are washed with 70% ethanol and foil changed between each sample. For each sample: In a 1.5 ml tube, we measured out 75mg (+/- 10%) of crushed placenta tissue and added 500 ul ATL & 30 ul PK. We then incubate them overnight in a thermomixer(shaking incubator). The total lysate was then transferred into the Qiasymphony SP and the DNA was extracted using Qiagen DNA Midi kit (Cat: 937255). DNA was quantified using Qubit Flex and quality was assessed using Nanodrop

tag: gender

value: Male

tag: sample type

value: maternal facing side placenta

tag: group

tag: ethnicity

value: chinese


title: female WT rep6 [MUP18]

source_name: female WT_liver

value: female


title: Mm_E11_5_MS252_189

source_name: Germ cells from E11.5 fetal ovary (Stella+Vasa-)

value: Dppa3-EGFPTg/0; mvh(Ddx4)-RFPTg/0


title: genomic DNA from maternal facing placenta tissue  [S0191]


title: female KO rep4 [MUP20]

source_name: female KO_liver

value: KO


title: Mm_E16_5_MS173_138

source_name: Somatic cells from E16.5 fetal ovary (Vasa-)

value: Gonadal somatic cells


title: female WT rep4 [MUP16]


title: female WT rep5 [MUP17]


title: genomic DNA from maternal facing placenta tissue  [S0177]


title: genomic DNA from maternal facing placenta tissue  [S0172]


title: genomic DNA from maternal facing placenta tissue  [S0182]


title: male WT rep2 [MUP15]


title: male KO rep6 [MUP14]

source_name: male KO_liver


title: genomic DNA from maternal facing placenta tissue  [S0170]


title: genomic DNA from maternal facing placenta tissue  [S0165]


title: female KO rep3 [MUP13]


title: female KO rep2 [MUP12]


title: genomic DNA from maternal facing placenta tissue  [S0169]

value: indian


title: genomic DNA from maternal facing placenta tissue  [S0166]


title: genomic DNA from maternal facing placenta tissue  [S0160]


title: male KO rep5 [MUP11]


title: genomic DNA from maternal facing placenta tissue  [S0164]


title: wild-type

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

country: USA

institute: Johns Hopkins University School of Medicine

data_processing:
Library strategy: Ribo-seq
The linker was trimmed using Skewer. Reads were aligned using Bowtie and allowing two mistmatches. Reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome version 2. Separately, the reads were mapped to the IRAGP_reporter plasmid sequence. In the WIG files, rpm values include the fraction of reporter reads in all the uniquely mapped reads, both the chromosome and the plasmid.
Genome_build: NC_000913.2 and separately the IRAGP_reporter plasmid
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

molecule: polyA RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell cultures

growth_protocol: Cultures with the IRAGP_reporter plasmid were harvested at OD600 = 0.3 at 37 C by filtration.

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. The lysis buffer contained Cm to arrest transation. Lysates were clarified and ribosomes were pelleted prior to digestion of mRNA with MNase. After digestion, 70S monosomes were purified over a sucrose gradient.
Ribosome footprints and total RNA fragments 15-45 nt in length were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

tag: genotype/variation

value: wild-type

tag: plasmids


title: maleKO rep4 [MUP10]


title: delta-ssrA_and_delta-smrB


title: delta-smrB

value: delta-smrB


title: genomic DNA from maternal facing placenta tissue  [S0162]


title: genomic DNA from maternal facing placenta tissue  [S0157]


title: control plasmid [plasmid BCSW]

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria St

department: Cancer Ecosystems Program

country: Australia

institute: Garvan Institute of Medical Research

description: target barcode amplified gDNA

data_processing:
Barcode counting using algorithm provided with barcode library (https://www.addgene.org/pooled-library/clontracer/)
Assembly: mm10 (GRCm38.p4)

organism: synthetic construct

source_name: plasmid

extract_protocol: phenol chloroform gDNA extraction

tag: tissue

value: plasmid

tag: cell line

tag: cell type

tag: treatment


title: genomic DNA from maternal facing placenta tissue  [S0154]

value: ART


title: genomic DNA from maternal facing placenta tissue  [S0153]


title: male WT rep4 [MUP21]


title: genomic DNA from maternal facing placenta tissue  [S0151]


title: female KO rep1 [MUP7]


title: genomic DNA from maternal facing placenta tissue  [S0148]

value: malay


title: genomic DNA from maternal facing placenta tissue  [S0147]


title: female WT rep3 [MUP8]


title: female WT rep2 [MUP6]


title: delta-ssrA

value: delta-ssrA


title: genomic DNA from maternal facing placenta tissue  [S0146]


title: female KO rep6 [MUP24]


title: genomic DNA from maternal facing placenta tissue  [S0145]


title: genomic DNA from maternal facing placenta tissue  [S0173]

value: Female


title: genomic DNA from maternal facing placenta tissue  [S0142]


title: genomic DNA from maternal facing placenta tissue  [S0140]


title: MB_M_T

city: Houston

first: Han

last: Liang

state: Texas

address: 1400 Pressler Street

department: Bipinformatics and computational biology

institute: MD Anderson Cancer Center

data_processing:
The RNA-Seq reads were mapped to the human genome UCSC hg19 with the v19 annotation file of the GENCODE database (https://www.gencodegenes.org/; file name: gencode.v19.annotation.gtf) using Tophat2.
The mapping result was input to HTSeq for reads quantification.
The resulted HTSeq counts were normalized using the R package “DESeq2” with default settings.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include reads count for all samples.

growth_protocol: The A549, SKOV3, and MDA-MB-231 cancer cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. To generate c-Myc over-expressed cell lines, HEK293LTX cells were co-transfected with lentiviral packaging mix (psPAX2 and pMD2.G) and either pCDH-puro-cMyc (lentiviral expression vector for full-length human c-Myc) or pCDH-CMV control plasmid to produce lentivirus. To generate the stable cell lines, A549, MDA-MB-231, and SKOV3 cells were transduced with lentivirus and cells with stable c-Myc overexpression were selected for puromycin resistance (A549, 3μg/ml; MDA-MB-231, 1μg/ml; SKOV3, 1.5μg/ml). Overexpression was confirmed by quantitative real-time PCR and western blot.

extract_protocol:
RNA was harvested using RNeasy plus mini kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The c-Myc over-expressed and control A549 cells were treated with 10μM Tipifarnib for 48 hours. The c-Myc over-expressed and control SKOV3 cells were treated with 20μM Tipifarnib for 48 hours. The c-Myc over-expressed and control MDA-MB-231 cells were treated with 20μM Tipifarnib for 48 hours.

value: Breast cancer cell line

value: c-Myc over-expression

value: 20μM Tipifarnib

tag: time

value: 48 hours


title: male KO rep3 [MUP4]

value: male


title: genomic DNA from maternal facing placenta tissue  [S0138]

value: maternal facing side placenta

value: chinese


title: genomic DNA from maternal facing placenta tissue  [S0137]


title: male KO rep2 [MUP3]

value: KO


title: genomic DNA from maternal facing placenta tissue  [S0136]


title: genomic DNA from maternal facing placenta tissue  [S0159]


title: genomic DNA from maternal facing placenta tissue  [S0135]


title: male WT rep1 [MUP2]

value: WT


title: MHC class II KO Vγ6 γδ T

type: RNA

city: Fukuoka

first: shinya

last: Hatano

address: 3-1-1, Maidashi, Higashi-ku,

institute: Kyushu University

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Transcriptome Array 1.0, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: Vγ6 γδ T cells, thymus, 0-day-old MHC class II KO mice

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Single-cell suspensions were isolated from thymus of 0-day-old WT and MHC class II KO mice. After cells were stained with mAbs, Vγ6 γδ T cell were sorted using a FACSAria (BD Bioscience).

tag: strain

value: MHC class II KO

tag: age

value: thymus

value: V<gamma>6 <gamma><delta> T cells


title: SK_M_T

value: Ovarian cancer cell line


title: WT Vγ6 γδ T

source_name: Vγ6 γδ T cells, thymus, 0-day-old WT mice


title: genomic DNA from maternal facing placenta tissue  [S0132]


title: SK_M_D

value: DMSO


title: MB_C_T


title: genomic DNA from maternal facing placenta tissue  [S0130]

value: ART


title: male KO rep1  [MUP1]


title: female WT rep1 [MUP5]

value: female


title: MB_M_D


title: genomic DNA from maternal facing placenta tissue  [S0125]

value: Female

value: indian


title: 4t1+Tcells.Vtn.55

city: Livermore

first: Claire

last: Robertson

state: CA

address: 7000 East Ave.

institute: Lawrence Livermore National Lab

data_processing:
Sequence reads were aligned against Mus musculus reference genome (mm10) using STAR (version 2.6).  After read alignment, the number of read counts per gene locus was summarized with ‘featureCounts’ from Rsubread package (version 1.30.5), using mm10 gene annotation. Read counts were subsequently normalized  using TMM normalization (edgeR version 3.31.7).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TMM normalized CPM values for each Sample .

source_name: cultured 4t1 cells+ C57Bl6 Splenic T cells

growth_protocol: 4T1 mammary gland carcinoma cells (ATCC CRL-2539) were maintained in ATCC formulated RPMI-1640 (ATCC 30-2001) supplemented with 10% FBS (ATCC 30-2020) and 100U/mL penicillin-streptomycin (ThermoFisher 15140148).  Cells were cultured in T75 flasks (Corning 430641U) at 37°C, 5% CO2 and passaged every 3 days by removing spent culture media, briefly washing with 0.25% trypsin-EDTA, incubation with fresh 0.25% trypsin-EDTA for 5 min until cells detach, then splitting 1:6 for subculturing.  Cells were routinely checked for mycoplasma contamination (Lonza MycoAlert LT07-705) and were used at <10 passages from ATCC.

extract_protocol:
Total RNA was harvested from frozen samples using the RNeasy Mini Kit (Qiagen, 74104).  Thawed, pelleted cells were disrupted with the RNeasy Mini Kit RLT lysis buffer containing β-mercaptoethanol and homogenized through a sterile, blunt 20-gauge needle.  On-column DNA digestions were performed using the RNase-Free DNase Set (Qiagen, 79254).  RNA yields were determined on a Qubit 4 Fluorometer using the Qubit RNA HS Assay Kit (ThermoFisher, Q32852).  RNA quality was assessed using an Agilent 2100 Bioanalyzer Instrument and the RNA 6000 Pico kit (Agilent, 5067-15103).
DNA libraries were generated from 0.1-1μg total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, RS-121-2001) and purified using AMPure XP magnetic beads (Beckman Coulter, A63881).  Libraries were normalized, pooled and sequenced on an Illumina NextSeq 550 System, generating single-end, 75 base pair reads.

treatment_protocol: 24-well plates (Corning 3524) were coated with 250μg/ml Col1 (Corning 354249), Col4 (Advanced Biomatrix 5022), Fn (Advanced Biomatrix 5080), or Vtn (Advanced Biomatrix 5051) using uncoated tissue culture polystyrene as a negative control. ECM proteins or PBS were distributed into well plates, incubated at 37°C for 30 min, then plates were wrapped with parafilm and stored at 4°C for 1-3 days.  Plates were then brought to room temperature, washed with PBS, then 4T1 at 10k/cm2 were seeded in each ECM condition.    4T1 were cultured overnight, then T cells at 80k/cm2 and interleukin 2 (IL2- Thermo PMC0025) at 30U/mL added to one 4T1 well and IL2 alone was added to the other.  Cells were then cultured for another 24 hours, then supernatants were collected, and any free cells were pelleted by centrifuging at 200g for 5min, then supernatants were transferred to a clean tube.  Cells were trypsinized & added to the cell pellet, then centrifuged, resuspended in RNA stabilizing agent (RNAprotect, Qiagen) and frozen at -80°C. Identical washes, centrifugation and trypsinization times were used for both MCC alone and MCC+ T cells.  Five biological replicates were undertaken: we obtained sufficient RNA for sequencing in 3-5 experiments per condition.

tag: condition

tag: culture substrate

value: Vitronectin

tag: experimental replicate

value: ECM 5.5


title: genomic DNA from maternal facing placenta tissue  [S0121]


title: 4t1+Tcells.Vtn.54

value: ECM 5.4


title: genomic DNA from maternal facing placenta tissue  [S0123]

value: Male


title: genomic DNA from maternal facing placenta tissue  [S0117]

value: maternal facing side placenta


title: MB_C_D

value: Breast cancer cell line

tag: genotype

value: 48 hours


title: SK_C_D

value: WT


title: 4t1+Tcells.Vtn.52

value: ECM 5.2


title: genomic DNA from maternal facing placenta tissue  [S0134]

tag: gender


title: SK_C_T

value: 20μM Tipifarnib


title: genomic DNA from maternal facing placenta tissue  [S0110]

tag: sample type


title: A5_M_D

value: Lung cancer cell line

value: c-Myc over-expression


title: genomic DNA from maternal facing placenta tissue  [S0109]

tag: group

value: malay


title: A5_C_T

value: 10μM Tipifarnib


title: 4t1.Vtn.55

source_name: cultured 4t1 mammary gland carcinoma cells


title: genomic DNA from maternal facing placenta tissue  [S0105]

value: ART

tag: ethnicity

value: chinese


title: genomic DNA from maternal facing placenta tissue  [S0108]

value: indian


title: genomic DNA from maternal facing placenta tissue  [S0102]

value: Female


title: A5_M_T


title: 4t1.Vtn.53

value: Vitronectin

value: ECM 5.3


title: 4t1.Vtn.52


title: genomic DNA from maternal facing placenta tissue  [S0095]


title: A5_C_D

value: DMSO


title: genomic DNA from maternal facing placenta tissue  [S0097]

value: Male

value: maternal facing side placenta


title: genomic DNA from maternal facing placenta tissue  [S0089]


title: genomic DNA from maternal facing placenta tissue  [S0116]


title: genomic DNA from maternal facing placenta tissue  [S0090]


title: genomic DNA from maternal facing placenta tissue  [S0093]


title: genomic DNA from maternal facing placenta tissue  [S0088]


title: 4t1+Tcells.PS.55

value: Uncoated Tissue Culture Polystyrene

value: ECM 5.5


title: Control rep2

city: Harbin

first: Guangyue

last: Li

state: heilongjang

address: No.26 Hexing Road Xiangfang District

department: College of Life Science

country: China

institute: Northeast Forestry University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Perl script.Firstly,trim Smart-seq2 public primer sequence from the Reads.Second, Remove the contaminated reads for adapters. Thrid, Remove the low quality reads. Lastly, Remove the reads whose N base more than 5% for total bases.
Trimmed reads were mapped to hg38 using HISAT2.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: HepG2 cell line were grown in DMEM medium and incubated at 37℃ in an atmosphere containing 5% carbon dioxide.

extract_protocol:
Total RNA was  extracted by Trizol reagent. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: HepG2 cell line was cultured in 10 cm plates using MEM medium. After 48h, cells were taken in the logarithmic growth phase and inoculated in 10 cm plates with a density of 1×106 per plate. The cells were incubated overnight. The plates were then randomly divided into two groups - control and treatment with three samples in each group. The cells were treated after 24h with about 80% confluence. The treatment group was treated with 336 μM of PD and the control group with DMSO. The cells were detached from the plates after 24h using Trizol reagent and RNA was extracted.

value: Liver

value: Hepatocellular carcinoma cells

value: Control


title: 4t1+Tcells.PS.54

value: ECM 5.4


title: genomic DNA from maternal facing placenta tissue  [S0087]


title: genomic DNA from maternal facing placenta tissue  [S0083]

value: malay


title: 4t1+Tcells.PS.52

value: ECM 5.2


title: Control rep1


title: Control rep3


title: 4t1+Tcells.PS.51

value: ECM 5.1


title: genomic DNA from maternal facing placenta tissue  [S0086]

value: chinese


title: Polydatin treatment rep3

value: PD treatment


title: Polydatin treatment rep2


title: 4t1.PS.55


title: Polydatin treatment rep1


title: genomic DNA from maternal facing placenta tissue  [S0079]

value: Female

value: indian


title: genomic DNA from maternal facing placenta tissue  [S0069]


title: genomic DNA from maternal facing placenta tissue  [S0070]


title: 4t1.PS.54


title: 4t1.PS.53

value: ECM 5.3


title: genomic DNA from maternal facing placenta tissue  [S0064]

value: ART


title: 4t1.PS.52


title: genomic DNA from maternal facing placenta tissue  [S0063]


title: Proliferation_Control_human_Adult_CPCs_Sample_3

city: Lausanne

first: Mohamed

last: Nemir

state: Vaud

address: Bugnon 27

department: Cœur et Vaisseau

institute: Lausanne University Hospital

data_processing:
Reads were pseudoaligned with kallisto software (version 0.44.0) to estimate the transcript level expression per sample
Gene level estimation was performed with sleuth R package (version 0.33.0) and transctipt expression was aggregated to gene level, followed by differential expression. For the transctipt to gene mapping gencode version 29 annotation was used.
Assembly: hg38
Supplementary files format and content: matrix table with TPM expression values for all genes and samples

source_name: Human Fetal CPCs

growth_protocol: Adult CPCs were expanded in expansion medium (3:1 DMEM 1g/l glucose/Medium 199 [Invitrogen] supplemented with 10% horse serum [Serotec, Kidlington, United Kingdom], 5% fetal bovine serum [Serotec], 100 U/ml penicillin [Invitrogen], and 100 μg/ml streptomycin [Invitrogen]). For inducing differentiation, cells were switched to MEM alpha (Invitrogen) containing 2% horse serum, 1 μmol/l dexamethasone (Sigma-Aldrich, St. Louis, Missouri), 50 μg/ml ascorbic acid (Sigma-Aldrich), 10 mmol/l β-glycerophosphate (Sigma-Aldrich), 100 U/ml penicillin (Invitrogen), and 100 μg/ml streptomycin (Invitrogen) (differentiation medium). Fetal CPCs  were expanded in culture in proliferation medium, a 3:1 mixture of DMEM 1 g/L glucose and Medium 199 (Invitrogen) supplemented with 10% Horse serum (Serotec), 5% fetal bovine serum (Serotec), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen). After three passages, cells were switched to a serum-free differentiation medium. Differentiation medium contained MEM alpha (Invitrogen) supplemented with 1 μM dexamethasone (Sigma-Aldrich), 50 μg/mL ascorbic acid (Sigma-Aldrich), 10 mM β-glycerophosphate (Sigma-Aldrich), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen)

extract_protocol:
Cells were lysed in Qiazol and RNA was purified using miRNeasy RNA prufication kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fetal CPCs


title: Proliferation_Control_human_Adult_CPCs_Sample_2


title: 4t1.Vtn.54

value: Vitronectin


title: EU_16_S6_L003_R1_001

city: Oxford

first: Madalena

last: Tarsounas

address: The Old Road Campus Research Building

country: United Kingdom

institute: Oxford Univerity

data_processing:
Sequencing reads were aligned using the Burrows-Wheeler Aligner software and reads with a quality score below 60 were removed.
Custom scripts were used to assign the aligned reads to 10 kb genomic bins and to calculate sigma (σ) values as the normalised number of reads per bin divided by its standard deviation (Macheret and Halazonetis, 2018)
Sigma values were used to identify MiDAS sites (peaks) by searching local maxima.
Assembly: human genome assembly (GRCh37/hg19
Supplementary files format and content: The “bamCoverage” function of deepTools (Ramirez et al., 2014)  was used to generate BigWig files.
Library strategy: EU-seq

growth_protocol: 1.5-2 million cells per T175 flask, 10-25 flasks per condition. BRCA2-deficient cells were grown with 2 ug/ml doxycylin for 2 days. Cells were synchronised with 1.5 mM thymidine for 16 hours, then 6 uM RO-3306 for 10.5 hours then 100 ng/ml nocodazole and 10 uM EdU for 3 hours.

extract_protocol: EU-seq- Cells were synchronised, RNA extracted with Trizol and then EU pulled down with streptavidin beads. Purified EU-labelled RNA was used for library preparation by TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina), omitting the ribo-depletion step, and high-throughput 100-base-pair single-end sequencing was performed on an Illumina Hi-Seq 4000 sequencer. RNA-seq

treatment_protocol: One BRCA2-proficient sample was also treated with 0.5 uM aphidicolin with the RO-3306 treatment.

tag: chip pull_down

value: EU Click-IT and streptavidin beads were used to pull down EdU-labelled fragments

value: Synchronised


title: genomic DNA from maternal facing placenta tissue  [S0059]

value: maternal facing side placenta


title: genomic DNA from maternal facing placenta tissue  [S0060]

value: Male


title: 4t1.PS.51

value: Uncoated Tissue Culture Polystyrene


title: genomic DNA from maternal facing placenta tissue  [S0076]


title: genomic DNA from maternal facing placenta tissue  [S0062]


title: genomic DNA from maternal facing placenta tissue  [S0067]


title: Proliferation_Control_human_Adult_CPCs_Sample_1


title: genomic DNA from maternal facing placenta tissue  [S0082]


title: 4t1+Tcells.Fn.55

value: Fibronectin

value: ECM 5.5


title: Proliferation_CARMEN_C201-deleted_human_Adult_CPCs_Sample_3


title: genomic DNA from maternal facing placenta tissue  [S0080]


title: genomic DNA from maternal facing placenta tissue  [S0052]


title: 4t1+Tcells.Fn.54

value: ECM 5.4


title: Proliferation_CARMEN_C201-deleted_human_Adult_CPCs_Sample_2


title: genomic DNA from maternal facing placenta tissue  [S0051]

value: malay


title: genomic DNA from maternal facing placenta tissue  [S0047]

value: chinese


title: genomic DNA from maternal facing placenta tissue  [S0048]


title: genomic DNA from maternal facing placenta tissue  [S0066]


title: genomic DNA from maternal facing placenta tissue  [S0045]


title: 4t1+Tcells.Fn.51

value: ECM 5.1


title: genomic DNA from maternal facing placenta tissue  [S0044]

value: Female


title: Proliferation_CARMEN_C201-deleted_human_Adult_CPCs_Sample_1


title: genomic DNA from maternal facing placenta tissue  [S0042]


title: 4t1+Tcells.Fn.52

value: ECM 5.2


title: genomic DNA from maternal facing placenta tissue  [S0043]


title: 4t1.Fn.55


title: Differentiation_CARMEN_C201-deleted_human_Adult_CPCs_Sample_2


title: genomic DNA from maternal facing placenta tissue  [S0057]


title: genomic DNA from maternal facing placenta tissue  [S0039]


title: Differentiation_CARMEN_C201-deleted_human_Adult_CPCs_Sample_1


title: genomic DNA from maternal facing placenta tissue  [S0038]

value: indian


title: genomic DNA from maternal facing placenta tissue  [S0037]

value: ART


title: 4t1.Fn.54


title: genomic DNA from maternal facing placenta tissue  [S0036]


title: Differentiation_Control_human_Adult_CPCs_Sample_3

value: Fetal CPCs


title: genomic DNA from maternal facing placenta tissue  [S0035]


title: 4t1.Fn.53

value: ECM 5.3


title: Differentiation_Control_human_Adult_CPCs_Sample_2


title: 4t1.Fn.52


title: genomic DNA from maternal facing placenta tissue  [S0033]


title: genomic DNA from maternal facing placenta tissue  [S0034]


title: genomic DNA from maternal facing placenta tissue  [S0032]


title: 4t1.Fn.51


title: genomic DNA from maternal facing placenta tissue  [S0029]


title: Differentiation_Control_human_Adult_CPCs_Sample_1


title: 4t1+Tcells.Col4.55

value: Collagen IV


title: genomic DNA from maternal facing placenta tissue  [S0026]


title: 4t1+Tcells.Col4.54


title: Differentiation_CARMEN_C201-deleted_human_Adult_CPCs_Sample_3


title: genomic DNA from maternal facing placenta tissue  [S0023]


title: 4t1+ Tcells.Col4.53


title: MiDAS_H1299_+BRCA2.fastq

data_processing:
Sequencing reads were aligned using the Burrows-Wheeler Aligner software and reads with a quality score below 60 were removed.
Custom scripts were used to assign the aligned reads to 10 kb genomic bins and to calculate sigma (σ) values as the normalised number of reads per bin divided by its standard deviation (Macheret and Halazonetis, 2018)
Sigma values were used to identify MiDAS sites (peaks) by searching local maxima.
Genome_build: human genome assembly (GRCh37/hg19
Supplementary_files_format_and_content: The “bamCoverage” function of deepTools (Ramirez et al., 2014)  was used to generate BigWig files.

source_name: Non-small-cell lung carcinoma

extract_protocol:
Cells were lysed with Triton X and DNA extracted with phenol chloroform. EdU Click-IT and streptavidin beads were used to pull down EdU-labelled fragments. Then DNA was purified.
TruSeq ChIP Library Preparation Kit, Illumina

value: Synchronised


title: genomic DNA from maternal facing placenta tissue  [S0018]

value: maternal facing side placenta


title: genomic DNA from maternal facing placenta tissue  [S0011]


title: genomic DNA from maternal facing placenta tissue  [S0009]


title: genomic DNA from maternal facing placenta tissue  [S0007]

value: Male


title: genomic DNA from maternal facing placenta tissue  [S0008]


title: EU_H1299_-BRCA2_R100

description: EU-seq- Cells were synchronised, RNA extracted with Trizol and then EU pulled down with streptavidin beads. Purified EU-labelled RNA was used for library preparation by TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina), omitting the ribo-depletion step, and high-throughput 100-base-pair single-end sequencing was performed on an Illumina Hi-Seq 4000 sequencer. RNA-seq


title: 4t1+ Tcells.Col4.52


title: genomic DNA from maternal facing placenta tissue  [S0006]


title: 4t1.Col4.55


title: MiDAS_H1299_-BRCA2.fastq


title: genomic DNA from maternal facing placenta tissue  [S0001]


title: 4t1.Col4.54


title: genomic DNA from maternal facing placenta tissue  [S0004]


title: MiDAS_H1299_+BRCA2+APH.fastq

value: Synchronised + Aphidicolin release


title: 4t1.Col4.53


title: CD8plus

city: Leiden

first: Martijn

last: Cordes

state: Zuid-Holland

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Centre

data_processing:
Sequencing data were demultiplexed and mapped against the GRCh38 genome using Cellranger 3.0.0.
BAM files were generated with the Cell Ranger 3.0.0 software using default parameters.
Gene-barcode matrices were generated from Cell Ranger 3.0.0 using default parameteres.
Genome_build: GRCh38
Supplementary_files_format_and_content: RDS files contain the final data objects generated after running the Seurat pipeline which contain the normalized, integrated data used for dimensionality reduction and clustering analysis in order to generate the final figures in the paper. All_thymus_samples.rds (Figure 2, Supplementary Figure 2), Sort1_DN123.rds (Figure 3, Supplementary Figure 3), Sort2_ISP_DP_SP.rds (Supplementary Figure 4), HCACD34BM_MantonBM_CordesThymus_integrated.rds (Figure 6, Supplementary Figure 7), Hao_Cordes_multimodal_mapping.rds (Figure 4, Supplementary Figure 5)

source_name: Human postnatal thymus

extract_protocol:
For the isolation of thymocyte subsets, thymocytes from six donors were pooled. To isolate DN1, DN2, and DN3 thymocytes, CD34 magnetic beads (CD34 MicroBead Kit UltraPure, Miltenyi Biotec) were used to enrich for CD34+ thymocytes after thawing, pooling, and Ficoll density separation.
Cell suspensions were barcoded through the 10x Chromium Single Cell platform using Chromium Single Cell 5’ Library, from Lin-CD34+CD38-CD1a- (DN1), Lin-CD34+CD38+CD1a- (DN2), Lin-CD34+CD38+CD1a+ (DN3) (Sort 1), and CD34-CD3lowCD4+ (ISP), CD34-CD3-CD4+CD8+ (DP CD3-), CD34-CD3+CD4+CD8+ (DP CD3+),, CD3-CD4+CD8- (CD4SP), CD3+CD4-CD8+ (CD8SP) (Sort 2) and used to generate 8 single-cell 5′ gene expression libraries. The loaded cell numbers range from 300-500,000 aiming for 5000 single cells per reaction. All libraries were sequenced on an Illumina HiSeq 4000 (paired-end 75bp reads) to an average depth of 50.000 reads per cell, resulting in 8 datasets (for each developmental thymocyte subset). Single-cell TCRαβ sequencing libraries were generated using the Chromium Single Cell 5′ Library Construction kit (PN-1000020, 10X Genomics) and Chromium Single Cell V(D)J Enrichment Kit for human T cell (PN-100005, 10X Genomics).  Single-cell TCRγδ sequencing libraries were generated using the Chromium Single Cell 5′ Library construction kit (PN-1000020, 10X Genomics) and custom primer sets. Pooled libraries were sequenced on an Illumina HiSeq4000 (paired-end 150 bp reads) aiming at an average depth of 5000 read pairs per cell.

value: CD3+CD4-CD8+ thymocytes

tag: developmental stage

value: Single Positive

tag: sort

value: Sort 2

tag: donor

value: 6 healthy donors (pooled)


title: CD4plus

tag: cell type

value: CD3-CD4+CD8- thymocytes


title: genomic DNA from fetal facing placenta tissue  [S0390]

source_name: fetal facing placenta tissue

value: fetal facing placenta

value: malay


title: genomic DNA from fetal facing placenta tissue  [S0384]


title: genomic DNA from fetal facing placenta tissue  [S0388]

value: chinese


title: DP_CD3plus

value: CD34-CD3+CD4+CD8+ thymocytes

value: Double Positive


title: genomic DNA from fetal facing placenta tissue  [S0383]

value: ART

value: indian


title: genomic DNA from fetal facing placenta tissue  [S0382]

value: Female


title: 4t1+Tcells.Col1.55

value: Collagen I

value: ECM 5.5

tag: cell line


title: DP_CD3min

value: CD34-CD3-CD4+CD8+ thymocytes


title: genomic DNA from fetal facing placenta tissue  [S0381]


title: ISP_CD4plus

value: CD34-CD3lowCD4+  thymocytes

value: Immature Single Positive


title: genomic DNA from maternal facing placenta tissue  [S0005]

source_name: maternal facing side placenta tissue

value: Male

value: maternal facing side placenta


title: genomic DNA from fetal facing placenta tissue  [S0376]


title: genomic DNA from fetal facing placenta tissue  [S0375]


title: genomic DNA from fetal facing placenta tissue  [S0374]


title: genomic DNA from fetal facing placenta tissue  [S0370]


title: 4t1+Tcells.Col1.52

value: ECM 5.2


title: 4t1.Col1.55


title: genomic DNA from fetal facing placenta tissue  [S0371]


title: DN3

value: Lin-CD34+CD38-CD1a+ thymocytes

value: Double Negative

value: Sort 1

value: 6 healthy donors (pooled)


title: genomic DNA from fetal facing placenta tissue  [S0363]

value: fetal facing placenta

value: chinese


title: genomic DNA from fetal facing placenta tissue  [S0367]


title: 4t1.Col1.54

value: ECM 5.4


title: genomic DNA from fetal facing placenta tissue  [S0365]

value: ART


title: genomic DNA from fetal facing placenta tissue  [S0362]

value: malay


title: DN1

value: Lin-CD34+CD38-CD1a- thymocytes


title: 4t1.Col4.52

value: Collagen IV


title: 4t1.Col1.53

value: Collagen I

value: ECM 5.3


title: genomic DNA from fetal facing placenta tissue  [S0359]


title: genomic DNA from fetal facing placenta tissue  [S0358]


title: mutESR1_Y537C_MCF7LTED_E2_EL_INput

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

institute: Institute of Cancer Research

description:
input LTED mutated ESR1 Y537C plus elacestrant
Y537CMCF7LTED_B1_E_RAD_ER_peaks.xls
Y537CMCF7LTED_B2_E_RAD_ER_peaks.xls

data_processing:
BWA alignement removing all reads with a quality score < 15
Peaks were called using MACS2 (v2.1.0.20150420) with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 excel file output files

source_name: breast cancer cell line

growth_protocol: Human breast cancer cell lines were cultured in phenol red-free RPMI1640 medium supplemented with 10% fetal bovine serum and 1nM E2. All cell lines were banked in multiple aliquots to reduce the risk of phenotypic drift and identity confirmed using STR. Long-term E deprived (LTED) cells modelling resistance to an AI were derived from all parental cell lines as previously described in  PMID: 29192207.

extract_protocol:
Cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes and then quenched with 125 mmol/L glycine. Samples were then lysed, sonicated, and chromatin was immunoprecipitated by overnight incubation at 4C with ER antibodies prebound with Protein G magnetic dynabeads (Invitrogen). Samples were then washed vigorously with RIPA buffer and reversed crosslinked by an overnight incubation in elution buffer at 65C. DNA was digested with RNase and Proteinase K, purify precipitated with phenol chloroform and eluted in Tris-HCl pH 8.0.
follows PMCID: PMC4052679

treatment_protocol: 10% DCC + 0.1nM E2 or 10% DCC + 0.1nM E2 + 1μM elacestrant or 10% DCC + 0.1nM E2 + 100nM fulvestrant

tag: long term estrogen deprivation (lted)

value: LTED

tag: esr1 mutation status

value: mutated ESR1 Y537C

tag: input or ip

value: input

tag: estradiol (e2)

tag: selective er modulator treatment

value: elacestrant


title: genomic DNA from fetal facing placenta tissue  [S0357]

value: Female


title: genomic DNA from fetal facing placenta tissue  [S0353]

value: Male


title: genomic DNA from fetal facing placenta tissue  [S0356]


title: 4t1.Col1.52

tag: condition

tag: culture substrate

tag: experimental replicate

value: ECM 5.2


title: 4t1+Tcells.Col1.54


title: mutESR1_Y537C_MCF7LTED_E2_Ful_INput

description:
input LTED mutated ESR1 Y537C plus fulvestrant
Y537CMCF7LTED_B1_E_FUL_ER_peaks.xls
Y537CMCF7LTED_B2_E_FUL_ER_peaks.xls

value: fulvestrant


title: mutESR1_Y537C_MCF7LTED__repl2_E2_ER

description:
immunoprecipitated LTED mutated ESR1 Y537C plus
Y537CMCF7LTED_B2_E2_ER_peaks.xls

value: immunoprecipitated

tag: biological replicate

value: replicate 2


title: shMYC_Dox_tumor_8602

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
For RNA-seq and 4SU-seq analysis, base calling was done with Illumina's FASTQ Generation software bcl2fastq Conversion v2.19 and overall sequencing quality was determined with FastQC
Reads (FASTQ files) were mapped to whole genome mm10, and in some cases to hg19, using Bowtie2 with default settings.
For RNA-seq, reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed and differentially expressed genes were called using EdgeR.
processed data files format and content: Matrix files (csv format) containing Ensembl gene ID, gene symbol, gene description and raw read counts for all genes of all samples.
Genome_build: mm10 and hg19

source_name: KPC derived pancreatic cancer tissue

growth_protocol:
For in vitro experiments, KPC cells were grown in DMEM, supplemented with 10% FBS and 1% penicillin/streptomycin.
For in vivo experiments, KPC cells were orthotopically transplanted into the pancreata of BL6 wild-type syngeneic mice. The tumors were allowed to grow for 7 or 14 days before the treatment was started.

extract_protocol:
For RNA-seq in vitro experiments, total RNA was isolated by using the RNeasy Mini Kit (Qiagen) including on-column DNaseI digestion. mRNA was isolated by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
For RNA-seq in vivo experiments, tissue samples were extracted and frozen on dry ice. Total RNA was isolated by using the RNeasy Mini Kit (Qiagen) including on-column DNaseI digestion. mRNA was isolated by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were generated with 1 µg of purified mRNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter). The quality, quantity and the size of the cDNA libraries were determined with the Fragment Analyzer (Thermo Fisher Scientific, previously Advanced Analytical Technologies). Libraries were sequenced on a NextSeq500 System (Illumina).

treatment_protocol:
For in vitro experiments, KPC cells of the various different genotypes were treated with 1 µg/ml doxycycline for 48 hours to induce shRNA-mediated knockdown of Myc or overexpression of exogenous Myc-WT or Myc-VD or IKBaM.
For in vivo experiments, feed the mice with established tumors doxycycline for 48 hours (or in some experiments until the mice were sacrificed).

value: pancreatic carcinoma

value: KPC

tag: myc manipulation

value: shRNA targeting Myc

tag: other manipulations

tag: treatment

value: Dox

tag: spike-in


title: genomic DNA from fetal facing placenta tissue  [S0350]

tag: gender

tag: sample type

value: fetal facing placenta

tag: group

tag: ethnicity

value: indian


title: DN2

tag: cell type

value: Lin-CD34+CD38+CD1a- thymocytes

tag: developmental stage

value: Double Negative

tag: sort

value: Sort 1

tag: donor

value: 6 healthy donors (pooled)


title: mutESR1_Y537C_MCF7LTED__repl2_E2_EL_ER

description:
immunoprecipitated LTED mutated ESR1 Y537C plus elacestrant
Y537CMCF7LTED_B2_E_RAD_ER_peaks.xls

tag: long term estrogen deprivation (lted)

value: LTED

tag: esr1 mutation status

value: mutated ESR1 Y537C

tag: input or ip

tag: estradiol (e2)

tag: selective er modulator treatment

value: elacestrant


title: genomic DNA from fetal facing placenta tissue  [S0348]

value: Female

value: chinese


title: genomic DNA from fetal facing placenta tissue  [S0349]

value: Male

value: malay


title: genomic DNA from fetal facing placenta tissue  [S0347]


title: shMYC_Dox_tumor_8600

value: pancreatic carcinoma

tag: cell line

tag: myc manipulation


title: genomic DNA from fetal facing placenta tissue  [S0346]


title: mutESR1_Y537C_MCF7LTED__repl1_E2_ER

description:
immunoprecipitated LTED mutated ESR1 Y537C plus
Y537CMCF7LTED_B1_E2_ER_peaks.xls

value: immunoprecipitated

tag: biological replicate

value: replicate 1


title: mutESR1_Y537C_MCF7LTED_E2_INput

description:
input LTED mutated ESR1 Y537C plus
Y537CMCF7LTED_B1_E2_ER_peaks.xls
Y537CMCF7LTED_B2_E2_ER_peaks.xls

value: input


title: genomic DNA from fetal facing placenta tissue  [S0345]

value: fetal facing placenta


title: genomic DNA from fetal facing placenta tissue  [S0343]

value: ART


title: shMYC_Dox_tumor_8599

value: KPC

value: shRNA targeting Myc

tag: other manipulations

tag: treatment

value: Dox

tag: spike-in


title: genomic DNA from fetal facing placenta tissue  [S0342]

tag: gender

tag: sample type

tag: group


title: genomic DNA from fetal facing placenta tissue  [S0338]

tag: ethnicity


title: shMYC_Dox_tumor_8598

tag: cell type


title: shMYC_Dox_tumor_8597


title: genomic DNA from fetal facing placenta tissue  [S0341]


title: mutESR1_Y537C_MCF7LTED__repl1_E2_EL_ER

description:
immunoprecipitated LTED mutated ESR1 Y537C plus elacestrant
Y537CMCF7LTED_B1_E_RAD_ER_peaks.xls


title: genomic DNA from fetal facing placenta tissue  [S0335]


title: genomic DNA from fetal facing placenta tissue  [S0334]


title: wtESR1_ptMCF7_repl2_E2_RAD_ER

description:
immunoprecipitated parental cell line wildtype ESR1 plus elacestrant
wtMCF7B2_E_RAD_ER_peaks.xls

value: parental cell line

value: wildtype ESR1

value: replicate 2


title: mutESR1_Y537C_MCF7LTED__repl1_E2_FUL_ER

description:
immunoprecipitated LTED mutated ESR1 Y537C plus fulvestrant
Y537CMCF7LTED_B1_E_FUL_ER_peaks.xls

value: LTED

value: mutated ESR1 Y537C

value: fulvestrant


title: genomic DNA from fetal facing placenta tissue  [S0326]

value: Female

value: chinese


title: wtESR1_ptMCF7_repl2_E2_ER

description:
immunoprecipitated parental cell line wildtype ESR1 plus
wtMCF7B2_E2_ER_peaks.xls


title: genomic DNA from fetal facing placenta tissue  [S0333]


title: mutESR1_Y537C_MCF7LTED__repl2_E2_FUL_ER

description:
immunoprecipitated LTED mutated ESR1 Y537C plus fulvestrant
Y537CMCF7LTED_B2_E_FUL_ER_peaks.xls


title: shMYC_EtOH_tumor_8594

value: pancreatic carcinoma

value: EtOH


title: genomic DNA from fetal facing placenta tissue  [S0325]

value: Male


title: wtESR1_ptMCF7_repl2_E2_Ful_ER

description:
immunoprecipitated parental cell line wildtype ESR1 plus fulvestrant
wtMCF7B2_E_FUL_ER_peaks.xls

value: immunoprecipitated


title: genomic DNA from fetal facing placenta tissue  [S0320]

value: fetal facing placenta


title: wtESR1_ptMCF7_repl1_E2_ER

description:
immunoprecipitated parental cell line wildtype ESR1 plus
wtMCF7B1_E2_ER_peaks.xls

value: replicate 1


title: genomic DNA from fetal facing placenta tissue  [S0316]


title: genomic DNA from fetal facing placenta tissue  [S0314]


title: genomic DNA from fetal facing placenta tissue  [S0313]

value: malay


title: shMYC_EtOH_tumor_7765

value: KPC

value: shRNA targeting Myc


title: genomic DNA from fetal facing placenta tissue  [S0336]


title: genomic DNA from fetal facing placenta tissue  [S0310]


title: shMYC_EtOH_tumor_7764


title: TBK1ko_IKBaM_shMYC_Dox_rep3

source_name: KPC cells

value: knockout of TBK1 and overexpression of IKBa or IKBaM

value: Dox


title: shMYC_EtOH_tumor_8596


title: genomic DNA from fetal facing placenta tissue  [S0304]


title: genomic DNA from fetal facing placenta tissue  [S0309]


title: genomic DNA from fetal facing placenta tissue  [S0299]


title: genomic DNA from fetal facing placenta tissue  [S0298]


title: TBK1ko_IKBaM_shMYC_Dox_rep1


title: genomic DNA from fetal facing placenta tissue  [S0323]

value: ART


title: shMYC_EtOH_tumor_8595


title: shMYC_Dox_tumor_8601


title: shMYC_EtOH_tumor_8593


title: wtESR1_ptMCF7_E2_Ful_INput

description:
input parental cell line wildtype ESR1 plus fulvestrant
wtMCF7B1_E_FUL_ER_peaks.xls
wtMCF7B2_E_FUL_ER_peaks.xls

value: parental cell line

value: wildtype ESR1

value: input


title: wtESR1_ptMCF7_repl1_E2_EL_ER

description:
immunoprecipitated parental cell line wildtype ESR1 plus elacestrant
wtMCF7B1_E_RAD_ER_peaks.xls

value: elacestrant


title: wtESR1_ptMCF7_E2_INput

description:
input parental cell line wildtype ESR1 plus
wtMCF7B1_E2_ER_peaks.xls
wtMCF7B2_E2_ER_peaks.xls


title: genomic DNA from fetal facing placenta tissue  [S0293]

value: chinese


title: TBK1ko_IKBaM_shMYC_Dox_rep2

value: pancreatic carcinoma


title: genomic DNA from fetal facing placenta tissue  [S0292]

value: indian


title: genomic DNA from fetal facing placenta tissue  [S0303]

value: Male


title: wtESR1_ptMCF7_E2_EL_INput

description:
input parental cell line wildtype ESR1 plus elacestrant
wtMCF7B1_E_RAD_ER_peaks.xls
wtMCF7B2_E_RAD_ER_peaks.xls


title: TBK1ko_IKBaM_shMYC_EtOH_rep2

value: EtOH


title: genomic DNA from fetal facing placenta tissue  [S0288]

value: fetal facing placenta


title: genomic DNA from fetal facing placenta tissue  [S0302]

value: Female


title: genomic DNA from fetal facing placenta tissue  [S0282]

value: malay


title: wtESR1_MCF7LTED_repl2_E2_EL_ER

description:
immunoprecipitated LTED wildtype ESR1 plus elacestrant
wtESR1MCF7LTEDB2_E_RAD_ER_peaks.xls

value: LTED

value: immunoprecipitated

value: replicate 2


title: TBK1ko_IKBaM_shMYC_EtOH_rep3

value: KPC

value: shRNA targeting Myc

value: knockout of TBK1 and overexpression of IKBa or IKBaM


title: wtESR1_ptMCF7_repl1_E2_FUL_ER

description:
immunoprecipitated parental cell line wildtype ESR1 plus fulvestrant
wtMCF7B1_E_FUL_ER_peaks.xls

value: parental cell line

value: wildtype ESR1

value: replicate 1

value: fulvestrant


title: wtESR1_MCF7LTED_repl2_E2_FUL_ER

description:
immunoprecipitated LTED wildtype ESR1 plus fulvestrant
wtESR1MCF7LTEDB2_E_FUL_ER_peaks.xls


title: genomic DNA from fetal facing placenta tissue  [S0291]

value: chinese


title: genomic DNA from fetal facing placenta tissue  [S0296]


title: genomic DNA from fetal facing placenta tissue  [S0281]


title: TBK1wt_IKBaM_shMYC_Dox_rep3

value: pancreatic carcinoma

value: Dox


title: wtESR1_MCF7LTED_repl1_E2_EL_ER

description:
immunoprecipitated LTED wildtype ESR1 plus elacestrant
wtESR1MCF7LTEDB1_E_RAD_ER_peaks.xls

value: elacestrant


title: genomic DNA from fetal facing placenta tissue  [S0280]

value: fetal facing placenta

value: ART


title: wtESR1_MCF7LTED_repl1_E2_ER

description:
immunoprecipitated LTED wildtype ESR1 plus
wtESR1MCF7LTEDB1_E2_ER_peaks.xls


title: genomic DNA from fetal facing placenta tissue  [S0272]

value: Male


title: genomic DNA from fetal facing placenta tissue  [S0267]


title: genomic DNA from fetal facing placenta tissue  [S0261]

value: Female


title: genomic DNA from fetal facing placenta tissue  [S0274]

value: indian


title: genomic DNA from fetal facing placenta tissue  [S0266]


title: TBK1wt_IKBaM_shMYC_Dox_rep2


title: genomic DNA from fetal facing placenta tissue  [S0259]

value: malay


title: TBK1wt_IKBaM_shMYC_Dox_rep1

value: KPC


title: TBK1wt_IKBaM_shMYC_EtOH_rep3

value: shRNA targeting Myc

value: EtOH


title: TBK1ko_IKBaM_shMYC_EtOH_rep1

value: knockout of TBK1 and overexpression of IKBa or IKBaM


title: genomic DNA from fetal facing placenta tissue  [S0276]


title: wtESR1_MCF7LTED_repl2_E2_ER

description:
immunoprecipitated LTED wildtype ESR1 plus
wtESR1MCF7LTEDB2_E2_ER_peaks.xls

value: LTED

value: wildtype ESR1

value: immunoprecipitated

value: replicate 2


title: TBK1wt_IKBaM_shMYC_EtOH_rep1

value: pancreatic carcinoma


title: wtESR1_MCF7LTED_repl1_E2_FUL_ER

description:
immunoprecipitated LTED wildtype ESR1 plus fulvestrant
wtESR1MCF7LTEDB1_E_FUL_ER_peaks.xls

value: replicate 1

value: fulvestrant


title: wtESR1_MCF7LTED_E2_INput

description:
input LTED wildtype ESR1 plus
wtESR1MCF7LTEDB1_E2_ER_peaks.xls
wtESR1MCF7LTEDB2_E2_ER_peaks.xls

value: input


title: TBK1ko_IKBa_shMYC_Dox_rep3

value: Dox


title: wtESR1_MCF7LTED_E2_Ful_INput

description:
input LTED wildtype ESR1 plus fulvestrant
wtESR1MCF7LTEDB1_E_FUL_ER_peaks.xls
wtESR1MCF7LTEDB2_E_FUL_ER_peaks.xls


title: TBK1wt_IKBaM_shMYC_EtOH_rep2


title: genomic DNA from fetal facing placenta tissue  [S0258]

value: Male

value: fetal facing placenta

value: chinese


title: genomic DNA from fetal facing placenta tissue  [S0255]

value: Female

value: indian


title: wtESR1_MCF7LTED_E2_EL_INput

description:
input LTED wildtype ESR1 plus elacestrant
wtESR1MCF7LTEDB1_E_RAD_ER_peaks.xls
wtESR1MCF7LTEDB2_E_RAD_ER_peaks.xls

value: elacestrant


title: genomic DNA from fetal facing placenta tissue  [S0254]


title: genomic DNA from fetal facing placenta tissue  [S0253]


title: TBK1ko_IKBa_shMYC_Dox_rep2

value: KPC

value: shRNA targeting Myc


title: genomic DNA from fetal facing placenta tissue  [S0252]

value: ART


title: TBK1ko_IKBa_shMYC_Dox_rep1

value: knockout of TBK1 and overexpression of IKBa or IKBaM


title: genomic DNA from fetal facing placenta tissue  [S0251]

value: malay


title: genomic DNA from fetal facing placenta tissue  [S0249]


title: BJDcdk_i

city: Charlestown

first: Ioannis

last: Sanidas

state: MA

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Sequencing reads were trimmed using trim-galore, aligned to the human genome (build hg19) using bwa-mem, then duplicate-marked using sambamba, and filtered to remove reads that were duplicates, had mapping quality <30, had >2 mismatches, or had >1/3 of their sequence soft-clipped.
Filtered BAMs were sorted and indexed, and deeptools-bamCoverage was used to generate CPM-normalized bigwig files for peak visualization, and bedtools-coverage was used to count reads in 200bp genomic windows tiling the genome.
Genome_build: human genome (build hg19)
Supplementary_files_format_and_content: CPM-normalized bigwig files were generated using deeptools-bamCoverage

source_name: skin fibroblasts BJ cells

growth_protocol: The telomerase-expressing non-transformed human retina epithelial cells RPE1 and skin fibroblasts BJ cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 5% Fetal Bovine Serum (FBS) and antibiotics (100 units/ml Penicillin and 100 μg/ml Streptomycin; P/S). The MCF10A human breast epithelial cell line were cultured in DMEM/Nutricient mixture F12 medium supplemented with 5% horse serum (Gibco, Cat. No. 16050122), 20 ng/ml human EGF (ThermoFisher, Cat. No. PHG0311), 0.5 µg/ml hydrocortisone (Sigma, Cat. No. H-0888), 100 ng/ml cholera toxin (Sigma, Cat. No. C-8052), 10 µg/ml insulin (Sigma, Cat. No. I-1882) and antibiotics (P/S). The human breast cancer cell line T47D was cultured in RPMI 1640 medium supplemented with 10% FBS and antibiotics (P/S).

extract_protocol:
ChIP assays were carried out on RPE1, BJ, MCF10A and T47D cell cultures using approximately 5 million cells per sample and per epitope. Cells were washed once with PBS and fixed with 1.5 mM ethylene glycol bis(succinimidyl succinate) (Thermo Scientific, Cat. No. 21565) for 30 min at 25oC and 1% formaldehyde (Sigma, Cat. No. F8775) for 10 min at 37oC. 20mM Tris-HCl pH7.5 and 150 mM Glycine were used to quench cross-linking. Cell pellets were washed twice with ice-cold PBS and lysates were prepared using 300 µl lysis buffer (50mM Tris-HCl pH 7.4, 1% SDS, 0.25% DOC) supplement with protease and phosphatase inhibitors cocktail (PPI) (Thermo Scientific, Cat. No. 78442) for 10 min on ice. Cell lysates were diluted with 900 µl ChIP dilution buffer (50mM Tris-HCl pH 7.4, 0.1% SDS, 150mM NaCl, 1.84% Triton-X) supplement with PPI and chromatin was fragmented to a size of 200 – 700 bases with Branson 250 sonifier. Solubilized chromatin was further diluted with 1800 µl ChIP dilution buffer and immunoprecipitated with the indicated antibodies overnight at 4°C. Anti-DYKDDDDK Tag (Cell Signaling, Cat. No. 14793) was used for FLAG-RB ChIP. Antibody-chromatin complexes were pulled down with protein G-Dynabeads (Life Technologies, Cat. No. 10004D) for 2 hours at 4°C and washed 3 times with RIPA 150 Wash Buffer (0.1% SDS, 0.1% DOC 1% Triton X-100, 1mM EDTA, 10mM Tris-HCl pH 8, 150mM NaCl), 3 times with RIPA 500 Wash Buffer (0.1% SDS, 0.1% DOC 1% Triton X-100, 1mM EDTA, 10mM Tris-HCl pH 8, 500mM NaCl), 3 times with LiCl wash buffer (10mM Tris-HCl, pH 8, 250mM LiCl, 0.5% Triton X-100, 0.5% DOC) and once with ice-cold 10mM Tris-HCl, pH 8. Chromatin complexes were eluted from the beads using elution buffer (10mM Tris-HCl pH 8, 0.1% SDS, 150mM NaCl, 5 mM DTT) for 1 hour at 65°C and treated with RNase A (Roche, Cat. No. 11119915001) for 30 min at 37oC. Proteinase K (Thermo Scientific, Cat. No. 25530049) treatment and reverse cross-linking was performed for 3 hours at 65°C. After crosslink reversal, immunoprecipitated DNA was extracted with AMP Pure XP beads (Beckman Coulter, Cat. No. A63881). ChIP DNA was quantified with Qubit dsDNA HS Assay kit (Thermo Scientific, Cat. No. Q32851).
1-2 ng ChIP DNA samples were used to prepare sequencing libraries, using the Ovation Ultralow System V2 kit (TECAN, Cat. No. 0344NB-A01).

treatment_protocol: RB1 knock down or replacement of the endogenous by exogenous RB protein in cells transduced with pINDUCER11 and/or pINDUCER20 constructs were induced by addition of 0.5 μg/ml DOX (Sigma, Cat. No. D9891) for the indicating time. Expression of the dominant negative A-FOS or the dominant negative DP1_aa127-410 in cells transduced with pLenti-CMVtight puro constructs were induced by addition of 0.5 μg/ml DOX for 48 hours. Contact inhibition experiments performed by maintaining RPE1 cells in confluent culture for 6 days.

value: BJ

tag: genotype

tag: chip antibody

value: 48 hours doxycycline


title: SubjectA and B adipose tissue

city: Orlando

first: Lauren

last: Sparks

state: Florida

address: 301 E Princeton St, 301

institute: AdventHealth

description: Subject A = subject 1, Subject B = subject 2

data_processing:
Initially FastQ files were processed using the Mappa Analysis pipeline. Following trimming, data was aligned to the GRCh38 reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include raw read count values  for each sample

source_name: subcutaneous abdominal fat

extract_protocol:
Adipose tissue biopsies were collected from subcutaneous abdominal adipose tissue. Tissue was digested with collagenase buffer (Type I collagenase in αMEM supplemented with 1% BSA) at 37 °C for 45 min. Adipocytes were collected by centrifugation at 200g for 5 minutes and washed twice with PBS prior to nuclei isolation (see below). After the adipocytes were collected, the SVF was isolated by additional centrifugation at 500g for 5 minutes and washed with RBC lysis buffer. The SVF solution was subsequently filtered through 100μm and 40μm strainer (BD Falcon) and counted with a countess II automated cell counter (Thermofisher). Following a wash, cells were resuspended in 1% BSA- nuclease free-water. Washed adipocytes (~150µL) were homogenized in a glass dounce with 1ml of homogenization buffer (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 250mM sucrose, 1µm DDT, 1 x protease inhibitor, 0.2 U/µL SUPERase•In RNase Inhibitor (Thermofisher Scientific) in nuclease-free water). Triton-X100 (0.1% v/v) was added to the homogenate prior to incubation on ice for 30 min with regular vortexing. Samples were filtered through a 100µm and 40µm strainer (BD Falcon), centrifuged at 1,000g for 10 min at 4°C, resuspended in 1mL nuclei isolation medium (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 1 mM EDTA, 0.2 U/µL Ribolock RNAase inhibitor, 1% BSA in nuclease-free water) and centrifuged at 1,000g for 10 min at 4°C. Nuclei was resuspended in 500µL nuclei isolation medium and filtered 10 x with a 25g syringe prior to being counted. Frozen adipose tissue (~100mg) was pulverized under liquid nitrogen and homogenized in 2mL of homogenization buffer (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 250mM sucrose, 1µm DDT, 1 x protease inhibitor, 0.2 U/µL SUPERase•In RNase Inhibitor (Thermofisher Scientific) in nuclease-free water) with a glasscol homogenizer. The homogenate was incubated for 30 minutes on ice with the addition of Triton-X100 (0.1% v/v) with regular vortexing. Samples were filtered through a 100µm and 40µm strainer (BD Falcon), centrifuged at 2,700g for 10 min at 4°C, resuspended in homogenization buffer and recentrifuged again at 2,700g for 10 min at 4°C. The pellet was then re-suspended in 1mL nuclei isolation medium (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 1 mM EDTA, 0.2 U/µL Ribolock RNAase inhibitor, 1% BSA in nuclease-free water) and centrifuged at 2,700g for 10 min at 4°C. Following re-suspension in 500µL nuclei isolation medium, sample was filtered 10 x with a 25g syringe prior to being counted. Single-nuclei suspension (40K/mL) or single-cell suspension (28L/mL) was distributed into eight wells of a 384-well source plate (Takara) and dispensed onto a ICELL8® 350v Chip (Takara) using an ICELL8 MultiSample NanoDispenser (MSND, Takara). Following dispense, the chip nanowells were imaged using the ICELL8 Imaging Station to identify nanowells containing a single nucleus/ a live single cell. Only these nanowells were subjected for downstream dispenses. After imaging, the chip was subjected to freeze-thaw to lyse the cells/nuclei, followed by a 3 min incubation at 72oC to denature the RNA.
Selected cell/nuclei were subjected to first-strand cDNA synthesis initiated by oligo dT primer (SMART-Seq ICELL8 CDS), followed by template switching with template switching oligo (SMART-Seq ICELL8 oligonucleotide) for 2nd strand cDNA synthesis, prior to unbiased amplification of full-length cDNA. Synthesized full-length cDNA was tagmented by TDE1 (Illumina Tagment DNA enzyme) and amplified using forward (i5) and reverse (i7) indexing primers. Each single cell/nucleus was indexed by a unique combination of 1 of 72 forward and 1 of 72 reverse indexing primers allowing for downstream identification. Collected cDNA was purified twice using a 1:1 proportion of AMPure XP beads (Beckman, A63880), further amplified according to manufacturer’s instructions and purified again at a 1:1 proportion of AMPure XP beads. The resultant sequencing-ready cDNA library was assessed for concentration by fluorometer (Qubit) and quality by electrophoresis (Agilent Bioanalyzer high sensitivity DNA chips) respectively. Libraries were sequenced with Illumina HiSeq 4000.

tag: subject

value: multiplexed sample (A and B)

tag: tissue

value: adipose tissue

tag: molecule subtype

value: single-nucleus RNA


title: SubjectB SVF and Adipocytes

description: subject 2

value: B

value: multiplexed sample (SVF and Isolated Adipocytes)

value: single-cell RNA (SVF) and single-nucleus RNA (Isolated Adipocytes)


title: TBK1ko_IKBa_shMYC_EtOH_rep2

value: pancreatic carcinoma

value: EtOH


title: BJ_W_i

value: pINDUCER10-shRB1, pINDUCER20-FLAG-RBWT

value: input


title: genomic DNA from fetal facing placenta tissue  [S0232]

value: Female

value: fetal facing placenta

value: chinese


title: genomic DNA from fetal facing placenta tissue  [S0247]


title: genomic DNA from fetal facing placenta tissue  [S0229]

value: Male

value: indian


title: SubjectA SVF and Adipocytes

description: subject 1

value: A


title: genomic DNA from fetal facing placenta tissue  [S0238]


title: BJDcdk_F

value: BJ

value: anti-DYKDDDDK Tag (Cell Signaling Technology, 14793)

value: 48 hours doxycycline


title: TBK1ko_IKBa_shMYC_EtOH_rep3

value: KPC

value: shRNA targeting Myc

value: knockout of TBK1 and overexpression of IKBa or IKBaM


title: genomic DNA from fetal facing placenta tissue  [S0233]

value: malay


title: genomic DNA from fetal facing placenta tissue  [S0234]


title: genomic DNA from fetal facing placenta tissue  [S0223]

value: ART


title: genomic DNA from fetal facing placenta tissue  [S0231]


title: TBK1ko_IKBa_shMYC_EtOH_rep1

value: pancreatic carcinoma

value: EtOH


title: TBK1wt_IKBa_shMYC_Dox_rep2

value: Dox


title: TBK1wt_IKBa_shMYC_Dox_rep1


title: genomic DNA from fetal facing placenta tissue  [S0222]


title: genomic DNA from fetal facing placenta tissue  [S0221]

value: Female


title: TBK1wt_IKBa_shMYC_Dox_rep3


title: genomic DNA from fetal facing placenta tissue  [S0227]

value: fetal facing placenta


title: genomic DNA from fetal facing placenta tissue  [S0215]

value: chinese


title: WTCHG_295177

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

growth_protocol: DMEM (Gibco, UK) containing 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was prepared from cell cultures using the Qiagen RNeasy kit.
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using PolyA capture.

treatment_protocol: Platinum-resistant HGSC lines were generated by culturing cells in increasing concentrations of cisplatin or carboplatin until a fold increase in IC50 of 2-10 was achieved.

tag: drug resistance

value: carboplatin resistant


title: genomic DNA from fetal facing placenta tissue  [S0226]


title: genomic DNA from fetal facing placenta tissue  [S0216]

value: Male


title: genomic DNA from fetal facing placenta tissue  [S0244]


title: WTCHG_296189

tag: cell line


title: genomic DNA from fetal facing placenta tissue  [S0214]


title: WTCHG_293153

value: cisplatin resistant


title: BJ_W_F

value: BJ

value: pINDUCER10-shRB1, pINDUCER20-FLAG-RBWT


title: TBK1wt_IKBa_shMYC_EtOH_rep2

tag: myc manipulation


title: WTCHG_292141


title: genomic DNA from fetal facing placenta tissue  [S0235]


title: WTCHG_291129

value: carboplatin cisplatin sensitive


title: genomic DNA from fetal facing placenta tissue  [S0213]


title: genomic DNA from fetal facing placenta tissue  [S0209]


title: TBK1wt_IKBa_shMYC_EtOH_rep3

value: KPC


title: 4SU_shMYC_Dox_chase120_rep2

data_processing:
Library strategy: 4sU-seq
For RNA-seq and 4SU-seq analysis, base calling was done with Illumina's FASTQ Generation software bcl2fastq Conversion v2.19 and overall sequencing quality was determined with FastQC
Reads (FASTQ files) were mapped to whole genome mm10, and in some cases to hg19, using Bowtie2 with default settings.
For 4SU-seq the mapping was done to the mouse genome mm10 and, for identification of the spike-in, also to the human genome hg19. First, exon reads, rRNA reads and reads in the 3'-UTR and the 5'-UTR were eliminated from the alignment files using bedtools intersect. The number of intron reads was determined for all cleaned alignment files using bedtools intersect. These read-numbers of samples were normalized according to the spike-in reads (mapped to hg19). Bed files were generated and the number of reads in introns of genes of interest were counted.
processed data files format and content: No processed data files were generated. Relevant read-counts in introns of genes of interest were extracted directly from bed files.
Genome_build: mm10 and hg19

extract_protocol:
For 4SU-seq in vitro experiments, KPC cells were labelled with 200 µM 4-thiouridine for 20 min, lysed with QIAzol reagent and spiked with 4sU-labelled U2OS cell-lysates. Total RNA was extracted with the miRNeasy kit (Qiagen) including on-column DNase digestion and quantified.
The isolated RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce) for 2 hours followed by purification of biotinylated RNA via chloroform-isoamylalcohol extration. Biotinylated RNA was pulled down using Dynabeads MyOne Streptavidin T1 beads (Invitrogen) . Following washing, 4sU-labelled RNA was eluted from the beads, purified with the RNeasy MinElute kit (Qiagen) and quantified with the RiboGreen Assay (Invitrogen).
About 10 ng of RNA was used as input material for library preparation. First, the rRNA was depleted using the NEBNext rRNA Depletion Kit (NEB), followed by cDNA preparation and library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB). The cDNA libraries were amplified with about 12 PCR cycles and quality and quantity and the size of the cDNA libraries were determined with the Fragment Analyzer (Thermo Fisher Scientific, previously Advanced Analytical Technologies). Libraries were sequenced on a NextSeq500 System (Illumina).

value: shRNA targeting Myc

value: 10% U2OS cells (human)


title: genomic DNA from fetal facing placenta tissue  [S0205]

data_processing:
R/Rstudio
Average Beta
The filtered and normalized (preprocessNoob) average Beta values are provided in the EPIC850k-GUSTO-Placenta-BetaNoob-708655Probes-Geo.txt.

extract_protocol: Frozen sections of placenta are chipped and crushed in liquid nitrogen on aluminum foil-lined mortar and pestle. Mortar and pestle are washed with 70% ethanol and foil changed between each sample. For each sample: In a 1.5 ml tube, we measured out 75mg (+/- 10%) of crushed placenta tissue and added 500 ul ATL & 30 ul PK. We then incubate them overnight in a thermomixer(shaking incubator). The total lysate was then transferred into the Qiasymphony SP and the DNA was extracted using Qiagen DNA Midi kit (Cat: 937255). DNA was quantified using Qubit Flex and quality was assessed using Nanodrop


title: WTCHG_290117


title: WTCHG_294165


title: genomic DNA from fetal facing placenta tissue  [S0201]


title: genomic DNA from fetal facing placenta tissue  [S0204]

value: indian


title: genomic DNA from fetal facing placenta tissue  [S0189]


title: genomic DNA from fetal facing placenta tissue  [S0188]


title: 4SU_shMYC_Dox_chase120_rep3


title: genomic DNA from fetal facing placenta tissue  [S0198]

value: ART


title: 4SU_shMYC_Dox_chase120_rep1

value: pancreatic carcinoma


title: genomic DNA from fetal facing placenta tissue  [S0190]


title: genomic DNA from fetal facing placenta tissue  [S0185]


title: genomic DNA from fetal facing placenta tissue  [S0210]


title: 4SU_shMYC_EtOH_chase120_rep3

value: EtOH


title: WTCHG_289105


title: 4SU_shMYC_EtOH_chase120_rep2


title: TBK1wt_IKBa_shMYC_EtOH_rep1

value: knockout of TBK1 and overexpression of IKBa or IKBaM


title: WTCHG_206166


title: 4SU_shMYC_Dox_chase60_rep3

value: Dox


title: WTCHG_204142


title: genomic DNA from fetal facing placenta tissue  [S0181]

value: fetal facing placenta


title: 4SU_shMYC_Dox_chase60_rep2


title: genomic DNA from fetal facing placenta tissue  [S0180]

value: Female

value: chinese


title: genomic DNA from fetal facing placenta tissue  [S0187]


title: 4SU_shMYC_EtOH_chase120_rep1


title: genomic DNA from fetal facing placenta tissue  [S0179]

value: Male


title: genomic DNA from fetal facing placenta tissue  [S0178]


title: genomic DNA from fetal facing placenta tissue  [S0202]


title: genomic DNA from fetal facing placenta tissue  [S0176]

value: malay


title: genomic DNA from fetal facing placenta tissue  [S0184]


title: genomic DNA from fetal facing placenta tissue  [S0195]


title: genomic DNA from fetal facing placenta tissue  [S0175]


title: 4SU_shMYC_EtOH_chase60_rep1


title: genomic DNA from fetal facing placenta tissue  [S0197]


title: genomic DNA from fetal facing placenta tissue  [S0167]


title: genomic DNA from fetal facing placenta tissue  [S0171]


title: genomic DNA from fetal facing placenta tissue  [S0168]


title: genomic DNA from fetal facing placenta tissue  [S0163]


title: genomic DNA from fetal facing placenta tissue  [S0183]


title: WTCHG_203130

value: carboplatin resistant


title: WTCHG_205154


title: 4SU_shMYC_Dox_chase60_rep1


title: WTCHG_202118


title: genomic DNA from fetal facing placenta tissue  [S0158]


title: 4SU_shMYC_EtOH_chase60_rep3


title: hE_28_2

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome or mm9 mouse transcriptome  (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19/mm9
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Human Embryonic Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

tag: Stage


title: hE_29_1

description: polyA RNA


title: 4SU_shMYC_EtOH_chase60_rep2

tag: other manipulations


title: WTCHG_201106


title: 4SU_shMYC_Dox_pulse_rep2

tag: treatment


title: hE_28_1

description: polyA RNA


title: hE_29_2

description: polyA RNA


title: genomic DNA from fetal facing placenta tissue  [S0174]


title: genomic DNA from fetal facing placenta tissue  [S0161]


title: genomic DNA from fetal facing placenta tissue  [S0156]


title: WTCHG_207178


title: genomic DNA from fetal facing placenta tissue  [S0155]


title: 4SU_shMYC_Dox_pulse_rep1

tag: spike-in


title: genomic DNA from fetal facing placenta tissue  [S0152]

tag: gender


title: genomic DNA from fetal facing placenta tissue  [S0149]

tag: sample type


title: 4SU_shMYC_EtOH_pulse_rep3


title: hE_27_2

description: polyA RNA


title: genomic DNA from fetal facing placenta tissue  [S0150]

tag: group


title: genomic DNA from fetal facing placenta tissue  [S0144]

tag: ethnicity


title: 4SU_shMYC_Dox_pulse_rep3

tag: cell type


title: genomic DNA from fetal facing placenta tissue  [S0143]


title: genomic DNA from fetal facing placenta tissue  [S0141]


title: 4SU_shMYC_EtOH_pulse_rep1


title: genomic DNA from fetal facing placenta tissue  [S0139]


title: genomic DNA from fetal facing placenta tissue  [S0133]


title: 4SU_shMYC_EtOH_pulse_rep2


title: ISK_2_scRNA-seq

value: Human Embryonic Cells


title: Sample49: E275_J2_IP_dox_PE_dsRNA-seq

data_processing:
For RNA-seq analysis and for J2-IP sequencing analysis, base calling was done with Illumina's FASTQ Generation software bcl2fastq Conversion v1.0.0 (for samples 1-16) and v2.19 (samples 17-49) and overall sequencing quality was determined with FastQC
dsRNA sequencing / J2 IP; Fastq files were trimmed for adapters and low quality reads by Trim Galore (v 0.6.4) with default parameters
Reads of trimmed fastq files were mapped to hg38 (spike-in) using Tophat2 (v 2.1.1) with default parameters and "-g 1 --no-coverage-search"
Unmapped bam files from the prevouse mapping were converted to fastq files by bamToFastq (bedtools, v 2.26.0)
Fastq files were subsequentially mapped to a reference of murine ribosomal DNA (BK000964.1), mitochondrial DNA (chrM of mm10) and to mm10 using Tophat2 as described before, with one additional paramater for mapping to mitochondrial DNA ("-- no-novel-junctions")
Mapped files were sorted, indexed and normalized by Samtools (v 1.9)
Bedgraphs were generated by Bedtools genomecov function
Genome_build: hg38, BK000964.1, mm10
Supplementary_files_format_and_content: bedgraphs of spike-in normalized files

extract_protocol:
Cells were lysed in the presence of NP-40. Lysates were treated with DNase I, RNase T1 and, where indicated, with RNase III. Double stranded RNA in the lysate was immuno-precipitated over-night using the J2 Antibody (Scicons). Following washing, RNA was extracted from the beads with TRIZOL and precipitated with isopropanol.
Ribosomal RNA was depleted from the immuno-precipitated RNA using the NEBNext rRNA depletion Kit (New England Biolabs) and the rRNA depleted samples were further processed using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter). The quality, quantity and the size of the cDNA libraries were determined with the Fragment Analyzer (Thermo Fisher Scientific, previously Advanced Analytical Technologies). Libraries were sequenced on a NextSeq500 System (Illumina).

treatment_protocol:
For in vitro experiments, KPC cells of the various different genotypes were treated with 1 µg/ml doxycycline for 48 hours to induce shRNA-mediated knockdown of Myc or overexpression of exogenous Myc-WT or Myc-VD.
For in vivo experiments, feed the mice with established tumors doxycycline for 48 hours

value: CRISPR/Cas9 knockout of Myc

value: Dox-inducible expression of Myc-WT

value: Dox and RNase T1

tag: antibody for ip

value: J2 (Scicons)

tag: library strategy

value: sequencing of double-stranded RNA


title: genomic DNA from fetal facing placenta tissue  [S0131]


title: genomic DNA from fetal facing placenta tissue  [S0129]


title: genomic DNA from fetal facing placenta tissue  [S0128]


title: genomic DNA from fetal facing placenta tissue  [S0127]


title: IS_5_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0126]


title: Sample48: E275_J2_IP_RIII_etoh_dsRNA-seq

value: EtOH, RNase T1 and RNase III

value: 10% U2OS cells (human)


title: hE_27_1

description: polyA RNA


title: genomic DNA from fetal facing placenta tissue  [S0122]


title: IS_4_scRNA-seq


title: Sample47: E275_J2_IP_RIII_dox_dsRNA-seq

value: pancreatic carcinoma

value: Dox, RNase T1 and RNase III


title: genomic DNA from fetal facing placenta tissue  [S0124]


title: genomic DNA from fetal facing placenta tissue  [S0120]

value: indian


title: Sample45: E275_J2_IP_dox_dsRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0119]

value: fetal facing placenta


title: IS_3_scRNA-seq


title: Sample46: E275_J2_IP_etoh_dsRNA-seq

value: EtOH and RNase T1


title: genomic DNA from fetal facing placenta tissue  [S0118]

value: Female

value: ART

value: chinese


title: IS_2_scRNA-seq


title: IF_2_scRNA-seq


title: ISK_1_scRNA-seq


title: Sample44: E275_IgG_etoh_dsRNA-seq

value: EtOH


title: IF_1_scRNA-seq

value: Human Embryonic Cells


title: IS_1_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0113]

value: Male


title: genomic DNA from fetal facing placenta tissue  [S0115]


title: IF_3_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0107]


title: genomic DNA from fetal facing placenta tissue  [S0114]


title: genomic DNA from fetal facing placenta tissue  [S0104]


title: Sample41: E275_input_dox_dsRNA-seq

value: CRISPR/Cas9 knockout of Myc

value: Dox-inducible expression of Myc-WT

value: Dox


title: Sample43: E275_IgG_dox_dsRNA-seq

value: sequencing of double-stranded RNA


title: genomic DNA from fetal facing placenta tissue  [S0112]


title: Sample42: E275_input_etoh_dsRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0106]


title: genomic DNA from fetal facing placenta tissue  [S0103]


title: Sample39: TBK1ko_shMyc_Dox_R2

description:
CA908_DE_TBK1ko_shMYC_Dox_vs_EV_shMYC_Dox
CA908_rawcount_matrix_all_samples.csv

data_processing:
For RNA-seq analysis, base calling was done with Illumina's FASTQ Generation software bcl2fastq Conversion v1.0.0 (for samples 1-16) and v2.19 (samples 17-40) and overall sequencing quality was determined with FastQC
Reads (FASTQ files) were mapped to whole genome mm9 (for samples 1-6) or to mm10 (samples 7-40) using Bowtie2 with default settings.
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed and differentially expressed genes were called using EdgeR.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: A matrix file (csv format) containing Ensembl gene ID, gene symbol, gene description and raw read counts for all genes of all samples.
Supplementary_files_format_and_content: A differential expression file (csv format) containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value (FDR) for the comparisons of all genes.

extract_protocol:
For in vitro experiments, total RNA was isolated by using the RNeasy Mini Kit (Qiagen) including on-column DNaseI digestion. mRNA was isolated by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
For in vivo experiments, tissue samples were extracted and frozen on dry ice. Total RNA was isolated by using the RNeasy Mini Kit (Qiagen) including on-column DNaseI digestion. mRNA was isolated by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were generated with 1 µg of purified mRNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter). The quality, quantity and the size of the cDNA libraries were determined with the Fragment Analyzer (Thermo Fisher Scientific, previously Advanced Analytical Technologies). Libraries were sequenced on a NextSeq500 System (Illumina).

value: shRNA targeting Myc

value: knockout of TBK1 and siRNA tageting IKBKE

value: mRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0100]


title: hE_25_scRNA-seq


title: hE_24_scRNA-seq


title: Sample40: TBK1ko_shMyc_Dox_R3

value: pancreatic carcinoma


title: genomic DNA from fetal facing placenta tissue  [S0099]


title: genomic DNA from fetal facing placenta tissue  [S0101]


title: hE_23_3_scRNA-seq


title: Sample38: TBK1ko_shMyc_Dox_R1


title: genomic DNA from fetal facing placenta tissue  [S0096]


title: genomic DNA from fetal facing placenta tissue  [S0094]


title: genomic DNA from fetal facing placenta tissue  [S0092]


title: hE_26_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0111]


title: hE_23_1_scRNA-seq


title: Sample36: TBK1ko_shMyc_EtOH_R2


title: genomic DNA from fetal facing placenta tissue  [S0091]

value: malay


title: genomic DNA from fetal facing placenta tissue  [S0084]

value: fetal facing placenta


title: Sample37: TBK1ko_shMyc_EtOH_R3


title: genomic DNA from fetal facing placenta tissue  [S0081]


title: genomic DNA from fetal facing placenta tissue  [S0078]

value: indian


title: hE_23_scRNA-seq


title: Sample34: EV_shMyc_Dox_R3


title: Sample35: TBK1ko_shMyc_EtOH_R1


title: genomic DNA from fetal facing placenta tissue  [S0098]


title: genomic DNA from fetal facing placenta tissue  [S0077]


title: hE_21_22_scRNA-seq


title: hE_23_2_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0074]

value: Female


title: hE_19_20_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0073]

value: ART


title: Sample32: EV_shMyc_Dox_R1


title: genomic DNA from fetal facing placenta tissue  [S0075]


title: Sample33: EV_shMyc_Dox_R2


title: genomic DNA from fetal facing placenta tissue  [S0072]


title: hE_18_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0071]


title: Sample31: EV_shMyc_EtOH_R3


title: hE_17_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0065]

value: chinese


title: genomic DNA from fetal facing placenta tissue  [S0068]


title: Sample30: EV_shMyc_EtOH_R2

value: EtOH


title: hE_16_scRNA-seq

value: Human Embryonic Cells


title: genomic DNA from fetal facing placenta tissue  [S0058]


title: Sample27: MycVD_EtOH_rep2

value: Dox-inducible expression of Myc-VD mutant


title: Sample29: EV_shMyc_EtOH_R1


title: genomic DNA from fetal facing placenta tissue  [S0055]

value: Male


title: hE_15_scRNA-seq


title: hE_15_1_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0056]


title: genomic DNA from fetal facing placenta tissue  [S0054]


title: hE_14_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0053]


title: genomic DNA from fetal facing placenta tissue  [S0049]


title: Sample26: MycVD_EtOH_rep1


title: genomic DNA from fetal facing placenta tissue  [S0046]


title: genomic DNA from fetal facing placenta tissue  [S0041]


title: hE_13_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0040]


title: hE_12_scRNA-seq


title: Sample25: MycVD_Dox_rep3

description:
CA893_DE_MycVD_Dox_vs_Myc_Dox
CA893_rawcount_matrix_all_samples.csv


title: Sample24: MycVD_Dox_rep2


title: genomic DNA from fetal facing placenta tissue  [S0031]


title: genomic DNA from fetal facing placenta tissue  [S0061]


title: Sample23: MycVD_Dox_rep1


title: hE_11_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0028]


title: genomic DNA from fetal facing placenta tissue  [S0027]


title: hE_10_scRNA-seq


title: Sample28: MycVD_EtOH_rep3


title: genomic DNA from fetal facing placenta tissue  [S0024]


title: hE_8_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0050]


title: genomic DNA from fetal facing placenta tissue  [S0022]


title: hE_9_scRNA-seq


title: Sample22: Myc_EtOH_rep3

value: Dox-inducible expression of Myc-WT


title: genomic DNA from fetal facing placenta tissue  [S0085]


title: Sample20: Myc_EtOH_rep1


title: genomic DNA from fetal facing placenta tissue  [S0020]


title: genomic DNA from fetal facing placenta tissue  [S0016]


title: genomic DNA from fetal facing placenta tissue  [S0021]


title: genomic DNA from fetal facing placenta tissue  [S0019]


title: Sample21: Myc_EtOH_rep2


title: genomic DNA from fetal facing placenta tissue  [S0015]


title: genomic DNA from fetal facing placenta tissue  [S0017]


title: hE_7_scRNA-seq


title: hE_4_1_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0030]


title: hE_5_6_scRNA-seq


title: Sample18: Myc_Dox_rep2

value: Dox


title: Sample19: Myc_Dox_rep3


title: genomic DNA from fetal facing placenta tissue  [S0013]


title: Sample17: Myc_Dox_rep1


title: genomic DNA from fetal facing placenta tissue  [S0010]


title: genomic DNA from fetal facing placenta tissue  [S0012]


title: genomic DNA from fetal facing placenta tissue  [S0025]


title: Sample16: tum_64A_withDox

description:
CA644_DE_tumor_shMYC_withDox_vs_noDox.csv
CA644_rawcount_matrix_all_samples.csv


title: hE_2_3_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0003]


title: Sample15: tum_63A_withDox


title: genomic DNA from fetal facing placenta tissue  [S0002]


title: Sample14: tum_61B_withDox


title: hE_1_scRNA-seq


title: genomic DNA from fetal facing placenta tissue  [S0014]


title: PMH_2456_AML

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences using Trim_galore with cutadapt
Reads were aligned to mouse genome assembly hg38 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: peripheral blood mononuclear cells (PBMCs)

extract_protocol:
RNA was isolated by TRIzol extraction
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

tag: disease state

value: blast phase disease (acute myeloid leukemia; AML)


title: PMH_2456_MF

value: peripheral blood mononuclear cells (PBMCs)

value: chronic phase myelofibrosis (MF)


title: hE_4_scRNA-seq

tag: tissue


title: 63552_AML


title: Sample11: tum_74A_noDox

value: shRNA targeting Myc

value: noDox

value: mRNA-seq


title: Sample12: tum_51B_withDox

value: pancreatic carcinoma


title: Sample13: tum_52A_withDox


title: 63552_MF


title: Sample10: tum_72A_noDox


title: 56932_AML


title: Sample9: tum_71A_noDox


title: 56932_MF


title: 56590_MF


title: Sample7: tum_54A_noDox


title: IMR32_EPZ-6438_D4 rep2

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to8x60K whole human genome oligonucleotide microarray (Agilent G4851B, grid ID 039494), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays (SureScan Microarray Scanner), and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background-subtracted and spatially detrended processed signal intensities.

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM, day4, replicate2

label_protocol: Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Human NB cell line SK-N-BE, SK-N-SH, NGP, IMR32 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). The total RNAs were extracted 3 days (SK-N-BE, SK-N-SH, NGP) or 4 days (IMR32) after the treatment.

treatment_protocol: NB cells were treated with 0.1% DMSO or EPZ-6438 1 μM on a 6 cm dish.

value: neuroblastoma cell line

value: EPZ-6438 1 µM, day4


title: NGP_EPZ-6438_D3_rep3

source_name: human neuroblastoma cell line NGP, EPZ-6438 1 µM, day3, replicate3

value: NGP

value: EPZ-6438 1 µM, day3


title: IMR32_EPZ-6438_D4 rep3

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM, day4, replicate3


title: NGP_DMSO_D3_rep2

source_name: human neuroblastoma cell line NGP, 0.1%DMSO, day3, replicate2

value: 0.1%DMSO, day3


title: NGP_DMSO_D3_rep3

source_name: human neuroblastoma cell line NGP, 0.1%DMSO, day3, replicate3


title: NGP_DMSO_D3_rep1

source_name: human neuroblastoma cell line NGP, 0.1%DMSO, day3, replicate1


title: IMR32_DMSO_D4_1

source_name: human neuroblastoma cell line IMR32, 0.1%DMSO, day4, replicate1

value: 0.1%DMSO, day4


title: NGP_EPZ-6438_D3_rep1

source_name: human neuroblastoma cell line NGP, EPZ-6438 1 µM, day3, replicate1


title: IMR32_DMSO_D4_3

source_name: human neuroblastoma cell line IMR32, 0.1%DMSO, day4, replicate3


title: IMR32_EPZ-6438_D4 rep1

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM, day4, replicate1


title: IMR32_DMSO_D4_2

source_name: human neuroblastoma cell line IMR32, 0.1%DMSO, day4, replicate2


title: NGP_EPZ-6438_D3_rep2

source_name: human neuroblastoma cell line NGP, EPZ-6438 1 µM, day3, replicate2


title: SK-N-SH_EPZ-6438_D3_rep2

source_name: human neuroblastoma cell line SK-N-SH, EPZ-6438 1 µM, day3, replicate2

value: SK-N-SH


title: SK-N-SH_EPZ-6438_D3_rep1

source_name: human neuroblastoma cell line SK-N-SH, EPZ-6438 1 µM, day3, replicate1


title: 56293_MF


title: 56293_AML


title: Sample6: KPC_shMYC_Dox_rep3

description:
CA619_DE_shMYC_Dox_vs_EtOH.csv
CA619_rawcount_matrix_all_samples.csv

source_name: KPC cells


title: Sample4: KPC_shMYC_Dox_rep1


title: 56590_AML


title: SK-N-SH_DMSO_D3_rep3

source_name: human neuroblastoma cell line SK-N-SH, 0.1%DMSO, day3, replicate3


title: 54910_MF

source_name: peripheral blood mononuclear cells (PBMCs)


title: 54910_AML


title: SK-N-SH_DMSO_D3_rep1

source_name: human neuroblastoma cell line SK-N-SH, 0.1%DMSO, day3, replicate1


title: SK-N-SH_DMSO_D3_rep2

source_name: human neuroblastoma cell line SK-N-SH, 0.1%DMSO, day3, replicate2


title: 52749_AML


title: 52749_MF


title: SK-N-SH_EPZ-6438_D3_rep3

source_name: human neuroblastoma cell line SK-N-SH, EPZ-6438 1 µM, day3, replicate3


title: Sample1: KPC_shMYC_EtOH_rep1

value: EtOH


title: SK-N-BE_DMSO_D3_rep2

source_name: human neuroblastoma cell line SK-N-BE, 0.1%DMSO, day3, replicate2

value: SK-N-BE


title: Sample2: KPC_shMYC_EtOH_rep2


title: SK-N-BE_EPZ-6438_D3_rep1

source_name: human neuroblastoma cell line SK-N-BE, EPZ-6438 1 µM, day3, replicate1


title: 46567_MF


title: SK-N-BE_DMSO_D3_rep1

source_name: human neuroblastoma cell line SK-N-BE, 0.1%DMSO, day3, replicate1


title: High_Fertility_9

city: Dunsany

first: Paul

last: Cormican

address: Grange

department: Bioscience

country: Ireland

institute: Teagasc

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to genome using STAR (v2.6.1b)
Read counts per gene for each sample were estimated using featurCounts from the subread package (v.1.6.3).
Supplementary files format and content: Bos_taurus_UMD_3.1.1
Supplementary files format and content: Individual matrix tables with raw gene counts for every gene in a sample

organism: Bos taurus

source_name: Uterine Post Mortem Biopsy

extract_protocol:
Uterine samples were taken, flash frozen before subsequent RNA extraction in TRIzol reagent. Total RNA concentration was quantified using the Nanodrop ND-1000 UV-Vis Spectophotometer. Quality of RNA was ascertained with the use of 2100 Agilent Bioanalyzer .
RNA libraries were prepared for sequencing using Illumina® TruSeq® Stranded mRNA Library preparation Kits

value: Uterine Post Mortem Biopsy

tag: breed

value: Holstein-Freisan

tag: Sex

value: Female

value: High Fertility


title: Sample3: KPC_shMYC_EtOH_rep3

value: shRNA targeting Myc


title: High_Fertility_10


title: IMR32_EPZ-6438 and 5-aza-dC_D4_rep3

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM and 5-aza-dC 1 µM, day4, replicate3

growth_protocol: Human NB cell line IMR32 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). The total RNAs were extracted 4 days after the treatment.

treatment_protocol: NB cells were treated with 0.1% DMSO, EPZ-6438 1 μM, 5-aza-dC 1 μM, EPZ-6438 1 μM and  5-aza-dC 1 μM on a 6 cm dish.

tag: cell line

value: EPZ-6438 1 µM and 5-aza-dC 1 µM, day4


title: Sample5: KPC_shMYC_Dox_rep2

tag: myc manipulation

value: Dox

value: mRNA-seq


title: Sample8: tum_55B_noDox

source_name: KPC derived pancreatic cancer tissue

value: pancreatic carcinoma

value: noDox


title: IMR32_5-aza-dC_D4_rep2

source_name: human neuroblastoma cell line IMR32, 5-aza-dC 1 µM, day4, replicate2

value: neuroblastoma cell line

value: 5-aza-dC 1 µM, day4


title: IMR32_5-aza-dC_D4_rep1

source_name: human neuroblastoma cell line IMR32, 5-aza-dC 1 µM, day4, replicate1


title: 46567_AML

value: peripheral blood mononuclear cells (PBMCs)

value: blast phase disease (acute myeloid leukemia; AML)


title: IMR32_EPZ-6438 and 5-aza-dC_D4_rep2

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM and 5-aza-dC 1 µM, day4, replicate2


title: 44786_MF

value: chronic phase myelofibrosis (MF)


title: High_Fertility_8


title: High_Fertility_7


title: IMR32_EPZ-6438 and 5-aza-dC_D4_rep1

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM and 5-aza-dC 1 µM, day4, replicate1


title: IMR32_5-aza-dC_D4_rep3

source_name: human neuroblastoma cell line IMR32, 5-aza-dC 1 µM, day4, replicate3


title: SK-N-BE_EPZ-6438_D3_rep3

source_name: human neuroblastoma cell line SK-N-BE, EPZ-6438 1 µM, day3, replicate3

value: EPZ-6438 1 µM, day3


title: High_Fertility_6


title: 29485_MF


title: IMR32_EPZ-6438_D4_rep3

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM, day4, replicate3

value: EPZ-6438 1 µM, day4


title: IMR32_EPZ-6438_D4_rep2

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM, day4, replicate2


title: 29485_AML

source_name: peripheral blood mononuclear cells (PBMCs)


title: IMR32_EPZ-6438_D4_rep1

source_name: human neuroblastoma cell line IMR32, EPZ-6438 1 µM, day4, replicate1


title: 44786_AML


title: 16345_MF


title: SK-N-BE_DMSO_D3_rep3

source_name: human neuroblastoma cell line SK-N-BE, 0.1%DMSO, day3, replicate3

value: SK-N-BE

value: 0.1%DMSO, day3


title: IMR32_DMSO_D4_rep2

source_name: human neuroblastoma cell line IMR32, 0.1%DMSO, day4, replicate2

value: 0.1%DMSO, day4


title: IMR32_DMSO_D4_rep3

source_name: human neuroblastoma cell line IMR32, 0.1%DMSO, day4, replicate3