title: Mouse mammary epithelial cells, Double_2

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19 for human samples, mm10 for mouse
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR

source_name: Mouse mammary epithelial cells

growth_protocol: All mice were housed at Memorial Sloan Kettering Cancer Center and All mouse procedures were completed in accordance with the Guidelines for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committees at MSKCC. Cell lines were maintained in 37°C incubator with 5% CO2 in humidified atmosphere. MCF7 cells were grown in DMEM/F12 supplemented with 10% FBS (Gibco), 100 μg/mL penicillin, 100 mg/mL streptomycin (Corning), and 4 mM glutamine, and MCF10A cells were grown in DMEM/F12 supplemented with 5% horse serum (Gibco), 20ng/mL EGF (Sigma-Aldrich), 10μg/mL insulin (Sigma-Aldrich), 0.5μg/mL hydrocortisone (Sigma-Aldrich),  0.1μg/mL cholera toxin (Sigma-Aldrich), 100 μg/mL penicillin, and 100 mg/mL streptomycin (Corning). T47D cells were cultured in RPMI1640 with 10% FBS (Gibco), 100 μg/mL penicillin and 100 mg/mL streptomycin (Corning).

extract_protocol:
Mammary gland epithelial cells were isolated from 4-month old mice. Breifly, mammary glands dissected from 4-month-old female mice were minced and digested with collagenase/trypsin mixture for 4 hours at 37C. After washed with L15 medium supplemented with 10% FBS, the red blood cells were lysed with Hybri-Max Red Blood Cell Lysing Buffer (Sigma). After washing with L15/10% FBS medium, the samples were incubated in serum-free Joklik’s medium and then treated with 0.05% trypsin and DNase I (Fisher Scientific). Trypsin was neutralized by adding L15/10% FBS medium and the samples were filtered through a 40m cell strainer to remove cell clumps and debris. Cells were pelleted and resuspended in L15/10% FBS medium. Fluorescence-activated cell sorting (FACS) was used to isolate mammary epithelial cells. The cells were incubated with antibodies against CD24 and CD45 in L15/10% FBS medium on ice for 45 min. DAPI was used to exclude dead cells. The mammary epithelial cells were sorted as CD24+/CD45- cells on FACS Aria sorter. Human cell lines were hearvested at 70% to 80% confluence. Total RNA was extracted with Direct-Zol RNA miniprep kit (Zymo).
Libraries were constructed with TruSeq RNA-seq prep kit by Genewiz or MSKCC Integrated Genomics Operation Core Facility.

treatment_protocol: MCF7 and T47D cell were treated with doxycycline to induce wild-type or mutant SF3B1 expression for 48 hours before hearvesting cells.

value: Mouse mammary epithelial cells

tag: genotype

value: Sf3b1 K700E & Pik3ca H1047R


title: A12.CD8.C4.rep5.b8.Healthy

status: Public on Jan 05 2021

type: SRA

city: San Francisco

first: Wilson

last: Liao

state: CA

address: 2340 Sutter St.

department: Dermatology

country: USA

institute: University of California, San Francisco

description: CountTable_SingleCellPsoCd8s_20200218.tsv

library_source: transcriptomic

data_processing:
Mapping was performed with STAR 2.4.2a to the human reference genome (GRCh38, GENCODE release 25) and the 92 reference sequences of the ERCC spike-in standard.
Read counts for each transcript were tallied using HTSeq 0.6.1p1
Filtering was performed to exclude cells that contained less than 100,000 mapped reads, less than 1,000 mapped genes, greater than 25% mapped reads on ERCC spike-ins, or greater than 25% mapped reads on mitochondrial genes. We also excluded genes that were not detected with at least 5 transcripts in at least two cells.
Read counts across libraries were normalized by RUVg, implemented in the RUVSeq 1.8.0 R package on ERCC spike-in counts to control for batch, depth, and other technical confounding effects
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file contains unnormalized read counts of each gene (rows) in each sample (columns)

molecule: polyA RNA

organism: Homo sapiens

source_name: Healthy skin

extract_protocol:
Skin punch biopsies were immediately stored at 4 °C in a container with sterile gauze and PBS until they were ready to be processed. The tissue was trimmed to remove hair and subcutaneous adipose before being finely minced and mixed with digestion buffer composed of Collagenase Type IV (Worthington LS04188), DNAse (Sigma-Aldrich DN25-1G), 10% FBS, 1% HEPES, and 1% Penicillin/Streptavidin in RPMI 1640. After overnight incubation in 5% CO2, cell suspensions were harvested, filtered, centrifuged, counted, and stained for CD45+CD3+CD8+ cells. These cells were directly sorted into 10X Reaction Buffer prepared from the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech cat. 634894) and snap frozen in liquid nitrogen for storage at −80 °C.
Full length cDNA synthesis of each cell was performed using the SMART-Seq v4 Ultra Low Input Kit with the following specifications and modifications. All reactions were prepared with a MANTIS liquid handler (Formulatrix) to allow miniaturization of the reaction volume to half of the manufacturer’s recommended volume.  0.4 µL of 1:4,000,000 diluted External RNA Controls Consortium (ERCC) RNA Spike-In (Thermo Fisher Scientific, cat. 4456740) was added to each cell lysate prior to the First-Strand Synthesis step. LD PCR was performed for 19 cycles. Purification of cDNA was performed using Agencourt AMPure XP beads (Beckman Coulter, cat. A63881) and quantified using the QuantIT PicoGreen dsDNA Assay Kit (Invitrogen, cat. P7589). Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina, cat. FC-131-1096), QC’d using the Bioanalyzer High Sensitivity DNA Kit (Agilent, cat. 5067-4626), and quantified by NEBNext library quantification kit for Illumina (New England Biolab, cat. E7630L). Read sequencing was performed on an Illumina HiSeq 4000.

tag: celltype

value: CD8+ T cell

tag: subjectid

tag: plate

tag: well

tag: sequencingbatch

tag: passedqc

value: FALSE

tag: cluster


title: Mouse mammary epithelial cells, PIK3CA_3

organism: Mus musculus

tag: cell type

value: Pik3ca H1047R


title: A12.CD8.C4.rep2.b7.Healthy

value: TRUE


title: Mouse mammary epithelial cells, Double_1


title: Mouse mammary epithelial cells, PIK3CA_2


title: A12.CD8.C4.rep3.b7.Healthy


title: Mouse mammary epithelial cells, PIK3CA_1


title: A12.CD8.C4.rep1.b7.Healthy


title: Mouse mammary epithelial cells, SF3B1_1

value: Sf3b1 K700E


title: Mouse mammary epithelial cells, SF3B1_2


title: A12.CD8.C13.rep2.b3.Healthy


title: A12.CD8.C13.rep1.b3.Healthy


title: A12.CD8.C14.rep1.b5.Healthy


title: Mouse mammary epithelial cells, WT-3

value: wild type


title: A11.CD8.P9.rep2.b6.PSO

source_name: Psoriasis lesion


title: Mouse mammary epithelial cells, WT-2


title: A11.CD8.P5.rep1.b2.PSO


title: A11.CD8.P5.rep2.b2.PSO


title: Mouse mammary epithelial cells, Double_3


title: hESC_untreated_rep4_TrAEL-seq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: hESC_replicates_rDNA_forward_reads_100bp_windows_spaced_10bp.txt

library_source: genomic

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified in windows: for dmc1 total read counts in 20bp windows, for hESC %reverse reads in 250kb windows every 10kb, for SfiI digests total read counts at 13bp cleavage sites, for other samples %reverse reads in 1kb windows
Genome_build: S. cerevisiae R64-1-1 or GRCh38

molecule: genomic DNA

source_name: hESC line H9

extract_protocol:
For yeast: Cells in ethanol (1-3x107 per plug) were pelleted in round bottom 2 ml tubes by centrifuging 30 s 20,000 g, washed once in 1 ml PFGE wash buffer (10 mM Tris HCl pH 7.5, 50 mM EDTA) and resuspended in 60 µl same with 1 µl lyticase (17 U/ µl in 10 mM KPO4 pH7, 50% glycerol, Merck >2000 U/mg L2524). Samples were heated to 50°C for 1-10 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl PFGE was buffer containing 10 µl 17 U/µl lyticase and incubated 1 hour at 37°. Solution was replaced with 500 µl PK buffer (100 mM EDTA pH 8, 0.2% sodium deoxycholate, 1% sodium N-lauroyl sarcosine, 1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were rinsed with 1 ml TE, then washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. RNase A was not used as it binds strongly to single stranded DNA [76]. For hESC: 1x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Washing as for yeast.
TrAEL-seq: ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.  END-seq: ½ an agarose plug of cells was equilibrated for 1 h at room temperature in 100µl NEBuffer 2 with 0.1mM dNTPs, then overnight at 37°C with 100 µl NEBuffer 2 with 0.1 mM dNTPs and 1 µl Klenow (NEB M0210S). Note that this is not the same blunting regimen used in END-seq [11] as Klenow performed best for SfiI-digested yeast genomic DNA in our hands. After rinsing twice with 1 ml tris buffer, plug was transferred to a 15 ml tube and washed three times for 15 min each with 10 ml tris buffer on rocker at room temperature before transfer to a new 2 ml tube. The plug was equilibrated with 100 µl CutSmart buffer containing 5 mM DTT and 1 mM dATP for 1 hour at room temperature before incubation for 2 h at 37°C in another 100 µl of the same buffer containing 1 µl Klenow exo- (NEB M0212S) and 1 µl T4 PNK (NEB M0201S). Plug was rinsed twice with 1 ml tris buffer then washed once with 10 ml of tris buffer for 15 min as above then returned to a 2 ml tube. The plug was equilibrated for 1 h at room temperature in 100 µl 1x Quick Ligation buffer (NEB B6058S) containing 2.7 µl END-seq adaptor 1 ([Phos]GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[BtndT]U[BtndT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC∗T), then overnight at 25°C with another 100 µl of the same buffer containing  2.7 µl END-seq adaptor 1 and 1 µl high concentration T4 DNA Ligase (NEB M0202M). After rinsing twice with 1 ml tris buffer, plug was transferred to a 15 ml tube and washed three times for 1-2 h each with 10 ml tris buffer on rocker at room temperature, then again overnight.  The plug was transferred to a 1.5 ml tube and equilibrated 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added to the plug. Plug was melted 20 min at 65°C then transferred for 5 min to a heating block pre-heated to 42°C, 1 µl beta-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 130 µl 1x TE, 15 min at 65°C.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ) or END-seq adaptor 2c ([Phos]GATCGGAAGAGCTATTATTTAAATTTTAATTUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA

tag: strain

value: hESC line H9

tag: growth and treatment

value: Maintained in E8 media

tag: fix and post-processing


title: Mouse mammary epithelial cells, WT-1


title: A11.CD8.P19.rep6.b19.PSO


title: A11.CD8.P19.rep5.b19.PSO


title: human gastric organoids TP53/ARID1A DKO; biological rep2; technical rep 2

city: Stanford

first: Andrey

last: Krokhotin

address: 279 Campus Drive W

institute: HHMI

data_processing:
Kallisto 0.44.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values for each Sample ...

molecule: total RNA

source_name: Human gastric organoids

growth_protocol: Human gastric organoids were established and grown as previously reported (Bartfeld et al. Gastroenterology. 2015;148:126–36.)

extract_protocol:
Total RNA from organoids was isolated with the RNeasy kit (Qiagen, #74106)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human gastric organoids


title: human gastric organoids TP53KO; biological rep2;


title: human gastric organoids TP53/ARID1A DKO; biological rep1; technical rep 2


title: hESC_untreated_rep3_TrAEL-seq


title: A11.CD8.P19.rep4.b19.PSO


title: A11.CD8.P18.rep6.b17.PSO


title: human gastric organoids TP53/ARID1A DKO; biological rep1; technical rep 1


title: A11.CD8.P18.rep5.b17.PSO


title: human gastric organoids TP53KO; biological rep1;


title: RNAseq gMYC transduced cells (replicate 3)

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
RNA-seq reads were mapped to the human reference genome with Star software. Reads counts were estimated for human Ensembl genes annotation.
Genome_build: hg19
Supplementary_files_format_and_content: xls

source_name: Primary HUVECs from pooled donors_gMYC

growth_protocol: Pooled human umbilical vein endothelial cells (HUVECs) were purchased from Lonza (#CC-2519) and cultured in endothelial basal medium (EBM, Lonza) supplemented with hydrocortisone (1 µg/mL), bovine brain extract (12 µg/mL), gentamicin (50 µg/mL), amphotericin B (50 ng/mL), human recombinant epidermal growth factor (10 ng/mL), and 10% fetal bovine serum (FBS, Life Technologies).

extract_protocol:
RNA was isolated from HUVECs using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a LabChip Gx Touch 24 (Perkin Elmer). 4 μg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).
Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 32M reads per library with 1x75bp single end setup.

treatment_protocol: A pool of gCTL or gMYC transduced HUVECs was selected with 0.5  μg of  Puromycin.

value: Primary HUVECs from pooled donors

tag: treatment

value: CRISRP/CAS9 - gMYC


title: A11.CD8.P18.rep4.b17.PSO


title: A11.CD8.P19.rep3.b19.PSO


title: RNAseq gMYC transduced cells (replicate 2)


title: RNAseq gCTL transduced cells (replicate 3)

source_name: Primary HUVECs from pooled donors_gCTL

value: CRISRP/CAS9 - gCTL


title: RNAseq gMYC transduced cells (replicate 1)


title: A11.CD8.P19.rep1.b19.PSO


title: A11.CD8.P18.rep2.b18.PSO


title: A11.CD8.P17.rep6.b16.PSO


title: Cs-137 irradiation, 80 cGy, replicate 2

type: RNA

city: New York

first: David

last: Goukassian

state: NY

address: 1470 Madison Ave

department: Cardiovascular Research Center

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: According to the manufacturer’s instructions.

scan_protocol: Chips were scanned with an Affymetrix GeneChip Scanner using 3000 Command Console Software.

data_processing: Arrays were processed and RMA normalized using oligo, pd.clariom.s.mouse, annotate and clariomsmousetranscriptcluster.db BioConductor packages .

source_name: Cs-137 irradiation_80 cGy_heart tissue

label_protocol: RNA fluorescent labeling reaction were performed using the Affymetrix WT-Plus kit according to the manufacturer’s instructions.

growth_protocol: 100-120-day old female CB6F1/Hsd mice were obtained from Harlan Laboratories Inc. (Indianapolis, IN). Animals  were shipped directly from the vendor to the animal facility at Brookhaven National Laboratory-BLAF (Upton, New York) approximately 1 week before irradiation. Mice were randomized by weight immediately prior to whole-body particle IR exposure. After exposure, mice were shipped to the animal facility at Lawrence Berkley National Laboratory (LBNL) and maintained for 16 months. All procedures were compliant with the standards of the Guide for the Care and Use of Laboratory Animals for the National Institutes of Health and approved by the Animal Care and Use Committees at Lawrence Berkley National Laboratory (Berkley, CA), Brookhaven National Laboratory (BNL) (Upton, NY) and SRI International (Menlo Park, CA).

extract_protocol: Total RNA was isolated from snap-frozen heart tissues using a total RNA isolation kit (Qiagen, Germantown, MD). RNA concentrations were assessed using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and quality assessment was performed using Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Female CB6F1/Hsd mice were irradiated with a single, full-body HZE dose (≤0.5 Gy) of 260 MeV/n silicon (14Si, LET ~ 70 keV/µm) and 1,000 MeV/n titanium (22Ti, LET ~ 100 keV/µm) Another group of animals were also irradiated with 137Cs gamma-ray that served as a low-LET reference. Control sham-treated animals were placed in clear plastic holders for equivalent exposure times but were not irradiated. Unanesthetized animals were briefly held in plastic boxes (40 x 40 x 73 mm) containing numerous holes to provide abundant airflow. Dosimetry studies, including depth-dose and dose-uniformity measurements, were conducted by beamline physicists.

tag: Sex

value: female

tag: treatment/group

value: Cs-137 irradiation, 80 cGy

tag: tissue

value: heart


title: A11.CD8.P18.rep1.b18.PSO


title: A11.CD8.P17.rep5.b16.PSO


title: human gastric organoids TP53/ARID1A DKO; biological rep2; technical rep 1


title: RNAseq gCTL transduced cells (replicate 2)


title: hESC_untreated_rep2_TrAEL-seq


title: RNAseq gCTL transduced cells (replicate 1)


title: A11.CD8.P19.rep2.b19.PSO


title: THZ531_3

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

description:
all_TALL_samples_peaks.narrowPeak
TALL_THZ531_forwardRawCov.bw
TALL_THZ531_reverseRawCov.bw

data_processing:
Single-end 50bp reads were filtered with bbduk.sh and parameters “k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=20 minlength=75 ref=truseq_rna.fa.gz”
STAR (v2.5.1b) was used to align reads to the human genome (GRCh38) with the following parameters “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate”.
Strand specific coverage profiles were created with the bamCoverage command (DeepTools v2.5.4) with parameters “--normalizeUsingRPKM –filterRNAstrand –bs 50".
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
PolyA-seq peaks were called using MACS2 (v 2.1.1) and parameters “--nomodel --extsize 100 --shift 0”.
Genome_build: GRCh38
Supplementary_files_format_and_content: Combined MACS narrow peak file and bedgrap coverage files for merged replicates of each treatment condition.

source_name: Jurkat cells

growth_protocol: Jurkat cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum

extract_protocol:
Biological duplicated were collected and RNA extraction was performed with TRIzol (Ambion) following the manufacturers’ instructions. Total RNA was treated with DNase I (Invitrogen).
Sequencing libraries were prepared with the RNA-seq library kit (QuantSeq 3’ mRNA Sequencing REV, Lexogen) following the manufacturers’ instructions.

treatment_protocol: Cells were incubated for 8 hours in the presence of DMSO or BSJ-4-116 (50 nM) or BSJ-4-116NC (100 nM) or THZ531 (250nM) before performing RNA extraction.

tag: origin

value: T-ALL


title: THZ531_2


title: A11.CD8.P17.rep2.b16.PSO


title: THZ531_1


title: A11.CD8.P17.rep1.b16.PSO


title: A11.CD8.P18.rep3.b18.PSO


title: A11.CD8.P16.rep6.b13.PSO


title: DMSO_1

description:
all_TALL_samples_peaks.narrowPeak
TALL_DMSO_forwardRawCov.bw
TALL_DMSO_forwardRawCov.bw

value: DMSO


title: A11.CD8.P16.rep4.b13.PSO

value: CD8+ T cell


title: CDK12nc_3

description:
all_TALL_samples_peaks.narrowPeak
TALL_CDK12NC_forwardRawCov.bw
TALL_CDK12NC_reverseRawCov.bw


title: CDK12nc_2


title: DMSO_2


title: A11.CD8.P16.rep2.b13.PSO


title: CDK12degr_3

description:
all_TALL_samples_peaks.narrowPeak
TALL_CDK12degr_forwardRawCov.bw
TALL_CDK12degr_reverseRawCov.bw


title: A11.CD8.P16.rep1.b13.PSO

value: FALSE


title: CDK12degr_2


title: A11.CD8.P15.rep6.b13.PSO


title: A11.CD8.P17.rep4.b16.PSO


title: A11.CD8.P15.rep4.b12.PSO


title: RNAseq Control at 32h (replicate 3)

description: polyA RNA

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
RNA-seq reads were mapped to the human reference genome with Star software. Reads counts were estimated for human Ensembl genes annotation.
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Primary HUVECs from pooled donors at 32h

value: HUVECs

tag: time

value: control


title: A11.CD8.P15.rep5.b13.PSO

tag: celltype

value: TRUE


title: CDK12degr_1


title: A11.CD8.P15.rep3.b12.PSO

tag: subjectid


title: A11.CD8.P17.rep3.b16.PSO

tag: plate


title: A11.CD8.P15.rep2.b12.PSO

tag: well


title: DMSO_3


title: RNAseq Control at 32h (replicate 1)

description: polyA RNA


title: RNAseq Control at 32h (replicate 2)

description: polyA RNA


title: RNAseq Control at 16h (replicate 3)

description: polyA RNA

source_name: Primary HUVECs from pooled donors at 16h


title: A11.CD8.P15.rep1.b12.PSO

tag: sequencingbatch


title: A11.CD8.P14.rep8.b10.PSO

tag: passedqc


title: Cs-137 irradiation, 160 cGy, replicate 2

source_name: Cs-137 irradiation_160 cGy_heart tissue

value: Cs-137 irradiation, 160 cGy


title: RNAseq Control at 16h (replicate 2)

description: polyA RNA


title: RNAseq Control at 16h (replicate 1)

description: polyA RNA


title: A11.CD8.P16.rep5.b13.PSO

tag: cluster


title: A11.CD8.P16.rep3.b13.PSO


title: RNAseq FOXO1A3 overexpression at 32h (replicate 3)

description: polyA RNA

tag: cell type

value: FOXO1A3 overexpression


title: A11.CD8.P14.rep6.b10.PSO


title: A11.CD8.P14.rep7.b10.PSO


title: A11.CD8.P14.rep5.b10.PSO


title: A11.CD8.P14.rep4.b10.PSO


title: RNAseq FOXO1A3 overexpression at 32h (replicate 2)

description: polyA RNA


title: RNAseq FOXO1A3 overexpression at 16h (replicate 3)

description: polyA RNA


title: A11.CD8.P14.rep3.b10.PSO


title: RNAseq FOXO1A3 overexpression at 16h (replicate 1)

description: polyA RNA


title: RNAseq FOXO1A3 overexpression at 16h (replicate 2)

description: polyA RNA


title: A11.CD8.P14.rep2.b10.PSO


title: A11.CD8.P13.rep4.b8.PSO


title: A11.CD8.P13.rep3.b7.PSO


title: H3K4me3 ChIPseq AdFOXO1A3

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
Reads were aligned to the human genome (hg38) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: Primary HUVECs from pooled donors at 24h

extract_protocol:
HUVECs were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 μg of antibody against FOXO1 (abcam), . Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: HUVECs transduced with an AKT-insensitive nuclear active FOXO1 encoding adenovirus compared to control HUVECs (Ad-Null). HUVECs were collected 24h after transduction.

value: HUVEC

tag: chip antibody

value: H3K4me3, Active Motif, #39159

tag: genotype

tag: fraction

value: H3K4me3 immunoprecipitated DNA


title: A11.CD8.P14.rep1.b10.PSO


title: A11.CD8.P13.rep2.b7.PSO


title: HUVEC_pooled_input

value: pooled samples (control and FOXO1A3 overexpression)

value: Input DNA


title: A11.CD8.P13.rep1.b7.PSO


title: H3K4me3 ChIPseq AdControl


title: H3K27ac ChIPseq AdFOXO1A3

value: H3K27ac, Active Motif, #39133

value: H3K27ac immunoprecipitated DNA


title: FOXO1 ChIPseq AdFOXO1A3

value: FOXO1 immunoprecipitated DNA


title: RNAseq FOXO1A3 overexpression at 32h (replicate 1)

description: polyA RNA

tag: treatment


title: A11.CD8.P10.rep1.b7.PSO


title: A11.CD8.P11.rep2.b6.PSO


title: RNAseq Control at 24h (replicate 3)


title: FOXO1 ChIPseq AdControl


title: RNAseq Control at 24h (replicate 2)


title: A11.CD8.P13.rep5.b8.PSO


title: A11.CD8.C7.rep7.b15.Healthy


title: RNAseq Control at 24h (replicate 1)


title: A11.CD8.C7.rep5.b15.Healthy


title: RNAseq FOXO1A3 overexpression at 24h (replicate 2)


title: A11.CD8.C7.rep4.b15.Healthy


title: A11.CD8.C7.rep3.b15.Healthy


title: RNAseq FOXO1A3 overexpression at 24h (replicate 1)


title: RNAseq S-2HG Treatment at 24h (replicate 3)

extract_protocol:
RNA was isolated from HUVEC cells using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a LabChip Gx Touch 24 (Perkin Elmer). 4 μg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).
Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 32M reads per library with 1x75bp single end setup.

treatment_protocol: HUVECs were treated for 24h with 800 µM of cell-permeable (2R)-Octyl-α-hydroxyglutarate or (2S)-Octyl-α-hydroxyglutarate (Cayman Chemical) compared to control vehicle (DMSO).


title: A11.CD8.P11.rep1.b6.PSO


title: A11.CD8.C7.rep2.b15.Healthy


title: RNAseq S-2HG Treatment at 24h (replicate 2)


title: A11.CD8.C7.rep1.b15.Healthy


title: A11.CD8.C6.rep5.b10.Healthy


title: H3K27ac ChIPseq AdControl


title: RNAseq R-2HG Treatment at 24h (replicate 3)


title: A11.CD8.C6.rep4.b10.Healthy


title: RNAseq FOXO1A3 overexpression at 24h (replicate 3)


title: RNAseq R-2HG Treatment at 24h (replicate 1)


title: RNAseq DMSO at 24h (replicate 3)


title: A11.CD8.C6.rep3.b10.Healthy


title: A11.CD8.C6.rep2.b11.Healthy


title: A11.CD8.C6.rep2.b10.Healthy


title: A11.CD8.C6.rep1.b10.Healthy


title: A11.CD8.C5.rep5.b9.Healthy


title: A11.CD8.C5.rep6.b9.Healthy


title: RNAseq DMSO at 24h (replicate 1)


title: A11.CD8.C6.rep6.b10.Healthy


title: A11.CD8.C5.rep4.b9.Healthy


title: RNAseq S-2HG Treatment at 24h (replicate 1)


title: CALM-AF10 in vitro final timepoint replicate 2

city: San Diego

first: Aniruddha

last: Deshpande

state: California

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
All analyses were performed using PinAPL-Py software (Spahn et al., 2017).
sgRNA raking was performed with BH p-value adjustment.
Gene ranking was performed through the adjusted robust-ranked aggregation algorithm.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Txt files containing sgRNA normalized read counts and Excel spreadsheet containing sgRNA- and gene- level statistics.

source_name: Mouse AML

growth_protocol: In vitro samples were cultured for 12 days in DMEM medium supplemented with 2 mM L-glutamine, 15% FBS and 50U/ml Penicillin/Streptomycin, in the presence of following cytokines: 10 ng/ml murine Interleukin 6 (mIL-6), 6 ng/ml murine Interleukin 3 (mIL3) and 20 ng/ml murine stem cell factor (mSCF) (all from Peprotech, Rocky Hill, NJ), and incubated in 5% CO2 at 37°C.

extract_protocol:
Extraction of genomic DNA was performed using the Zymo Quick-DNA™ Miniprep Plus Kit (Zymo Research, Cat. D4068) according to manufacturer’s instructions.
Library construction was performed according to Canver et al. (2018), with custom primers to achieve sequencing with 1x75 bp single-end.
Aplicon sequencing

tag: sample type

value: Mouse CALM-AF10 AML

tag: strain


title: CALM-AF10 in vitro final timepoint replicate 1


title: CALM-AF10 in vivo final timepoint replicate 2


title: CALM-AF10 in vivo final timepoint replicate 1


title: CALM-AF10 T0 replicate 2


title: A11.CD8.C5.rep1.b9.Healthy


title: RNAseq R-2HG Treatment at 24h (replicate 2)


title: A11.CD8.C5.rep2.b9.Healthy


title: CALM-AF10 T0 replicate 1


title: A11.CD8.C4.rep6.b8.Healthy


title: RNAseq DMSO at 24h (replicate 2)

value: DMSO


title: iCALM_AF10_Dox_H3K27Ac_input

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq  Sequence reads were aligned to  mouse genome assembly mm9 using Bowtie (Langmead et al., 2009)
Reads that aligned to multiple loci in the genome were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools

source_name: CALM-AF10 AML cells

growth_protocol: Murine CALM-AF10 AML cells were grown in DMEM supplemented with 15% FBS and 1% Penicilin+ Streptomycin  with 10ng/ml of IL6, 20 ng/ml of SCF and 6ng/ml of IL3.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with the H3K27ac antibody.
Libraries were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina following the manufacturer's protocols.

treatment_protocol: Cells were treated with either DMSO (vehicle) or 4ug/ml Doxycycline for 72 hours before fixing cells for ChIP.

value: mouse AML cell lines

value: input

value: DOX treated


title: iCALM_AF10_Dox_H3K27Ac_R2

value: Abcam, ab4729


title: A11.CD8.C4.rep5.b8.Healthy

value: CD8+ T cell

value: TRUE


title: A11.CD8.C4.rep3.b7.Healthy


title: iCALM_AF10_Dox_H3K27Ac_R1


title: iCALM_AF10_DMSO_H3K27Ac_input

value: DMSO treated


title: iCALM_AF10_DMSO_H3K27Ac_R2


title: iCALM_AF10_DMSO_H3K27Ac_R1


title: A11.CD8.C4.rep4.b8.Healthy


title: A11.CD8.C14.rep1.b5.Healthy

value: FALSE


title: CALM_AF10_Jak1_null_R3

data_processing:
Illumina Casava1.7 software or Rosalind software (OnRamp Bio) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with normalized FPKM values or every gene and every sample.

source_name: Leukemia Cells

growth_protocol: Cells were grown in DMEM medium supplemented with 15% fetal bovine serum, 1% penicillin and streptomycin, and 20ng per ml of SCF, 6 ng per ml of IL3 and 100ng per ml of IL6.

extract_protocol:
AML cells were grown in murine bone marrow medium,pelleted, and washed with PBS before pelleting again. RNA was harvested using Trizol reagent and cleaned up by repurification using the RNEasy Mini Kit (Qiagen) . Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with Dox (for On/Off experiments) or 4-OHT (for Cre-ER mediated Jak1 deletion),

tag: tissue

value: Bone marrow

tag: age

value: cultured and treared

value: Jak1 deleted


title: A11.CD8.C13.rep1.b3.Healthy


title: CALM_AF10_Jak1_null_R1


title: A10.CD8.P9.rep2.b6.PSO


title: A11.CD8.C4.rep2.b7.Healthy


title: CALM_AF10_Jak1_null_R2


title: A10.CD8.P5.rep1.b2.PSO


title: A11.CD8.C13.rep2.b3.Healthy


title: CALM_AF10_Jak1_floxed_R2

value: Jak1 floxed


title: A10.CD8.P19.rep6.b19.PSO


title: CALM_AF10_Jak1_floxed_R3


title: A10.CD8.P19.rep5.b19.PSO


title: iMLL_AF9_DOX_R3

value: wild type


title: CALM_AF10_Jak1_floxed_R1


title: opcBulk_150dpi_WT_22064_tdTpositive

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description:
opcBulk_150dpi_WT_22064_tdTpositive
rsem_opc.csv

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the mouse (GRCm38.82) transcriptome using RSEM. Reference ERCC sequences were also provided for the alignment.
RSEM options for pool-and-split controls and 10-cell samples: --bowtie2 --single-cell-prior --paired-end (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts, paired end reads)
RSEM options for bulk samples: --bowtie2 (Bowtie2 transcriptome aligner)
Comma-separated values (CSV) file includes read counts from RSEM
Genome_build: GRCm38.82
Supplementary_files_format_and_content: 2020_03_20_opc_allcompiled.csv (read counts)

source_name: Brain oligodendrocyte precursor cells

extract_protocol:
T7-based linear amplification
Double-stranded cDNA was mechanically sheared to between 150 and 600 bp by sonication using a Bioruptor (Diagenode)
All samples were cryoembedded and sectioned onto glass slides. Cell samples were isolated via laser capture microdissection prior to RNA extraction, reverse transcription, and RNA amplification

value: wild-type

tag: time

value: 150 dpi (days following tamoxifen treatment start)

value: bulk

tag: Sex

value: female

tag: section thickness (µm)


title: A11.CD8.C5.rep3.b9.Healthy

tag: celltype

tag: subjectid

tag: plate


title: iMLL_AF9_DOX_R1


title: iMLL_AF9_DOX_R2


title: opcBulk_150dpi_WT_22062_tdTpositive

description:
opcBulk_150dpi_WT_22062_tdTpositive
rsem_opc.csv


title: opcBulk_150dpi_WT_21592_tdTpositive

description:
opcBulk_150dpi_WT_21592_tdTpositive
rsem_opc.csv

value: male


title: A11.CD8.C4.rep1.b7.Healthy

tag: well

tag: sequencingbatch

tag: passedqc


title: iMLL_AF9_DMSO_R3


title: opcBulk_150dpi_WT_21591_tdTpositive

description:
opcBulk_150dpi_WT_21591_tdTpositive
rsem_opc.csv


title: A10.CD8.P19.rep2.b19.PSO

tag: cluster


title: A10.CD8.P5.rep2.b2.PSO


description:
opcBulk_150dpi_Tumor_21354_tdTpositive_TGTGC
rsem_opc.csv

source_name: Brain tumor cells

tag: genotype


description:
opcBulk_150dpi_Tumor_21354_tdTpositive_ACGTA
rsem_opc.csv


title: opcBulk_150dpi_WT_21590_tdTpositive

description:
opcBulk_150dpi_WT_21590_tdTpositive
rsem_opc.csv


title: A10.CD8.P19.rep1.b19.PSO


description:
opcBulk_150dpi_Tumor_21349_tdTpositive_TCTTC
rsem_opc.csv


title: A10.CD8.P18.rep6.b17.PSO


title: A10.CD8.P18.rep5.b17.PSO


description:
opcBulk_150dpi_Tumor_21256_tdTpositive_GAACA
rsem_opc.csv


title: iMLL_AF9_DMSO_R1


title: iMLL_AF10_DOX_R3


description:
opcBulk_150dpi_Tumor_21256_tdTpositive_TTTAG
rsem_opc.csv


description:
opcBulk_150dpi_Tumor_16844_tdTpositive_TTGGT
rsem_opc.csv


description:
opcBulk_150dpi_Tumor_16844_tdTpositive_AACAA
rsem_opc.csv


description:
opcBulk_150dpi_Tumor_16840_tdTpositive_GGCTG
rsem_opc.csv


title: iMLL_AF10_DOX_R1


title: A10.CD8.P18.rep4.b17.PSO

description: CountTable_SingleCellPsoCd8s_20200218.tsv


title: A10.CD8.P18.rep3.b18.PSO


description:
opcBulk_150dpi_Tumor_16840_tdTpositive_GAATG
rsem_opc.csv


description:
opcBulk_150dpi_Tumor_16839_tdTpositive_GTTGG
rsem_opc.csv


title: iMLL_AF10_DMSO_R3


title: opcBulk_150dpi_WT_21593_tdTpositive

description:
opcBulk_150dpi_WT_21593_tdTpositive
rsem_opc.csv


title: A10.CD8.P18.rep2.b18.PSO


title: iMLL_AF10_DMSO_R2


description:
opcBulk_150dpi_Tumor_16839_tdTpositive_CTAAA
rsem_opc.csv


description:
opcBulk_150dpi_Tumor_21349_tdTpositive_CTTCG
rsem_opc.csv


title: A10.CD8.P18.rep1.b18.PSO


description:
opcBulk_150dpi_Tumor_16713_tdTpositive_TAATT
rsem_opc.csv


title: iMLL_AF10_DOX_R2


title: opcBulk_90dpi_WT_22255_tdTpositive

description:
opcBulk_90dpi_WT_22255_tdTpositive
rsem_opc.csv

value: 90 dpi (days following tamoxifen treatment start)


title: A10.CD8.P17.rep6.b16.PSO


title: opcBulk_90dpi_WT_22254_tdTpositive

description:
opcBulk_90dpi_WT_22254_tdTpositive
rsem_opc.csv


title: opcBulk_90dpi_WT_22184_tdTpositive

description:
opcBulk_90dpi_WT_22184_tdTpositive
rsem_opc.csv


title: iCALM_AF10_DOX_R3


title: opcBulk_90dpi_WT_21167_tdTpositive

description:
opcBulk_90dpi_WT_21167_tdTpositive
rsem_opc.csv


title: A10.CD8.P17.rep5.b16.PSO


title: iMLL_AF10_DMSO_R1


title: opcBulk_90dpi_WT_22185_tdTpositive

description:
opcBulk_90dpi_WT_22185_tdTpositive
rsem_opc.csv


description:
opcBulk_90dpi_CKO_22212_tdTpositive_AGAAG
rsem_opc.csv


title: iMLL_AF9_DMSO_R2


title: opcBulk_90dpi_CKO_22154_tdTpositive

description:
opcBulk_90dpi_CKO_22154_tdTpositive
rsem_opc.csv


title: iCALM_AF10_DOX_R1


description:
opcBulk_90dpi_CKO_22212_tdTpositive_AAAGC
rsem_opc.csv


title: iCALM_AF10_DOX_R2


title: A10.CD8.P17.rep4.b16.PSO


title: opcBulk_90dpi_CKO_22152_tdTpositive

description:
opcBulk_90dpi_CKO_22152_tdTpositive
rsem_opc.csv


title: iCALM_AF10_DMSO_R3


title: A10.CD8.P19.rep4.b19.PSO


title: opcBulk_90dpi_CKO_22149_tdTpositive

description:
opcBulk_90dpi_CKO_22149_tdTpositive
rsem_opc.csv


title: A10.CD8.P17.rep3.b16.PSO

description: CountTable_SingleCellPsoCd8s_20200218.tsv


title: A10.CD8.P17.rep2.b16.PSO


description:
opcBulk_150dpi_Tumor_16713_tdTpositive_GTGGA
rsem_opc.csv


title: opcBulk_90dpi_CKO_22146_tdTpositive

description:
opcBulk_90dpi_CKO_22146_tdTpositive
rsem_opc.csv


title: iCALM_AF10_DMSO_R2


title: iCALM_AF10_DMSO_R1


description:
opcBulk_90dpi_CKO_20647_tdTpositive_GAGCT
rsem_opc.csv


title: A10.CD8.P17.rep1.b16.PSO


description:
opcBulk_90dpi_CKO_20647_tdTpositive_ACTAA
rsem_opc.csv


title: A10.CD8.P16.rep6.b13.PSO


title: opc90-96_ten-cell_female_1

description:
opc90-96
rsem_opc.csv

extract_protocol:
PCR amplification
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads
All samples were cryoembedded and sectioned onto glass slides. Cell samples were isolated via laser capture microdissection prior to RNA extraction, reverse transcription, and RNA amplification

value: 10-cell sample


title: A10.CD8.P16.rep5.b13.PSO


description:
opcBulk_90dpi_CKO_20642_tdTpositive_GTGCC
rsem_opc.csv


description:
opcBulk_90dpi_CKO_20642_tdTpositive_CACCC
rsem_opc.csv


title: opc90-95_ten-cell_female_1

description:
opc90-95
rsem_opc.csv


title: opc90-94_ten-cell_female_1

description:
opc90-94
rsem_opc.csv


title: opcBulk_12dpi_WT_22180_tdTpositive

description:
opcBulk_12dpi_WT_22180_tdTpositive
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)


title: opcBulk_12dpi_WT_22280_tdTpositive

description:
opcBulk_12dpi_WT_22280_tdTpositive
rsem_opc.csv


title: opc90-93_ten-cell_male_2

description:
opc90-93
rsem_opc.csv


title: opcBulk_12dpi_WT_22281_tdTpositive

description:
opcBulk_12dpi_WT_22281_tdTpositive
rsem_opc.csv


title: A10.CD8.P16.rep4.b13.PSO

value: CD8+ T cell


title: opcBulk_12dpi_WT_22178_tdTpositive

description:
opcBulk_12dpi_WT_22178_tdTpositive
rsem_opc.csv


title: opcBulk_12dpi_CKO_22363_tdTpositive

description:
opcBulk_12dpi_CKO_22363_tdTpositive
rsem_opc.csv


title: A10.CD8.P16.rep3.b13.PSO


title: A10.CD8.P16.rep1.b13.PSO

value: TRUE


title: opcBulk_12dpi_WT_22056_tdTpositive

description:
opcBulk_12dpi_WT_22056_tdTpositive
rsem_opc.csv


title: opc90-92_ten-cell_male_2

description:
opc90-92
rsem_opc.csv


title: A10.CD8.P16.rep2.b13.PSO


title: opcBulk_12dpi_CKO_22210_tdTpositive

description:
opcBulk_12dpi_CKO_22210_tdTpositive
rsem_opc.csv


title: opc90-91_ten-cell_male_2

description:
opc90-91
rsem_opc.csv


description:
opcBulk_12dpi_CKO_22208_tdTpositive_AGCTC
rsem_opc.csv


title: A10.CD8.P15.rep6.b13.PSO


title: opcBulk_12dpi_CKO_21724_tdTpositive

description:
opcBulk_12dpi_CKO_21724_tdTpositive
rsem_opc.csv


title: A10.CD8.P15.rep5.b13.PSO


title: opcBulk_12dpi_CKO_21725_tdTpositive

description:
opcBulk_12dpi_CKO_21725_tdTpositive
rsem_opc.csv


title: opc90-89_ten-cell_male_1

description:
opc90-89
rsem_opc.csv


title: A10.CD8.P15.rep4.b12.PSO

description: CountTable_SingleCellPsoCd8s_20200218.tsv


title: BOP27_R2

city: La Jolla

first: Ke

last: Chen

address: Bioengineering Department, 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20.
Raw sequencing reads were mapped to the reference genome NC_000913.3 using Bowtie 2.3.4.3 with the following options "-X 1000 -N 1 -3 3".
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with the following options "mode="IntersectionStrict", singleEnd=FALSE, ignore.strand=FALSE, preprocess.reads=invertStrand".
Transcripts per Million (TPM) were calculated by DESeq2.
Genome_build: Reference genome: E. coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: deseq2-tpm.csv: Comma-separated text file containing normalized abundance measurements (TPM) for each sample.

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

source_name: bacteria cells

growth_protocol: Cultures were inoculated from -80°C glycerol stocks into M9 minimal medium with 4g/L glucose supplementation, and grown aerated at 37°C overnight. Physiological adaptation was achieved by growing cell cultures exponentially over 2 passages for 5 to 10 generations at the target temperature. Next, cultures growing at the exponential growth phase were passaged to a 15 mL working volume tube and grown fully aerated until mid-log phase (OD600 ≈ 0.6) for RNA-Seq sample extraction.

extract_protocol:
3 mL of cell broth was taken at OD600~0.6 and immediately added to 2 volumes Qiagen RNAprotect Bacteria Reagent (6 mL). Then, the sample was vortexed for 5 seconds, incubated at room temperature for 5 minutes, and immediately centrifuged for 10 minutes at 5000 x g. The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the RNeasy Plus Mini Kit (Qiagen) columns following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria). The quantity was determined by Nanodrop 1000 spectrophotometer (Thermo Scientific). The quality was checked using RNA 6000 Pico Kit using Agilent 2100 Bioanalyzer (Agilent). Paired-end, strand-specific RNA-seq library was built with the KAPA RNA Hyper Prep kit (Kapa Biosystems) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: Wild type

tag: medium

value: glucose M9 minimal

tag: temperature

tag: growth phase

value: mid-log


title: opcBulk_12dpi_CKO_22364_tdTpositive

description:
opcBulk_12dpi_CKO_22364_tdTpositive
rsem_opc.csv

tag: sample type


title: A10.CD8.P15.rep3.b12.PSO

source_name: Psoriasis lesion


title: BOP27_R1


title: opc90-87_ten-cell_female_2

description:
opc90-87
rsem_opc.csv


title: opc90-86_ten-cell_female_2

description:
opc90-86
rsem_opc.csv


description:
opcBulk_12dpi_CKO_22208_tdTpositive_GGGTT
rsem_opc.csv


title: opc90-90_ten-cell_male_1

description:
opc90-90
rsem_opc.csv


title: opc90-85_ten-cell_female_2

description:
opc90-85
rsem_opc.csv


title: A10.CD8.P15.rep1.b12.PSO


title: A10.CD8.P14.rep8.b10.PSO


title: opc90-84_ten-cell_female_1

description:
opc90-84
rsem_opc.csv


title: A10.CD8.P14.rep7.b10.PSO


title: opc90-83_ten-cell_female_1

description:
opc90-83
rsem_opc.csv


title: opc90-88_ten-cell_male_1

description:
opc90-88
rsem_opc.csv


title: A10.CD8.P14.rep6.b10.PSO


title: A10.CD8.P15.rep2.b12.PSO


title: opc90-82_ten-cell_female_1

description:
opc90-82
rsem_opc.csv


title: A10.CD8.P14.rep5.b10.PSO


title: opcBulk_12dpi_CKO_22017_tdTpositive

description:
opcBulk_12dpi_CKO_22017_tdTpositive
rsem_opc.csv


title: opc90-81_ten-cell_male_2

description:
opc90-81
rsem_opc.csv


title: TCE Rep 3 T2

first: Jason

last: Papin

address: 415 Lane Rd

department: Biomedical Engineering

data_processing:
Illumina 1.9 was used for basecalling
Sequenced reads were pseudo-aligned to the rno reference transcriptome using Kallisto v. 0.43. with parameters -b 100
Genome_build: rno
Supplementary_files_format_and_content: tab-separated value files include estimated counts and transcripts per million for each Sample

organism: Rattus norvegicus

source_name: Renal Proximal Tubule Epithelial Cell

extract_protocol:
After supernatants were collected, cells from each time point were treated with TRIzol® and then scraped and collected into tubes. Chloroform was added to each tube and after shaking, cells were poured into pre-spun phase-lock gel tubes (5PRIME). Tubes were then spun in a cold room, the upper phase was collected, and IPA and glycogen were added to each tube followed by gentle inversion. Supernatants were again spun in a cold room and the resulting pellet was washed twice with 75% ethanol. The pellet was semi-dried and then dissolved in nuclease-free H2O. RNA samples were treated with DNA-free DNA removal kit (Ambion/Invitrogen), according to manufacturer’s instructions, to remove any remaining DNA. RNA was quantified using the Qubit RNA broad range kit and sample integrity assessed using Agilent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Renal Proximal Tubule Epithelial Cell

tag: treatment

value: Trichloroethylene

tag: time point

value: 24 hours


title: TCE Rep 2 T2


title: opc90-80_ten-cell_male_2

description:
opc90-80
rsem_opc.csv

tag: time

tag: Sex

tag: section thickness (µm)


title: TCE Rep 1 T2


title: A10.CD8.P14.rep3.b10.PSO

tag: celltype

tag: subjectid

tag: plate


title: TCE Rep 2 T1

value: 6 hours


title: opc90-78_ten-cell_male_1

description:
opc90-78
rsem_opc.csv


title: A10.CD8.P14.rep1.b10.PSO

tag: well

tag: sequencingbatch

tag: passedqc

value: FALSE


title: TCE Rep 1 T1


title: TCE Rep 3 T1


title: opc90-79_ten-cell_male_1

description:
opc90-79
rsem_opc.csv

tag: genotype


title: TCDD Rep 1 T2


title: A10.CD8.P14.rep2.b10.PSO

tag: cluster


title: opc90-76_ten-cell_male_1

description:
opc90-76
rsem_opc.csv


title: A10.CD8.P19.rep3.b19.PSO


title: TCDD Rep 1 T1


title: Gent Rep 2 T2

value: Gentamicin


title: TCDD Rep 2 T2


title: opc90-74_ten-cell_female_2

description:
opc90-74
rsem_opc.csv


title: TCDD Rep 3 T2


title: A10.CD8.P13.rep2.b7.PSO


title: Gent Rep 1 T2


title: TCDD Rep 2 T1


title: A10.CD8.P13.rep4.b8.PSO


title: A10.CD8.P13.rep5.b8.PSO


title: opc90-75_ten-cell_female_2

description:
opc90-75
rsem_opc.csv


title: Gent Rep 3 T2


title: A10.CD8.P13.rep3.b7.PSO


title: opc90-72_ten-cell_female_2

description:
opc90-72
rsem_opc.csv


title: Control Rep 3 T2

value: Control


title: Gent Rep 3 T1


title: Control Rep 1 T2


title: A10.CD8.P14.rep4.b10.PSO


title: Control Rep 2 T2


title: A10.CD8.P10.rep1.b7.PSO


title: opc90-73_ten-cell_female_2

description:
opc90-73
rsem_opc.csv

value: female


title: A10.CD8.P11.rep1.b6.PSO


title: Gent Rep 1 T1


title: Control Rep 3 T1


title: opc90-77_ten-cell_male_1

description:
opc90-77
rsem_opc.csv

value: male


title: APAP Rep 3 T2

value: Acetaminophen


title: A10.CD8.P13.rep1.b7.PSO


title: opc90-71_ten-cell_female_1

description:
opc90-71
rsem_opc.csv

value: 90 dpi (days following tamoxifen treatment start)

value: 10-cell sample


title: opc90-69_ten-cell_female_1

description:
opc90-69
rsem_opc.csv


title: APAP Rep 2 T2


title: TCDD Rep 3 T1


title: CMC-003i-Nestin.EGFP_p10

type: genomic

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

country: South Korea

institute: Korea National Institute of Health

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix Chromosome Anaysis Suite Software (ChAS version 4.0).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: biotin

source_name: cord blood

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: human induced pluripotent stem cells

tag: cell line


title: A10.CD8.C7.rep7.b15.Healthy

source_name: Healthy skin

value: CD8+ T cell


title: APAP Rep 1 T2


title: opc90-68_ten-cell_female_1

description:
opc90-68
rsem_opc.csv


title: A10.CD8.C7.rep5.b15.Healthy


title: opc90-67_ten-cell_female_1

description:
opc90-67
rsem_opc.csv


title: A10.CD8.C7.rep4.b15.Healthy

value: TRUE


title: A10.CD8.P11.rep2.b6.PSO


title: APAP Rep 1 T1


title: NU01-EiPS07_p13

source_name: Urine


title: CMC-hiPSC-011_p26


title: hAdMSiPS1_p18

source_name: Adipocyte


title: opc90-65_ten-cell_male_2

description:
opc90-65
rsem_opc.csv


title: Gent Rep 2 T1


title: PB01-EiPS21_p21

source_name: PBMC


title: A10.CD8.C7.rep2.b15.Healthy


title: A10.CD8.C7.rep3.b15.Healthy


title: opc90-66_ten-cell_male_2

description:
opc90-66
rsem_opc.csv


title: CMC-003i-Pdx1.EGFP_p13


title: opc90-64_ten-cell_male_2

description:
opc90-64
rsem_opc.csv


title: DHK-005iA_p6


title: opc90-70_ten-cell_female_1

description:
opc90-70
rsem_opc.csv


title: CHA-hES15_p28

source_name: humen embryonic stem cells

value: human embryonic stem cells


title: DHK-090iA_p6


title: opc90-63_ten-cell_male_2

description:
opc90-63
rsem_opc.csv


title: A10.CD8.C6.rep6.b10.Healthy


title: opc90-62_ten-cell_male_1

description:
opc90-62
rsem_opc.csv


title: A10.CD8.C6.rep5.b10.Healthy


title: CMC-hiPSC-005_p20


title: opc90-61_ten-cell_male_1

description:
opc90-61
rsem_opc.csv


title: CMC-hiPSC-022_p19


title: A10.CD8.C7.rep1.b15.Healthy


title: hFSiPS3-1_p30

source_name: fibroblast


title: A10.CD8.C6.rep4.b10.Healthy


title: CMC-hiPSC-003_p18


title: A10.CD8.C6.rep3.b10.Healthy


title: opc90-59_ten-cell_male_1

description:
opc90-59
rsem_opc.csv


title: A10.CD8.C6.rep2.b11.Healthy


title: CMC-hiPSC-009_p26


title: A10.CD8.C6.rep2.b10.Healthy


title: opc90-57_ten-cell_female_2

description:
opc90-57
rsem_opc.csv


title: A10.CD8.C6.rep1.b10.Healthy


title: Control Rep 2 T1


title: opc90-56_ten-cell_female_2

description:
opc90-56
rsem_opc.csv


title: A10.CD8.C5.rep6.b9.Healthy


title: APAP Rep 3 T1


title: APAP Rep 2 T1


title: opc90-60_ten-cell_male_1

description:
opc90-60
rsem_opc.csv


title: opc90-55_ten-cell_female_2

description:
opc90-55
rsem_opc.csv


title: A10.CD8.C5.rep5.b9.Healthy


title: opc90-54_ten-cell_female_1

description:
opc90-54
rsem_opc.csv


title: A10.CD8.C5.rep4.b9.Healthy


title: opc90-53_ten-cell_female_1

description:
opc90-53
rsem_opc.csv


title: opc90-58_ten-cell_female_2

description:
opc90-58
rsem_opc.csv


title: A10.CD8.C5.rep3.b9.Healthy


title: Pat 63_bile duct control - normal - ITPN-P

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

description: Infinium MethylationEPIC

hyb_protocol: supplier protocol (Illumina)

scan_protocol: supplier protocol (Illumina)

data_processing: supplier software (GenomeStudio)

label: Cy5 and Cy3

source_name: Pat 63

label_protocol: supplier protocol (Illumina)

extract_protocol: AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) as recommended by the manufacturer with following modifications: After addition of xylene, samples were incubated at 56°C for 2 min followed by two ethanol washes. The first proteinase K digestion was done with 20 µl at 56°C for 30 min. The DNA was eluted twice with 30 µl H2O.

tag: disease state

value: bile duct control - normal - ITPN-P


title: opc90-52_ten-cell_female_1

description:
opc90-52
rsem_opc.csv

tag: sample type


title: Pat 63_ITPN-P - premalignant

description: Infinium MethylationEPIC

value: ITPN-P - premalignant


title: Pat 62_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC

source_name: Pat 62


title: Pat 60_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC

source_name: Pat 60


title: A10.CD8.C5.rep2.b9.Healthy

extract_protocol:
Skin punch biopsies were immediately stored at 4 °C in a container with sterile gauze and PBS until they were ready to be processed. The tissue was trimmed to remove hair and subcutaneous adipose before being finely minced and mixed with digestion buffer composed of Collagenase Type IV (Worthington LS04188), DNAse (Sigma-Aldrich DN25-1G), 10% FBS, 1% HEPES, and 1% Penicillin/Streptavidin in RPMI 1640. After overnight incubation in 5% CO2, cell suspensions were harvested, filtered, centrifuged, counted, and stained for CD45+CD3+CD8+ cells. These cells were directly sorted into 10X Reaction Buffer prepared from the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech cat. 634894) and snap frozen in liquid nitrogen for storage at −80 °C.
Full length cDNA synthesis of each cell was performed using the SMART-Seq v4 Ultra Low Input Kit with the following specifications and modifications. All reactions were prepared with a MANTIS liquid handler (Formulatrix) to allow miniaturization of the reaction volume to half of the manufacturer’s recommended volume.  0.4 µL of 1:4,000,000 diluted External RNA Controls Consortium (ERCC) RNA Spike-In (Thermo Fisher Scientific, cat. 4456740) was added to each cell lysate prior to the First-Strand Synthesis step. LD PCR was performed for 19 cycles. Purification of cDNA was performed using Agencourt AMPure XP beads (Beckman Coulter, cat. A63881) and quantified using the QuantIT PicoGreen dsDNA Assay Kit (Invitrogen, cat. P7589). Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina, cat. FC-131-1096), QC’d using the Bioanalyzer High Sensitivity DNA Kit (Agilent, cat. 5067-4626), and quantified by NEBNext library quantification kit for Illumina (New England Biolab, cat. E7630L). Read sequencing was performed on an Illumina HiSeq 4000.


title: opc90-51_ten-cell_male_2

description:
opc90-51
rsem_opc.csv


title: Pat 62_ITPN-P - premalignant

description: Infinium MethylationEPIC


title: Pat 60_ITPN-P - premalignant

description: Infinium MethylationEPIC


title: Pat 58_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC

source_name: Pat 58


title: Pat 61_ITPN-P - premalignant

description: Infinium MethylationEPIC

source_name: Pat 61


title: A10.CD8.C5.rep1.b9.Healthy


title: Pat 59_ITPN-P - premalignant

description: Infinium MethylationEPIC

source_name: Pat 59


title: opc90-50_ten-cell_male_2

description:
opc90-50
rsem_opc.csv

source_name: Brain oligodendrocyte precursor cells


title: Pat 57_ITPN-P - premalignant

description: Infinium MethylationEPIC

source_name: Pat 57


title: A10.CD8.C4.rep6.b8.Healthy


title: opc90-49_ten-cell_male_2

description:
opc90-49
rsem_opc.csv


title: Pat 55_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC

source_name: Pat 55


title: Pat 54_pCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 54

value: pCCA - invasive


title: Pat 55_ITPN-P - premalignant

description: Infinium MethylationEPIC


title: Pat 57_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC


title: A10.CD8.C4.rep5.b8.Healthy


title: Pat 58_ITPN-P - premalignant

description: Infinium MethylationEPIC


title: Pat 53_dCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 53

value: dCCA - invasive


title: opc90-48_ten-cell_male_2

description:
opc90-48
rsem_opc.csv


title: opc90-47_ten-cell_male_2

description:
opc90-47
rsem_opc.csv


title: Pat 51_dCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 51


title: A10.CD8.C4.rep3.b7.Healthy

source_name: Healthy skin


title: Pat 59_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC


title: Pat 53_bile duct control - normal

description: Infinium MethylationEPIC

value: bile duct control - normal


title: A10.CD8.C4.rep2.b7.Healthy

value: FALSE


title: Pat 56_ITPN-P - premalignant

description: Infinium MethylationEPIC

source_name: Pat 56


title: Pat 51_IPNB - premalignant

description: Infinium MethylationEPIC

value: IPNB - premalignant


title: opc90-45_ten-cell_male_1

description:
opc90-45
rsem_opc.csv


title: opc90-46_ten-cell_male_1

description:
opc90-46
rsem_opc.csv


title: Pat 61_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC


title: A10.CD8.C4.rep4.b8.Healthy


title: Pat 54_bile duct control - normal

description: Infinium MethylationEPIC


title: A10.CD8.C4.rep1.b7.Healthy


title: A10.CD8.C14.rep1.b5.Healthy


title: opc90-43_ten-cell_female_2

description:
opc90-43
rsem_opc.csv


title: Pat 54_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 49_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 49


title: opc90-42_ten-cell_female_2

description:
opc90-42
rsem_opc.csv


title: Pat 48_dCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 48


title: Pat 50_ITPN - premalignant

description: Infinium MethylationEPIC

source_name: Pat 50

value: ITPN - premalignant


title: Pat 48_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 49_IPNB - premalignant

description: Infinium MethylationEPIC


title: opc90-44_ten-cell_male_1

description:
opc90-44
rsem_opc.csv


title: opc90-41_ten-cell_female_2

description:
opc90-41
rsem_opc.csv

value: female


title: Pat 47_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 47


title: A1.CD8.P9.rep2.b6.PSO

source_name: Psoriasis lesion


title: A1.CD8.P5.rep2.b2.PSO


title: Pat 51_bile duct control - normal

description: Infinium MethylationEPIC


title: A10.CD8.C13.rep2.b3.Healthy


title: Pat 47_iCCA - invasive

description: Infinium MethylationEPIC

value: iCCA - invasive


title: Pat 48_bile duct control - normal

description: Infinium MethylationEPIC


title: A1.CD8.P19.rep6.b19.PSO


title: opc90-39_pooled_female_1

description:
opc90-39
rsem_opc.csv

value: pool-and-split control


title: Pat 44_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 44


title: Pat 56_bile duct control - normal - ITPN-P

description: Infinium MethylationEPIC


title: A10.CD8.C13.rep1.b3.Healthy


title: Pat 44_iCCA - invasive

description: Infinium MethylationEPIC


title: opc90-40_pooled_female_1

description:
opc90-40
rsem_opc.csv

value: 90 dpi (days following tamoxifen treatment start)


title: opc90-37_pooled_male_2

description:
opc90-37
rsem_opc.csv

value: male


title: opc90-38_pooled_female_1

description:
opc90-38
rsem_opc.csv


title: Pat 46_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 46


title: A1.CD8.P19.rep4.b19.PSO


title: opc90-36_pooled_male_2

description:
opc90-36
rsem_opc.csv


title: A1.CD8.P19.rep3.b19.PSO


title: A1.CD8.P19.rep5.b19.PSO


title: opc90-35_pooled_male_2

description:
opc90-35
rsem_opc.csv


title: Pat 41_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 41


title: Pat 45_ITPN - premalignant

description: Infinium MethylationEPIC

source_name: Pat 45


title: Pat 42_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 42


title: opc90-34_pooled_male_1

description:
opc90-34
rsem_opc.csv

source_name: Brain oligodendrocyte precursor cells


title: Pat 42_iCCA - invasive

description: Infinium MethylationEPIC


title: Pat 43_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 43


title: Pat 42_bile duct control - normal

description: Infinium MethylationEPIC


title: A1.CD8.P19.rep2.b19.PSO


title: A1.CD8.P18.rep5.b17.PSO


title: Pat 41_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 40_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 40


title: Pat 46_bile duct control - normal

description: Infinium MethylationEPIC


title: opc90-32_pooled_male_1

description:
opc90-32
rsem_opc.csv


title: A1.CD8.P18.rep4.b17.PSO


title: Pat 53_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 53


title: opc90-33_pooled_male_1

description:
opc90-33
rsem_opc.csv


title: opc90-31_pooled_female_2

description:
opc90-31
rsem_opc.csv


title: A1.CD8.P18.rep3.b18.PSO


title: A1.CD8.P18.rep6.b17.PSO


title: Pat 40_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 44_ITPN - premalignant

description: Infinium MethylationEPIC


title: Pat 45_iCCA - invasive

description: Infinium MethylationEPIC


title: opc90-30_pooled_female_2

description:
opc90-30
rsem_opc.csv


title: Pat 39_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 39


title: Pat 47_ITPN - premalignant

description: Infinium MethylationEPIC


title: Pat 38_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 38


title: opc90-29_pooled_female_2

description:
opc90-29
rsem_opc.csv


title: A1.CD8.P18.rep2.b18.PSO


title: A1.CD8.P17.rep6.b16.PSO


title: Pat 43_IPNB - premalignant

description: Infinium MethylationEPIC


title: opc90-28_pooled_female_1

description:
opc90-28
rsem_opc.csv


title: Pat 39_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 37_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 37


title: Pat 36_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 36


title: A1.CD8.P17.rep4.b16.PSO


title: opc90-26_pooled_female_1

description:
opc90-26
rsem_opc.csv


title: opc90-27_pooled_female_1

description:
opc90-27
rsem_opc.csv


title: Pat 38_IPNB - premalignant

description: Infinium MethylationEPIC


title: A1.CD8.P17.rep5.b16.PSO


title: Pat 37_dCCA - invasive

description: Infinium MethylationEPIC


title: A1.CD8.P17.rep3.b16.PSO


title: Pat 35_iCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 35


title: A1.CD8.P17.rep2.b16.PSO


title: opc90-24_pooled_male_2

description:
opc90-24
rsem_opc.csv


title: A1.CD8.P16.rep6.b13.PSO


title: opc90-25_pooled_male_2

description:
opc90-25
rsem_opc.csv


title: Pat 35_bile duct control - normal

description: Infinium MethylationEPIC


title: Pat 35_ITPN - premalignant

description: Infinium MethylationEPIC


title: opc90-23_pooled_male_2

description:
opc90-23
rsem_opc.csv


title: Pat 33_ITPN - premalignant

description: Infinium MethylationEPIC

source_name: Pat 33


title: opc90-22_pooled_male_2

description:
opc90-22
rsem_opc.csv


title: Pat 33_bile duct control - normal

description: Infinium MethylationEPIC


title: Pat 37_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 34_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 34


title: A1.CD8.P16.rep5.b13.PSO

source_name: Psoriasis lesion


title: opc90-21_pooled_male_1

description:
opc90-21
rsem_opc.csv


title: Pat 32_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 32


title: Pat 34_IPNB - premalignant

description: Infinium MethylationEPIC


title: A1.CD8.P16.rep4.b13.PSO


title: opc90-20_pooled_male_1

description:
opc90-20
rsem_opc.csv


title: A1.CD8.P16.rep3.b13.PSO


title: Pat 32_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 30_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 30


title: opc90-19_pooled_female_2

description:
opc90-19
rsem_opc.csv


title: Pat 31_ITPN - premalignant

description: Infinium MethylationEPIC

source_name: Pat 31


title: Pat 30_dCCA - invasive

description: Infinium MethylationEPIC


title: opc90-18_pooled_female_2

description:
opc90-18
rsem_opc.csv


title: Pat 31_bile duct control - normal

description: Infinium MethylationEPIC


title: Pat 30_IPNB - premalignant

description: Infinium MethylationEPIC


title: A1.CD8.P15.rep5.b13.PSO


title: Pat 26_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 26


title: A1.CD8.P16.rep2.b13.PSO


title: Pat 29_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 29


title: Pat 28_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 28


title: opc90-17_pooled_female_1

description:
opc90-17
rsem_opc.csv

source_name: Brain oligodendrocyte precursor cells


title: Pat 28_dCCA - invasive

description: Infinium MethylationEPIC


title: opc90-16_pooled_male_2

description:
opc90-16
rsem_opc.csv


title: A1.CD8.P15.rep3.b12.PSO


title: Pat 28_IPNB - premalignant

description: Infinium MethylationEPIC


title: A1.CD8.P15.rep6.b13.PSO


title: A1.CD8.P15.rep4.b12.PSO


title: Pat 23_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 23


title: opc90-15_pooled_male_2

description:
opc90-15
rsem_opc.csv


title: A1.CD8.P15.rep2.b12.PSO


title: opc90-14_pooled_male_1

description:
opc90-14
rsem_opc.csv


title: A1.CD8.P14.rep8.b10.PSO


title: Pat 29_bile duct control - normal

description: Infinium MethylationEPIC


title: opc90-13_pooled_male_1

description:
opc90-13
rsem_opc.csv


title: Pat 26_dCCA - invasive

description: Infinium MethylationEPIC


title: Pat 24_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 24


title: A1.CD8.P14.rep7.b10.PSO


title: Pat 25_ITPN - premalignant

description: Infinium MethylationEPIC

source_name: Pat 25


title: Pat 25_bile duct control - normal

description: Infinium MethylationEPIC


title: Pat 23_IPNB - premalignant

description: Infinium MethylationEPIC


title: opc90-12_pooled_female_2

description:
opc90-12
rsem_opc.csv


title: opc90-11_pooled_female_2

description:
opc90-11
rsem_opc.csv


title: Pat 23_dCCA - invasive

description: Infinium MethylationEPIC


title: Pat 22_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 22


title: A1.CD8.P14.rep5.b10.PSO


title: Spinal cord cells - GFAP::EGFP+

city: Santiago

first: Juan

last: Larraín

address: Portugal 49

department: Cellular and Molecular Biology

country: Chile

institute: Pontificia Universidad Catolica de Chile

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
Paired-end reads were mapped to Xenopus laevis model transcriptome v9.1 (Xenbase) using Bowtie 1.2.2, including EGFP sequence and allowing up to 2 mismatches. Gene expression level was quantified by RSEM 1.3.0.

organism: Xenopus laevis

source_name: Spinal cord cells

extract_protocol:
Spinal cords from animals at R-stage were dissected from the transgenic line Xla.Tg(Dre.gfap:EGFP)Larra. Posteriorly, EGFP+ and EGFP- cells were separated using Fluorescence-Activated Cell Sorting (FACS) and the purification of total RNA from both cell populations was performed using the RNeasy Micro Kit.
RNA libraries were prepared by Macrogen (South Korea) using SMTer Universal low amount RNA library kit. Posterioly these were sequenced on the Illumina HiSeq 4000.

tag: Stage

value: NF stage 50

tag: tissue

value: Spinal cord


title: Pat 22_pCCA - invasive

description: Infinium MethylationEPIC


title: A1.CD8.P14.rep4.b10.PSO

data_processing:
Mapping was performed with STAR 2.4.2a to the human reference genome (GRCh38, GENCODE release 25) and the 92 reference sequences of the ERCC spike-in standard.
Read counts for each transcript were tallied using HTSeq 0.6.1p1
Filtering was performed to exclude cells that contained less than 100,000 mapped reads, less than 1,000 mapped genes, greater than 25% mapped reads on ERCC spike-ins, or greater than 25% mapped reads on mitochondrial genes. We also excluded genes that were not detected with at least 5 transcripts in at least two cells.
Read counts across libraries were normalized by RUVg, implemented in the RUVSeq 1.8.0 R package on ERCC spike-in counts to control for batch, depth, and other technical confounding effects
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file contains unnormalized read counts of each gene (rows) in each sample (columns)

value: CD8+ T cell


title: A1.CD8.P14.rep6.b10.PSO

value: TRUE


title: Pat 29_pCCA - invasive

description: Infinium MethylationEPIC


title: opc90-10_pooled_female_1

description:
opc90-10
rsem_opc.csv


title: Pat 22_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 20_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 20


title: opc90-09_pooled_female_1

description:
opc90-09
rsem_opc.csv


title: Spinal cord cells - GFAP::EGFP-


title: A1.CD8.P14.rep3.b10.PSO


title: opc90-08_pooled_female_1

description:
opc90-08
rsem_opc.csv


title: Pat 27_ITPN - premalignant

description: Infinium MethylationEPIC

source_name: Pat 27


title: A1.CD8.P13.rep5.b8.PSO


title: Pat 20_IPNB - premalignant

description: Infinium MethylationEPIC


title: opc90-06_pooled_male_1

description:
opc90-06
rsem_opc.csv


title: Pat 20_pCCA - invasive

description: Infinium MethylationEPIC


title: Pat 25_pCCA - invasive

description: Infinium MethylationEPIC


title: Uveal melanoma_Early metastasis_#16

city: OSLO

first: Agate

last: Noer

address: Kirkeveien 166

department: Ophthalmology

country: Norway

institute: Oslo University Hospital, Ullevaal

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix.

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing:
The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.
RMA signal estimated from Partek Genomics Suite software, Log2 values

label: Biotin

source_name: Uveal melanoma

label_protocol: Total RNA (50 ng) was subjected to the GeneChip™ WT Pico Reagent Kit and WT Labeling Kit (Affymetrix).

growth_protocol: not applicable

extract_protocol: RNA was isolated from sections of the FFPE tumor. Extraction was carried out using the Qiagen MiRNEASY FFPE kit (Qiagen) according to the manufacturers’ recommendations. RNA was purified using the Zymo PCR inhibitor removal kit (Zymo). RNA concentration and purity were determined using NanoDrop (Thermo Fisher Scientific) and Bioanalyzer (Agilent 2100, Agilent, Santa Clara, CA, US). The RNA integrity number (RIN) values and 260/280 ratio were within the ranges recommended by Qiagen.

treatment_protocol: not applicable

tag: metastasis

value: Early


title: Pat 19_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 19


title: opc90-05_pooled_male_1

description:
opc90-05
rsem_opc.csv

tag: time


title: Uveal melanoma_Early metastasis_#15


title: A1.CD8.P14.rep2.b10.PSO

source_name: Psoriasis lesion


title: Uveal melanoma_Early metastasis_#17


title: A1.CD8.P13.rep3.b7.PSO


title: Uveal melanoma_Early metastasis_#2


title: A1.CD8.P13.rep4.b8.PSO


title: Pat 19_iCCA - invasive

description: Infinium MethylationEPIC


title: Pat 21_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 21


title: A1.CD8.P11.rep2.b6.PSO


title: Pat 19_bile duct control - normal

description: Infinium MethylationEPIC


title: Pat 14_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 14


title: opc90-07_pooled_male_2

description:
opc90-07
rsem_opc.csv

tag: Sex


title: A1.CD8.C7.rep7.b15.Healthy

source_name: Healthy skin


title: Pat 17_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 17


title: opc90-02_pooled_female_2

description:
opc90-02
rsem_opc.csv

tag: section thickness (µm)


title: Uveal melanoma_No metastasis_#12

value: No


title: opc90-04_pooled_male_1

description:
opc90-04
rsem_opc.csv


title: Pat 15_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 15


title: Pat 16_pCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 16

value: pCCA - invasive


title: opc90-03_pooled_female_2

description:
opc90-03
rsem_opc.csv

source_name: Brain oligodendrocyte precursor cells


title: A1.CD8.C7.rep5.b15.Healthy

tag: celltype


title: A1.CD8.C7.rep4.b15.Healthy

tag: subjectid


title: Pat 15_pCCA - invasive

description: Infinium MethylationEPIC


title: opc12-96_ten-cell_male_1

description:
opc12-96
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)

value: 10-cell sample


title: A1.CD8.C7.rep3.b15.Healthy

tag: plate


title: opc90-01_pooled_female_2

description:
opc90-01
rsem_opc.csv


title: opc12-95_ten-cell_female_2

description:
opc12-95
rsem_opc.csv


title: Uveal melanoma_No metastasis_#7


title: Uveal melanoma_No metastasis_#11


title: Pat 16_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 16_bile duct control - normal

description: Infinium MethylationEPIC

value: bile duct control - normal


title: Pat 17_IPNB - premalignant

description: Infinium MethylationEPIC

value: IPNB - premalignant


title: Uveal melanoma_No metastasis_#13


title: opc12-94_ten-cell_female_2

description:
opc12-94
rsem_opc.csv


title: Pat 17_iCCA - invasive

description: Infinium MethylationEPIC


title: A1.CD8.C7.rep2.b15.Healthy

tag: well

value: FALSE


title: A1.CD8.C6.rep6.b10.Healthy

tag: sequencingbatch


title: opc12-93_ten-cell_male_2

description:
opc12-93
rsem_opc.csv


title: A1.CD8.C6.rep5.b10.Healthy

tag: passedqc


title: Pat 14_dCCA - invasive

description: Infinium MethylationEPIC

value: dCCA - invasive


title: Pat 13_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 13


title: opc12-92_ten-cell_male_2

description:
opc12-92
rsem_opc.csv

tag: genotype


title: Pat 13_IPNB - premalignant

description: Infinium MethylationEPIC


title: opc12-91_ten-cell_female_2

description:
opc12-91
rsem_opc.csv

value: female


title: A1.CD8.C6.rep4.b10.Healthy

tag: cluster


title: A1.CD8.C6.rep3.b10.Healthy


title: opc12-90_ten-cell_male_1

description:
opc12-90
rsem_opc.csv


title: A1.CD8.C6.rep2.b11.Healthy


title: opc12-89_pooled_female_1

description:
opc12-89
rsem_opc.csv

value: pool-and-split control


title: Pat 12_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 12


title: A1.CD8.C6.rep2.b10.Healthy


title: 22.No.Spi

description: Genomic DNA from formalin-fixed paraffin-embedded uveal melanoma sections

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan system

data_processing: Illumina’s GenomeStudio V2011.1 Methylation Module V1.9

source_name: uveal melanoma

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extraction was carried out using the QIAamp DNA FFPE Tissue Kit (Qiagen, Venlo, NL) according to the manufacturers’ recommendations. DNA was purified using the Zymo PCR inhibitor removal kit (Zymo, Irvine, CA, US). DNA concentration was determined using Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, US). Quality control of DNA samples was performed using the Infinium HD FFPE QC Assay (Illumina, San Diego, CA, US) protocol according to Illumina’s recommendations. Samples were kept at -20 C˚ until bisulphite conversion using Zymo EZ DNA Methylation kit (Zymo). 500 ng of genomic DNA from each sample was converted. Samples underwent restoration using the Illumina Infinium HD Restore protocol (Illumina), and 4 μl of bisulphite-converted restored DNA was used for hybridization on the Infinium Human Methylation 450 BeadChip (Illumina), following the Illumina Infinium HD Methylation protocol (Illumina).

tag: gender

value: F

tag: histology

value: Spi

tag: relapse


title: Pat 12_pCCA - invasive

description: Infinium MethylationEPIC

tag: disease state


title: 23.No.Epi

value: M

value: Epi


title: Pat 12_IPNB - premalignant

description: Infinium MethylationEPIC


title: A1.CD8.C5.rep6.b9.Healthy

value: CD8+ T cell


title: opc12-88_ten-cell_female_1

description:
opc12-88
rsem_opc.csv

tag: sample type


title: A1.CD8.C5.rep5.b9.Healthy


title: opc12-87_ten-cell_female_1

description:
opc12-87
rsem_opc.csv


title: 21.Early.Epi


title: Pat 11_iCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 11

value: iCCA - invasive


title: opc12-86_pooled_male_2

description:
opc12-86
rsem_opc.csv

value: male


title: A1.CD8.C5.rep4.b9.Healthy

value: TRUE


title: Pat 11_bile duct control - normal

description: Infinium MethylationEPIC


title: opc12-84_pooled_female_2

description:
opc12-84
rsem_opc.csv


title: 20.Late.Spi

value: Late


title: opc12-85_pooled_male_2

description:
opc12-85
rsem_opc.csv

value: 12 dpi (days following tamoxifen treatment start)


title: 17.Early.Spi

value: Early


title: Pat 09_ITPN - premalignant

description: Infinium MethylationEPIC

source_name: Pat 09

value: ITPN - premalignant


title: 19.Late.Mix

value: Mix


title: A1.CD8.C5.rep2.b9.Healthy


title: Pat 07_iCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 07


title: A1.CD8.C5.rep3.b9.Healthy

value: FALSE


title: Pat 08_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 08

value: IPNB - premalignant


title: Pat 07_IPNB - premalignant

description: Infinium MethylationEPIC


title: A1.CD8.C4.rep6.b8.Healthy


title: opc12-83_ten-cell_female_2

description:
opc12-83
rsem_opc.csv

value: 10-cell sample

value: female


title: 16.Early.Mix

source_name: Uveal melanoma

value: F


title: opc12-82_pooled_female_1

description:
opc12-82
rsem_opc.csv

value: pool-and-split control


title: 15.Early.Mix

value: M


title: opc12-81_pooled_female_1

description:
opc12-81
rsem_opc.csv


title: 18.Late.Mix


title: 14.Early.Epi

value: Epi


title: opc12-80_pooled_male_2

description:
opc12-80
rsem_opc.csv


title: A1.CD8.C13.rep2.b3.Healthy

value: CD8+ T cell


title: Pat 06_dCCA - invasive

description: Infinium MethylationEPIC

source_name: Pat 06

value: dCCA - invasive


title: P14.CD8.Lung.KO2

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.2.1
Aligned reads are converted to BAM files using samtools. BAM files are subsequently converted to BED files using bedtools. Unpublished python scripts were used to calculate raw reads and RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes among different conditions.
Genome_build: mm10

source_name: lung

growth_protocol: Naïve WT and Tslpr-/- P14 T cells were isolated for use in vitro and in vivo from the spleens of naïve WT and Tslpr-/- P14 mice and purified using a negative selection CD8+ T cell kit (Stem Cell Technologies). To generate memory CD8+ T cells for use in vivo or in vitro, 5 x 104 (influenza infections) or 105 (LCMV infections) WT or Tslpr-/- naïve P14 cells were injected i.v. into naïve C57BL/6 mice, and the following day the mice were infected with either 103 EID50 of PR8-33 i.n. or 2 x 106 pfu LCMV Armstrong i.p. At >30 days p.i. the spleens were harvested and memory WT and Tslpr-/- P14 cells purified using a negative selection CD8+ T cell kit (Stem Cell Technologies). A sample of the cells were stained with Thy1.1, Thy1.2, CD8, CD44, Va2 and Live/Dead stain to determine the number of P14 T cells. Equal numbers of naïve or memory WT and Tslpr-/- P14 were combined; verification that equal numbers of WT and Tslpr-/- were added was determined by flow cytometry using the same antibodies listed above, and 2.5 x 104 (influenza) or 103 (LCMV) naive P14 T cells or 104 (influenza) or 103 (LMCV) memory P14 T cells of each population (WT and Tslpr-/-) were co-transferred i.v. into naive C57BL/6 mice. On the day following cell transfer, the mice were infected with either 103 EID50 of PR8-33 i.n. or 2 x 106 pfu LCMV Armstrong i.p.  For the assessment of the homeostasis of naïve and memory P14 cells in vivo, equal numbers of naïve or memory WT and Tslpr-/- P14 T cells (~1-2 x 106 total cells) were co-transferred into naïve C57BL/6 mice.

extract_protocol:
For RNA-seq, RNA was isolated from sorted P14 T cells at the indicated time points using the Zymo RNA miniprep kit (Zymo Research), and 500 ng RNA was used for RNA-Seq library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were excised and purified with Zymoclean Gel DNA Recovery Kit (Zymo Research).
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq3000 system.

treatment_protocol: 1 x 106 CD8+ T cells were plated in 0.75 ml/well in 48 well plates or 2 x 106 CD8+ T cells were plated in 1.5 ml/well total volume in 24 well plates with either medium or 100 ng/ml TLSP (R&D systems) with or without stimulation. For in vitro stimulation of naïve cells, the plates were pre-coated with 2 mg/ml anti-CD3e (BioXcell) and 1 mg/ml of soluble anti-CD28 was added. For in vitro stimulation of memory cells, 1 mg/ml of soluble anti-CD3 was added.

tag: strain

tag: cell type

value: lung cells

tag: genotype/variation

value: KO


title: Pat 06_IPNB - premalignant

description: Infinium MethylationEPIC


title: Pat 07_bile duct control - normal

description: Infinium MethylationEPIC

value: bile duct control - normal


title: 12.No.Spi

value: Spi

value: No


title: opc12-79_ten-cell_female_2

description:
opc12-79
rsem_opc.csv

tag: time

value: 12 dpi (days following tamoxifen treatment start)

tag: Sex

tag: section thickness (µm)


title: PBMCs from Healthy 2 co-cultured with Huh7

city: Bangkok

first: Natthaya

last: Chuaypen

address: 1873 Rama 4 road, Pathumwan

country: Thailand

institute: Chulalongkorn University

description:
Treatment Huh8
Controls_vs_Treatments Huh7.txt
TV5

data_processing:
The quality of the raw sequencing reads were assessed with the FastQC v.0.11.2 software. The raw sequencing reads were subjected to trimming process with Trimmomatic v.0.32 software. The surviving paired-end reads were aligned to the Homo sapiens reference genome (Ensembl GRCh38 genome) with HISAT2 v.2.1.0 software. The alignment files were analyzed individually with the StringTie version 1.3.3b software to detect and quantify previously known transcripts. Invidual annotation files generated from transcript assembly process were merged together parsimoniously using StringTie version 1.3.3b. With the merged annotation file.
The expression unit calculated is FPKM, Fragments Per Kilobase Million. Besides, differential expression (DE) analysis was performed according to the given comparison groups . The expression fold change between each comparison group were calculated and log-transformed. Multiple output files were generated by DESeq2 version 1.16.1 and the detail files information are described in the table of result files below. Significant DE genes or transcripts (q-value < 0.05) were extracted for each comparison groups and cancer type.
Genome_build: HG19
Supplementary_files_format_and_content: text files were generated using DESeq2 version 1.16.1 and represented FPKM for each sample , fold change and p-value compared between Control and Treatment groups

source_name: PBMCs

growth_protocol: The liver cancer cells were obtained from Nation Institutes of Biomedical Innovation, Health and Nutrition JCRB Cell Bank (Osaka, Japan) including HepG2 (JCRB1054) and Huh7 (JCRB0403). The Cells were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37 ºc 5 % CO2 in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

extract_protocol:
PBMCs were collected from Transwell culture six well plates and RNA was harvested using Trizol reagent.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified (by AxyPrep Mag PCR Clean-up (Axygen)) double-stranded cDNA was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer ( Agilent Technologies, Palo Alto, CA, USA ) , and quantified by Qubit 2.0 Fluorometer ( Invitrogen, Carlsbad, CA, USA ).

treatment_protocol: Indirect or co-culture liver cancer cells with PBMCs from healthy were performed in Transwell culture six well plates (Costar, France). The liver cancer cells were seeded into plate (106 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37 ºc 5 % CO2. The PBMCs from healthy were plated on permanent membrane culture of Transwell (2 × 106 cells) and incubated for 4 hours at 37 ºc 5 % CO2.

tag: cell line

tag: blood

value: PBMCs


title: P14.CD8.Lung.WT2

value: WT


title: P14.CD8.Lung.WT1


title: P14.CD8.Lung.KO1


title: PBMCs from Healthy 3 co-cultured with Huh7

description:
Treatment Huh9
Controls_vs_Treatments Huh7.txt
TV6


title: A1.CD8.C4.rep3.b7.Healthy

tag: celltype

tag: subjectid

tag: plate

tag: well

tag: sequencingbatch

value: TRUE


title: Pat 05_IPNB - premalignant

description: Infinium MethylationEPIC

source_name: Pat 05

value: IPNB - premalignant


title: Pat 04_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 04


title: opc12-78_pooled_female_2

description:
opc12-78
rsem_opc.csv

tag: genotype

value: female


title: 13.No.Spi

tag: gender

value: F

tag: histology

tag: relapse


title: opc12-77_ten-cell_male_1

description:
opc12-77
rsem_opc.csv

tag: sample type

value: 10-cell sample

value: male


title: Pat 11_IPNB - premalignant

description: Infinium MethylationEPIC

tag: disease state


title: PBMCs from Healthy 1 co-cultured with Huh7

description:
Treatment Huh7
Controls_vs_Treatments Huh7.txt
TV4


title: 10.No.Mix

value: Mix


title: opc12-76_pooled_male_1

description:
opc12-76
rsem_opc.csv

value: pool-and-split control


title: memory.CD8.TCR+media.24h 3

source_name: sleen

tag: strain

tag: cell type

value: CD8+ T cells

tag: sorted cell

value: memory

tag: treatment

value: TCR+media 24h


title: memory.CD8.TCR+TSLP.24h 3

value: TCR+TSLP 24h


title: PBMCs from Healthy 2 co-cultured with HepG2

description:
Treatment HepG2
Controls_vs_Treatments HepG2.txt
TV2

tag: cell line


title: PBMCs from Healthy 3 co-cultured with HepG2

description:
Treatment HepG2
Controls_vs_Treatments HepG2.txt
TV3

tag: blood


title: memory.CD8.media+TSLP.24h 3

value: media+TSLP 24h


title: PBMCs from Healthy 1 co-cultured with HepG2

description:
Treatment HepG2
Controls_vs_Treatments HepG2.txt
TV1


title: opc12-74_pooled_female_1

description:
opc12-74
rsem_opc.csv

tag: time

tag: Sex

tag: section thickness (µm)


title: memory.CD8.TCR+TSLP.4h 3

value: TCR+TSLP 4h


title: PBMCs from Healthy 3

description:
Control
Controls_vs_Treatments HepG2.txt,Controls_vs_Treatments Huh7.txt
RCM6


title: Pat 03_bile duct control - normal

description: Infinium MethylationEPIC

source_name: Pat 03

value: bile duct control - normal