title: OAA-treated Aged Digit D21 [C1]

city: Dallas

first: Robert

middle: J

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

data_processing:
SpaceRanger
Seurat
Genome_build: mm10
Supplementary_files_format_and_content: spatial folder, matrix.h5 files and text file for digit coordinates and genotype

source_name: Aged mice injected daily D10-D21 with OAA

extract_protocol:
enzymatic permeabilization (manufacturer's protocol)
10X Visium Spatial Gene Expression (manufacturer's protocol)

tag: day

value: Day 21

tag: agent

value: OAA


title: ANON3005 May HA III (classical) [14935]

status: Public on Jun 01 2022

type: SRA

city: Hamilton

first: Sarah

last: Anzick

state: MT

address: 903 South 4th Street

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

library_source: transcriptomic

data_processing:
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to GRCh38 reference genome using HISAT2, version 2.1.0.
Reads mapping to genes were counted using htseq-count, version 0.9.1
Gene normalization and differential expression analysis were performed using Deseq2, version 1.18.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
direct lysate
Cells were sorted directly into Takara lysis buffer and a volume of lysate corresponding to 4 or fewer cells was used as input for cDNA synthesis and library construction using the SMART-Seq V4 Ultra Low Input RNA kit (Takara) and SMARTer ThruPLEX DNA-Seq kit, respectively.  Libraries were sequenced as 2 X 150 bp reads

treatment_protocol: flow cytometry and B cell selection

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ classical

tag: season

value: May


title: 961272

type: RNA

city: Durham

first: Wendell

middle: D

last: Jones

state: NC

address: 2400 Ellis Rd

institute: Q2 Solutions

description:
USC33M
Censored data (time=outcome)

hyb_protocol: Samples were hybed (capture probes) based on the typical NanoString protocol

scan_protocol: Samples were scanned based on the typical NanoString protocol on the nCounter instrument

data_processing: Samples were normalized between batches using common samples that had sufficient detection.  Some samples have more than 1 NanoString cartridge.  The cartridge with the highest level of detection was brought forward.  Genes were then separated into cancer-related and immune related genes.  Immune genes were scaled to a common log2 value of 8 across samples using the entire NanoString sample profile(immune and cancer gene expression).  Cancer genes were normalized separately to attempt to estimate the relative expression in non-immune cells as samples varied widely in tumor purity.  Cancer genes were also normalized to a common log2 value of 8 but only using the sample profile of the cancer (non-immune) genes.

molecule: total RNA

source_name: uterine serous cancer

label_protocol: Isolated RNA was assessed by sample source using TapeStation for the percentage of fragments (fragmentation score) between 50 and 300 nt.  Based on a linear function that increased input for higher fragmentation scores, the input level for samples ranged from 100 ng to 1000 ng in proportion to the fragmentation score (higher scores implied higher levels of fragmentation which led to higher input levels to the assay).  After the first round of testing, all 60 samples were evaluated for provenance and consistency between paired samples.  Several samples were repeated at the same or higher input levels to potentially boost detection rates for some samples that initially had low detection rates.  Analysis went forward with the best of the two runs for each sample based on detection rates. A small subset of samples (patient ID #1 Met, patient ID #9 Met and Primary, patient ID #12 Met, patient ID #20 Distant Met, and patient ID#28, Primary) yielded unacceptable NanoString results from either run.

extract_protocol: Archived formalin-fixed paraffin-embedded tumor blocks of paired primary and metastatic tumor from 29 patients with complete clinical treatment/response information were used to obtain 5-8 unstained slides sectioned at 10-micron thickness. The unstained tissue sections were used for extraction of RNA and DNA.  We used Qiagen’s Allprep DNA/RNA FFPE kit to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections.  DNA and RNA were released sequentially by differential solubilization of the same FFPE sample.  FFPE tissue sections were first deparaffinized using xylene.  The tissue was then digested with proteinase K to enable cell lysis and release of the RNA into the supernatant while the DNA and other insoluble material are precipitated.  The sample was then centrifuged to separate the RNA containing supernatant from the DNA containing pellet.  The RNA containing supernatant was heated to partially reverse formalin crosslinks before application to a RNeasy Mini spin column where the total RNA was bound to the membrane.  An on-column DNase digestion was performed to ensure purification of DNA-free RNA.  Following DNase digestion, contaminants were removed through column washing and total RNA was eluted in Nuclease-free water.

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

value: Gain

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: OAA-treated Aged Digit D21 [D1]

organism: Mus musculus

tag: day

tag: agent


title: RS58

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were trimmed with SolexaQA++ dynamic trim [54] and the aligned to GRCh38 with STAR.
Counts were normalized to transcripts per million (TPM) and then log + 1 transformed for all visualizations.
Differential expression was calculated using the software edgeR (v3.26.8) [56]. Raw counts were formatted into a DGE list and filtered for genes with counts > 1 in at least 3 samples. In order to capture all gene expression changes in response to VPA all genes with counts > 0 in at least 1 sample were used. Counts were then normalized with the TMM method. Dispersion was estimated in three steps. First common dispersion was calculated with the conditional maximum likelihood method, followed by tagwise dispersion as a moving average, and then trended dispersion calculated as a spline. These dispersions were then used to calculate differential expression between the relevant two groups. P-values were then adjusted for multiple-testing using the p.adjust function in R (v3.6.1) with the fdr method. To identify the number of genes differentially expressed we used an FDR < 0.05 with no minimum logFC. In the case where differences in expression were calculated as a function of time, these were calculated using the edgeR GLM function with expression as a function of time + disease status. For bulk analyses, days 8-42 were combined and tested as a function of disease status using the described exact test functions. Results were reported as volcano plots with fold change transformed using base 2 and raw p-values transformed using base exp(1).
Functional enrichment analysis was performed using DAVID bioinformatics (v6.8) [57, 58]. All genes with FDR < 0.05 for a given differential expression test were uploaded as a gene list in official gene symbol format and corrected against the Homo sapiens background. A functional annotation chart was then calculated from the results.
Principal component analysis was performed on TPM values using the package pcaMethods (v1.76.0) with the svd algorithm.
LEF1 predicted downstream targets were identified using the Transfac database (gene id = 51176).
Genome_build: hg38
Supplementary_files_format_and_content: Transcripts Per Million normalized expression table as a tab-separated text file

source_name: neurons

growth_protocol: NPCs were differentiated to dentate gyrus-like neurons in N2B27 media supplemented with 200 nM ascorbic acid (STEMCELL Technologies), 500 μg/ml cyclic AMP (Tocris Bioscience), 20 ng/ml brain-derived neurotrophic factor (BDNF, PeproTech), 20 ng/ml Wnt3a (R&D Systems) and 5 μg/ml laminin for 3 weeks. Media was changed three times a week and Wnt3a was removed after 3 weeks.

extract_protocol:
 Cells (~5x106 cells) were collected in RNA-Bee solution (Tel-Test, Inc) and total RNA was extracted using the DNA-Free RNA Kit (Zymo Research) according to the manufacturer’s instructions.
Stranded mRNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions. All libraries were then quantified, pooled and sequenced at single-end 50 bp reads on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing (NGS) Core at a depth of approximately 40 million reads per library.
stranded mRNA

treatment_protocol: 24h treatment with 1 mM LiCl, 1 mM valproic acid, vehicle (water)

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Sorted

tag: treatment

value: VPA

tag: clone

tag: passage number


title: RS59

value: Li


title: 961274

description:
USC34M
Censored data (time=outcome)

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable


title: 961270

tag: tissue

value: metastatic USCD

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

value: M-Metastatic,   D-Distant,   P-Primary:MD

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: OAA-treated Aged Digit D21 [B1]

tag: day

value: Day 21

tag: agent

value: OAA


title: OAA-treated Aged Digit D21 [A1]


title: 961271

value: primary USC

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)


title: RS57

tag: cohort

tag: disease state

tag: cell line

tag: sorted/bulk

tag: treatment

value: CTRL

tag: clone

tag: passage number


title: ANON3005 Conv Pf II (activated) [14931]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: Pf+ activated

tag: season

value: Convalescence


title: 961269

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IV

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: Lung

value: X

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: RS109

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Bulk

tag: treatment

value: 6 week of induction

tag: clone

tag: passage number


title: ANON3005 Conv Pf I (atypical) [14930]

tag: cell type

tag: gender

tag: age

tag: subset

value: Pf+ atypical

tag: season


title: CD4 vhl cKO  6

city: Solna

first: Martin

last: Rottenberg

address: Solna vägen 9

country: Sweden

institute: Karolinska Institutet

description: Lungs  from M. tuberculosis  infected mic were removed, mechanically minced into small pieces and digested with 3 mg/ ml Collagenase D and 30 mg/ ml DNase I for 1 h at 37oC, and single-cell suspensions prepared by filtering lung tissue through 70 µm nylon cell strainers. To enrich the suspension in lymphocytes, cells were loaded into an isotonic 40-70% Percoll density gradient and centrifuged for 30 min at room temperature. Cells in the gradient interphase were collected and washed. CD4 T cells  were obtained after positive selection using CD4 Macs bead (Milteny).

data_processing:
Base calling: Casava 1.8 version base recognition
Read alignement software: Sequenced reads were trimmed for adaptor sequence, containing ploy-N and low quality reads from raw data.   Index of the reference genome was built using Hisat2 v2.0.5. Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.then mapped to mm10 whole genome.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 FPKM values for each Sample , and the log10 p value and the fold changes over log2 FPKM means for each gene,

source_name: Lung CD4 T cell

extract_protocol:
RNA was extracted using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: Vhl fl/fl cd4 cre

value: M. tuberculosis infection


title: CD4 vhl cKO  5


title: 961267

description:
USC30P
Censored data (time=outcome)

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: 961268

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IV

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

value: Ov, Omentum

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: RS60

source_name: neuronal progenitor cells

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Bulk

tag: treatment

value: Neural Progenitor Cells (NPC)

tag: clone

tag: passage number


title: CD4 vhl cKO  4

tag: strain

tag: genotype

value: Vhl fl/fl cd4 cre

value: M. tuberculosis infection


title: RS108

value: 4 week of induction


title: ANON3005 May HA I (atypical) [14933]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ atypical

tag: season

value: May


title: ANON3005 Conv HA III (classical) [14929]

value: HA+ classical

value: Convalescence


title: CD4 vhl cKO  2


title: CD4 vhl cKO  3


title: RS106

value: 1 week of induction


title: RS107

value: 2 week of induction


title: ANON3004 May Pf II (activated) [14925]

value: male

value: Pf+ activated


title: ANON3005 Conv HA I (atypical) [14927]


title: ANON3004 May Pf III (classical) [14926]

value: Pf+ classical


title: 961266

description:
USC30M
Censored data (time=outcome)

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

tag: plk3 est. cn

tag: plk3 cna call

value: Gain

tag: tp53 cna call

value: Normal

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: ANON3005 Conv Pf III (classical) [14932]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

tag: season


title: 961263

description:
USC29P
Censored data (time=outcome)

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

value: IV

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ovary/Omentum

tag: site of recurrence

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: CD4 vhl cKO  1

tag: strain

tag: genotype

value: Vhl fl/fl cd4 cre

tag: treatment

value: M. tuberculosis infection


title: 961262

description:
USC29M
Censored data (time=outcome)

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: RS105

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Bulk

value: Neural Progenitor Cells (NPC)

tag: clone

tag: passage number


title: RS55

value: Sorted

tag: treatment

value: VPA


title: CD4 WT   4

tag: strain

tag: genotype

value: Wild type


title: CD4 WT   5


title: ANON3004 May HA I (atypical) [14921]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: HA+ atypical

tag: season

value: May


title: RS54

value: CTRL


title: ANON3004 May HA III (classical) [14923]

value: HA+ classical


title: CD4 WT   3


title: ANON3004 Conv Pf III (classical) [14920]

value: Pf+ classical

value: Convalescence


title: 961261

description:
USC28P
Not used in the study due to very low levels of detection, and thus we feel the expression values may not be valid.

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ovary, LN

tag: site of recurrence

value: Mesentary

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

value: X

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

value: Loss

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: 961260

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: nanostring io 360 expression data (x if present)

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: RS89

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Bulk

tag: treatment

value: 6 week of induction

tag: clone

tag: passage number


title: ANON3004 Conv Pf II (activated) [14919]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: Pf+ activated

tag: season

value: Convalescence


title: 961259

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

value: Lung

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: CD4 WT   1

tag: strain

tag: genotype

value: Wild type

tag: treatment

value: M. tuberculosis infection


title: CD4 WT   2


title: RS87

tag: cohort

tag: disease state

tag: cell line

tag: sorted/bulk

value: 2 week of induction

tag: clone

tag: passage number


title: ANON3004 Conv Pf I (atypical) [14918]

tag: cell type

tag: gender

tag: age

tag: subset

value: Pf+ atypical

tag: season


title: ANON3004 Conv HA III (classical) [14917]

value: HA+ classical


title: CD4 WT  + unstimulated rep 3

data_processing:
Base calling: Casava 1.8 version base recognition
Read alignement software: Sequenced reads were trimmed for adaptor sequence, containing ploy-N and low quality reads from raw data.   Index of the reference genome was built using Hisat2 v2.0.5. Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.then mapped to mm10 whole genome.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Spleen CD4 T cell

treatment_protocol:
Single cell suspensions were obtained from spleens of mice by mechanical disruption, filtering over a nylon cell strainer and lysis of erythrocytes. Label-free naïve CD4+CD44- T cells were further isolated by negative selection using magnetic beads (MACS, Miltenyi Biotec).
CD4 T cells were stimulated in vitro with either  plate-bound anti-CD3 antibody (145-2C11, Invitrogen) and soluble anti-CD28 antibody (37.51, BD Pharmingen). and cultured at CO2 incubator at 37°C and 5% CO2

value: Untreated


title: RS88

value: iPSC-derived ("Alda cohort")

value: Control

value: Bulk

value: 4 week of induction


title: RS56

value: Sorted

value: Li


title: RS86

value: 1 week of induction


title: CD4 WT  + unstimulated rep 1


title: CD4 WT  + unstimulated rep 2


title: RS85

value: Neural Progenitor Cells (NPC)


title: 961256

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

value: Liver

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: 961254

description:
USC24M
Censored data (time=outcome)

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IIIA

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

value: Bowel

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: 961255

description:
USC24P
Censored data (time=outcome)

value: primary USC

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

value: Loss


title: 961257

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

value: IIIC

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: ANON3004 Conv HA II (activated) [14916]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: HA+ activated

tag: season

value: Convalescence


title: 961258

value: metastatic USC

value: PtS

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ovary, LN

tag: site of recurrence

value: Lung

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3004 Conv HA I (atypical) [14915]

tag: cell type

tag: gender

tag: age

tag: subset

value: HA+ atypical

tag: season


title: ANON3013 Conv Pf III (classical) [14910]

value: Pf+ classical


title: CD4 dcKO  + a-CD3/CD28 rep 4

tag: strain

tag: genotype

value: hif1a fl/fl Vhl fl/fl cd4 cre

tag: treatment

value: Anti CD3/CD38


title: RS44

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Sorted

value: Li

tag: clone

tag: passage number


title: RS43

value: VPA


title: CD4 dcKO  + a-CD3/CD28 rep 3

value: Anti CD3/CD37


title: ANON3013 Conv Pf I (atypical) [14908]

value: primary B cells

value: male

value: Pf+ atypical


title: CD4 dcKO  + a-CD3/CD28 rep 2

value: Anti CD3/CD36


title: RS42

value: CTRL


title: ANON3013 Conv HA III (classical) [14907]

value: HA+ classical

value: Convalescence


title: 961253

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

value: Lung

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: 961252

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: 961251

description:
USC21P
Censored data (time=outcome)

value: PtS-NED

value: CEU+Unk

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn


title: 961250

description:
USC21M
Censored data (time=outcome)

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

tag: plk3 cna call

tag: tp53 cna call

value: Gain

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: RS79

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Bulk

tag: treatment

value: 6 week of induction

tag: clone

tag: passage number


title: ANON3013 Conv HA II (activated) [14906]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: HA+ activated

tag: season

value: Convalescence


title: 961249

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IVB

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: LN

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3011 Conv Pf III (classical) [14904]

tag: cell type

tag: gender

tag: age

tag: subset

value: Pf+ classical

tag: season


title: CD4 vhl cKO  + a-CD3/CD28 rep 3

tag: strain

tag: genotype

value: Vhl fl/fl cd4 cre

tag: treatment

value: Anti CD3/CD34


title: CD4 vhl cKO  + a-CD3/CD28 rep 2

value: Anti CD3/CD33


title: 961248

description:
USC20MD
Not used in the study due to very low levels of detection, and thus we feel the expression values may not be valid.

tag: tissue

value: metastatic USCD

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

value: M-Metastatic,   D-Distant,   P-Primary:MD

value: X

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

value: Unk

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: RS76

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Bulk

tag: treatment

value: 1 week of induction

tag: clone

tag: passage number


title: RS77

value: 2 week of induction


title: CD4 vhl cKO  + a-CD3/CD28 rep 1

tag: strain

tag: genotype

value: Anti CD3/CD32


title: WRKY37_CR_3

city: Beijing

first: Wang

middle: Zhi

last: rong

address: 2#, Yuanmingyuan West Road,100193 Beijing, China

country: China

institute: China Agricultural University

data_processing:
Illumina Novaseq 6000 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SL4.0 whole genome.
Transcripts Per Million reads of library size were calculated.
Genome_build: SL4.0
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
Total RNA was isolated from the tomato samples with the RNAeasy Plant Kit (Huayueyang Company) . RNA-seq 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: the fourth leaf of three-week-old WT, slwrky37-CR and SlWRKY37-OE plants were individually collected with three biological replicates for RNA-seq

tag: tissue

value: leaf

tag: tag

value: WRKY37 mutant

tag: age

value: three-week


title: RS37

value: Sorted

value: VPA


title: RS75

value: Neural Progenitor Cells (NPC)


title: CD4 WT  + a-CD3/CD28 rep 3

value: Wild type

value: Anti CD3/CD30


title: ANON3011 Conv HA I (atypical) [14899]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: subset

value: HA+ atypical

tag: season

value: Convalescence


title: CD4 WT  + a-CD3/CD28 rep 4

value: Anti CD3/CD31


title: 961247

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IVB

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: LN

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Gain

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: CD4 dcKO  + a-CD3/CD28 rep 1

tag: strain

tag: genotype

value: hif1a fl/fl Vhl fl/fl cd4 cre

tag: treatment

value: Anti CD3/CD35


title: 961243

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Lung, peritoneum

value: Loss


title: RS38

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Sorted

value: Li

tag: clone

tag: passage number


title: ANON3014 May Pf III (classical) [14898]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: Pf+ classical

tag: season

value: May


title: RS78

value: Bulk

tag: treatment

value: 4 week of induction


title: 961242

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IV

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

value: Ov, Omentum

tag: site of recurrence

value: Lung

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Gain+

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3011 Conv Pf II (activated) [14903]

tag: cell type

tag: gender

tag: age

tag: subset

value: Pf+ activated

tag: season

value: Convalescence


title: CD4 WT  + a-CD3/CD28 rep 2

tag: strain

tag: genotype

value: Wild type

tag: treatment

value: Anti CD3/CD29


title: 961241

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

value: Gain

value: Loss


title: RS36

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

value: Sorted

tag: treatment

value: CTRL

tag: clone

tag: passage number


title: ANON3011 Conv Pf I (atypical) [14902]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: Pf+ atypical

tag: season


title: 961244

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

value: Lung, peritoneum

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3014 May HA III (classical) [14896]

tag: cell type

tag: gender

tag: age

tag: subset

value: HA+ classical

tag: season

value: May


title: ANON3011 Conv HA III (classical) [14901]

value: Convalescence


title: CD4 WT  + a-CD3/CD28 rep 1

tag: strain

tag: genotype

value: Wild type

tag: treatment

value: Anti CD3/CD28


title: 961240

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

value: Amer Ind

tag: tumor stage

value: IVB

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: Abdomen

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

value: Normal


title: KLF7_IP

city: Guangzhou

first: Jun

last: Liu

state: Guangdong

address: No.2 Lujing Road

department: Dermatology Hospital

institute: Southern Medical University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using EasyAlign version 3.2.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg18
Supplementary_files_format_and_content: KLF7_genes_with_peak.txt

molecule: genomic DNA

source_name: epidermal

extract_protocol:
Lysates were clarified from sonicated nuclei and KLF7-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: chip antibody

value: FLAG (Cell Signaling technology, 14793)


title: Mucosal ileum scrapings - PBS [F09774]

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

country: United Kingdom

institute: University of Warwick

data_processing:
The read quality of all samples were assessed separately using FASTQC
Raw reads were pre-processed using Cutadapt to remove adapter and low quality sequences
The paired end reads were aligned using TopHat 2.0.14 to a combined mouse/human reference genome.  Parameters: "-p 8 -G <combined or mouse gft file> --library-type fr-firststrand --b2-very-sensitive <Combined or mouse genomic index> <file_R1.fastq> <file_R2.fastq>"
For xenograft samples the alignments for the two species were then separated
HTSeq-count 0.6.1p1 was then used to produce read counts for each gene based on the reference annotations Homo_sapiens.GRCh38.80.gtf and genes_mm10_ens.gtf.  Parameters: "-f bam -i gene_id -m intersection-nonempty -s reverse <bam file> <gtf file>"
Genome_build: GRCh38 (human, Ensembl release 83); GRCm38 (mouse, Ensembl release 83)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ileum mucosal scrapings

growth_protocol: For xenograft samples, human small bowel 12-18 weFeks gestational age was implanted subcutaneously on the dorsum of the mouse. Before surgery, carprofen (5 mg/kg) was administered subcutaneously. After surgery, the mice were provided with enrofloxacin-medicated water for 7 days. Grafts developed in situ for 12-16 weeks prior to manipulation.

extract_protocol:
RNA from source tissue was purified using GenElute Mammalian Total RNA kit (Sigma) and RNA samples were quantified using a NanoDrop ND-1000 spectrophotometer.
Libraries were made with the TruSeq Stranded total RNA library prep kit. An average of ~30 million 125-nt paired-end reads was sequenced for each sample.

treatment_protocol: Mice were subjected to systemic LPS  or PBS by intraperitoneal injection.

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

tag: tissue

value: Ileum mucosal scrapings

tag: treatment

value: PBS

tag: xenograft source


title: Mucosal ileum scrapings - PBS [F09775]


title: ANON3014 Conv Pf III (classical) [14893]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: Pf+ classical

tag: season


title: KLF7_In

value: Non


title: ANON3014 Conv Pf I (atypical) [14891]

value: Pf+ atypical

value: Convalescence


title: Mucosal ileum scrapings - PBS [F09772]


title: 961239

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Gain+

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: HCT116.3

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

hyb_protocol: Labeled cell line cRNA was paired with the differentially labeled normal colonic epithelial cRNA and, using the Agilent In situ Hybridization Kit according to manufacturer's specifications. A total of three hybridizations, one of which was a dye swap, were performed and the data pooled in further analysis. Samples were hybridized to the Agilent 44K Whole Genome Oligo Microarray for 17 hours at 60 degree C according to the manufacturer's protocol. After hybridization samples were washed once in Agilent wash buffer I (2X, 0.005% Triton X102) for 5 min., once in wash buffer II (0.006X SSPE, 0.005% N-lauoylsarcosine), and then dried in Agilent Stabilization and Drying Solution.

scan_protocol: Scanned on an Axon 4000B scanner and initial fluorescence data generated with Axon’s GenePix Pro 5.1 software

data_processing:
Axon generated fluorescence intensities for test and reference channels were processed as follows: median background fluorescence was subtracted from median signal for each probe; the 75th percentile over probes in each channel was then standardized to the arbitrary level of 1000 with a multiplicative constant.The  esulting expressions were then truncated at a lower minimum value of 25. These values were then Log base 2 transformed. A linear mixed affects model, including factors for experimental (“Date” of hybridization) and biological (“Patient” source of cell lines, status of “Metastasis”) variation, was fitted to each probe. Date was assumed to be a random Axon generated fluorescence intensities for test and reference channels were processed as follows: median background fluorescence was subtracted from median signal for each probe; the 75th percentile over probes in each channel was then standardized to the arbitrary level of 1000 with a multiplicative constant. The resulting expressions were then truncated at a lower minimum value of 25. These values were then Log base 2 transformed. A linear mixed affects model, including factors for experimental (“Date” of hybridization) and biological (“Patient” source of cell lines, status of “Metastasis”) variation, was fitted to each probe. Date was assumed to be a random affect, and Patient and Metastasis within Patient were fixed affects. Comparisons testing each parameter against zero with t-statistics were performed and the pvalues as well as the fold change (FC) in each cell line versus normal expression was calculated. The FC for each cell line j in each probe g was computed as FC = 2^(β(gj)) . The parameters tested for each probe include the average of all cell lines (cancer) to normal, and the average of the three metastasis-derived cell line to the average of both primary-derived cell lines.
Matrix table includes Log_2_normalized_fold_change_values

source_name: Normal colonic epithelial RNA (BD Biosciences)

label_protocol: total RNA from cell lines and commercially available normal colonic epithelial RNA (BD Biosciences Clontech, Mountain View, CA) labeled using Agilent's Low RNA Input Labeling Kit (5184-3523) according to manufacturer's specifications

growth_protocol: SW480 and SW620 were cultured according to ATCC protocol; KM12 cell lines were grown according to published protocols of the laboratory from which they were obtained (Morikawa et al, 1988)

extract_protocol: Total cellular RNA isolated from the cells using TRIZOL reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol.

tag: tissue

value: Normal colonic epithelial RNA

source_name: HCT116 colon cancer cell RNA

value: HCT116 colon cancer cell RNA


title: ANON3014 Conv Pf II (activated) [14892]

tag: cell type

tag: gender

tag: age

tag: subset

value: Pf+ activated

tag: season


title: KM12C.4

source_name: KM12C colon cancer cell RNA

value: KM12C colon cancer cell RNA


title: KM12SM.3

source_name: KM12SM colon cancer cell RNA

value: KM12SM colon cancer cell RNA


title: ANON3014 Conv HA III (classical) [14890]

value: primary B cells

value: HA+ classical


title: Mucosal ileum scrapings - PBS [F09768]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: Ileum mucosal scrapings

tag: treatment

value: PBS

tag: xenograft source


title: Mucosal ileum - 0.1mg/kg LPS [F09771]

value: LPS 0.1mg/kg


title: 961237

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IVB

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: Peritoneum

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

value: Gain*


title: ANON3014 Conv HA II (activated) [14889]

tag: cell type

tag: gender

value: male

tag: age

tag: subset

value: HA+ activated

tag: season

value: Convalescence


title: 961235

description:
USC12M
Not used in the study due to very low levels of detection, and thus we feel the expression values may not be valid.

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU+Unk

tag: ethnicity (self-reported)

value: Indian

tag: tumor stage

value: IIIA

tag: date of last chemo- therapy

tag: date of recurrence

value: Progressed after 3 cycles

tag: date of death

value: Ov, FT

value: Abdomen/Lung

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

value: Unk

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3009 May HA III (classical) [14884]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ classical

tag: season

value: May


title: Mucosal ileum - 0.1mg/kg LPS [F09769]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

tag: tissue

value: Ileum mucosal scrapings

tag: treatment

value: LPS 0.1mg/kg

tag: xenograft source


title: 961238

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IVB

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: Peritoneum

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis


title: Mucosal iIleum - 10mg/kg LPS [F09773]

tag: strain

tag: tissue

tag: treatment

value: LPS 10mg/kg

tag: xenograft source


title: 961234

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IIIB

tag: date of last chemo- therapy

tag: date of recurrence

value: FT,Vagina

value: Abdomen

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3009 Conv Pf III (classical) [14881]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: Pf+ classical

tag: season

value: Convalescence


title: KM12SM.5

tag: tissue

value: KM12SM colon cancer cell RNA

value: Normal colonic epithelial RNA


title: 961233

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

value: Loss


title: ANON3009 May HA I (atypical) [14882]

tag: cell type

tag: gender

tag: age

tag: subset

value: HA+ atypical

tag: season

value: May


title: Ileum - PBS [F09763]

source_name: Ileum

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

tag: tissue

value: Full thickness Ileum section

tag: treatment

value: PBS

tag: xenograft source


title: ANON3009 Conv HA II (activated) [14877]

value: HA+ activated


title: KM12L4A.4

source_name: KM12L4A colon cancer cell RNA line RNA

value: KM12L4A colon cancer cell RNA line RNA


title: KM12SM.4


title: 961236

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU+Unk

tag: ethnicity (self-reported)

value: Indian

tag: tumor stage

value: IIIA

tag: date of last chemo- therapy

tag: date of recurrence

value: Progressed after 3 cycles

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

value: Ov, FT

value: Abdomen/Lung

value: M-Metastatic,   D-Distant,   P-Primary:P

value: X

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3009 Conv HA I (atypical) [14876]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ atypical

tag: season

value: Convalescence


title: Ileum - PBS [F09759]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

tag: tissue

value: Full thickness Ileum section

tag: treatment

value: PBS

tag: xenograft source


title: HCT116.2

value: HCT116 colon cancer cell RNA

value: Normal colonic epithelial RNA


title: 961290

description:
USC9P
Not used in the study due to very low levels of detection, and thus we feel the expression values may not be valid.

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

value: Unk

value: Loss


title: KM12L4A.2

tag: tissue

value: KM12L4A colon cancer cell RNA line RNA


title: Ileum - PBS [F09758]

tag: strain

tag: treatment

tag: xenograft source


title: 961231

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: II

tag: date of last chemo- therapy

tag: date of recurrence

value: Cervix

value: Lung

value: M-Metastatic,   D-Distant,   P-Primary:M

value: X

tag: nanostring io 360 expression data (x if present)

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: 961289

description:
USC9M
Not used in the study due to very low levels of detection, and thus we feel the expression values may not be valid.

tag: tissue

value: PtS

value: CEU

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

value: Gain+


title: ANON3012 May HA III (classical) [14874]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: HA+ classical

tag: season

value: May


title: SW620.2

tag: tissue

value: Normal colonic epithelial RNA

source_name: SW620 colon cancer cell RNA

value: SW620 colon cancer cell RNA


title: Ileum - 0.1mg/kg LPS [F09762]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: Full thickness Ileum section

tag: treatment

value: LPS 0.1mg/kg

tag: xenograft source


title: ANON3012 Conv Pf II (activated) [14870]

value: Pf+ activated

value: Convalescence


title: HCT116.1

value: HCT116 colon cancer cell RNA


title: Mucosal iIleum - 10mg/kg LPS [F09766]

value: Ileum mucosal scrapings

value: LPS 10mg/kg


title: 961232

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: II

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

value: Cervix

value: Lung

value: M-Metastatic,   D-Distant,   P-Primary:P

value: X

tag: nanostring io 360 expression data (x if present)

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: Ileum - 0.1mg/kg LPS [F09761]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

tag: tissue

value: Full thickness Ileum section

tag: treatment

value: LPS 0.1mg/kg

tag: xenograft source


title: ANON3012 Conv Pf I (atypical) [14869]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: Pf+ atypical

tag: season

value: Convalescence


title: 961288

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

value: IV

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov/Omentum

tag: site of recurrence

value: Abdomen

tag: sample_name (matched primary-met)

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

value: Gain+


title: KM12SM.2

tag: tissue

value: Normal colonic epithelial RNA

value: KM12SM colon cancer cell RNA


title: Ileum - 10mg/kg LPS [F09764]

tag: strain

tag: treatment

value: LPS 10mg/kg

tag: xenograft source


title: 961287

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

value: M-Metastatic,   D-Distant,   P-Primary:M

value: X

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: SW480.2

tag: tissue

source_name: SW480 colon cancer cell RNA

value: SW480 colon cancer cell RNA


title: Ileum - 0.1mg/kg LPS [F09760]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: Full thickness Ileum section

tag: treatment

value: LPS 0.1mg/kg


title: ANON3012 Conv HA III (classical) [14868]

source_name: PBMC

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: HA+ classical

tag: season

value: Convalescence


title: ANON3012 Conv HA II (activated) [14867]

value: HA+ activated


title: 961286

source_name: uterine serous cancer

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU+Unk

tag: ethnicity (self-reported)

value: Arabic

tag: tumor stage

value: IV

tag: date of last chemo- therapy

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: Abdomen

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

value: Normal


title: KM12C.3

tag: tissue

value: Normal colonic epithelial RNA

value: KM12C colon cancer cell RNA


title: Ileum - 10mg/kg LPS [F09756]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: Full thickness Ileum section

tag: treatment

value: LPS 10mg/kg

tag: xenograft source


title: KM12C.2


title: 961285

value: metastatic USCD

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

value: M-Metastatic,   D-Distant,   P-Primary:MD

value: X

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3012 Conv HA I (atypical) [14866]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: HA+ atypical

tag: season

value: Convalescence


title: ANON3010 May Pf III (classical) [14865]

value: female

value: Pf+ classical

value: May


title: Ileum - 10mg/kg LPS [F09757]

tag: strain

tag: tissue

tag: treatment

tag: xenograft source


title: Mucosal human xenograft - PBS [E07137]

source_name: Mucosal Xenograft

value: Mucosal scrapings

value: PBS

value: human fetal gut


title: KM12L4A.1

value: Normal colonic epithelial RNA

value: KM12L4A colon cancer cell RNA line RNA


title: KM12SM.6

value: KM12SM colon cancer cell RNA


title: ANON3010 May Pf I (atypical) [14864]

value: Pf+ atypical


title: Mucosal human xenograft - PBS [E07138]

value: C.B-17/IcrHsd-Prkdcscid (SCID)


title: 961284

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU+Unk

tag: ethnicity (self-reported)

value: Arabic

tag: tumor stage

value: IV

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: Ov, Omentum

tag: site of recurrence

value: Abdomen

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

value: Gain+


title: SW620.1

tag: tissue

value: SW620 colon cancer cell RNA


title: 961282

description:
USC6M
Censored data (time=outcome)

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

value: IIIA

value: FT

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: 961281

value: primary USC

value: Afr

value: AA

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

value: LN/Peritoneum

tag: sample_name (matched primary-met)

value: M-Metastatic,   D-Distant,   P-Primary:P


title: ANON3010 May HA I (atypical) [14861]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ atypical

tag: season

value: May


title: SW480.1

tag: tissue

value: SW480 colon cancer cell RNA

value: Normal colonic epithelial RNA


title: Mucosal human xenograft - PBS [E07136]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: Mucosal scrapings

tag: treatment

value: PBS

tag: xenograft source

value: human fetal gut


title: KM12C.1

value: KM12C colon cancer cell RNA


title: 961279

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

value: LN, Uterine Sero

tag: tumor type

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: 961278

tag: tissue

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: AA

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

value: LN

tag: sample_name (matched primary-met)

value: M-Metastatic,   D-Distant,   P-Primary:M

value: Loss


title: KM12SM.1

value: KM12SM colon cancer cell RNA

value: Normal colonic epithelial RNA


title: 961280

tag: ethnicity (self-reported)

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

value: LN/Peritoneum

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Gain


title: Mucosal human xenograft - 0.1mg/kg LPS [E07130]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

tag: tissue

value: Mucosal scrapings

tag: treatment

value: LPS 0.1mg/kg

tag: xenograft source

value: human fetal gut


title: ANON3010 Conv HA II (activated) [14856]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ activated

tag: season

value: Convalescence


title: Mucosal human xenograft - PBS [E07132]

value: PBS


title: ANON3010 Conv Pf III (classical) [14860]

value: Pf+ classical


title: 961283

description:
USC6P
Censored data (time=outcome)

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

tag: ethnicity (self-reported)

value: W

tag: tumor stage

value: IIIA

tag: date of last chemo- therapy

tag: date of recurrence

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: FT

tag: site of recurrence

tag: sample_name (matched primary-met)

value: M-Metastatic,   D-Distant,   P-Primary:P

value: X

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: ANON3010 Conv Pf II (activated) [14859]

tag: cell type

tag: gender

tag: age

tag: subset

value: Pf+ activated

tag: season


title: ANON3010 Conv HA I (atypical) [14855]

value: HA+ atypical


title: ANON3010 Conv HA III (classical) [14857]

value: primary B cells

value: HA+ classical


title: Mucosal human xenograft - 0.1mg/kg LPS [E07129]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

tag: tissue

value: Mucosal scrapings

tag: treatment

value: LPS 0.1mg/kg

tag: xenograft source

value: human fetal gut


title: Mucosal human xenograft - PBS [E07131]

value: PBS


title: 961265

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtR

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

value: Peritoneum

tag: tumor type

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Loss


title: ANON3015 May HA III (classical) [14852]

tag: cell type

tag: gender

value: male

tag: age

tag: subset

tag: season

value: May


title: ANON3015 May HA II (activated) [14851]

value: HA+ activated


title: Mucosal human xenograft - 0.1mg/kg LPS [E07127]

tag: strain

tag: tissue

tag: treatment

tag: xenograft source


title: 961264

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of recurrence

tag: sample_name (matched primary-met)

value: M-Metastatic,   D-Distant,   P-Primary:M

value: X

value: Gain

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: 961246

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: CEU

value: W

value: IV

tag: site of metastasis

value: Ov, Omentum

value: Oment/Periotoneum

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

value: Normal


title: Mucosal human xenograft - 10mg/kg LPS [E07135]

tag: strain

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: Mucosal scrapings

tag: treatment

value: LPS 10mg/kg

tag: xenograft source

value: human fetal gut


title: 961245

description:
USC1M
Not used in the study due to very low levels of detection, and thus we feel the expression values may not be valid.

value: PtR

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

value: Unk

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: ANON3015 May HA I (atypical) [14850]

tag: cell type

value: primary B cells

tag: gender

value: male

tag: age

tag: subset

value: HA+ atypical

tag: season

value: May


title: sBPD, 100

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description:
severe BPD
Sample name: 100

data_processing:
Data were analyzed in Excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
Data table shows miRNA Ct values normalized to global mean ΔCt = (Ct_miRNA − Ct_global mean)
Supplementary file non-normalized_data.txt:  raw Ct values.
Supplementary file fold-change.txt:  For fold-change calculations (using the livak method), ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 25 was considered as cutoff.

label: SYBR Green

source_name: tracheal aspirate

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of TAs with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Tracheal aspirates were obtained from premature babies with sBPD and BPD-PH. Total RNA was purified from TAs and the expression of 1066 human miRNAs was detected with a PCR array.

tag: developmental stage

value: premature neonate

tag: tissue

value: tracheal aspirate

tag: sbpd

value: yes

tag: bpd-ph

value: no


title: Mucosal human xenograft - 0.1mg/kg LPS [E07128]

tag: strain

tag: treatment

value: LPS 0.1mg/kg

tag: xenograft source


title: ANON3015 Conv Pf III (classical) [14849]

value: Pf+ classical

value: Convalescence


title: HOVON95: Newly diagnosed MM_239

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

hyb_protocol: 13 ug of fragmented and biotin labeled cRNA hybridized to the microarray in an Affymetrix GeneChip® Hybridization Oven 645 and washed / stained in Affymetrix GeneChip Fluidics Station FS450DX2v2

scan_protocol: Affymetrix GeneChip® System 3000Dx v.2

data_processing: MAS5.0 (Bioconductor affy package v1.36.2) default values with a trimmed mean target intensity value set to 1500. Values below 30 were truncated.

label: biotin

source_name: bone marrow aspirate

label_protocol: Affymetrix Gene Profiling MDx IVD Expression Reagent Kit in accordance with Affymetrix protocols.

growth_protocol: Samples obtained from patients

extract_protocol: RNeasy

treatment_protocol: Patients were treatment naive

value: Female

value: bone marrow aspirate

tag: disease state

value: multiple myeloma


title: HOVON95: Newly diagnosed MM_240

value: Male


title: HOVON95: Newly diagnosed MM_236


title: sBPD, 96

description:
severe BPD
Sample name: 96


title: sBPD, 95

description:
severe BPD
Sample name: 95


title: HOVON95: Newly diagnosed MM_237


title: Mucosal human xenograft - 10mg/kg LPS [E07133]

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: Mucosal scrapings

value: LPS 10mg/kg

value: human fetal gut


title: ANON3015 Conv HA III (classical) [14846]

value: primary B cells

value: male

value: HA+ classical


title: ANON3015 Conv Pf I (atypical) [14847]

value: Pf+ atypical


title: HOVON95: Newly diagnosed MM_238


title: Whole gut human xenograft - PBS [E07122]

source_name: Mouse gut Xenograft

value: Full thickness gut sections

value: PBS


title: ANON3015 Conv Pf II (activated) [14848]

value: Pf+ activated


title: HOVON95: Newly diagnosed MM_234


title: Whole gut human xenograft - PBS [E07126]


title: ANON3015 Conv HA II (activated) [14845]

value: HA+ activated


title: Whole gut human xenograft - PBS [E07123]


title: BPD+PH, 93

description:
BPD with Pulmonary Hypertension
Sample name: 93

value: premature neonate

value: tracheal aspirate

value: no

value: yes


title: ANON3015 Conv HA I (atypical) [14844]

value: HA+ atypical

value: Convalescence


title: sBPD, 91

description:
severe BPD
Sample name: 91


title: BPD+PH, 84

description:
BPD with Pulmonary Hypertension
Sample name: 84


title: Whole gut human xenograft - PBS [E07121]

value: C.B-17/IcrHsd-Prkdcscid (SCID)


title: Mucosal human xenograft - 10mg/kg LPS [E07134]

value: Mucosal scrapings

value: LPS 10mg/kg


title: Whole gut human xenograft - 1mg/kg LPS [E07125]

value: LPS 1mg/kg

value: human fetal gut


title: sBPD, 80

description:
severe BPD
Sample name: 80


title: ANON3016 Conv Pf I (atypical) [14843]

value: primary B cells

value: female


title: sBPD, 77

description:
severe BPD
Sample name: 77


title: HOVON95: Newly diagnosed MM_233

value: Male

value: bone marrow aspirate

value: multiple myeloma


title: Whole gut human xenograft - 1mg/kg LPS [E07124]

value: Full thickness gut sections


title: HOVON95: Newly diagnosed MM_232


title: HOVON95: Newly diagnosed MM_230


title: BPD+PH, 76

description:
BPD with Pulmonary Hypertension
Sample name: 76

value: premature neonate


title: ANON3016 Conv Pf II (activated) [14842]

value: Pf+ activated


title: HOVON95: Newly diagnosed MM_235

value: Female


title: Whole gut human xenograft - 10mg/kg LPS [E07120]


title: HOVON95: Newly diagnosed MM_231


title: sBPD, 74

description:
severe BPD
Sample name: 74

value: tracheal aspirate

value: yes

value: no


title: ANON3016 Conv Pf III (classical) [14841]

value: Pf+ classical

value: Convalescence


title: Whole gut human xenograft - 10mg/kg LPS [E07119]

value: C.B-17/IcrHsd-Prkdcscid (SCID)

value: LPS 10mg/kg


title: HOVON95: Newly diagnosed MM_228


title: HOVON95: Newly diagnosed MM_229


title: ANON3016 Conv HA III (classical) [14840]

value: HA+ classical


title: Whole gut human xenograft - 10mg/kg LPS [E07118]

value: human fetal gut


title: BPD+PH, 70

description:
BPD with Pulmonary Hypertension
Sample name: 70


title: CMm_EV_3

city: Oeiras

first: Ana

middle: Filipa

last: Louro

address: Av. República, Qta. do Marquês Edifício iBET/ITQB

department: Animal Cell Technology Unit

country: Portugal

institute: iBET

description:
Sample 12
SV18531_0012_S30

data_processing:
Data was processed through the Genboree exceRpt small RNA-seq Pipeline, Version 4.6.2
Exogenous alignment: endogenous-only; Endogenous Library Order: miRNA, tRNA, piRNA, gencode, circRNA. Within the exceRpt 4.6.2 database the sources for small RNA library mapping are: annotations for miRNAs from miRBAse version 21, tRNAs from gtRNAdb, piRNAs from RNAdb, genome from Gencode version 21 (hg38), CircularRNAs from circBase
Filtering by expression performed with EdgeR (version 3.24.0). Filtering cut-off: CPM equivalent to a minimum of 5 counts
Normalization performed by TMM method using EdgeR
Genome_build: Gencode version 21 (hg38)
Supplementary_files_format_and_content: Tab-delimited text files include Read Count or Read Count Per Million for all Samples corresponding to Genboree exceRpt small RNA-seq Pipeline (4.6.2) output or Trimmed-mean of M-values (TMM) files obtained through EdgeR pipeline

source_name: Conditioned Culture Medium

extract_protocol:
Total RNA was isolated from EV samples (N=3 biological replicates corresponding to EV preparations from three independent cultures) using Norgen Biotek Exosomal RNA Isolation Kit (Cat.58000).
microRNA library preparation was performed by PCR amplification using Norgen Biotek Small RNA Library Prep Kit (Cat. 63600) and library quality control was achieved using Bioanalyzer to estimate library size and concentration. Libraries were denatured and diluted to the required concentration and then applied onto the suitable flowcell and sequenced using Illumina NextSeq 500 sequencing platforms
Small RNA-seq

tag: cell line

tag: differentiation stage

value: mature cardiomyocyte

tag: sample type

value: EV


title: CMm_EV_2

description:
Sample 11
SV18531_0011_S29


title: CMm_EV_1

description:
Sample 10
SV18531_0010_S28


title: sBPD, 67

description:
severe BPD
Sample name: 67


title: BPD+PH, 66

description:
BPD with Pulmonary Hypertension
Sample name: 66


title: HOVON95: Newly diagnosed MM_225

value: bone marrow aspirate


title: HOVON95: Newly diagnosed MM_227

value: Male

value: multiple myeloma


title: CMi_EV_3

description:
Sample 9
SV18531_0009_S27

value: immature cardiomyocyte


title: CMi_EV_2

description:
Sample 8
SV18531_0008_S26


title: CMi_EV_1

description:
Sample 7
SV18531_0007_S25


title: sBPD, 60

description:
severe BPD
Sample name: 60

value: premature neonate


title: BPD+PH, 64

description:
BPD with Pulmonary Hypertension
Sample name: 64


title: HOVON95: Newly diagnosed MM_224


title: BPD+PH, 62

description:
BPD with Pulmonary Hypertension
Sample name: 62


title: HOVON95: Newly diagnosed MM_226


title: sBPD, 59

description:
severe BPD
Sample name: 59


title: SW480-Calcitriol_16hours-rep2

city: Edinburgh

first: Peter

middle: G

last: Vaughan-Shaw

address: Crewe Road

department: IGMM

institute: University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: limma normexp background correction using negative control probes and quantile normalization using negative and positive control probes

source_name: SW480 cell line

label_protocol: For HT12 analysis, total RNA was converted to double-stranded cDNA, followed by in vitro transcription amplification to generate labelled cRNA (Illumina TotalPrep™ RNA Amplification Kit).

growth_protocol: Established colorectal cancer cell lines were used (SW480, LS174T, SW48, DLD1, HCT116, COLO205, T84, LOVO, VACO425, CaCO-2), cultured under standard conditions . When cells reached 80% confluency, standard cell culture techniques were used for cell passaging and maintenance. Cells were treated with 1α,25-dihydroxyvitamin D3 (calcitriol; Sigma) diluted in 100% ethanol, or ethanol control, once 70% confluence was reached. Harvesting of cells for protein and RNA was routinely performed after 16 hours from addition of calcitriol,

extract_protocol: RNA was extracted from cells and organoids using a proprietary RNA extraction kit (Ribopure kit, Applied Biosystems) according to the manufacturer’s protocol. This process initially involved homogenising samples in 1 mL TRIzol. The homogenates were then incubated for 5 minutes at room temperature to enable the nucleoprotein complexes to completely dissociate. 200 μl of chloroform was added and the tubes vortexed at 2800 rpm for 15 seconds. After 5 minutes’ incubation at room temperature, the homogenate was centrifuged at 12,000 x g for 10 min at 4°C. This separated the homogenate into a lower, red, organic phase (phenol-BCP phase); an interphase; and a colourless, upper, aqueous phase. 400 μl of the aqueous phase was withdrawn to which 200 μl of ethanol was added. The mixture was vortexed at maximum speed for 5 seconds and added to a filter cartridge-collection tube. This was centrifuged at 12,000 x g for 30 seconds at room temperature and the flow-through discarded. Two wash cycles using 500 μl of provided wash solution were undertaken, with a final spin of 12,000 x g for 30 seconds to ensure all wash solution had left the filter. Finally, 50 μl of provided elution buffer was added to the filter cartridge within a new collection tube and spun at 12,000 x g for 30 seconds to elute the RNA.

treatment_protocol: Cell line culture was performed in a class 1 biological safety cabinet.  Tissue culture medium used was Dulbecco's Modified Eagle Medium (high glucose, with L-glutamine; DMEM) (Gibco) supplemented with Foetal Calf Serum (10%), or charcoal-treated FCS (10%, Sigma for treatments) and Penicillin/Streptomycin (100 I.U./mL penicillin and 100 μg/mL streptomycin 1%).

value: Calcitriol


title: BPD+PH, 63

description:
BPD with Pulmonary Hypertension
Sample name: 63

value: tracheal aspirate


title: CPC_EV_3

description:
Sample 6
SV18531_0006_S24

value: cardiac progenitor cell


title: BPD+PH, 58

description:
BPD with Pulmonary Hypertension
Sample name: 58

value: no

value: yes


title: SW480-Calcitriol_16hours-rep3


title: HOVON95: Newly diagnosed MM_221


title: SW480-Calcitriol_16hours-rep1


title: CPC_EV_1

description:
Sample 4
SV18531_0004_S22


title: HOVON95: Newly diagnosed MM_223


title: SW480-Ethanol_16hours-rep2

value: ethanol


title: HOVON95: Newly diagnosed MM_218


title: HOVON95: Newly diagnosed MM_219

value: Female


title: HOVON95: Newly diagnosed MM_220


title: LS174T-Calcitriol_16hours-rep3

source_name: LS174T cell line


title: SW480-Ethanol_16hours-rep3


title: HOVON95: Newly diagnosed MM_217


title: BPD+PH, 55

description:
BPD with Pulmonary Hypertension
Sample name: 55


title: HOVON95: Newly diagnosed MM_222