title: Tumor DNA from Pediatric Adrenocortical Tumor_068

source_name: Pediatric Adrenocortical Tumor 068

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Androgen and cortisol

tag: tumor stage

tag: histopathological classification

value: Adenoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: Unavailable

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

value: Wild-type

value: Alive and disease free


title: xenopus tropicalis sperm-H3K27me3_rep2

status: Public on Jan 26 2023

type: SRA

city: Shenzhen

first: Chuihui

last: Hou

state: Guangdong

address: Xueyuan Avenue

country: China

institute: Southern University of Science and Technology

library_source: genomic

data_processing:
Low-quality raw ChIP reads and adapter sequences were removed by Trimmomatic v0.38. Clean reads were then aligned to the X.tropicalis v10.0 reference genome using bwa with default parameters. ChIP-seq signal tracks for visualization were also generated by bamCoverage with options “--binSize 10 --extendReads --minMappingQuality 20 --ignoreDuplicates --normalizeUsing RPKM”.
Genome_build: xv10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Xenopus tropicalis

source_name: xenopus tropicalis sperm

extract_protocol:
Male Xenopus tropicalis were injected with 150 U HCG. After 2 hours, two X. tropicalis testes collected in 1 ml 1xMBS and homogenized using razor blades. The solution was filtered with 40um strainer and its volume was brought down to 14ml. Then, through twice 180G horizontal centrifugation, we can obtain pure sperm in the supernatant.
The ChIP assay was performed as described. Briefly, 5-20 millions sperm were crosslinked with 1% formaldehyde for 10 min using vacuum infiltration. Chromatin was sheared to an average size of 150 bp using a sonicator (Bioruptor Pico, Diagenode). Sonicated chromatin fragments were immunoprecipitated with 3-5 μg of antibody. Chromatin-bound antibodies were recovered with 30μl Protein A/G magnetic beads (Millipore 16-663). After reverse crosslinking, ChIPed DNA was recovered using the MinElute Reaction Cleanup Kit (Qiagen 28206) and amplified with the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme ND607). Amplified ChIP libraries were sequenced on the Illumina HiSeq X10 platform.

tag: tissue

value: sperm

tag: antibody


title: Mouse_kidney_3month_rep1 [SN7640244]

city: Köln

first: Antonios

last: Papadakis

address: Fürvelser Str. 15

country: Germany

institute: CECAD

description:
Mouse_kidney_3month_rep1
Replicate 1

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic version 0.33 ILLUMINACLIP:(TruSeq3-PE.fa:2:30:10 or TruSeq3-SE.fa:2:30:10) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:45 then mapped using STAR version 2.5.1b ‘--outFilterType BySJout --outWigNorm None
Isoform abundancy estimated using Kallisto version 0.42.5
Differential gene expression obtained using DESeq2 version 1.8.2 with RUVr normalization on gene counts obtained by summing kallisto isoform abundancy
Genome_build: hg19,rn5,mm10,dm6,ce10
Supplementary_files_format_and_content: tab-delimited text files with gene counts and differential expression analysis for each contrast

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol:
TruSeq stranded total RNA (Illumina) protocol
RNeasy mini Kit and Trizol

value: kidney

tag: age

value: 3 months

tag: sexe

value: Male

tag: feeding

value: AL

tag: genotype


title: Mouse_liver_16month_DR_rep3

description:
Mouse_liver_16month_DR_rep3
Replicate 3

source_name: liver

value: liver

value: 16 months

value: DR


title: xenopus tropicalis sperm-H3K27me3_rep1


title: xenopus tropicalis sperm-H3K9me2_rep2


title: Mouse_hypothalamus_26month_rep1

description:
Mouse_hypothalamus_26month_rep1
Replicate 1

source_name: hypothalamus

value: hypothalamus

value: 26 month


title: Pituitary neuroendocrine tumors (PitNETs)-008

type: genomic

city: Ribeirão Preto

first: Junier

middle: Marrero

last: Gutiérrez

state: São Paulo

address: Av Bandeirantes, 3900

department: Pediatric

country: Brazil

institute: Ribeirão Preto Medical School-University of São Paulo

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_008
PitNET008

hyb_protocol: Standard Illumina protocol

scan_protocol: Raw methylation data were obtained using the Illumina iScan system (RRID:SCR_016388) according to Illumina protocol.

data_processing: Minfi software program in R computing language (RRID:SCR_012830)

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: DNA from microdissected, fresh frozen tumor samples was extracted using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instruction. DNA quantification was performed by fluorometry using the Qubit dsDNA BR Assay (Thermo Fisher Scientific, Waltham, MA), and the integrity was assessed by electrophoresis using the Tape Station 4200 System (Agilent, Santa Clara, CA). DNA integrity number (DIN) ≥ 6 was considered adequate.

tag: methylation group

tag: gender

value: Female

value: Acromegaly (GH-secreting)

tag: ihc

value: GH+

tag: tumor size

tag: invasion

value: Yes

tag: surgery number

tag: age years

tag: mutations

value: WT

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes


title: Mouse_kidney_24month_rep3

description:
Mouse_kidney_24month_rep3
Replicate 3

value: 24 months


title: Mouse_hypothalamus_26month_rep2

description:
Mouse_hypothalamus_26month_rep2
Replicate 2


title: Pituitary neuroendocrine tumors (PitNETs)-013

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_013
PitNET013

tag: clinical presentation

value: Cushing disease (ACTH-secreting)

value: ACTH+

value: No

value: Undefined

value: ACTH


title: Tumor DNA from Pediatric Adrenocortical Tumor_075

data_processing:
Minfi software program in R computing language (RRID:SCR_012830)
Matrix-processed-Mvalues.csv: Average Beta

source_name: Pediatric Adrenocortical Tumor 075

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Virilization

value: Androgen

tag: tumor stage

value: I

tag: histopathological classification

value: Adenoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

value: Surgery

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)

tag: outcome

value: Alive and disease free


title: Mouse_kidney_24month_rep2

description:
Mouse_kidney_24month_rep2
Replicate 2

tag: tissue

value: kidney

tag: age

tag: sexe

value: Male

tag: feeding

value: AL

tag: genotype


title: Mouse_liver_16month_DR_rep2

description:
Mouse_liver_16month_DR_rep2
Replicate 2

value: liver

value: 16 months

value: DR


title: xenopus tropicalis sperm-H3K27ac_rep2

value: sperm

tag: antibody


title: Mouse_kidney_3month_rep1 [SN7640229]

description:
Mouse_kidney_3month_rep1
Replicate 1

value: 3 months


title: Tumor DNA from Pediatric Adrenocortical Tumor_067

source_name: Pediatric Adrenocortical Tumor 067

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Boldrini's Children Center - State University of Campinas

tag: tumor steroid-secretion

tag: clinical presentation

value: Unavailable

tag: tumor stage

value: II

tag: histopathological classification

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

value: No


title: xenopus tropicalis sperm-H3K27ac_rep1

tag: tissue


title: Mouse_kidney_24month_rep1

description:
Mouse_kidney_24month_rep1
Replicate 1

tag: age

value: 24 months

tag: sexe

tag: feeding

tag: genotype


title: Tumor DNA from Pediatric Adrenocortical Tumor_061

source_name: Pediatric Adrenocortical Tumor 061

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

value: Asymptomatic

value: III

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

value: Surgery and chemotherapy

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)

tag: outcome

value: Alive with active disease


title: Mouse_liver_16month_rep1

description:
Mouse_liver_16month_rep1
Replicate 1

tag: tissue

tag: age

tag: sexe

value: Male


title: fly_heads_50day_dilp2,3-5_rep2

description:
fly_heads_50day_dilp2,3-5_rep2
Replicate 2

organism: Drosophila melanogaster

source_name: heads

value: heads

value: 50 days

tag: feeding

value: AL

tag: genotype


title: Tumor DNA from Pediatric Adrenocortical Tumor_065

source_name: Pediatric Adrenocortical Tumor 065

tag: methylation group

tag: gender

tag: age (years)

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

tag: tumor stage

tag: histopathological classification

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

value: Surgery

value: Mutant

value: Wild-type

value: Alive and disease free


title: Mouse_liver_16month_rep2

description:
Mouse_liver_16month_rep2
Replicate 2

tag: tissue

value: liver

tag: age

value: 16 months

tag: sexe


title: xenopus tropicalis sperm-H3_rep2

value: sperm

tag: antibody


title: WT EC D30 rep3

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequences were removed, then mapped to GRCh38 whole genome using hisat2
Gene counts were calculated using featureCounts with provided GTF file (GENCODE)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Induced pluripotent stem cell

growth_protocol: Human induced pluripotent stem cells were cultured in Essential 8 medium (Thermo Fisher Scientific). Cardiac and endothelial differentiation was performed by chemical modulation of WNT signaling as we previously published (PMID: 33645570; 34611813).

extract_protocol:
Cells were lysed by the TRIzol Reagent (Thermo Fisher Scientific) and total RNA was extracted using the Direct-Zol RNA Miniprep kit (Zymo Research).
RNA libraries were prepared using standard in-house library prep protocols (Novogene)

treatment_protocol: Early iPSC-CMs were treated with 2 mM of CHIR99021 for 4 days for cardiomyocyte proliferation experiment as we previously described (PMID: 33645570).

tag: cell line

value: Endothelial cell

tag: day

value: day 30

tag: genotype

value: wild type


title: Mouse_liver_16month_rep3

description:
Mouse_liver_16month_rep3
Replicate 3

tag: feeding


title: Mouse_liver_16month_DR_rep1

description:
Mouse_liver_16month_DR_rep1
Replicate 1

value: DR


title: Pituitary neuroendocrine tumors (PitNETs)-005

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_005
PitNET005

tag: methylation group

tag: gender

tag: clinical presentation

value: Acromegaly (GH-secreting)

tag: ihc

value: GH+/PRL+

tag: tumor size

tag: invasion

value: No

tag: surgery number

tag: age years

tag: mutations

value: WT

value: Somatotroph

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes

value: GH


title: fly_heads_30day_dilp2,3-5_rep1

description:
fly_heads_30day_dilp2,3-5_rep1
Replicate 1

tag: tissue

value: heads

tag: age

value: 30 days

tag: sexe

value: AL


title: xenopus tropicalis sperm-H3K4me3_rep1

tag: antibody


title: Tumor DNA from Pediatric Adrenocortical Tumor_064

source_name: Pediatric Adrenocortical Tumor 064

value: Male

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Cushing’s Syndrome

value: Androgen and cortisol

tag: tumor stage

value: II

tag: histopathological classification

value: Uncertain malignant potential

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

value: Yes

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

value: Surgery and chemotherapy

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)

tag: outcome

value: Deceased


title: WT EC D30 rep2

tag: cell line

value: Endothelial cell

tag: day

value: day 30

tag: genotype

value: wild type


title: Tumor DNA from Pediatric Adrenocortical Tumor_058

source_name: Pediatric Adrenocortical Tumor 058

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

tag: tumor stage

value: I

tag: histopathological classification

value: Carcinoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

value: Surgery

value: Alive and disease free


title: NOTCH1-KO EC D30 rep3


title: Tumor DNA from Pediatric Adrenocortical Tumor_062

source_name: Pediatric Adrenocortical Tumor 062

value: Boldrini's Children Center - State University of Campinas

value: Asymptomatic

value: Unavailable

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)


title: Mouse_kidney_3month_rep3 [SN7640229]

description:
Mouse_kidney_3month_rep3
Replicate 3

tag: tissue

value: kidney

tag: age

value: 3 months

tag: sexe

value: Male

tag: feeding

value: AL

tag: genotype


title: xenopus tropicalis sperm-H3K4me3_rep2

value: sperm

tag: antibody


title: Tumor DNA from Pediatric Adrenocortical Tumor_059

source_name: Pediatric Adrenocortical Tumor 059

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

tag: clinical presentation

tag: tumor stage

tag: histopathological classification

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

value: Mutant

tag: outcome


title: Mouse_kidney_3month_rep2 [SN7640229]

description:
Mouse_kidney_3month_rep2
Replicate 2

tag: tissue

tag: age

tag: sexe

tag: feeding

tag: genotype


title: fly_heads_30day_dilp2,3-5_rep3

description:
fly_heads_30day_dilp2,3-5_rep3
Replicate 3

value: heads

value: 30 days


title: xenopus tropicalis sperm-H3K4me1_rep2

tag: antibody


title: fly_heads_50day_dilp2,3-5_rep1

description:
fly_heads_50day_dilp2,3-5_rep1
Replicate 1

value: 50 days


title: NOTCH1-KO EC D30 rep2

tag: cell line

value: Endothelial cell

tag: day

value: day 30


title: fly_heads_30day_dilp2,3-5_rep2

description:
fly_heads_30day_dilp2,3-5_rep2
Replicate 2


title: Tumor DNA from Pediatric Adrenocortical Tumor_053

source_name: Pediatric Adrenocortical Tumor 053

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Androgen and cortisol

tag: tumor stage

value: I

value: Uncertain malignant potential

value: No

value: Yes

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)

value: Lost to follow-up


title: fly_heads_50day_dilp2,3-5_rep3

description:
fly_heads_50day_dilp2,3-5_rep3
Replicate 3

tag: tissue

tag: age

tag: sexe

tag: feeding

value: AL

tag: genotype


title: Tumor DNA from Pediatric Adrenocortical Tumor_060

source_name: Pediatric Adrenocortical Tumor 060

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Asymptomatic

tag: clinical presentation

value: II

tag: histopathological classification

value: Adenoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

value: Surgery

tag: outcome

value: Alive and disease free


title: xenopus tropicalis sperm-H3K4me1_rep1

tag: tissue

value: sperm

tag: antibody


title: fly_heads_50day_rep3 [AA]

description:
fly_heads_50day_rep3
Replicate 3

value: heads

tag: age

value: 50 days

tag: sexe

tag: feeding

tag: genotype

value: wDah


title: Tumor DNA from Pediatric Adrenocortical Tumor_055

source_name: Pediatric Adrenocortical Tumor 055

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

value: Virilization

value: Androgen and cortisol

tag: tumor stage

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)


title: xenopus tropicalis sperm-H3_rep1

source_name: xenopus tropicalis sperm

tag: tissue

tag: antibody


title: NOTCH1-KO EC D30 rep1

tag: cell line

value: Endothelial cell

tag: day

value: day 30

tag: genotype


title: WT EC D30 rep1

value: wild type


title: NOTCH1-KO CM D30 rep3

value: Cardiomyocyte


title: Tumor DNA from Pediatric Adrenocortical Tumor_050

source_name: Pediatric Adrenocortical Tumor 050

tag: methylation group

tag: gender

value: Male

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Cushing’s Syndrome

tag: clinical presentation

value: IV

tag: histopathological classification

value: Carcinoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

value: Yes

tag: vascular invasion

value: Surgery and chemotherapy

tag: outcome

value: Deceased


title: fly_heads_50day_rep2 [Z]

description:
fly_heads_50day_rep2
Replicate 2

tag: tissue

value: heads

tag: age

value: 50 days

tag: sexe

tag: feeding

value: AL

value: wDah


title: xenopus tropicalis sperm-RPB2_rep2

value: sperm

tag: antibody


title: Tumor DNA from Pediatric Adrenocortical Tumor_054

source_name: Pediatric Adrenocortical Tumor 054

tag: methylation group

tag: gender

value: Female

tag: age (years)

value: Boldrini's Children Center - State University of Campinas

value: Virilization

value: Unavailable

tag: tumor stage

value: II

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

value: Surgery

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)

value: Alive and disease free


title: fly_heads_50day_rep1 [Y]

description:
fly_heads_50day_rep1
Replicate 1

tag: tissue

tag: age

tag: sexe

tag: genotype


title: xenopus tropicalis sperm-SMC_rep1

tag: antibody

value: SMC


title: Tumor DNA from Pediatric Adrenocortical Tumor_049

source_name: Pediatric Adrenocortical Tumor 049

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

tag: clinical presentation

value: Androgen

value: I

tag: histopathological classification

value: Adenoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

tag: vascular invasion

tag: outcome


title: fly_heads_30day_rep3

description:
fly_heads_30day_rep3
Replicate 3

tag: tissue

value: heads

tag: age

value: 30 days

tag: sexe

tag: feeding

value: AL

value: wDah


title: xenopus tropicalis sperm-RPB2_rep1

value: sperm

tag: antibody


title: fly_heads_30day_rep2

description:
fly_heads_30day_rep2
Replicate 2

tag: genotype


title: NOTCH1-KO CM D30 rep1

tag: cell line

value: Cardiomyocyte

tag: day

value: day 30


title: NOTCH1-KO CM D30 rep2


title: Tumor DNA from Pediatric Adrenocortical Tumor_048

source_name: Pediatric Adrenocortical Tumor 048

tag: methylation group

tag: gender

value: Male

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

tag: tumor stage

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

value: Yes

tag: post-surgery recurrence or metastasis

tag: treatment

value: Surgery

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)


title: Tumor DNA from Pediatric Adrenocortical Tumor_046

source_name: Pediatric Adrenocortical Tumor 046

tag: methylation group

value: Female

value: Androgen and cortisol

tag: histopathological classification

value: Carcinoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

value: Mutant

tag: outcome

value: Alive and disease free


title: S2 cells, Arp6 KD, OE WT, replicate 2

city: Taoyuan City

first: Yun-Ling

last: Hsiao

state: Guishan Dist.

address: No. 259, Wenhua 1st Road

country: Taiwan

institute: Chang Gung University

description: Arp6 KD_WT, replicate 2

data_processing:
Partek® Flow® Genomic Analysis Software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek® Flow® Genomic Analysis Software
Trimmed sequence reads were mapped to BDGP6.32 using Partek® Flow® Genomic Analysis Software
Read count extraction and normalization were performed using Partek® Flow® Genomic Analysis Software
Assembly: BDGP6.32
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: S2 cell line

growth_protocol: Drosophila S2 cells were maintained in Schneider's Drosophila medium supplemented with 10% fetal bovine serum (FBS) at 25C

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Kit or TruSeq strandard mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Description in the Materials and Methods section of paper.

tag: cell line

value: S2 cell line

tag: cell type

value: late embryonic stage

tag: genotype

value: Arp6 knockdown

value: transfection Ac-Da


title: xenopus tropicalis sperm-SMC_rep2

tag: tissue

tag: antibody

value: SMC


title: xenopus tropicalis sperm-CTCF_rep1

value: sperm

value: CTCF


title: WT CM D30 rep2

value: Cardiomyocyte

tag: day

value: day 30

value: wild type


title: Jurkat LAI HUEPI vRNA Rep2

city: SEATTLE

first: Vanessa

last: Montoya

state: Washington

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Center

description:
HuEpi guide RNA library generated by Emerman lab. The library targets 841 human epigenome genes and 252 non-targeting controls.
viral RNA
Jurkat_HuEpi_200205.anno.txt

data_processing:
For the HiSeq2500 datasets, image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4. For the NextSeq2000 datasets Real Time Analysis v3.7.17 was used, followed by bcl2fastq v2.20.
Samples were demultiplexed using FASTX toolkit. Specifically, FASTX barcode splitter was used to separate reads by barcode matching.
HiSeq dataset reads were trimmed and aligned to the respective guide libraries using Bowtie v1.0.0, followed by tabulation of read counts using R. Guide-level quantification for the NextSeq data was performed using Liu lab's MAGeCK software.
Liu lab's CRISPR analysis tool, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK), was used to perform differential guide analysis between various groups of interest. PMID: 25476604.
Assembly: Described in samples section on a per sample basis. [description field]
Supplementary files format and content: Tab delimited files with read counts for each guide sequence
Library strategy: CRISPR

growth_protocol: Jurkat-CCR5 ZAP KO cells are grown in RPMI-1640 supplemented with 10% FBS, 10nM HEPES, and Pen/Strep. Cells are passaged between 2 x 10^5 cells/mL and 2 x 10^6 cells/mL.

extract_protocol:
Viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen, Cat No 52904)
Described in samples section on a per sample basis.
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

treatment_protocol: 3 x 10^6 (>500X coverage) Jurkat-CCR5 ZAP KO cells were each transduced with the TKOv3, HuEpi, PIKA, or HIVDEP libraries (MOI<1) and selected in  0.4 ug/mL puromycin for 10-14 days. Knockout cell pools were infected with viral strains LAI, VSV-G psuedotyped LAI, LAIΔVpr, Q23.BG505, or CH470 TF . Each condition is performed with two replicates. After the treatment, cells and viral supernatants were harvested.

value: Human T lymphocyte

tag: treatment

value: Pooled KO cells containing HuEpi library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)

tag: group

value: Jurkat LAI HUEPI


title: fly_heads_30day_rep1

description:
fly_heads_30day_rep1
Replicate 1

source_name: heads

value: heads

tag: age

value: 30 days

tag: sexe

tag: feeding

value: AL

value: wDah


title: Tumor DNA from Pediatric Adrenocortical Tumor_040

source_name: Pediatric Adrenocortical Tumor 040

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Androgen and cortisol

tag: tumor stage

value: I

tag: histopathological classification

value: Uncertain malignant potential

tag: tumor weight (grams)

tag: tumor size (cm)

value: Unavailable

value: No

value: Yes

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

value: Surgery

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)

value: Alive and disease free


title: WT CM D30 rep3

source_name: Induced pluripotent stem cell

tag: cell line

value: Cardiomyocyte

tag: day

value: day 30

tag: genotype

value: wild type


title: Jurkat LAI HUEPI gDNA

description:
HuEpi guide RNA library generated by Emerman lab. The library targets 841 human epigenome genes and 252 non-targeting controls.
Jurkat_HuEpi_200205.anno.txt

extract_protocol:
Genomic DNA was extracted using a QIAamp DNA Blood Midi kit (Qiagen, Cat No 51183)
Described in samples section on a per sample basis.
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

tag: cell type

value: Human T lymphocyte

tag: treatment

value: Pooled KO cells containing HuEpi library, infected with LAI and gDNA extracted 3dpi (gDNA Replicate 2)

tag: group

value: Jurkat LAI HUEPI


title: Tumor DNA from Pediatric Adrenocortical Tumor_038

source_name: Pediatric Adrenocortical Tumor 038

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Asymptomatic

tag: clinical presentation

tag: tumor stage

tag: histopathological classification

value: Adenoma

tag: tumor weight (grams)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

tag: outcome


title: Tumor DNA from Pediatric Adrenocortical Tumor_037

source_name: Pediatric Adrenocortical Tumor 037

value: Virilization

value: Androgen and cortisol

value: I

tag: tumor size (cm)

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)


title: xenopus tropicalis sperm-CTCF_rep2

tag: tissue

value: sperm

tag: antibody

value: CTCF


title: S2 cells, Arp6 KD, OE WT, replicate 1

description: Arp6 KD_WT, replicate 1

tag: cell line

value: S2 cell line

tag: cell type

value: late embryonic stage

tag: genotype

value: Arp6 knockdown

tag: treatment

value: transfection Ac-Da


title: WT CM D30 rep1

value: Cardiomyocyte

tag: day

value: day 30

value: wild type


title: S2 cells, Luc KD, OE WT, replicate 2

description: ctrl Luc KD_WT, replicate 2

value: Luc knockdown


title: NOTCH1-KO CM drug D20 rep2

value: day 20

value: CHIR99021 treatment


title: Jurkat_TKOv3_LAI_vRNA Rep1

description:
TKOv3 library generated by Emerman lab. It consists of 18053 genes and 142 non-targeting controls.
viral RNA
Jurkat_TKOv3_LAI_200205.txt

value: Human T lymphocyte

value: Pooled KO cells containing TKOv3 library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)

tag: group

value: Jurkat LAI TKOV3


title: NOTCH1-KO CM drug D20 rep1


title: NOTCH1-KO CM drug D20 rep3


title: Tumor DNA from Pediatric Adrenocortical Tumor_035

source_name: Pediatric Adrenocortical Tumor 035

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Androgen and cortisol

tag: tumor stage

value: II

tag: histopathological classification

value: Carcinoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

value: Yes

tag: vascular invasion

tag: soft-tissue invasion

value: Surgery and chemotherapy

value: Mutant

value: Wild-type

tag: outcome

value: Deceased


title: fly_heads_50day_RpII2154_rep2

description:
fly_heads_50day_RpII2154_rep2
Replicate 2

tag: tissue

value: heads

tag: age

value: 50 days

tag: sexe

tag: feeding

value: AL

tag: genotype


title: NOTCH1-KO CM D20 rep3

tag: cell line

value: Cardiomyocyte

tag: day

value: day 20


title: Jurkat_TKOv3_LAI_gDNA Rep2

description:
TKOv3 library generated by Emerman lab. It consists of 18053 genes and 142 non-targeting controls.
Jurkat_TKOv3_LAI_200205.txt

tag: cell type

value: Human T lymphocyte

tag: treatment

value: Pooled KO cells containing TKOv3 library, infected with LAI, and gDNA extracted 3dpi (Replicate 2)

tag: group

value: Jurkat LAI TKOV3


title: NOTCH1-KO CM D20 rep2


title: Jurkat_TKOv3_LAI_gDNA Rep1

value: Pooled KO cells containing TKOv3 library, infected with LAI, and gDNA extracted 3dpi (Replicate 1)


title: Tumor DNA from Pediatric Adrenocortical Tumor_029

source_name: Pediatric Adrenocortical Tumor 029

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Cushing’s Syndrome

tag: clinical presentation

value: Androgen and cortisol

tag: tumor stage

value: IV

tag: histopathological classification

tag: tumor weight (grams)

tag: tumor size (cm)

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)


title: NOTCH1-KO CM D20 rep1

tag: cell line

tag: day

tag: genotype


title: Tumor DNA from Pediatric Adrenocortical Tumor_030

source_name: Pediatric Adrenocortical Tumor 030

tag: methylation group

tag: gender

value: Male

tag: age (years)

tag: reference center

value: Boldrini's Children Center - State University of Campinas

tag: tumor steroid-secretion

value: Virilization

value: Unavailable

value: II

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

value: No

tag: treatment

value: Surgery

value: Mutant

tag: outcome

value: Alive and disease free


title: Jurkat_plusIFN_LAI_ HUEPI gDNA

tag: cell type

value: Human T lymphocyte

value: Pooled KO cells containing HuEpi library, treated with Interferon, infected with LAI and gDNA extracted 3dpi (gDNA Replicate 1)

tag: group

value: Jurkat LAI HUEPI


title: S2 cells, Luc KD, OE WT, replicate 1

description: ctrl Luc KD_WT, replicate 1

tag: cell line

value: S2 cell line

value: late embryonic stage

value: Luc knockdown

value: transfection Ac-Da


title: Tumor DNA from Pediatric Adrenocortical Tumor_045

source_name: Pediatric Adrenocortical Tumor 045

value: Female

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: clinical presentation

value: Androgen

tag: tumor stage

value: I

tag: histopathological classification

value: Adenoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: necrosis

value: Yes

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)


title: NOTCH1-KO CM D13 rep3

value: Cardiomyocyte

tag: day

value: day 13

tag: genotype


title: fly_heads_50day_RpII2154_rep1

description:
fly_heads_50day_RpII2154_rep1
Replicate 1

tag: tissue

value: heads

tag: age

value: 50 days

tag: sexe

tag: feeding

value: AL


title: Tumor DNA from Pediatric Adrenocortical Tumor_036

source_name: Pediatric Adrenocortical Tumor 036

tag: methylation group

tag: gender

value: Male

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

tag: tumor stage

value: II

tag: histopathological classification

value: Uncertain malignant potential

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: treatment

value: Surgery and chemotherapy

value: Mutant

tag: outcome

value: Alive and disease free


title: Tumor DNA from Pediatric Adrenocortical Tumor_028

source_name: Pediatric Adrenocortical Tumor 028

value: Female

value: Boldrini's Children Center - State University of Campinas

value: Unavailable

value: I

tag: tumor weight (grams)

tag: tumor size (cm)

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

value: Surgery

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)


title: Tumor DNA from Pediatric Adrenocortical Tumor_025

source_name: Pediatric Adrenocortical Tumor 025

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Asymptomatic

tag: clinical presentation

tag: tumor stage

value: IV

tag: histopathological classification

tag: tumor volume (cm3)

value: Yes

value: Wild-type

value: Deceased


title: Tumor DNA from Pediatric Adrenocortical Tumor_026

source_name: Pediatric Adrenocortical Tumor 026

value: Male

value: Ribeirao Preto Medical School - University of Sao Paulo

value: Virilization

value: Androgen and cortisol

value: Carcinoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: treatment

tag: outcome

value: Alive with active disease


title: Jurkat_TKOv3_LAI_vRNA Rep2

tag: cell line

tag: cell type

value: Human T lymphocyte

value: Pooled KO cells containing TKOv3 library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)

tag: group

value: Jurkat LAI TKOV3


title: Jurkat LAI HUEPI vRNA Rep1

value: Pooled KO cells containing HuEpi library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)

value: Jurkat LAI HUEPI


title: Jurkat LAIdelVpr HUEPI vRNA Rep2

value: Pooled KO cells containing HuEpi library infected with LAIdeltaVpr, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)

value: Jurkat LAIdeltaVpr HUEPI


title: NOTCH1-KO CM D13 rep2

value: Cardiomyocyte

tag: day

value: day 13

tag: genotype


title: fly_heads_50day_rep2 [K002000083]

description:
fly_heads_50day_rep2
Replicate 2

tag: tissue

value: heads

tag: age

value: 50 days

tag: sexe

tag: feeding

value: AL

value: wDah


title: fly_heads_10day_RpII2154_rep3

description:
fly_heads_10day_RpII2154_rep3
Replicate 3

value: 10 days


title: Tumor DNA from Pediatric Adrenocortical Tumor_021

source_name: Pediatric Adrenocortical Tumor 021

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Androgen and cortisol

tag: tumor stage

value: II

tag: histopathological classification

value: Unavailable

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

value: No

value: Yes

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

value: Surgery

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)

value: Alive and disease free


title: WT CM drug D20 rep2

tag: cell line

value: Cardiomyocyte

tag: day

value: day 20

tag: genotype

value: wild type

tag: treatment

value: CHIR99021 treatment


title: Jurkat CH470TF PIKA gDNA

description:
PIKA-HIV library developed by Emerman lab. It consists of 1906 genes and 200 non-targeting controls.
Jurkat_PIKA_counts.anno.txt

tag: cell type

value: Human T lymphocyte

value: Pooled KO cells containing PIKA library, treated with Interferon, infected with CH470 TF and gDNA extracted 3dpi (gDNA Replicate 2)

tag: group

value: Jurkat PIKA


title: WT CM drug D20 rep1


title: Jurkat LAI PIKA vRNA Rep2

description:
PIKA-HIV library developed by Emerman lab. It consists of 1906 genes and 200 non-targeting controls.
viral RNA
Jurkat_PIKA_counts.anno.txt

value: Pooled KO cells containing PIKA library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)


title: fly_heads_10day_rep3

description:
fly_heads_10day_rep3
Replicate 3

tag: tissue

value: heads

tag: age

value: 10 days

tag: sexe

tag: feeding

value: AL

value: wDah


title: fly_heads_50day_RpII2154_rep3

description:
fly_heads_50day_RpII2154_rep3
Replicate 3

value: 50 days


title: WT CM D20 rep2


title: fly_heads_10day_RpII2154_rep1

description:
fly_heads_10day_RpII2154_rep1
Replicate 1


title: fly_heads_50day_rep1 [K002000083]

description:
fly_heads_50day_rep1
Replicate 1


title: fly_heads_50day_rep3 [K002000083]

description:
fly_heads_50day_rep3
Replicate 3


title: NOTCH1-KO CM D13 rep1

value: day 13


title: WT CM drug D20 rep3


title: WT CM D20 rep1


title: Jurkat LAI-VSVg HIVDEP vRNA Rep2

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
viral RNA
Jurkat_HIVDEP_201231.anno.txt

value: Pooled KO cells containing HIVDEP library infected with LAI-VSV-G, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)

value: Jurkat LAI-VSVG HIVDEP


title: Tumor DNA from Pediatric Adrenocortical Tumor_009

source_name: Pediatric Adrenocortical Tumor 009

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Androgen and cortisol

tag: tumor stage

value: II

tag: histopathological classification

value: Uncertain malignant potential

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

value: Yes

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

value: Surgery

value: Mutant

tag: outcome

value: Alive and disease free


title: WT CM D13 rep3

tag: cell line

value: Cardiomyocyte

tag: day

tag: genotype

value: wild type


title: WT CM D20 rep3

value: day 20


title: Jurkat LAI-VSVg HIVDEP vRNA Rep1

tag: cell type

value: Human T lymphocyte

tag: treatment

value: Pooled KO cells containing HIVDEP library infected with LAI-VSV-G, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)

tag: group


title: Jurkat LAIdelVpr HUEPI vRNA Rep1

description:
HuEpi guide RNA library generated by Emerman lab. The library targets 841 human epigenome related genes and 252 non-targeting controls.
viral RNA
Jurkat_HuEpi_200205.anno.txt

value: Pooled KO cells containing HuEpi library infected with LAIdeltaVpr, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)

value: Jurkat LAIdeltaVpr HUEPI


title: WT CM D13 rep2

value: day 13


title: Jurkat LAI PIKA vRNA Rep1

value: Pooled KO cells containing PIKA library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)

value: Jurkat PIKA


title: Tumor DNA from Pediatric Adrenocortical Tumor_014

source_name: Pediatric Adrenocortical Tumor 014

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Boldrini's Children Center - State University of Campinas

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Unavailable

tag: tumor stage

value: I

tag: histopathological classification

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

tag: overall survival (years)


title: Tumor DNA from Pediatric Adrenocortical Tumor_020

source_name: Pediatric Adrenocortical Tumor 020

value: Ribeirao Preto Medical School - University of Sao Paulo

value: Androgen and cortisol

value: II

value: Carcinoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

value: Yes

tag: mitosis > 15/20 high powered fields

value: Surgery and chemotherapy

value: Mutant

tag: outcome

value: Alive and disease free


title: fly_heads_10day_RpII2154_rep2

description:
fly_heads_10day_RpII2154_rep2
Replicate 2

source_name: heads

tag: tissue

value: heads

tag: age

value: 10 days

tag: sexe

tag: feeding

value: AL

tag: genotype


title: fly_heads_10day_rep2

description:
fly_heads_10day_rep2
Replicate 2

value: wDah


title: Tumor DNA from Pediatric Adrenocortical Tumor_013

source_name: Pediatric Adrenocortical Tumor 013

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

tag: tumor stage

tag: histopathological classification

value: Uncertain malignant potential

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

value: Surgery

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)


title: Jurkat CH4706mo PIKA gDNA

tag: cell line

tag: cell type

value: Human T lymphocyte

value: Pooled KO cells containing PIKA library, treated with Interferon, infected with CH470 6mo and gDNA extracted 3dpi (gDNA Replicate 1)

tag: group

value: Jurkat PIKA


title: border zone, FapKO-1

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 mouse genome using STAR.
Aligned reads with high quality were quantified by HTSeq.
Counts per million reads (CPM) were calculated.
Unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts were calculated by UMI number to get rmdup.count file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: border zone

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were constructed by a modified Smartseq2 method with UMI barcodes (Nature 533:487, 2016).

tag: tissue

value: border zone

tag: genotype

value: FapKO

value: MI

tag: time


title: Tumor DNA from Pediatric Adrenocortical Tumor_017

source_name: Pediatric Adrenocortical Tumor 017

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

value: Cushing’s Syndrome

value: Androgen and cortisol

value: I

value: Adenoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

value: Yes

tag: mitosis > 15/20 high powered fields

value: Wild-type

tag: overall survival (years)

tag: outcome


title: HIVDEP plasmid Rep1

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
Plasmid
Jurkat_HIVDEP_201231.anno.txt

extract_protocol:
Plasmid
Described in samples section on a per sample basis.
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

tag: cell line

tag: cell type

tag: treatment

value: HIVDEP plasmid Rep1

tag: group


title: Tumor DNA from Pediatric Adrenocortical Tumor_012

source_name: Pediatric Adrenocortical Tumor 012

tag: methylation group

tag: gender

value: Male

tag: age (years)

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

tag: tumor stage

value: IV

tag: histopathological classification

value: Carcinoma

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

value: Surgery and chemotherapy

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

value: Deceased


title: worms_14day_daf2_rep2

description:
worms_14day_daf2_rep2
Replicate 2

organism: Caenorhabditis elegans

source_name: whole body

tag: tissue

value: whole body

tag: age

value: 14 days

tag: sexe

tag: feeding

value: AL

tag: genotype


title: Jurkat LAI HIVDEP vRNA Rep2

tag: cell line

tag: cell type

value: Human T lymphocyte

tag: treatment

value: Pooled KO cells containing HIVDEP library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)

tag: group

value: Jurkat LAI HIVDEP


title: Tumor DNA from Pediatric Adrenocortical Tumor_003

source_name: Pediatric Adrenocortical Tumor 003

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Asymptomatic

tag: clinical presentation

value: Androgen and cortisol

value: Adenoma

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: overall survival (years)

tag: outcome

value: Alive and disease free


title: border zone, FapKO-4

tag: tissue

value: border zone

tag: genotype

value: FapKO

tag: treatment

value: MI

tag: time


title: G1_Il13ra1-/-_OXA_esophagus

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.28.0
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized_counts.csv

source_name: esophagus

extract_protocol:
RNA extraction using TRIZOL (Ambion)
The CEL-Seq library was run on an Illumina NextSeq550 sequencer

treatment_protocol: Mice underwent a murine experimental EoE model using the chemical Allergan 4-Ethoxymethylene-2-phenyl-2-oxazolin-5-one (OXA) or control (Vehicle ) treatment.

value: esophagus

tag: strain

value: OXA


title: Tumor DNA from Pediatric Adrenocortical Tumor_006

source_name: Pediatric Adrenocortical Tumor 006

tag: methylation group

tag: gender

value: Male

tag: age (years)

tag: reference center

value: Boldrini's Children Center - State University of Campinas

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

value: Unavailable

tag: tumor stage

value: II

tag: histopathological classification

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

value: Surgery

tag: p53 p.r337h germline mutation genotype

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)


title: HeLa_replicate3_initial [HeLa_R3_D5]

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: HeLa initial replicate 3

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
Reads were aligned to the guide library  using Bowie and counted for gene associations against the guide library used.
Raw counts for each guide are supplied for every sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample.

growth_protocol: Cells were cultured in DMEM+10% FBS at 37C 5% CO2

extract_protocol:
Followed the standard protocol for the Qiagen QIAamp DNA Blood Mini Kit
Nested PCR was used to amplify integrated sgRNAs out of gDNA.  Illumina adapters were added on as part of the primers for the second round PCR.

treatment_protocol: Cells were treated with puromycin to kill untransduced cells at the start of the experiement

tag: cell line

value: HeLa

tag: cell type

value: Cervical Cancer Cells

tag: timepoint

value: intial


title: Tumor DNA from Pediatric Adrenocortical Tumor_010

source_name: Pediatric Adrenocortical Tumor 010

value: Female

value: I

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: treatment

value: Mutant

value: Wild-type

tag: overall survival (years)

tag: outcome


title: WT CM D13 rep1

source_name: Induced pluripotent stem cell

value: Cardiomyocyte

tag: day

value: day 13

tag: genotype

value: wild type


title: Jurkat LAI HIVDEP vRNA Rep1

tag: cell line

value: Human T lymphocyte

value: Pooled KO cells containing HIVDEP library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)

tag: group

value: Jurkat LAI HIVDEP


title: HeLa_replicate3_outgrowth [HeLa_R3_D13]

description: HeLa eight days outgrowth replicate 3

tag: cell type

tag: timepoint

value: final


title: border zone, FapKO-2

tag: tissue

value: border zone

value: FapKO

value: MI

tag: time


title: Jurkat LAI HIVDEP gDNA Rep1

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
Jurkat_HIVDEP_201231.anno.txt

value: Pooled KO cells containing HIVDEP library infected with LAI and gDNA extracted 3dpi (Replicate 1)


title: HeLa_replicate2_initial [HeLa_R2_D5]

description: HeLa initial replicate 2

value: HeLa

value: Cervical Cancer Cells


title: border zone, FAPI-4

value: WT

value: MI+FAPI


title: F3_Il13ra1-/-_OXA_esophagus

value: esophagus

tag: strain

value: OXA


title: border zone, MI-4


title: HeLa_replicate2_outgrowth [HeLa_R2_D13]

description: HeLa eight days outgrowth replicate 2


title: border zone, MI-3


title: border zone, FAPI-3


title: F2_Il13ra1-/-_OXA_esophagus


title: HeLa_replicate1_initial [HeLa_R1_D5]

description: HeLa initial replicate 1

value: intial


title: worms_14day_ama1_rep2

description:
worms_14day_ama1_rep2
Replicate 2

value: whole body

tag: age

value: 14 days

tag: sexe

tag: feeding

value: AL


title: E5_Il13ra1-/-_Vehicle_esophagus

value: Vehicle


title: fly_heads_10day_rep1

description:
fly_heads_10day_rep1
Replicate 1

value: heads

value: 10 days

value: wDah


title: HIVDEP plasmid Rep2

value: HIVDEP plasmid Rep2


title: HeLa_replicate1_outgrowth [HeLa_R1_D13]

description: HeLa eight days outgrowth replicate 1

value: final


title: border zone, FapKO-3

value: border zone

value: FapKO

value: MI


title: worms_14day_daf2_rep3

description:
worms_14day_daf2_rep3
Replicate 3


title: border zone, MI-1

value: WT


title: worms_14day_rep3 [K002000093]

description:
worms_14day_rep3
Replicate 3


title: E3_Il13ra1-/-_Vehicle_esophagus


title: HCT116_replicate1_outgrowth [HCT116_R1_D8]

description: HCT116 eight days outgrowth replicate 1

value: Colorectal Cancer Cells


title: HCT116_replicate3_initial [HCT116_R3_D0]

description: HCT116 initial replicate 3


title: border zone, FAPI-2

value: MI+FAPI


title: Jurkat LAI HIVDEP gDNA Rep2

value: Human T lymphocyte

value: Pooled KO cells containing HIVDEP library infected with LAI and gDNA extracted 3dpi (Replicate 2)

value: Jurkat LAI HIVDEP


title: E2_Il13ra1-/-_Vehicle_esophagus

value: esophagus


title: border zone, sham-3

value: sham


title: border zone, sham-1


title: HCT116_replicate2_initial [HCT116_R2_D0]

description: HCT116 initial replicate 2

value: intial


title: HCT116_replicate1_initial [HCT116_R1_D0]

description: HCT116 initial replicate 1


title: border zone, FAPI-1


title: S7_S6_5E1_anti-HH, rep3

city: New York

first: Matthias

middle: C

last: Kugler

state: NY

address: 550 First Avenue, Medical Science Building, MSB-594

department: Medicine

institute: NYU School of Medicine

description: P8 5E1

data_processing:
Reads were mapped to the reference genome (mm10) using the STAR aligner (v2.5.0c) and aligned guided by a Gene Transfer Format (GTF) file.
Mean read insert sizes and corresponding standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard).
The Read Per Million (RPM) normalized BigWig files were created using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4)
Read count tables wre generated in HTSeq (v0.6.0)
The DESeq2 package (v.1.10.0) was used in R (v.3.5.1; http://www.R-project.org/) to normalize samples based on their library size factors and to carry out differential expression analysis among the different sample groups
Assembly: mm10
Supplementary files format and content: bw, tab-delimited text files include RPKM values for each Sample

source_name: lung

extract_protocol:
Lungs were harvested genotyped PdgraEGFP/+ pups at P8, single cell suspensions were generated and live EGFP+ expressing cells were sorted by FACS for RNA library prep
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Prep following manufacturer's protocols.

treatment_protocol: Timed pregnant PdgfraEGFP/+ dams were treated at E18.5 with either anti-HH antibody 5E1 or control IgG by intraperitoneal injection.

value: lung

value: EGFP+ cell population

value: PdgfraEGFP/+


title: D1_WT_OXA_esophagus

value: OXA


title: F4_Il13ra1-/-_OXA_esophagus


title: S6_S5_5E1_anti-HH, rep2

description: P8 5E1


title: C3_WT_OXA_esophagus


title: Tumor DNA from Pediatric Adrenocortical Tumor_001

source_name: Pediatric Adrenocortical Tumor 001

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Androgen and cortisol

tag: clinical presentation

value: Cushing’s Syndrome

tag: tumor stage

value: III

tag: histopathological classification

value: Uncertain malignant potential

tag: tumor weight (grams)

tag: tumor size (cm)

tag: tumor volume (cm3)

tag: vena cava invasion

value: No

tag: capsular invasion

value: Yes

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

value: UUnavailablevailable

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

value: Surgery and chemotherapy

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

tag: disease-free survival (years)

value: Deceased


title: border zone, MI-2

tag: tissue

value: border zone

tag: genotype

value: WT

tag: treatment

value: MI

tag: time


title: worms_14day_ama1_rep1

description:
worms_14day_ama1_rep1
Replicate 1

value: whole body

tag: age

value: 14 days

tag: sexe

tag: feeding

value: AL


title: worms_14day_ama1_rep3

description:
worms_14day_ama1_rep3
Replicate 3


title: S3_S3_IgG, rep3

description: P8 IgG

value: lung

tag: cell type

value: EGFP+ cell population

value: PdgfraEGFP/+

value: IgG


title: HCT116_replicate3_outgrowth [HCT116_R3_D8]

description: HCT116 eight days outgrowth replicate 3

tag: cell line

value: Colorectal Cancer Cells

tag: timepoint

value: final


title: S2_S2_IgG, rep2

description: P8 IgG


title: RAS_replicate3_initial [RAS_R3_D0]

description: Ras transformed ARPE19 initial replicate 3

value: RAS

value: Ras Transformed retinal pigment epithelial cells

value: intial


title: worms_14day_daf2_rep1

description:
worms_14day_daf2_rep1
Replicate 1


title: border zone, sham-2

value: sham


title: RAS_replicate2_initial [RAS_R2_D0]

description: Ras transformed ARPE19 initial replicate 2


title: D2_WT_OXA_esophagus

value: esophagus

tag: strain

value: OXA


title: HCT116_replicate2_outgrowth [HCT116_R2_D8]

description: HCT116 eight days outgrowth replicate 2


title: A2_WT_Vehicle_esophagus

value: WT

value: Vehicle


title: E4_Il13ra1-/-_Vehicle_esophagus


title: 3D-culture-rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 mouse genome using STAR.
For RNA-seq data, aligned reads with high quality were quantified by HTSeq.
For RNA-seq data, counts per million reads (CPM) were calculated.
For RNA-seq data, unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts were calculated by UMI number to get rmdup.count file.
Genome_build: mm10
Supplementary_files_format_and_content: We provided tab-delimited text files including raw count values for each sample.

molecule: polyA RNA

source_name: mouse cardiac fibroblast

growth_protocol: Mouse cardiac fibroblasts were isolated from mouse heart ventricles and cultured in low-glucose DMEM media (Corning, 10-014-CV) supplemented with 10% FBS (Gibco, 10270-106), 10 μM ROCK inhibitor (MedExpress, HY-15720) and 1% penicillin/streptomycin (Thermo). Mouse endothelial cells were isolated from mouse heart and lung and cultured in dishes pre-coated with 1% fibronectin with EGM-2 MV media (Lonza, CC-3202).

extract_protocol:
Cardiac fibroblasts cultured alone were extracted directly from 3D GelMA dissosiation, cardiac fibroblasts (CD45-CD31-Pdgfr-α+) co-cultured with endothelial cells were flow cytometrically sorted from 3D GelMA co-culture system.
RNA-seq libraries were constructed by a modified Smart-seq2 method with UMI barcodes (Nature 533:487, 2016).

treatment_protocol: Cardiac fibroblasts were cultured alone or co-cultured with endothelial cells for 7 days in 5% 3D GelMa system (EFL, EFL-GM-90).

value: mouse heart ventricle

tag: condition

value: 3D culture in GelMA system

value: cardiac fibroblast cultured alone


title: B1_WT_Vehicle_esophagus


title: worms_21day_rep2

description:
worms_21day_rep2
Replicate 2

value: whole body

value: 21 days

value: AL


title: ARPE19_replicate3_outgrowth [ARPE19_R3_D8]

description: ARPE19 eight days outgrowth replicate 3

value: Retinal pigment epithelial cells


title: S1_S1_IgG, rep1

description: P8 IgG

value: lung

value: EGFP+ cell population

value: PdgfraEGFP/+

value: IgG


title: worms_14day_rep2 [K002000093]

description:
worms_14day_rep2
Replicate 2

value: 14 days


title: worms_7day_rep1

description:
worms_7day_rep1
Replicate 1

value: 7 days


title: 3D-culture-rep1


title: worms_14day_rep1 [K002000093]

description:
worms_14day_rep1
Replicate 1


title: RAS_replicate3_outgrowth [RAS_R3_D8]

description: Ras transformed ARPE19 eight days outgrowth replicate 3

value: RAS

value: Ras Transformed retinal pigment epithelial cells

value: final


title: worms_21day_rep3

description:
worms_21day_rep3
Replicate 3


title: worms_7day_rep3

description:
worms_7day_rep3
Replicate 3


title: S5_S4_5E1_anti-HH, rep1

description: P8 5E1


title: worms_14day_rep3 [SN7640275]

description:
worms_14day_rep3
Replicate 3


title: 3D-culture-rep2


title: ARPE19_replicate1_outgrowth [ARPE19_R1_D8]

description: ARPE19 eight days outgrowth replicate 1


title: worms_1day_rep2

description:
worms_1day_rep2
Replicate 2

value: 1 days


title: A4_WT_Vehicle_esophagus

value: esophagus

value: WT

value: Vehicle


title: RAS_replicate2_outgrowth [RAS_R2_D8]

description: Ras transformed ARPE19 eight days outgrowth replicate 2


title: worms_14day_rep2 [SN7640275]

description:
worms_14day_rep2
Replicate 2

value: whole body


title: worms_21day_rep1

description:
worms_21day_rep1
Replicate 1

value: 21 days


title: A3_WT_Vehicle_esophagus


title: C1_WT_OXA_esophagus

value: OXA


title: ARPE19_RAS_mixed_replicate1_initial [ARPE19_RAS_R1_D0]

description: ARPE19 and Ras initial replicate 1 mixed

value: Retinal pigment epithelial cells

value: intial


title: worms_1day_rep1

description:
worms_1day_rep1
Replicate 1

value: AL


title: co-culture-rep1

value: mouse heart ventricle

value: 3D culture in GelMA system

value: cardiac fibroblast co-cultured with endothelial cell


title: ARPE19_replicate2_outgrowth [ARPE19_R2_D8]

description: ARPE19 eight days outgrowth replicate 2


title: RAS_replicate1_outgrowth [RAS_R1_D8]

description: Ras transformed ARPE19 eight days outgrowth replicate 1


title: ovarian cells, 22h, rep2

status: Public on Jan 25 2023

city: Nanjing

first: Qiuzhen

last: Chen

address: 101 Longmian Rd, Nanjing, Jiangsu, 211166 China

institute: Nanjing Medical University

data_processing:
Checked the quality control of reads data by FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to Sscrofa11 using STAR
Read count extraction and normalization were performed using HTSeq and RSEM
Assembly: Sscrofa11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample,  each file contain 2 columns, the first column represents gene id, the second column represents the FPKM value

organism: Sus scrofa

source_name: ovary

extract_protocol:
Oocytes were isolated from the column oocyte complexes after in vitro mature for 0h, 22h, and 46h, respectively.
RNA-seq library preparation was used the SMART-Seq2 protocol.

value: ovary

value: oocyte

value: in vitro mature for 22h

tag: replicate


title: ovarian cells, 0h, rep1

value: in vitro mature for 0h


title: ovarian cells, 0h, rep2


title: ovarian cells, 46h, rep2

value: in vitro mature for 46h


title: ovarian cells, 22h, rep4


title: worms_14day_rep1 [SN7640275]

description:
worms_14day_rep1
Replicate 1

value: 14 days


title: ovarian cells, 22h, rep1


title: CD15M_CM2_IgG

city: Wuhan

first: Weiwei

last: Wang

address: Hongshan District

institute: Huazhong Agricultural University

data_processing:
The clean data were mapped to the Sus scrofa genome assembly 11.1 with BWA (v0.7.17-r1188).
The duplicate reads and low-quality reads (MAPQ < 25) were filtered out using SAMtools (v1.9) and Picard (v2.8.3).
To identify the H3K4me3 and H3K27ac peaks, replicates of ChIP-seq data were pooled and the peak calling was performed by MACS2 (v2.2.6) with a 3 kb extension regions.
Assembly: Sus scrofa genome assembly 11.1
Supplementary files format and content: Merge_peaks (except for IgG samples)

source_name: Myometrium

extract_protocol:
The samples were lysed with precooled lysis buffer at 4°C for 10 min, and resuspended in wash buffer. Then the number of nuclei was counted. Approximately 100,000 nuclei were resuspended in wash buffer, mixed with 10 µL equilibrated Concanavalin A beads. Then the beads were resuspended in a mixture containing diluted primary antibody to obtain the immunoprecipitated DNA.
The immunoprecipitated DNA and immunoprecipitated control (IgG) were purified. ChIP-seq libraries were constructed following the manufacturer’s instructions for Illumina, and were sequenced on an Illumina NovaSeq PE150 platform (Yingzi gene technology, Wuhan, China).

value: Myometrium

tag: tissue type

value: Circular muscle

tag: chip antibody

value: IgG (ABclonal, #AC005)


title: CD15M_CM1_IgG


title: TELS hybrid tail-HiC_rep2

data_processing:
Hi-C raw sequencing reads were aligned to reference genome using distiller-nf mapping pipeline with default parameters (https://github.com/mirnylab/distiller-nf).
Genome_build: xv10
Supplementary_files_format_and_content: hic contact map

organism: Xenopus tropicalis x Xenopus laevis

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids tail

extract_protocol:
Male Xenopus tropicalis were injected with 150 U HCG. After 2 hours, two X. tropicalis testes collected in 1 ml 1xMBS and homogenized using razor blades. The solution was filtered with 40um strainer and its volume was brought down to 14ml. Then, through twice 180G horizontal centrifugation, we can obtain pure sperm in the supernatant. Ovulation and cross-fertilization were carried out according to the protocol described previously with some modification (Gibeaux., 2018). Briefly, Female Xenopus laevis were injected with 500 U HCG. After 12 hours, male Xenopus tropicalis were injected with 150 U HCG. After 2 hours, X. laevis females were squeezed gently to deposit eggs onto clean 9 cm Petri dishes and two X. tropicalis testes collected in 0.5 ml 1xMBS and homogenized using razor blades. Any liquid in the Petri dishes was removed and the per dish eggs were fertilized with mix solution containing 0.1 ml of sperm and 0.9 ml H2O. Eggs were swirled in the solution to individualize eggs as much as possible and incubated for 10 min. Jelly coats were removed with a 2% cysteine solution (add NaOH adjust the pH to 7.8-8.0). After extensive washing (at least four times) with 0.1xMBS, embryos were incubated at 23 °C.
1-2 millions sperm（or 50-200 X.laevis x X.tropicalis embryos） were cross-linked with 1% formaldehyde for 10 min using vacuum infiltration. (Human K562 cells were added as spike-in control.) Isolated nuclei were digested with 80U of DpnII (NEB, R0543L) at 37°C for 4 hrs. Restriction fragment overhangs were marked with biotin-labeled nucleotides. After labeling, chromatin fragments in proximity were ligated with 4000U T4 DNA ligase for 6 hrs at 16°C. Chromatin was reverse cross-linked, purified, and precipitated using ethanol. Biotinylated ligation DNA was sheared to 250-500bp fragments followed by pull-down with MyOne Streptavidin T1 beads (Life technologies, 65602). Immobilized DNA fragments were end-repaired, A-tailed, and ligated with adaptors. Fragments were then amplified with the Q5 master mix (NEB, M0492L). Hi-C libraries were sequenced on the Illumina HiSeq X10 platform (PE 2×150 bp reads).

value: tail


title: co-culture-rep3


title: TELS hybrid tail-HiC_rep1


title: TELS hybrid S33-HiC_rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S33

value: embryo


title: ovarian cells, 46h, rep1


title: worms_1day_rep3

description:
worms_1day_rep3
Replicate 3

value: whole body

value: 1 days


title: ovarian cells, 46h, rep4


title: ovarian cells, 46h, rep3


title: GD15M_LM1_H3K27ac

value: Longitudinal muscle

value: H3K27ac (Abcam, #ab4729)


title: GD15M_LM2_H3K4me3

value: H3K4me3 (Abcam, #ab8580)


title: ARPE19_replicate2_initial [ARPE19_R2_D0]

description: ARPE19 initial replicate 2

value: Retinal pigment epithelial cells

value: intial


title: CD15M_CM2_H3K4me3


title: worms_7day_rep2

description:
worms_7day_rep2
Replicate 2

value: 7 days

value: AL


title: CD15M_CM1_H3K27ac


title: GD15M_CM2_H3K27ac


title: ovarian cells, 0h, rep3

value: ovary

value: oocyte

value: in vitro mature for 0h


title: co-culture-rep2

value: mouse heart ventricle

value: 3D culture in GelMA system

value: cardiac fibroblast co-cultured with endothelial cell


title: CD15M_CM1_H3K4me3

value: Myometrium

value: Circular muscle


title: GD15M_LM1_IgG

value: IgG (ABclonal, #AC005)


title: TELS hybrid S33-HiC_rep1

value: embryo


title: ARPE19_replicate3_initial [ARPE19_R3_D0]

description: ARPE19 initial replicate 3


title: GD15M_CM2_IgG


title: ovarian cells, 22h, rep3

value: in vitro mature for 22h


title: GD15M_LM2_IgG

value: Longitudinal muscle


title: GD15M_CM1_IgG


title: HPMCs from patient 2958 untreated

city: Chicago

first: Hilary

last: Kenny

state: IL

address: 927 E 57TH STREET, ROOM W107K, CHICAGO, IL 60637

institute: University of Chicago

description: C2 P2958

data_processing:
Raw reads of FASTQ format were first processed through fastp. In this step, clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Paired-end clean reads were aligned to a reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software. FeatureCounts was used to count the read numbers mapped of each gene. RPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were identified as differentially expressed.  Differential expression analysis of two conditions without biological replicates was performed using EdgeR R package, A corrected p-value of 0.005 and log2 (Fold CHANGE) of 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample, Group and gene name

source_name: Human Primary mesothelial cells(HPMCs)

growth_protocol: Human Primary mesothelial cells were maintained in RPMI supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from primary human mesothelial cells 36 hours after treatment with Tyk-nu spheroid conditioned media, ascites, or control media using RNeasy Mini kit (Qiagen) following manufacturer’s instructions. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN). RNA integrity and quantitation were assessed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Library preparation and next generation RNA sequencing was carried out by Novogene
Sequencing libraries were generated using NEBNext® Ultra™ RNA library Prep kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample. The library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina platform and paired- end reads were generated

treatment_protocol: . Mesothelial cells were treated with control media, OvCa conditioned media or ascites from three different patients (n=10 patients/group).

value: Human Primary mesothelial cells(HPMCs)

value: Control media


title: HPMCs from patient 3016 treated with ascites sample2

description: A2 P3016


title: ovarian cells, 0h, rep4


title: HPMCs from patient 2960 untreated

description: C1 P2960


title: HPMCs from patient 2963 untreated

description: C1 P2963


title: HPMCs from patient 3016 treated with ascites sample3

description: A3 P3016


title: GD15M_LM2_H3K27ac

value: H3K27ac (Abcam, #ab4729)


title: HPMCs from patient 2960 treated with conditioned media

description: T2 P2960

value: Conditioned media


title: HPMCs from patient 3049 treated with ascites sample2

description: A2 P3049


title: HPMCs from patient 2823 treated with ascites sample2

description: A2 P2823


title: GD15M_CM1_H3K27ac


title: CD15M_CM2_H3K27ac


title: HPMCs from patient 3049 treated with ascites sample1

description: A1 P3049


title: GD15M_LM1_H3K4me3

value: H3K4me3 (Abcam, #ab8580)


title: HPMCs from patient 3049 treated with conditioned media

description: T1 P3049


title: HPMCs from patient 2934 treated with ascites sample3

description: A3 P2934


title: HPMCs from patient 3016 treated with conditioned media

description: T1 P3016


title: GD15M_CM1_H3K4me3


title: HPMCs from patient 1715 treated with ascites sample3

description: A3 P1715


title: HPMCs from patient 3052 treated with ascites sample3

description: A3 P3052


title: HPMCs from patient 3049untreated

description: C1 P3049


title: HPMCs from patient 2963 treated with conditioned media

description: T1 P2963


title: HPMCs from patient 3016 treated with ascites sample1

description: A1 P3016


title: GD15M_CM2_H3K4me3


title: HPMCs from patient 2823 untreated

description: C1 P2823


title: HPMCs from patient 3049 treated with ascites sample3

description: A3 P3049


title: HPMCs from patient 2823 treated with ascites sample3

description: A3 P2823


title: HPMCs from patient 2823 treated with ascites sample1

description: A1 P2823


title: HPMCs from patient 3052 untreated

description: C2 P3052


title: HPMCs from patient 2958 treated with conditioned media

description: T2 P2958


title: HPMCs from patient 2817 treated with ascites sample2

description: A2 P2817


title: HPMCs from patient 3052 treated with conditioned media

description: T2 P3052


title: HPMCs from patient 2934 untreated

description: C2 P2934


title: HPMCs from patient 2817 treated with ascites sample3

description: A3 2817


title: HPMCs from patient 2934 treated with ascites sample2

description: A2 P2934


title: HPMCs from patient 2817 treated with conditioned media

description: T1 P2817


title: HPMCs from patient 2817 treated with ascites sample1

description: A1 P2817


title: HPMCs from patient 3016 untreated

description: C2 P3016


title: HPMCs from patient 3052 treated with ascites sample1

description: A1 P3052


title: HPMCs from patient 3052 treated with ascites sample2

description: A2 P3052


title: HPMCs from patient 2823 treated with conditioned media

description: T1 P2823


title: HPMCs from patient 2934 treated with ascites sample1

description: A1 P2934


title: HPMCs from patient 2934 treated with conditioned media

description: T1 P2934


title: HPMCs from patient 1715 treated with conditioned media

description: T2 P1715


title: HPMCs from patient 1715 untreated

description: C2 P1715


title: GBM, Recurrent, Patient 30

city: Cleveland

first: Andrew

last: Dhawan

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing:
Raw reads from Fastq files from the sequencing runs underwent adapter trimming using the TrimGalore package (Barbraham Informatics), version 0.6.2.
Fastq files were then checked for quality using FastQC version 2.
Reads were aligned using Salmon version 0.8.2 to the ENSEMBL reference human transcriptome, version 37.75, hg1910. Reads were aligned using the --gcbias filter. Default settings were used otherwise.
The txImport package, version 1.16.1 was used to import the reads into an R script from which further analyses were carried out
Assembly: GrCh 37.75
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Glioblastoma

extract_protocol:
Library preparation was performed with 1-50 ng of total RNA
cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma-Aldrich, St. Louis, MO, USA) per manufacturer's protocol, and Illumina sequencing adapters were ligated to the ends of cDNA fragments. These were amplified for 12 cycles using primers incorporating unique index tags.

value: Glioblastoma

tag: disease state

value: Recurrent

tag: patient


title: GBM, Primary, Patient 30

tag: tissue

value: Primary


title: HPMCs from patient 2817 untreated

description: C3 P2817


title: GBM, Recurrent, Patient 26


title: GBM, Primary, Patient 26


title: HPMCs from patient 1715 treated with ascites sample1

description: A1 P1715


title: HPMCs from patient 1715 treated with ascites sample2

description: A2 P1715


title: GBM, Primary, Patient 19


title: GBM, Recurrent, Patient 19


title: GBM, Primary, Patient 12


title: GBM, Recurrent, Patient 25


title: GBM, Recurrent, Patient 24


title: GBM, Recurrent, Patient 12


title: GBM, Recurrent, Patient 27


title: GBM, Recurrent, Patient 14


title: GBM, Primary, Patient 11


title: GBM, Recurrent, Patient 50


title: GBM, Primary, Patient 27


title: GBM, Primary, Patient 13


title: GBM, Primary, Patient 24


title: GBM, Primary, Patient 14


title: GBM, Recurrent, Patient 17


title: GBM, Recurrent, Patient 13


title: HeLa, Ctrl, C7orf26, Serum 1, biol rep2

city: Philadelphia

first: Sarah

middle: R

last: Offley

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

description: INTS15 ChIP-seq in s serum-starved HeLa cells

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment (ChIPseq): BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM high glucose media, supplemented with 10%(v/v) super calf serum (GEMcell) and 2 mM of L-glutamine. HL-60 cells were maintained in RPMI high glucose media, supplemented with 10% (v/v) super calf serum and 2mM L-glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei (Covaris S220), and protein-DNA complexes were isolated with antibody-conjugated Dynabeads
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Inc.)

treatment_protocol: WT HeLa cells were starved in DMEM media containing 0.3% super calf serum for 72 hours and then treated with 0.1ug/mL EGF for 15 minutes. HL-60 cells were differentiated with 100nM phorbol myristate acetate (PMA) for 16 hours where noted. Where noted, HeLa cells were infected with lentivirus containing shRNAs for Luciferase (control),  starved overnight in 0.3% serum containing-DMEM media and then treated with 0.1ug/mL EGF.

value: HeLa

value: cervical epithelial

tag: genotype

value: wt

value: Serum starved in DMEM media containing 0.3% serum for 72 hours

value: INTS15 (Serum 1, Offley et al., 2023, in press)


title: HeLa, EGF, C7orf26, Serum 1, biol rep2

description: INTS15(C7orf26) ChIP-seq in serum-starved HeLa cells treated with 0.1ug/mL EGF

tag: treatment

value: Serum starved in DMEM media containing 0.3% serum for 72 hours and then treated with epidermal growth factor (EGF) for 15 minutes


title: HeLa, EGF, INTS10, biol rep1

description: INTS10 ChIP-seq in serum-starved HeLa cells treated with 0.1ug/mL epidermal growth factor (EGF)

value: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes

value: INTS10 (Proteintech, 15271-1-AP)


title: GBM, Recurrent, Patient 47


title: HeLa, EGF, C7orf26, Serum 1, biol rep1


title: HeLa, Ctrl, INTS10, biol rep1

description: INTS10 ChIP-seq in serum-starved HeLa cells

value: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight


title: GBM, Recurrent, Patient 48


title: HeLa, Ctrl, C7orf26, Serum 1, biol rep1

description: INTS15 (C7orf26) ChIP-seq in  serum-starved HeLa cells


title: GBM, Primary, Patient 49


title: GBM, Recurrent, Patient 49


title: GBM, Recurrent, Patient 11


title: GBM, Primary, Patient 47


title: GBM, Primary, Patient 17


title: GBM, Recurrent, Patient 46


title: GBM, Primary, Patient 25


title: GBM, Primary, Patient 45


title: HL-60, NT, INTS10, biol rep1

description: INTS10 ChIP-seq in untreated HL-60 cells

value: promyeloblast

value: No treatment


title: HL-60, NT, INTS10, biol rep2


title: GBM, Primary, Patient 50


title: GBM, Primary, Patient 48


title: HeLa, shC7orf26, Ctrl, RNAPII, biol rep2

description: RNAPII ChIP-seq in C7orf26-KD, serum-starved HeLa cells

treatment_protocol: WT HeLa cells were starved in DMEM media containing 0.3% super calf serum for 72 hours and then treated with 0.1ug/mL EGF for 15 minutes. HL-60 cells were differentiated with 100nM phorbol myristate acetate (PMA) for 16 hours where noted. Where noted, HeLa cells were either infected with lentivirus containing shRNAs for Luciferase (control) or C7orf26, starved overnight in 0.3% serum containing-DMEM media and then treated with 0.1ug/mL EGF.

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight

value: RNAPII (Barbieri et al., Mol Cell, 2018, 71, 103-116 e107.)


title: GBM, Recurrent, Patient 43


title: GBM, Primary, Patient 46


title: HeLa, shLUC, EGF, RNAPII, biol rep2

description: RNAPII ChIP-seq in shLuciferase(Control), serum-starved HeLa cells treated with 0.1ug/mL EGF


title: HL-60, PMA, INTS10, biol rep1

description: INTS10 ChIP-seq in PMA-treated HL-60 cells

value: Differentiated with 100nM phorbol myristate acetate (PMA) for 16 hours


title: HeLa, shLUC, Ctrl, RNAPII, biol rep2

description: RNAPII ChIP-seq in shLuciferase(control), serum-starved HeLa cells


title: HL-60, PMA, INTS10, biol rep2


title: GBM, Recurrent, Patient 44

value: Glioblastoma


title: HL-60, NT, C7orf26, biol rep2

description: C7orf26 ChIP-seq in untreated HL-60 cells

value: C7orf26 (Sigma, HPA042899)


title: HeLa, EGF, C7orf26, biol rep2

description: C7orf26 ChIP-seq in serum-starved HeLa cells treated with 0.1ug/mL epidermal growth factor (EGF)


title: HeLa, Ctrl, INTS10, biol rep2


title: GBM, Recurrent, Patient 45

value: Recurrent


title: GBM, Primary, Patient 43

value: Primary


title: HeLa, shC7orf26, EGF, RNAPII, biol rep2

description: RNAPII ChIP-seq in C7orf26-KD, serum-starved HeLa cells treated with 0.1ug/mL EGF

value: HeLa

value: cervical epithelial

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes


title: HL-60, PMA, C7orf26, biol rep2

description: C7orf26 ChIP-seq in PMA-treated HL-60 cells

value: wt


title: HeLa, EGF, INTS10, biol rep2


title: Colletotrichum camelllae treated rep3

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

data_processing:
Firstly, fastp and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was also verified using fastp. including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0.
Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.kegg.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM.
The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Colletotrichum camelliae

source_name: fungi

growth_protocol: 2-years old tea plants were grown in soil under a microbe free climate chamber with the 10 h light and 14 h dark.The plants were watered once a week and kept growing.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Colletotrichum camelliae was grown in PDA (200 g potato, 20 g glucose, 20 g agar and 1 L water) plate to produce the conidia spores. For incubation, the plant leaves were droplet infected with 1*106 spores mL-1. The spores without infection were used as untreated control (CK). All leaves were harvest at 24 hours and frozen at -80℃ for RNA sequencing.

value: fungi

value: 24h old

value: Colletotrichum camelliae sample that infected tea plants


title: Colletotrichum camelllae treated rep1


title: GBM, Recurrent, Patient 42


title: HeLa, Ctrl, C7orf26, biol rep2

description: C7orf26 ChIP-seq in serum-starved HeLa cells

value: Serum starved in DMEM media containing 0.3% serum for 72 hours


title: GBM, Primary, Patient 38


title: GBM, Recurrent, Patient 41


title: GBM, Recurrent, Patient 40


title: GBM, Primary, Patient 42


title: GBM, Primary, Patient 40


title: GBM, Primary, Patient 44


title: GBM, Recurrent, Patient 38


title: GBM, Recurrent, Patient 37


title: CK rep1

value: uninfected control sample


title: GBM, Primary, Patient 41


title: CK rep2


title: CD15M_LM2

data_processing:
Sus scrofa genome assembly 11.1
Sequence reads were mapped to the Sus scrofa genome assembly 11.1 with HISAT2 (v2.1.0)
The mapped reads were assembled and count by HTSeq (v0.9.1)
Normalize the readscount in data to TPM
Assembly: Sus scrofa genome assembly 11.1
Supplementary files format and content: RNA-seq_data_TPM file include TPM values for each sample

extract_protocol:
Total RNA was isolated using the HP Total RNA Kit (R6812, Omega Bio-tek, USA)
A total of 18 RNA libraries were constructed for RNA sequencing using Illumina HiSeq X Ten (PE150) platform according to the manufacturer’s instructions.

value: Myometrium

value: Longitudinal muscle

tag: time

value: day 15 of estrous cycle


title: CK rep3

tag: age


title: CD15M_LM3


title: GBM, Primary, Patient 39


title: GD15M_LM3

value: day 15 of pregnancy


title: GBM, Recurrent, Patient 36

value: Glioblastoma


title: CD15M_LM1


title: GBM, Recurrent, Patient 39


title: GBM, Primary, Patient 37


title: GBM, Primary, Patient 35


title: GD15M_LM1


title: GD15M_LM2


title: GBM, Recurrent, Patient 35


title: GBM, Primary, Patient 36


title: GD12M_LM3

value: day 12 of pregnancy


title: GD12M_LM2


title: CD15M_CM2

value: Circular muscle


title: CD15M_CM3


title: Colletotrichum camelllae treated rep2


title: GBM, Primary, Patient 33

value: Primary


title: GBM, Primary, Patient 34


title: GD12M_LM1


title: GD15M_CM2


title: GBM, Primary, Patient 32


title: GBM, Recurrent, Patient 33

value: Recurrent


title: CD15M_CM1


title: GD12M_CM2


title: GD12M_CM3


title: GBM, Primary, Patient 31


title: GBM, Primary, Patient 9


title: GBM, Recurrent, Patient 32


title: GBM, Recurrent, Patient 31


title: GD15M_CM3


title: GBM, Primary, Patient 10


title: GBM, Recurrent, Patient 10


title: GBM, Recurrent, Patient 8


title: GD15M_CM1


title: GBM, Recurrent, Patient 9


title: GBM, Recurrent, Patient 34


title: GD12M_CM1


title: GBM, Primary, Patient 8


title: 21-2454_1082/1157_072821-ROI 012-Segment 2

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

data_processing:
Raw basecall files were demultiplexed into individual fastqs corresponding to each ROI using bclconvert software (v3.7.5)
Fastqs were converted to Digital Count Conversion files (DCC files) using NanoString’s GeoMx NGS Pipeline v.2.0.0 using default parameters.
DCC files were processed using the GeoMX tools workflow.  ROIs with less than 1000 raw reads, 65% trimmed/stitched/aligned reads, or 50% sequencing saturation were removed, along with samples containing fewer than 20 cells per region of interest. Probe data was filtered using a minProbeRatio value of 0.1 and a percentFailGrubbs value of 20. The background noise within the study is defined as the expression signal from negative control probes. ROIs with 2 geometric standard deviations above the background were kept along with those containing > 15% gene detection rate (82 ROIs).  Genes detected in 30% of ROIs were kept.  Q3 normalization was then performed on the filtered data.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx .pkc file.
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode).

source_name: Thymoma

extract_protocol:
The FFPE tissue blocks were cut at 5um, and the slides were subjected for in-situ mRNA hybridization. The slides were incubated at 60C for 35m and moved into Leica BOND RX for RNA antigen retrieval, using proteinase K (1ug/ml) for 5 minutes and HIER2 for 20m. RNA probes (NanoString GeoMx Mouse Whole Transcriptome Atlas) were added for hybridization at 37 C for 16h. The stringent washes were performed according to the manufacturer's instructions. The slides were blocked with W buffer for 1h and then incubated with primary antibody cocktail for 1h at room temperature. The cocktail contains CD3 (1:100 dilution, Ab135372) and B220 (1:60 dilution, BD #550286) antibodies. The slides were washed with SSC buffer two times and subjected to incubation with secondary antibodies, AF594 Goat anti Rat at 1:100 dilution and AF647 Goat anti Rabbit at 1:100 dilution, for 45 minutes at RT. The slides were washed with SCC buffer twice and incubated with morphology markers cocktail, which contains Pancytokeratin-AF532 (1:40 dilution) and Syto13 (1:10 dilution), for at RT for 1h.  After washing with ASSC buffer twice, the slides were immediately loaded on to the GeoMX DSP and scanned for selection of regions of interest (ROIs). Upon ROI selection, segmentation was performed by masking for desired markers.  ROIs within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform.
Each collection of oligo tags from one well representing an ROI was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed ROIs were pooled and purified in two rounds of AMPure XP PCR purification and sequenced on the NextSeq 2000 using a P3 flow cell kit (27 x 27 and index 8 x 8).

value: Thymoma

value: thymoma 1157 T cells

value: Gtf2ifl/wt Foxn1-Cre/wt

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: roi

tag: segment

value: Segment 2

tag: aoi

value: Segment 2-aoi-001

tag: ab positivity

tag: number of_cells

tag: area (um^2)


title: 21-2454_1082/1157_072821-ROI 010-Segment 1

tag: cell type

value: thymoma 1157 epithelial cells

value: Segment 1

value: Segment 1-aoi-001

value: PanCK


title: GBM, Recurrent, Patient 7


title: 21-2454_1082/1157_072821-ROI 012-Segment 1


title: GBM, Recurrent, Patient 5


title: GBM, Primary, Patient 7


title: GBM, Primary, Patient 4


title: 21-2454_1082/1157_072821-ROI 010-Segment 2


title: 21-2454_1082/1157_072821-ROI 007-Segment 3

value: thymoma 1157 B cells

value: Segment 3

value: Segment 3-aoi-001


title: 21-2454_1082/1157_072821-ROI 009-Segment 1


title: GBM, Primary, Patient 5

value: Glioblastoma


title: GBM, Recurrent, Patient 1


title: 21-2454_1082/1157_072821-ROI 008-Segment 3


title: GBM, Primary, Patient 3


title: GBM, Recurrent, Patient 3


title: 21-2454_1082/1157_072821-ROI 006-Segment 2

value: thymoma 1082 T cells


title: GBM, Recurrent, Patient 2


title: 21-2454_1082/1157_072821-ROI 005-Segment 2


title: 21-2454_1082/1157_072821-ROI 013-Segment 3


title: 21-2454_1082/1157_072821-ROI 004-Segment 1

value: thymoma 1082 epithelial cells


title: 21-2454_1082/1157_072821-ROI 006-Segment 1


title: 21-2454_1082/1157_072821-ROI 004-Segment 2


title: 21-2454_1082/1157_072821-ROI 009-Segment 2


title: GBM, Primary, Patient 1

value: Primary


title: 21-2454_1082/1157_072821-ROI 005-Segment 1

value: Thymoma