title: ToCSV isolate from susceptible tomato line, 35 dpi, rep3

city: Johannesburg

first: Gerrit

last: Koorsen

address: Corner of Kingsway and University Avenue

country: South Africa

institute: University of Johannesburg

data_processing:
Raw sequence reads were filtered using Trimmomatic to remove low-quality sequences and sequencing adapters.
Processed reads were mapped to the reference ToCSV-genome (OK813888.1) using Bismark v0.23.1, powered by the Bowtie2 aligner. Methylation bias was corrected by end-trimming reads (7-13 nt) as guided by M-bias plots.
Methylated cytosines (in CG, CHG and CHH sequence contexts, respectively), were called using the Bismark v0.23.1 methylation extractor.
Assembly: OK813888.1
Supplementary files format and content: Bismark methylation extractor output text in tab-delimited text format, containing the positions of cytosines in the viral genome (OK813888.1) and their methylation status (+ or -).

organism: Tomato curly stunt virus

source_name: infected leaves

growth_protocol: Plants were grown and maintained under a controlled environment in an insect-free chamber at 28 °C with a 16/8-h (light/dark) photoperiod.

extract_protocol:
The leaf tissue was snap-frozen in liquid nitrogen and stored at -80 °C until needed. Total DNA was extracted from the harvested leaf tissue using the modified cetyltrimethylammonium bromide (CTAB) extraction method. Harvested snap-frozen leaf tissue was crushed to a fine powder using a micro pestle and resuspended in 500 µL of CTAB buffer (2% (w/v) CTAB, 5 M NaCl, 0.2% 2-mercaptoethanol, 0.5 M EDTA, 1 M Tris-HCI, pH 8.0 and 2% w/v PVP) and incubated at 65 °C for 60 min. For phase separation, 500µl of chloroform: isoamyl alcohol (24:1) was added, followed by centrifugation at 13 000 g for 10 min at room temperature. The aqueous phase was extracted to a new microfuge tube, and an equal amount of isopropanol was added to precipitate the DNA. The mixture was centrifuged at 13 000 g for 10 min, and the supernatant was removed. The pellet was washed twice in 1 ml of ice-cold 70% ethanol (v/v) followed by centrifugation at 13 000 g for 5 min. The pellet was air-dried and resuspended in TE buffer (1 M Tris, pH 8, and 0.5 M EDTA) supplemented with 200 µg/ml RNase A and stored overnight at 4°C. Total DNA was subjected to restriction digestion using the restriction endonuclease BamH1 (Thermo Scientific, Waltham, USA). The endonuclease digestion was carried out in a reaction that contained 1X FastDigest ® buffer (Thermo Scientific, Waltham, USA), 1.25 U/µL BamH1 enzyme and DNA template. The reactions were incubated at 37 °C for 16 hours and inactivated at 80 °C for 5 min. Followed by the addition of proteinase K (20mg/ml) and subsequent incubation for 15 min at room temperature and 10 min. Following the proteinase K treatment, the digested DNA was purified using the DNA clean-up (Zymo Research, Irvine, CA, USA). A total of 500 ng of purified DNA was used for bisulfite conversion, using the Zymo EZ DNA methylation Gold™ kit. Bisulfite-modified DNA was used as a PCR template using Epimark Taq polymerase (New England Biolabs). PCR was carried out in a final volume of 20 µL, containing, 1X Epimark buffer, 200 µM dNTPs, 0.2 µM primer, 0.0125 U/µL PCR of the EpiMark Hot Start Taq DNA Polymerase and 100 ng DNA template. PCR for each primer set was performed independently using the Eppendorf master cycler (Merck, US) with the following cycling conditions; initial denaturation 95 °C for 30 sec, followed by 40 cycles of denaturation 95 °C for 30 sec, annealing at specific temperatures for each primer set (see supplementary file) for 60 sec, extension 68°C for 1 min and a final extension at 68°C for 5 min. To confirm positive amplification, 5µL of the PCR amplicons were separated on a 1 % agarose gel stained with 10 µg/mL ethidium bromide and visualized under ultraviolet light, using a ChemiDoc MP imaging system (Bio-Rad, USA).
TruSeq Nano (low molecular weight/adapter ligation)

treatment_protocol: Agrobacterium tumefaciens C58C1 cultures were used for inoculation containing ToCSV infectious viral clone (Accession: OK813888.1) in YEP media supplemented with 50 μg/ml of rifampicin and 50 μg/ml of kanamycin. Additionally, Agrobacterium tumefaciens C58C1 culture harbouring an empty pCambia2300 plasmid, functioned as a negative control (mock-inoculated) containing 50 μg/ml of rifampicin when inoculated in YEP media. Both cultures were incubated at 30 ˚C for 48 hours at 200 rpm followed by co-cultivation into fresh YEP media supplemented with rifampicin (50 μg/ml) and kanamycin (50 μg/ml) until an OD600 of 0.8 was reached.  Agrobacterium cultures were centrifuged at 8000 g for 5 mins followed by the removal of the supernatant. The pellet was then washed in sterile water followed by centrifugation at 8000 g for 5 min. Thereafter, the pellet was resuspended in YEP and used for inoculation of tomato seedlings. The four-week-old seedlings were wounded along the stem using a hypodermic needle and each seedling was inoculated with 100 µL of resuspended YEP media. For mock-inoculated plants, a volume of 100 µL of the A. tumefaciens strain C58C1 (pCambia2300) was inoculated in each seedling. The experiment was repeated three times independently, each consisting of four mock-inoculated plants and four ToCSV-inoculated plants.

value: infected leaves

value: 35 dpi

value: susceptible tomato line


title: ToCSV isolate from susceptible tomato line, 35 dpi, rep2

status: Public on Jan 26 2023

type: SRA

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: cell line

tag: treatment

tag: group


title: ToCSV isolate from susceptible tomato line, 35 dpi, rep1


title: 148-PEARL_057_1

city: Valencia

first: Antonio

last: Fernandez-Serra

address: Beltraan Baguena, 8-11

department: Molecular Biology Lab

country: Spain

institute: Fundacion Instituto Valenciano de Oncologia

library_source: transcriptomic

data_processing:
Sequencing was performed by using Oncology Biomarker Panel from HTG Edgeseq which interrogates the expression of 2560 genes.
Base-calling: Illumina Basespace
Generation of read counts: HTG Edgeseq Parser v. 5,2,823,5648
Normalization: R Bioconductor DESeq2 v. 1,28,1
Assembly: hg19
Supplementary files format and content: Table with median transformation normalized counts
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Breast Cancer

extract_protocol:
Total RNA was prepared from 5µm FFPE tissue sections of microdissected ITF using the Agencourt FormaPure kit (A33341; Beckman Coulter, Indianapolis, IN, USA) and following the manufacturer’s instructions. RNA concentration was determined with Qubit 4 Fluorometer and Qubit® RNA HS Reagent (Thermo Fisher Scientific, Waltham, MA, USA).
HTG EdgeSeq Chemistry was employed to synthetize the RNA-Seq library. Briefly, target capture was performed by hybridizing the mRNA with Nuclease Protection Probes (NPPs). The S1 nuclease was added to the mix, producing a stoichiometric amount of target mRNA/NPP duplexes. This reaction was blocked by enzyme heat denaturation of S1. The samples were randomized before inclusion in the HTG EdgeSeq system to reduce potential biases in the run. Each hybridized sample was used as template to set up PCR reactions with specially designed tags, sharing common sequences that are complementary to both 5’-end and 3’-sequences of the probes, and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode used for sample identification and multiplexing. After PCR amplification, a clean-up procedure was performed using Agencourt AMPure XP (Beckman Coulter). The library was quantified by quantitative PCR, using KAPA Library Quantification (Roche), according to the manufacturer’s instructions. All samples and controls were quantified in triplicate and no template control was included in any run.

value: Breast Cancer

tag: cell type

value: Tumor

value: Capecitabine


title: 148-PEARL_055_1


title: ToCSV isolate from tolerant tomato line, 35 dpi, rep3

value: tolerant tomato line


title: 148-PEARL_053_1

value: Palbociclib


title: ToCSV isolate from tolerant tomato line, 35 dpi, rep1


title: ToCSV isolate from tolerant tomato line, 35 dpi, rep2


title: 148-PEARL_051_1


title: Frozen DTAN4047, 2

city: Palo Alto

first: Siddhartha

last: Jaiswal

state: CA

address: 240 Pasteur Dr

department: Pathology

country: USA

institute: Stanford University School of Medicine

library_source: transcriptomic single cell

data_processing:
Gene counts quantified with CellRanger 3.0
Assembly: GRCh38
Supplementary files format and content: Gene counts

source_name: Carotid Artery

extract_protocol:
Vessels were digested into single cell suspensions using a simple Liberase digestion protocol. The cells were then sorted for CD45+ cells and a live/dead exclusion was performed using AQUA.
V3’ 10x Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit

value: Carotid

tag: celltype

value: CD45+ hematopoetic cells

tag: plaque severity

value: moderate

tag: age

tag: Sex

value: Male

tag: diabetes

value: No

tag: chd

value: Yes


title: TELS S3 embryos hybrid RNA-seq__rep2

city: Shenzhen

first: Chuihui

last: Hou

state: Guangdong

address: Xueyuan Avenue

country: China

institute: Southern University of Science and Technology

data_processing:
Raw fastq RNA-seq reads and adapter sequences were removed by Trimmomatic v0.38. Clean reads were mapped to the combined X.tropicalis v10.0 and X.laevis v9.2 reference genome using STAR v2.7.9a
Genome_build: xv10_xl9
Supplementary_files_format_and_content: gene abundance

organism: Xenopus tropicalis x Xenopus laevis

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S3

extract_protocol:
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.
Total RNA was isolated from hybrid embryos using the TransZol Up Plus RNA Kit (Transgen, ER501-01). Libraries were prepared with a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L) according to the manufacturer's instructions. The libraries were sequenced on an Illumina HiSeq 2500 platform, and 150-base paired-end reads were produced. Two biological replicates were generated for control and dark-treated seedlings.

value: embryo


title: TELS S5 embryos hybrid RNA-seq__rep1

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S5


title: Fresh DTAN4047, 2


title: Fresh ROB2026, 2


title: 148-PEARL_046_1


title: 148-PEARL_047_1


title: Frozen ROB2026, 2


title: 148-PEARL_050_1


title: Frozen 1700

source_name: Coronary Artery

value: Coronary


title: 148-PEARL_054_1


title: 148-PEARL_044_1


title: 148-PEARL_049_1


title: Frozen 1667, 2

value: severe


title: Fresh 1667, 2


title: 148-PEARL_042_1


title: Fresh 1495


title: 148-PEARL_041_1


title: 148-PEARL_040_1


title: Frozen 1495


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_074

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

data_processing:
FASTQ’s were merged and aligned to GRCh37(hs37d5) using STAR (v2.5.3a)
Picard Mark Duplicates (v1.128) identified duplicate reads in the aligned BAM files (.bam). Star-Fusion (v0.8.0) identified potential fusion transcripts, also using the STAR aligner. Fusion catcher (v0.99.7b) identified novel and known somatic fusion genes, chimeras, and translocations.
Salmon (v0.7.2) quantified transcripts, produced a quantification file, commanded information and auxiliary files. Read counts were normalized by the size of each library using a counts per million scaling (CPM)
HTSeq (v0.6.0) processed and analyzed aligned RNA data
DESeq2 package identified differentially expressed genes (DEGs)
Assembly: GRCh37(hs37d5)
Supplementary files format and content: tab-delimited files (txt) includes the output to DESeq for comparison between A1 vs B1, A1 vs C1, B1 vs C1, and FPT vs NFPT.

source_name: Tissue

extract_protocol:
RNA from 65 microdissected, fresh frozen pituitary tumor samples was extracted using the QIAamp RNeasy Mini Kit (QIAGEN, Hilden, Germany).
NEBNext® Ultra™ II Directional RNA Library Prep Kit (E7765)

value: Tissue

tag: clinical presentation

value: Non-functioning PitNET

tag: immunohistochemistry

value: LH+/FSH+

tag: tumor size

tag: tumor invasion

tag: surgery number

value: M

tag: mutation

value: WT

tag: rna seq_id

tag: tumor id

tag: transcriptome group_1

tag: transcriptome group_2

tag: 3 description


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_077

tag: tissue

value: Acromegaly (GH-secreting)

value: GH+/PRL+

value: F


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_076

value: All negative


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_075

value: ACTH+


title: 148-PEARL_038_1

value: Breast Cancer

tag: cell type

value: Tumor

tag: treatment

value: Palbociclib


title: 148-PEARL_039_1


title: 148-PEARL_036_1


title: Fresh 1700

tag: celltype

value: CD45+ hematopoetic cells

tag: plaque severity

value: moderate

tag: age

tag: Sex

value: Male

value: No

value: Yes


title: 148-PEARL_037_1

value: Capecitabine


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_073

value: Tissue

tag: clinical presentation

value: Non-functioning PitNET

tag: immunohistochemistry


title: 148-PEARL_034_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_072

tag: tumor size

tag: tumor invasion

value: WT


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_067

value: Acromegaly (GH-secreting)

tag: surgery number

value: M

tag: mutation

value: GNAS


title: 148-PEARL_043_1


title: 148-PEARL_032_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_068

value: All negative

value: F

tag: rna seq_id

tag: tumor id


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_069

tag: transcriptome group_1

tag: transcriptome group_2


title: 148-PEARL_033_1

tag: tissue

value: Breast Cancer


title: 148-PEARL_027rep_1

tag: cell type

value: Tumor


title: 148-PEARL_031_1

tag: treatment

value: Palbociclib


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_064

value: ACTH+

tag: 3 description


title: 148-PEARL_026_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_063

value: LH+/FSH+


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_066

value: Undefined


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_065

value: No


title: 148-PEARL_025_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_062

value: LH+

value: Yes


title: 148-PEARL_024_1

value: Capecitabine


title: 148-PEARL_023_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_060

value: Tissue

value: Non-functioning PitNET


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_057

value: WT


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_059

value: M


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_061


title: 148-PEARL_021_1


title: 148-PEARL_020_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_056


title: 148-PEARL_018_1


title: 148-PEARL_028_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_055


title: 148-PEARL_015_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_054


title: 148-PEARL_017_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_051

value: Acromegaly (GH-secreting)

value: GH+ and other(s)


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_053

value: F


title: 148-PEARL_013_1

value: Breast Cancer


title: 148-PEARL_014_1

value: Tumor


title: 148-PEARL_012_1

value: Palbociclib


title: 148-PEARL_011_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_049

value: All negative


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_048

value: LH+/FSH+


title: 148-PEARL_009_1


title: 148-PEARL_022_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_047


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_046

value: Not reported


title: 148-PEARL_006_1


title: 148-PEARL_010_1


title: 148-PEARL_005_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_045


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_044


title: 148-PEARL_003_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_042


title: 148-PEARL_002_1


title: 30052-119

city: Örebro

first: Robert

last: Kruse

address: Södra Grev Rosengatan 32

department: Kliniskt forskningslaboratorium

country: Sweden

institute: Örebro University

description:
name in processed data file:
30052-119

data_processing:
Raw data were demultiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina, San Diego, CA, USA). FASTQ data were checked using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Supplementary files format and content: counts per million in the file "NGS_miRNA_expression_normalised_counts_per_million.txt"

extract_protocol:
Extraction of the miRNA and NGS were done by Qiagen. According to Qiagen miRNA was purified from the serum-EDTA samples using miRNeasy Kit (Qiagen) according to the manufacturer’s instructions. Purified miRNA quality was checked by qPCR to evaluate if the expression levels of selected miRNAs in our samples were within the expected range.
The library preparation was done using the QIAseq miRNA Library Kit (Qiagen) according to manufactures instructions.
Adapters containing UMIs were ligated to the RNA which was subsequently converted to cDNA. The cDNA was amplified using PCR and purified. Library preparation QC was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Based on the quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pool(s) were quantified using qPCR and sequenced on a NextSeq550 sequencing instrument according to the manufacturer’s instructions.

tag: patient diagnosis

value: Type 2 Diabetes

value: serum

tag: visit

value: G


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_041

value: Yes

tag: age

tag: Sex


title: 148-PEARL_004_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_050

value: Tissue

tag: clinical presentation

tag: immunohistochemistry

value: LH+

value: No


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_039

value: Non-functioning PitNET

tag: tumor size

tag: tumor invasion

value: WT


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_037

tag: surgery number

tag: mutation


title: 30052-113

description:
name in processed data file:
30052-113

value: M


title: 30052-111

description:
name in processed data file:
30052-111

value: F


title: 30052-110

description:
name in processed data file:
30052-110

value: L


title: 30052-115

description:
name in processed data file:
30052-115


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_038

value: LH+/PRO+

tag: rna seq_id

tag: tumor id


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_036

tag: transcriptome group_1

tag: transcriptome group_2


title: 30052-118

description:
name in processed data file:
30052-118

tag: tissue


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_035


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_034

value: ACTH+ and other(s)+


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_033

value: Undefined


title: 30052-106

description:
name in processed data file:
30052-106

tag: treatment


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_043

value: All negative

tag: 3 description


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_030


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_031


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_029

value: LH+/FSH+


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_032


title: 30052-103

description:
name in processed data file:
30052-103

tag: patient diagnosis

value: Type 2 Diabetes


title: 30052-102

description:
name in processed data file:
30052-102

value: serum

tag: visit


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_027

value: Cushing disease (ACTH-secreting)

value: ACTH+

tag: age


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_024

value: Tissue

tag: Sex


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_025

tag: clinical presentation


title: 30052-101

description:
name in processed data file:
30052-101


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_023

tag: immunohistochemistry


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_022

tag: tumor size

value: Yes


title: 30052-100

description:
name in processed data file:
30052-100

value: G


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_021

tag: tumor invasion


title: 30052-099

description:
name in processed data file:
30052-099


title: 30052-107

description:
name in processed data file:
30052-107


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_016

value: Non-functioning PitNET

tag: surgery number


title: 30052-096

description:
name in processed data file:
30052-096


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_014

tag: mutation

value: WT


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_015

tag: rna seq_id


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_012

value: Acromegaly (GH-secreting)

value: Not reported

value: No

value: M

tag: tumor id


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_011

value: GH+ and other(s)

value: F

value: GNAS

tag: transcriptome group_1


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_010

tag: transcriptome group_2


title: Adult PMN

type: RNA

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: R/Bioconductor, rma normalization, default parameters

label: biotin

source_name: Peripheral venous blood from adult donor.

label_protocol: Standard Affymetrix protocol.

extract_protocol: Human neutrophils were isolated from umbilical cord or peripheral venous blood by layering cells on a Polymorphprep density gradient (AXIS-SHIELD PoC AS, Dundee, Scotland) followed by centrifugation (500g, 30 min, room temperature). RNA of neutrophils (>90% purity) was extracted with the RNeasy Mini Kit (Qiagen).

tag: tissue

value: Peripheral venous blood


title: Adult PMN A


title: SSW 32+4

source_name: Cord blood sample from neonates delivered at gestational week (SSW) 32+4.

value: Cord blood


title: 30052-089

description:
name in processed data file:
30052-089

value: Type 2 Diabetes

value: serum

tag: treatment


title: 30052-090

description:
name in processed data file:
30052-090

value: L


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_007

value: Tissue

tag: 3 description


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_006


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_018

value: All negative


title: SSW 40+2

source_name: Cord blood sample from neonates delivered at gestational week (SSW) 40+2.


title: SSW 30+5

source_name: Cord blood sample from neonates delivered at gestational week (SSW) 30+5.


title: SSW 32+0

source_name: Cord blood sample from neonates delivered at gestational week (SSW) 32+0.


title: Adult PMN B


title: SSW 38+0

source_name: Cord blood sample from neonates delivered at gestational week (SSW) 38+0.


title: SSW 38+6

source_name: Cord blood sample from neonates delivered at gestational week (SSW) 38+6.


title: 30052-087

description:
name in processed data file:
30052-087

tag: patient diagnosis


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_013

value: Cushing disease (ACTH-secreting)

value: ACTH+


title: CDCs,cultured on the OPC substrate, biol rep3

city: Guangzhou

first: Qi

last: Li

address: Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou City, Guangdong Province, China

department: Department of Developmental and Regenerative Biology

institute: Jinan University

description:
primary culture cell
OPC_3

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.1 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) following the manufacturer's procedure, the total RNA  quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano Lapchip Kit (Agilent, America). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols

value: heart

tag: cell type

value: cardiosphere derived cells

tag: genotype

value: WT

value: culturing on the OPC substrate


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_004

value: Acromegaly (GH-secreting)

value: GH+/PRL+

value: No

tag: age

tag: Sex

value: M


title: CDCs,cultured on the ULA substrate, biol rep3

description:
primary culture cell
LV_3

value: culturing on the ULA substrate


title: CDCs,cultured on the OPC substrate, biol rep2

description:
primary culture cell
OPC_2


title: CDCs,cultured on the OPC substrate, biol rep1

description:
primary culture cell
OPC_1


title: 30052-084

description:
name in processed data file:
30052-084

tag: visit


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_003

tag: clinical presentation

tag: immunohistochemistry

tag: tumor size

value: Yes


title: 30052-092

description:
name in processed data file:
30052-092

value: Type 2 Diabetes

value: G


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_002

value: GH+ and other(s)

tag: tumor invasion

tag: surgery number

tag: mutation


title: CDCs,cultured on the ULA substrate, biol rep2

description:
primary culture cell
LV_2


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_005

value: Tissue

tag: rna seq_id

tag: tumor id

tag: transcriptome group_1


title: 30052-083

description:
name in processed data file:
30052-083

tag: tissue

value: serum

tag: treatment

value: L


title: Tumor RNA from Pituitary neuroendocrine tumors (PitNETs)_001

value: F

tag: transcriptome group_2

tag: 3 description


title: CDCs,cultured on the ULA substrate, biol rep1

description:
primary culture cell
LV_1

value: heart

tag: cell type

tag: genotype


title: 30052-081

description:
name in processed data file:
30052-081

tag: patient diagnosis

tag: Sex


title: DI318 CSCs + DMSO rep4

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

data_processing:
Library strategy: CUT&Tag
Sequencing was performed using a NovaSeq SP100 and employed a paired-end sequencing strategy with the following parameters: Read1:i7:i5:Read2=28:10:10:90
Reads were aligned to the guide library using Bowtie2 and peaks were called using MACS2
Raw FASTQ files for each replicate are provided
Assembly: hg38
Supplementary files format and content: narrowPeak files for each replicate are provided

source_name: GBM CSCs

growth_protocol: DI318 were grown in sphere culture in neurobasal media supplemented with L-glutamine, NaPyr, P/S, B27, EGF and FGF2 in subconfluent conditions.

extract_protocol:
Cells were harvested, counted and CUT&Tag-IT Assay and library preparation was performed on 500,000 cells per replicate, according to the Manufacturer’s Manual (Active Motif). Rabbit anti-human Tri-Methyl-Histone H3 (Lys4) (C42D8) (Cell Signaling Technologies 9751) antibody was used for the CUT&Tag procedure.
Sample indices for multiplexing (unique combination of one i7 Indexed Primer and one i5 Indexed Primer) were attached through 14 rounds of PCR.

treatment_protocol: Cells were plated at 0.5x10^6 cells/ml and treated with 3μM C16 or DMSO. 72 hrs after treatment, treated cells were collected for CUT&Tag.

tag: disease state

value: Glioblastoma (GBM)

tag: cell line

value: cancer stem cells (CSCs)

value: DMSO


title: DI318 CSCs + C16 rep3


title: 30052-080

description:
name in processed data file:
30052-080

tag: visit


title: DI318 CSCs + C16 rep2


title: CDCs,cultured on the PS substrate,  biol rep3

description:
primary culture cell
NC_3

value: cardiosphere derived cells

value: WT

value: culturing on the PS substrate


title: CDCs,cultured on the PS substrate,  biol rep2

description:
primary culture cell
NC_2


title: DI318 CSCs + DMSO rep3


title: CDCs,cultured on the PS substrate, biol rep1

description:
primary culture cell
NC_1


title: DI318 CSCs + DMSO rep2


title: DI318 CSCs + DMSO rep1


title: 30052-078

description:
name in processed data file:
30052-078


title: 30052-079

description:
name in processed data file:
30052-079

value: M


title: 30052-077

description:
name in processed data file:
30052-077


title: 30052-076

description:
name in processed data file:
30052-076


title: Neuroblastoma_usi_PARDEA

city: Los angeles

first: Xiangming

last: Ding

state: California

address: 4650 Sunset Blvd

institute: CHLA

data_processing:
RNA-seq data were aligned using Hisat2 (version 2.2.0), reads were counted using featureCounts (version 2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 150ng of total RNA was used for the construction of sequencing libraries.
150ng of total RNA was used to enrich for poly-adenylated RNA, which were heat-fragmented to a target size of 180bp and converted to cDNA using random primers with Superscript II (Invitrogen), then used for library prep using the Illumina TruSeqRNA library kit.

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: DI318 CSCs + C16 rep1

tag: treatment


title: 30052-074

description:
name in processed data file:
30052-074

tag: tissue


title: DI318 CSCs + C16 rep4


title: Neuroblastoma_usi_PAUICI

source_name: Neuroblastoma (Schwannian stroma-poor)

value: Neuroblastoma (Schwannian stroma-poor)

value: Not Hispanic or Latino


title: 30052-073

description:
name in processed data file:
30052-073

value: Type 2 Diabetes

value: G


title: Neuroblastoma_usi_PAPAEH

source_name: Neuroblastoma

value: Neuroblastoma


title: 30052-070

description:
name in processed data file:
30052-070

value: serum


title: Neuroblastoma_usi_PARUTJ


title: Neuroblastoma_usi_PATRUL

value: Unknown


title: Neuroblastoma_usi_PATJEY


title: Neuroblastoma_usi_PANBVG


title: Neuroblastoma_usi_PAUJLW


title: 30052-068

description:
name in processed data file:
30052-068

value: L


title: 30052-069

description:
name in processed data file:
30052-069

value: F


title: 30052-065

description:
name in processed data file:
30052-065


title: 30052-067

description:
name in processed data file:
30052-067


title: Neuroblastoma_usi_PARALN


title: Neuroblastoma_usi_PAUFVW


title: 30052-064

description:
name in processed data file:
30052-064


title: Neuroblastoma_usi_PATTFB


title: 30052-063

description:
name in processed data file:
30052-063


title: Neuroblastoma_usi_PATGVK


title: 30052-062

description:
name in processed data file:
30052-062


title: Neuroblastoma_usi_PASYAA


title: Neuroblastoma_usi_PASWSZ


title: 30052-059

description:
name in processed data file:
30052-059


title: 30052-061

description:
name in processed data file:
30052-061


title: Neuroblastoma_usi_PASSVJ


title: Pituitary neuroendocrine tumors (PitNETs)-075

type: genomic

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_075
PitNET075

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

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

tag: clinical presentation

value: Non-functioning PitNET

tag: ihc

value: ACTH+

tag: tumor size

tag: invasion

value: Yes

tag: surgery number

tag: age years

tag: mutations

value: Corticotroph

value: pituitary tumor

value: PitNETs

tag: subtypes

value: NS


title: Pituitary neuroendocrine tumors (PitNETs)-069

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_069
PitNET069

value: Acromegaly (GH-secreting)

value: All negative

value: No

value: WT

value: Somatotroph

tag: disease state

value: GH


title: Pituitary neuroendocrine tumors (PitNETs)-068

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_068
PitNET068


title: Pituitary neuroendocrine tumors (PitNETs)-077

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_077
PitNET077

value: GH+/PRL+


title: Pituitary neuroendocrine tumors (PitNETs)-076

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_076
PitNET076

value: Male


title: Pituitary neuroendocrine tumors (PitNETs)-063

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_063
PitNET063

value: LH+/FSH+

value: Gonadotroph


title: Pituitary neuroendocrine tumors (PitNETs)-065

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_065
PitNET065

value: Female

value: Non-functioning PitNET


title: Pituitary neuroendocrine tumors (PitNETs)-072

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_072
PitNET072


title: Pituitary neuroendocrine tumors (PitNETs)-061

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_061
PitNET061

value: Yes


title: Pituitary neuroendocrine tumors (PitNETs)-058

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_058
PitNET058


title: 30052-058

description:
name in processed data file:
30052-058

tag: patient diagnosis

value: Type 2 Diabetes

value: serum

tag: Sex

value: M

tag: visit

value: L


title: Pituitary neuroendocrine tumors (PitNETs)-074

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_074
PitNET074

value: pituitary tumor

value: PitNETs

value: NS


title: Pituitary neuroendocrine tumors (PitNETs)-066

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_066
PitNET066

value: All negative

value: Undefined

value: Undefined tPit+/ Pit1+


title: Neuroblastoma_usi_PASRSG

value: Neuroblastoma (Schwannian stroma-poor)

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Neuroblastoma_usi_PARUPT

tag: tissue


title: 30052-055

description:
name in processed data file:
30052-055

value: F

tag: treatment


title: 30052-053

description:
name in processed data file:
30052-053

value: G


title: Pituitary neuroendocrine tumors (PitNETs)-053

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_053
PitNET053

tag: methylation group

tag: gender

value: Female

tag: clinical presentation

tag: ihc

value: LH+

tag: tumor size

tag: invasion

tag: surgery number

value: WT

value: Gonadotroph


title: Pituitary neuroendocrine tumors (PitNETs)-056

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_056
PitNET056

value: Non-functioning PitNET

value: Yes

tag: age years

tag: mutations

tag: disease state

tag: subtypes


title: Pituitary neuroendocrine tumors (PitNETs)-055

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_055
PitNET055

value: LH+/FSH+

value: No


title: Pituitary neuroendocrine tumors (PitNETs)-059

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_059
PitNET059

value: Male

value: pituitary tumor

value: PitNETs


title: Pituitary neuroendocrine tumors (PitNETs)-050

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_050
PitNET050

value: NS


title: Neuroblastoma_usi_PARSIJ

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

tag: efstime


title: Pituitary neuroendocrine tumors (PitNETs)-062

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_062
PitNET062

tag: tissue


title: Neuroblastoma_usi_PARLHV

tag: stime

tag: efscens

tag: scens


title: 30052-051

description:
name in processed data file:
30052-051

tag: patient diagnosis

value: Type 2 Diabetes

value: serum

tag: Sex

tag: visit

tag: treatment


title: Pituitary neuroendocrine tumors (PitNETs)-051

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_051
PitNET051

tag: methylation group

tag: gender

tag: clinical presentation

value: Acromegaly (GH-secreting)

tag: ihc

value: GH+ and other(s)

tag: tumor size

tag: invasion

tag: surgery number

value: Undefined Pit1+/ SF1+

value: GH


title: Pituitary neuroendocrine tumors (PitNETs)-057

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_057
PitNET057

value: All negative

tag: age years

tag: mutations

tag: disease state

tag: subtypes


title: Pituitary neuroendocrine tumors (PitNETs)-060

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_060
PitNET060

value: Female

tag: tissue


title: Pituitary neuroendocrine tumors (PitNETs)-064

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_064
PitNET064

value: ACTH+

value: WT

value: Corticotroph


title: Neuroblastoma_usi_PAPTRJ

value: Neuroblastoma

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Unknown

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Pituitary neuroendocrine tumors (PitNETs)-054

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_054
PitNET054

tag: methylation group

tag: gender

tag: clinical presentation

value: Non-functioning PitNET

value: Yes


title: 30052-050

description:
name in processed data file:
30052-050

tag: patient diagnosis

tag: Sex

value: F

tag: visit

tag: treatment

value: L


title: Pituitary neuroendocrine tumors (PitNETs)-052

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_052
PitNET052

tag: ihc

tag: tumor size

tag: invasion

tag: surgery number

tag: age years

tag: mutations

value: pituitary tumor

tag: disease state

value: PitNETs

value: NS


title: Pituitary neuroendocrine tumors (PitNETs)-071

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_071
PitNET071

value: Cushing disease (ACTH-secreting)

value: No

tag: tissue

tag: subtypes


title: 30052-047

description:
name in processed data file:
30052-047

value: Type 2 Diabetes

value: serum

value: M


title: 30052-046

description:
name in processed data file:
30052-046

value: G


title: Neuroblastoma_usi_PAPRVP

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Pituitary neuroendocrine tumors (PitNETs)-070

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_070
PitNET070

tag: methylation group

tag: gender

value: Female

tag: clinical presentation

value: ACTH+


title: 30052-043

description:
name in processed data file:
30052-043

tag: patient diagnosis

tag: Sex

tag: visit

tag: treatment


title: Neuroblastoma_usi_PAPCDN

value: Neuroblastoma


title: Neuroblastoma_usi_PANBLP

value: Hispanic or Latino


title: Pituitary neuroendocrine tumors (PitNETs)-067

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_067
PitNET067

value: Male

value: Acromegaly (GH-secreting)

tag: ihc

value: GH+/PRL+

tag: tumor size

tag: invasion

tag: surgery number

tag: age years

tag: mutations

value: GNAS

value: Somatotroph

tag: disease state

value: GH


title: 30052-041

description:
name in processed data file:
30052-041

tag: tissue

value: L


title: Pituitary neuroendocrine tumors (PitNETs)-073

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_073
PitNET073

value: Non-functioning PitNET

value: All negative

value: No

value: WT

value: Gonadotroph

value: pituitary tumor

value: PitNETs

tag: subtypes

value: NS


title: 30052-042

description:
name in processed data file:
30052-042

value: Type 2 Diabetes

value: serum

value: M

value: G


title: Neuroblastoma_usi_PAMRWL

value: Neuroblastoma

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Pituitary neuroendocrine tumors (PitNETs)-049

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_049
PitNET049

tag: methylation group

tag: gender

value: Male

tag: clinical presentation

value: Yes


title: Neuroblastoma_usi_PAUGNL

value: Neuroblastoma (Schwannian stroma-poor)


title: 30052-040

description:
name in processed data file:
30052-040

tag: patient diagnosis

tag: Sex

tag: visit

tag: treatment


title: 30052-036

description:
name in processed data file:
30052-036

value: L


title: Neuroblastoma_usi_PATUZF


title: 30052-039

description:
name in processed data file:
30052-039


title: Neuroblastoma_usi_PATRJK


title: 30052-032

description:
name in processed data file:
30052-032


title: Pituitary neuroendocrine tumors (PitNETs)-046

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_046
PitNET046

value: Non-functioning PitNET

tag: ihc

value: Not reported

tag: tumor size

tag: invasion

tag: surgery number

tag: age years

tag: mutations

tag: disease state


title: Neuroblastoma_usi_PATVXD

tag: tissue

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

tag: efstime

tag: stime


title: Neuroblastoma_usi_PATLNM

tag: efscens

tag: scens


title: Pituitary neuroendocrine tumors (PitNETs)-047

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_047
PitNET047

tag: methylation group

tag: gender

tag: clinical presentation

value: LH+

value: WT

tag: subtypes


title: Pituitary neuroendocrine tumors (PitNETs)-048

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_048
PitNET048

value: Female

tag: ihc

value: LH+/FSH+

tag: tumor size

tag: invasion

value: Gonadotroph

value: pituitary tumor


title: 30052-030

description:
name in processed data file:
30052-030

tag: patient diagnosis

value: Type 2 Diabetes

value: serum

tag: Sex

tag: visit

tag: treatment


title: Neuroblastoma_usi_PATHUU

tag: tissue

tag: age at_diag

tag: age at_first_event_or_censor


title: Pituitary neuroendocrine tumors (PitNETs)-045

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_045
PitNET045

tag: surgery number

tag: age years

tag: mutations

tag: disease state

value: PitNETs

value: NS


title: 30052-029

description:
name in processed data file:
30052-029

value: M

value: G


title: Pituitary neuroendocrine tumors (PitNETs)-038

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_038
PitNET038

tag: methylation group

tag: gender

value: Male

value: LH+/PRO+

value: Yes


title: S2 cells, H2A.Z 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: H2A.Z  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

organism: Drosophila melanogaster

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: H2A.Z knockdown

value: transfection Ac-Da


title: Neuroblastoma_usi_PASTNT

tag: ethnicity

value: Not Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Pituitary neuroendocrine tumors (PitNETs)-027

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_027
PitNET027

value: Female

tag: clinical presentation

value: Cushing disease (ACTH-secreting)

tag: ihc

value: ACTH+

tag: tumor size

tag: invasion

value: No

value: WT

value: Corticotroph

tag: tissue

tag: subtypes

value: ACTH


title: Pituitary neuroendocrine tumors (PitNETs)-034

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_034
PitNET034

value: Non-functioning PitNET

value: ACTH+ and other(s)+

tag: surgery number

tag: age years

tag: mutations

value: Gonadotroph

value: pituitary tumor

tag: disease state

value: PitNETs

value: NS


title: Pituitary neuroendocrine tumors (PitNETs)-044

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_044
PitNET044

tag: methylation group

tag: gender

value: Male

value: All negative

value: Yes

value: Undefined tPit+/ Pit1+


title: 30052-014

description:
name in processed data file:
30052-014

tag: patient diagnosis

value: Type 2 Diabetes

value: serum

tag: Sex

value: M

tag: visit

tag: treatment

value: L


title: Pituitary neuroendocrine tumors (PitNETs)-035

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_035
PitNET035

value: LH+/FSH+

value: WT


title: S2 cells, H2A.Z KD, OE WT, replicate 1

description: H2A.Z KD_WT, replicate 1

tag: cell line

value: S2 cell line

tag: cell type

value: late embryonic stage

tag: genotype

value: H2A.Z knockdown

value: transfection Ac-Da


title: Pituitary neuroendocrine tumors (PitNETs)-041

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_041
PitNET041

value: Female

tag: clinical presentation

value: Non-functioning PitNET

tag: ihc

tag: tumor size

value: Gonadotroph

value: pituitary tumor


title: Pituitary neuroendocrine tumors (PitNETs)-031

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_031
PitNET031

value: Male

value: LH+

tag: invasion

tag: tissue

value: PitNETs

tag: subtypes

value: NS


title: Neuroblastoma_usi_PASSEC

value: Neuroblastoma (Schwannian stroma-poor)

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Pituitary neuroendocrine tumors (PitNETs)-040

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_040
PitNET040

tag: methylation group

tag: gender

value: All negative

value: No

tag: surgery number

tag: age years

tag: mutations

tag: disease state


title: Pituitary neuroendocrine tumors (PitNETs)-033

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_033
PitNET033

tag: clinical presentation

tag: ihc

tag: tumor size

value: Undefined

value: WT


title: 30052-013

description:
name in processed data file:
30052-013

tag: patient diagnosis

value: Type 2 Diabetes

tag: tissue

value: serum

tag: Sex

value: M

tag: visit

tag: treatment

value: G


title: S2 cells, Control KD, OE R29G, replicate 2

description: Luc ctrl KD_R29G, replicate 2

tag: cell line

value: S2 cell line

tag: cell type

value: late embryonic stage

tag: genotype

value: Luc knockdown

value: transfection AcR29G-Da


title: Pituitary neuroendocrine tumors (PitNETs)-032

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_032
PitNET032

tag: methylation group

value: Male

value: Non-functioning PitNET

tag: invasion

value: Yes

value: Gonadotroph

value: pituitary tumor

tag: subtypes


title: Neuroblastoma_usi_PASJNX

value: Neuroblastoma (Schwannian stroma-poor)

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Pituitary neuroendocrine tumors (PitNETs)-043

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_043
PitNET043

tag: gender

value: Female

tag: clinical presentation

tag: ihc

value: All negative

tag: tumor size

tag: surgery number

tag: age years

tag: mutations

value: Undefined tPit+/ Pit1+

tag: tissue

tag: disease state

value: PitNETs

value: NS


title: Pituitary neuroendocrine tumors (PitNETs)-037

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_037
PitNET037

tag: methylation group

value: LH+/FSH+

tag: invasion

value: No

value: WT

tag: subtypes


title: Pituitary neuroendocrine tumors (PitNETs)-025

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_025
PitNET025

value: Cushing disease (ACTH-secreting)

value: ACTH+ and other(s)+

value: Corticotroph

value: ACTH


title: Pituitary neuroendocrine tumors (PitNETs)-030

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_030
PitNET030

value: Non-functioning PitNET

value: Yes


title: Pituitary neuroendocrine tumors (PitNETs)-039

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_039
PitNET039

value: Gonadotroph

value: pituitary tumor


title: Pituitary neuroendocrine tumors (PitNETs)-028

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_028
PitNET028


title: Pituitary neuroendocrine tumors (PitNETs)-029

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_029
PitNET029

value: Male


title: Neuroblastoma_usi_PASHKU

value: Neuroblastoma (Schwannian stroma-poor)

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino


title: Pituitary neuroendocrine tumors (PitNETs)-026

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_026
PitNET026

value: Female


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

description: Luc ctrl KD_WT, replicate 2

tag: cell line

value: S2 cell line

tag: cell type

value: late embryonic stage

tag: genotype

value: Luc knockdown

tag: treatment

value: transfection Ac-Da


title: 30052-009

description:
name in processed data file:
30052-009

tag: patient diagnosis

value: Type 2 Diabetes

value: serum

tag: Sex

value: F

tag: visit

value: G


title: Neuroblastoma_usi_PARZZC

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Neuroblastoma_usi_PARUJP

tag: tissue


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

description: Luc ctrl KD_WT, replicate 1


title: 30052-008

description:
name in processed data file:
30052-008

value: M

value: L


title: 30052-007

description:
name in processed data file:
30052-007


title: Colon26 tumors from mice treated with DMSO, replicate 3

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing:
FASTQ files were trimmed to remove adapters and low-quality bases with TrimGalore v0.4.3
The trimmed reads were aligned to the human and mouse reference genomes (mm10) with STAR aligner v.2.7 with two mismatches allowed
Differential gene expression analysis was done with DESeq2 R Bioconductor package (v.1.22), using read counts data provided by the aligner
Genes were considered differentially expressed if the adjusted P-value, calculated using Benjamini-Hochberg method was less than 0.01.
lncRNA expression was quantified with kallisto using GENCODE lncRNA annotation. The tpm values produced by kallisto have been converted into DESeq2 format and analyzed the same way which was used for protein-coding genes.
Genome_build: mm10
Supplementary_files_format_and_content: processed data files contain raw read counts for EnsEMBL gene IDs as calculated by STAR aligner

molecule: polyA RNA

organism: Mus musculus

source_name: Colon26 tumor model (Balb/c)

growth_protocol: CT26 cell lines were grown in high glucose Dulbecco’s modified Eagle medium supplemented with 10% (v/v) FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Zymo DirectZol kit or Trizol. Samples quality was analysed with Agilent 2100.
cDNA libraries were made using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina. CT26 and Colon26 RNAseq were perfomed with  BGISeq500.
RNA-seq transcriptome

treatment_protocol: PRMT5 inhibition was induced with 1uM T1-44 for 72h in CT26 cells. Treatment of mouse Colon26 syngeneic  model was conducted with 100mg/kg of T1-44 daily for 19 days.

value: Colorectal carcinoma

value: Colon26 tumor

value: DMSO treated


title: 30052-005

description:
name in processed data file:
30052-005


title: 30052-010

description:
name in processed data file:
30052-010


title: Pituitary neuroendocrine tumors (PitNETs)-036

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_036
PitNET036

tag: methylation group

tag: gender

value: Male

tag: clinical presentation

value: Non-functioning PitNET

tag: ihc

value: LH+

tag: tumor size

tag: invasion

value: No

tag: surgery number

tag: age years

tag: mutations

value: WT

value: Gonadotroph

value: pituitary tumor

tag: disease state

value: PitNETs

value: NS


title: Neuroblastoma_usi_PARTRP

value: Neuroblastoma (Schwannian stroma-poor)

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino


title: Neuroblastoma_usi_PARICL

value: Neuroblastoma

tag: efstime

tag: stime


title: Pituitary neuroendocrine tumors (PitNETs)-024

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_024
PitNET024

value: Female

value: Cushing disease (ACTH-secreting)

value: ACTH+

value: Corticotroph

tag: subtypes

value: ACTH


title: 30052-004

description:
name in processed data file:
30052-004

tag: patient diagnosis

value: Type 2 Diabetes

tag: tissue

value: serum

tag: Sex

value: M

tag: visit

tag: treatment

value: L


title: Pituitary neuroendocrine tumors (PitNETs)-021

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_021
PitNET021

tag: methylation group

tag: gender

tag: clinical presentation

tag: ihc

tag: tumor size

value: Yes

value: WT


title: Pituitary neuroendocrine tumors (PitNETs)-023

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_023
PitNET023

value: ACTH+ and other(s)+

tag: invasion

value: No

tag: surgery number

tag: age years

tag: mutations

value: pituitary tumor

tag: disease state


title: 30052-003

description:
name in processed data file:
30052-003

value: G


title: Colon26 tumors from mice treated with T1-44, replicate 3

tag: cell type

value: Colorectal carcinoma

value: Colon26 tumor

value: PRMT5 inhibitor (T1-44) treated:100mg/kg, once per day


title: Neuroblastoma_usi_PARETD

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino

tag: efstime

tag: stime

tag: efscens

tag: scens


title: Colon26 tumors from mice treated with DMSO, replicate 1

tag: tissue

tag: treatment

value: DMSO treated


title: Neuroblastoma_usi_PARCXV


title: Pituitary neuroendocrine tumors (PitNETs)-022

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_022
PitNET022

tag: methylation group

tag: gender

value: Male

tag: clinical presentation

value: Non-functioning PitNET

tag: ihc

value: Corticotroph

value: PitNETs

tag: subtypes

value: NS


title: 30052-002

description:
name in processed data file:
30052-002

tag: patient diagnosis

value: Type 2 Diabetes

value: serum

tag: Sex

value: M

tag: visit

value: L


title: Colon26 tumors from mice treated with T1-44, replicate 2

tag: cell type


title: Neuroblastoma_usi_PAPSVY

value: Neuroblastoma

tag: age at_diag

tag: age at_first_event_or_censor


title: 30052-001

description:
name in processed data file:
30052-001


title: Colon26 tumors from mice treated with T1-44, replicate 1


title: Neuroblastoma_usi_PAPPPX

tag: ethnicity

tag: efstime


title: Pituitary neuroendocrine tumors (PitNETs)-020

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_020
PitNET020

value: Female

value: Cushing disease (ACTH-secreting)

value: ACTH+

tag: tumor size

tag: invasion

value: Yes

tag: surgery number

tag: age years

tag: mutations

value: pituitary tumor

tag: disease state


title: CT26 cell line treated with DMSO, replicate 3

source_name: CT26 (Colon26) cells

value: Colorectal carcinoma

tag: cell line

tag: treatment


title: Neuroblastoma_usi_PANLCE

tag: tissue

value: Not Hispanic or Latino

tag: stime

tag: efscens

tag: scens


title: Neuroblastoma_usi_PAMMGU

value: Hispanic or Latino


title: Pituitary neuroendocrine tumors (PitNETs)-019

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_019
PitNET019

tag: methylation group

tag: gender

tag: clinical presentation

tag: ihc

value: No

tag: subtypes


title: S26

city: guangzhou

first: Yingqin

state: guangdong

address: Guangzhou, 510060, P.R. China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: Array hybridization and washing was performed using GeneChip Hybridization, Wash and Stain Kit (Cat#900720) in a Hybridization Oven 645 and a Fluidics Station 450 followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip Scanner 3000 (Cat#00-00213). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing:
The raw data were normalized by  Expression Console.
Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

source_name: S26 cells without any treatment

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix WT PLUS Reagent Kit(Cat#902280) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: S18/S26 (two human NPC cells) were grown in 10% fetal bovine serum (FBS, Gibco) contained DMEM.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer’ s instructions.

treatment_protocol: Without any treatment

value: nasopharyngeal carcinoma cell lines

tag: cell type

value: low metastatic NPC cell line


title: Pituitary neuroendocrine tumors (PitNETs)-017

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_017
PitNET017

value: Acromegaly (GH-secreting)

value: GH+/PRL+

tag: tumor size

tag: invasion

value: PitNETs


title: CT26 cell line treated with DMSO, replicate 2

value: DMSO treated


title: Neuroblastoma_usi_PAMKGY

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

tag: efstime


title: Ctcf_KO_STAG2

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

institute: CNIO

data_processing:
Alignment of reads to the reference mouse genome (mm9) was performed using ‘Bowtie2′ (version 2.4.2) under default settings.
Duplicates were removed using GATK4 (version 4.1.9.0).
Peak calling was carried out using MACS2 (version 2.2.7.1) after setting the q value (FDR) to 0.05 and using the ‘–extsize’ argument with the values obtained in the ‘macs2 predictd’ step.
Assembly: mm9
Supplementary files format and content: bigWig files

source_name: MEF

growth_protocol: MEFs were isolated from E12.5 embryos and cultured in DMEM supplemented with 20% FBS at 37 ºC under 90% humidity and 5% CO2.

extract_protocol:
Cells were fixed for 15 min in 1% formaldehyde and after quenching and lysis, sonication with performed in Covaris instrument. Around 50 micrograms of antibody was added to immunoprecipitated chromatin from 10 million cells. 5% mouse ES cell chromatin was added for calibration.
At least 5 ng of DNA were processed through subsequent enzymatic treatments with "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" from New England BioLabs (ref. E7805). Briefly, a short fragmentation of 10 min was followed by end-repair, dA-tailing, and ligation to adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8-12 cycles). Resulting average fragment size is 300 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on Illumina NextSeq 500 (with v2.5 reagent kits) following manufacturer's recommendations.

treatment_protocol: Conditional knock out MEFs (Stag2 f/Y; Cre-ERT2 and Pds5A f/f; Pds5B f/f; Cre-ERT2) were cultured in medium with 1 μM 4-hydroxy tamoxifen for 4 and 5 days, respectively. For CTCF elimination, a clone of immortalized Ctcf f/f MEFs was infected with Adeno-Cre viruses (University of Iowa) at 250 pfu/cell in DMEM supplemented with 2% FBS. Medium was replaced after 24 h and cells were collected 9 days later for immunoblot and chromatin immunoprecipitation analyses.

tag: cell line

value: MEF

value: Embryonic fibroblasts

tag: genotype

value: Ctcf KO

tag: treatment

value: Adeno-Cre virus

tag: antibody

value: STAG2, custom made


title: Pituitary neuroendocrine tumors (PitNETs)-042

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_042
PitNET042

value: Female

value: Non-functioning PitNET

value: All negative

value: Yes

tag: surgery number

tag: age years

tag: mutations

value: WT

value: Gonadotroph

tag: tissue

tag: disease state

value: NS


title: Pituitary neuroendocrine tumors (PitNETs)-016

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_016
PitNET016

tag: methylation group

tag: gender

value: Male

tag: clinical presentation

tag: ihc

value: LH+/FSH+

value: pituitary tumor

tag: subtypes


title: CT26 cell line treated with DMSO, replicate 1

tag: cell type

value: Colorectal carcinoma


title: Ctcf_KO_SMC1

value: SMC1A, custom made


title: Neuroblastoma_usi_PALWKV

value: Neuroblastoma

tag: age at_diag

tag: age at_first_event_or_censor

tag: ethnicity

value: Not Hispanic or Latino

tag: stime

tag: efscens

tag: scens


title: CT26 cell line treated with T1-44, replicate 3

tag: cell line

tag: treatment

value: PRMT5 inhibitor (T1-44) treated:1uM, 48h


title: CT26 cell line treated with T1-44, replicate 2


title: Ctcf_WT_STAG2

value: MEF

value: Embryonic fibroblasts

tag: genotype

value: Ctcf WT

tag: antibody


title: Neuroblastoma_usi_PALUKI

tag: tissue

tag: efstime


title: Ctcf_WT_SMC1


title: CT26 cell line treated with T1-44, replicate 1


title: S2 cells, Control KD, OE R29G, replicate 1

description: Luc ctrl KD_R29G, replicate 1

value: S2 cell line

value: late embryonic stage

value: Luc knockdown

value: transfection AcR29G-Da


title: Ctcf_KO_INPUT

value: Ctcf KO

value: Adeno Cre virus


title: IMR90_Late_passage_rep2

city: Köln

first: Antonios

last: Papadakis

address: Fürvelser Str. 15

institute: CECAD

description:
Nascent RNA
IMR90_Late_passage_rep2
Replicate 2

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

extract_protocol:
isolation of factory RNA + illumina platform libraries
RNeasy mini Kit and Trizol

tag: age

value: Late passage

tag: sexe

tag: feeding


title: xenopus tropicalis sperm-Ring1B_rep2

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 and mm10 reference genome using bowtie2 with default parameters.
Assembly: xv10
Supplementary files format and content: bigWig

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. (Mouse cells were added as spike-in control.) 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.

value: sperm


title: Ctcf_WT_INPUT


title: IMR90_Early_passage_rep2

description:
Nascent RNA
IMR90_Early_passage_rep2
Replicate 2

value: Early passage


title: Tumor DNA from Pediatric Adrenocortical Tumor_102

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

source_name: Pediatric Adrenocortical Tumor 102

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: 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

value: No

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: Tumor DNA from Pediatric Adrenocortical Tumor_098

source_name: Pediatric Adrenocortical Tumor 098

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: treatment


title: Stag2_KO_SMC1_R4

tag: cell line

value: MEF

tag: cell type

value: Embryonic fibroblasts

tag: genotype

value: Stag2 KO

value: 4 days 1 uM 4OHT

tag: antibody

value: SMC1A, custom made


title: Pituitary neuroendocrine tumors (PitNETs)-010

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_010
PitNET010

value: Acromegaly (GH-secreting)

tag: ihc

value: GH+ and other(s)

tag: tumor size

tag: invasion

tag: surgery number

tag: age years

tag: mutations

value: WT

value: Somatotroph

tag: tissue

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes

value: GH


title: Stag2_KO_SMC1_R3


title: Pituitary neuroendocrine tumors (PitNETs)-014

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_014
PitNET014

tag: methylation group

tag: gender

value: Female

tag: clinical presentation

value: Non-functioning PitNET

value: All negative

value: Yes

value: Corticotroph

value: NS


title: xenopus tropicalis sperm-Ring1B_rep1

value: sperm


title: IMR90_Early_passage_rep1

description:
Nascent RNA
IMR90_Early_passage_rep1
Replicate 1

tag: age

value: Early passage

tag: sexe

tag: feeding


title: Pituitary neuroendocrine tumors (PitNETs)-012

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_012
PitNET012

value: Male

value: Not reported

value: No


title: xenopus tropicalis sperm-H2AK119ub1_rep2


title: xenopus tropicalis sperm-H2AK119ub1_rep1


title: Tumor DNA from Pediatric Adrenocortical Tumor_097

source_name: Pediatric Adrenocortical Tumor 097

tag: age (years)

tag: reference center

value: Ribeirao Preto Medical School - University of Sao Paulo

tag: tumor steroid-secretion

value: Asymptomatic

value: 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

tag: capsular invasion

tag: vascular invasion

tag: soft-tissue invasion

tag: necrosis

tag: mitosis > 15/20 high powered fields

value: Unavailable

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

tag: treatment

value: Surgery and chemotherapy

tag: p53 p.r337h germline mutation genotype

value: Wild-type

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)

tag: outcome

value: Alive with active disease


title: HUVECs_Late_passage_rep3

description:
HUVECs_Late_passage_rep3
Replicate 3

source_name: HUVECs

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

tag: cell line

value: HUVECs

tag: age

value: Late passage

tag: sexe

tag: feeding

tag: genotype


title: Tumor DNA from Pediatric Adrenocortical Tumor_101

source_name: Pediatric Adrenocortical Tumor 101

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

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

tag: tumor steroid-secretion

value: Virilization

tag: clinical presentation

tag: tumor stage

value: III

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: Yes

value: Mutant

value: Deceased


title: xenopus tropicalis sperm-SUZ12_rep2

tag: tissue

value: sperm

tag: antibody


title: Pituitary neuroendocrine tumors (PitNETs)-015

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_015
PitNET015

value: Female

value: Cushing disease (ACTH-secreting)

tag: ihc

value: ACTH+

tag: tumor size

tag: invasion

tag: surgery number

tag: age years

tag: mutations

value: Corticotroph

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes

value: ACTH


title: S18

source_name: S18 cells without any treatment

tag: cell line

value: nasopharyngeal carcinoma cell lines

tag: cell type

value: high metastatic NPC cell line


title: Tumor DNA from Pediatric Adrenocortical Tumor_096

source_name: Pediatric Adrenocortical Tumor 096

tag: methylation group

tag: gender

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Virilization and Cushing’s Syndrome

tag: clinical presentation

value: Unavailable

tag: tumor stage

value: II

tag: histopathological classification

tag: tumor weight (grams)

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: treatment

value: Surgery and chemotherapy

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)

tag: outcome


title: Stag2_WT_SMC1_R4

tag: cell line

value: MEF

tag: cell type

value: Embryonic fibroblasts

tag: genotype

value: Stag2 WT

tag: antibody

value: SMC1A, custom made


title: HUVECs_Late_passage_rep2

description:
HUVECs_Late_passage_rep2
Replicate 2

value: HUVECs

tag: age

value: Late passage

tag: sexe

tag: feeding


title: Colon26 tumors from mice treated with DMSO, replicate 2

value: Colorectal carcinoma

tag: tissue

value: Colon26 tumor

value: DMSO treated


title: HUVECs_Late_passage_rep1

description:
HUVECs_Late_passage_rep1
Replicate 1


title: Tumor DNA from Pediatric Adrenocortical Tumor_095

source_name: Pediatric Adrenocortical Tumor 095

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

tag: tumor stage

value: I

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

tag: necrosis

tag: mitosis > 15/20 high powered fields

value: No

value: Surgery

value: Mutant

value: Alive and disease free


title: Stag2_WT_SMC1_R3

tag: cell line

value: MEF

tag: cell type

tag: genotype

tag: treatment

tag: antibody


title: Pituitary neuroendocrine tumors (PitNETs)-009

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_009
PitNET009

tag: methylation group

tag: gender

tag: clinical presentation

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

tag: tissue

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes


title: xenopus tropicalis sperm-EZH2_rep2

value: sperm


title: HUVECs_Early_passage_rep3

description:
HUVECs_Early_passage_rep3
Replicate 3

tag: cell line

value: HUVECs

tag: age

value: Early passage

tag: sexe

tag: feeding


title: Pituitary neuroendocrine tumors (PitNETs)-006

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_006
PitNET006

value: Female

value: GH+ and other(s)

value: Somatotroph

value: GH


title: Pituitary neuroendocrine tumors (PitNETs)-007

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_007
PitNET007

value: Male

value: No


title: Stag2_pool-WT-KO_INPUT_R3R4

tag: cell type

value: Embryonic fibroblasts

tag: genotype

tag: treatment

value: None + 4 days 1 uM 4OHT

tag: antibody


title: xenopus tropicalis sperm-EZH2_rep1


title: WT_Control_R3_RNA-seq

data_processing:
Fastq files with 86-nt single-end sequenced reads were quality-checked with FastQC (S. Andrews, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were aligned to the mouse genome with Nextpresso executing TopHat-2.0.0 using Bowtie 0.12.7 and Samtools 0.1.16 allowing two mismatches and five multi-hits (Graña et al., 2018).
Reads were mapped to mm9 genes using HTSeq (Anders et al., 2015).
Assembly: mm9
Supplementary files format and content: counts_rnaseq.txt

extract_protocol:
Total RNA was extracted with total RNA (RNeasy Mini Kit, Qiagen) following manufacturer’s instructions and treated with DNaseI (Ambion).
PolyA+ RNA was purified with the Dynabeads mRNA purification kit (Invitrogen), randomly fragmented and converted to double-stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing and ligation to adapters as in Illumina's ‘TruSeq RNA Sample Preparation Guide’ (Part # 15031047 Rev. D). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers and applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on HiSeq2000 or Illumina HiSeq2500 instrument by following manufacturer's protocols.

value: MEF


title: Tumor DNA from Pediatric Adrenocortical Tumor_094

source_name: Pediatric Adrenocortical Tumor 094

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

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

value: Surgery

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

tag: disease-free survival (years)

tag: overall survival (years)

tag: outcome

value: Alive and disease free


title: HUVECs_Early_passage_rep2

description:
HUVECs_Early_passage_rep2
Replicate 2

tag: cell line

value: HUVECs

tag: age

value: Early passage

tag: sexe

tag: feeding

tag: genotype


title: WT_Control_R2_RNA-seq

tag: cell type

value: WT


title: Tumor DNA from Pediatric Adrenocortical Tumor_093

source_name: Pediatric Adrenocortical Tumor 093

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

value: Cushing’s Syndrome

tag: clinical presentation

value: Cortisol

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

value: Yes

tag: vascular invasion

tag: treatment

value: Wild-type


title: IMR90_Late_passage_rep1

description:
Nascent RNA
IMR90_Late_passage_rep1
Replicate 1

tag: cell line

tag: age

value: Late passage

tag: sexe

tag: feeding

tag: genotype


title: xenopus tropicalis sperm-HiC_spikein_rep1

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

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).

tag: tissue

value: sperm


title: Mouse_kidney_3month_DR_rep4

description:
Mouse_kidney_3month_DR_rep4
Replicate 4

source_name: kidney

value: kidney

value: 3 months

value: Male

value: DR


title: Pituitary neuroendocrine tumors (PitNETs)-003

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_003
PitNET003

tag: methylation group

tag: gender

value: Acromegaly (GH-secreting)

tag: ihc

value: GH+/PRL+

tag: tumor size

tag: invasion

tag: surgery number

tag: age years

tag: mutations

value: Somatotroph

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes

value: GH


title: Tumor DNA from Pediatric Adrenocortical Tumor_090

source_name: Pediatric Adrenocortical Tumor 090

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: 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: 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

tag: disease-free survival (years)

tag: overall survival (years)

tag: outcome

value: Alive and disease free


title: Tumor DNA from Pediatric Adrenocortical Tumor_092

source_name: Pediatric Adrenocortical Tumor 092

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

tag: clinical presentation

tag: tumor stage

tag: histopathological classification

value: Carcinoma

tag: tumor weight (grams)

value: Yes

value: Wild-type


title: xenopus tropicalis sperm-HiC_spikein_rep2

tag: tissue

value: sperm


title: xenopus tropicalis sperm-HiC_rep2


title: WT_Control_R1_RNA-seq

tag: cell line

value: MEF

tag: cell type

value: Embryonic fibroblasts

tag: genotype

value: WT


title: HUVECs_Early_passage_rep1

description:
HUVECs_Early_passage_rep1
Replicate 1

value: HUVECs

tag: age

value: Early passage

tag: sexe

tag: feeding


title: xenopus tropicalis sperm-HiC_rep1


title: Tumor DNA from Pediatric Adrenocortical Tumor_087

source_name: Pediatric Adrenocortical Tumor 087

value: Ribeirao Preto Medical School - University of Sao Paulo

value: Virilization

value: Androgen

value: III

value: Unavailable

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 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: Lost to follow-up


title: Pituitary neuroendocrine tumors (PitNETs)-002

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_002
PitNET002

tag: methylation group

tag: gender

value: Male

tag: clinical presentation

value: Acromegaly (GH-secreting)

tag: ihc

value: GH+ and other(s)

tag: tumor size

tag: invasion

value: No

tag: surgery number

tag: age years

tag: mutations

value: Somatotroph

tag: tissue

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes

value: GH


title: xenopus tropicalis sperm-SUZ12_rep1

value: sperm

tag: antibody


title: Pituitary neuroendocrine tumors (PitNETs)-011

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_011
PitNET011

value: Female

value: GNAS


title: Pituitary neuroendocrine tumors (PitNETs)-004

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_004
PitNET004

value: GH+/PRL+


title: Tumor DNA from Pediatric Adrenocortical Tumor_107

source_name: Pediatric Adrenocortical Tumor 107

tag: age (years)

tag: reference center

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

tag: tumor steroid-secretion

value: Virilization

tag: tumor stage

value: IV

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

tag: necrosis

tag: mitosis > 15/20 high powered fields

tag: atypical mitosis

tag: post-surgery recurrence or metastasis

value: Yes

tag: treatment

tag: p53 p.r337h germline mutation genotype

value: Mutant

tag: ctnnb1 (exon 3) somatic genotype

value: Wild-type

value: Alive and disease free


title: Mouse_kidney_3month_DR_rep3

description:
Mouse_kidney_3month_DR_rep3
Replicate 3

tag: tissue

value: kidney

tag: age

value: 3 months

tag: sexe

value: Male

tag: feeding

value: DR

tag: genotype


title: Mouse_kidney_3month_DR_rep1

description:
Mouse_kidney_3month_DR_rep1
Replicate 1


title: Mouse_hypothalamus_26month_IRS1-/-_rep2

description:
Mouse_hypothalamus_26month_IRS1-/-_rep2
Replicate 2

source_name: hypothalamus

value: hypothalamus

value: 26 month

value: AL


title: Mouse_kidney_3month_rep4

description:
Mouse_kidney_3month_rep4
Replicate 4


title: xenopus tropicalis sperm-ATAC_rep2

data_processing:
Raw fastq ATAC-seq reads were trimmed and aligned to X.tropicalis v10.0 genome using bwa. ATAC-seq signal tracks for visualization were also generated by bamCoverage with option “--normalizeUsing RPKM”.
Genome_build: xv10
Supplementary_files_format_and_content: bigWig

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.
About 50000 sperms were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.5% NP-40) for 10 min on ice to prepare the nuclei. Then, nuclei were spun at 1500g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme，TD501).  Following incubation, sperm were treated with Proteinase K at 63°C for 2 hr, and gDNA was purified with the 1.2× DNA clean beads. PCR was performed to amplify the library for 12 cycles and libraries were purified with the 1.2×DNA clean beads. Amplified ATAC libraries were sequenced on the Illumina HiSeq X10 platform.

value: sperm


title: Pituitary neuroendocrine tumors (PitNETs)-001

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_001
PitNET001

tag: methylation group

tag: gender

value: Female

tag: clinical presentation

value: Acromegaly (GH-secreting)

tag: ihc

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: Mouse_kidney_3month_DR_rep2

description:
Mouse_kidney_3month_DR_rep2
Replicate 2


title: Matthias, 5E1 anti-HH

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:
10x Genomics
metadata.tsv.gz
my.obj.Robj

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
A sequence containing the tdTomato coding sequence (GenBank accession no. AY678269.1), the 3Æ-prime Woodchuck hepatitis virus Posttranscriptional Regulatory Element (WPRE) and the polyA signal was added to the raw dataset in order to identify tdTom expressing cells in the dataset
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx), my.obj.Robj

source_name: lung

extract_protocol:
P6 lungs were perfused with PBS through the RV, minced with a razor blade, pooled (n=3 per condition), and digested  in 2.4 U/mL Dispase II/0.1% collagenase A in 150 mM NaCl, 10 mM Hepes pH 7.4, 2 mM CaCl2 for 45 min at 37C. Enzymes were inactivated with 10 mM EDTA and cells were passed through 70-um and 40-um filters. Spun-down cell pellets were washed twice and resuspended in 0.5% BSA-PBS. Life cell numbers were counted (Trypan Blue dye). Single cells (~20,000/sample) were loaded onto a GEM code instrument (10xGenomics).
GEM generation and library prep was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics).

treatment_protocol: Gli1creERT2/+;R26RtdTom pups were treated with tamoxifen SC at P1 followed by treatment with anti-HH antibody 5E1 or IgG control SC at P3.

value: lung

tag: cell type

value: whole lung single cells

tag: treatment


title: Mouse_hypothalamus_26month_IRS1-/-_rep1

description:
Mouse_hypothalamus_26month_IRS1-/-_rep1
Replicate 1

tag: tissue

tag: age


title: Mouse_hypothalamus_26month_IRS1-/-_rep3

description:
Mouse_hypothalamus_26month_IRS1-/-_rep3
Replicate 3

tag: sexe

tag: feeding


title: Matthias, IgG

tag: genotype

value: IgG


title: Tumor DNA from Pediatric Adrenocortical Tumor_078

source_name: Pediatric Adrenocortical Tumor 078

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

value: Androgen and cortisol

tag: tumor stage

value: III

tag: histopathological classification

value: Unavailable

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

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: Alive and disease free


title: Tumor DNA from Pediatric Adrenocortical Tumor_088

source_name: Pediatric Adrenocortical Tumor 088

tag: methylation group

tag: gender

value: Female

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

tag: clinical presentation

tag: tumor stage

value: I

tag: histopathological classification

value: Adenoma

value: No

value: Yes

tag: treatment

value: Surgery

value: Lost to follow-up


title: xenopus tropicalis sperm-ATAC_rep3

tag: tissue

value: sperm


title: Tumor DNA from Pediatric Adrenocortical Tumor_085

source_name: Pediatric Adrenocortical Tumor 085

value: Ribeirao Preto Medical School - University of Sao Paulo

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


title: Mouse_hypothalamus_26month_rep3

description:
Mouse_hypothalamus_26month_rep3
Replicate 3

value: hypothalamus

tag: age

value: 26 month

tag: sexe

value: Male

tag: feeding

value: AL

tag: genotype


title: Tumor DNA from Pediatric Adrenocortical Tumor_081

source_name: Pediatric Adrenocortical Tumor 081

tag: methylation group

tag: gender

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

tag: histopathological classification

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)

tag: outcome


title: xenopus tropicalis sperm-H2AZ_rep1

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

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

tag: antibody


title: xenopus tropicalis sperm-ATAC_rep1


title: Tumor DNA from Pediatric Adrenocortical Tumor_073

source_name: Pediatric Adrenocortical Tumor 073

value: II

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: treatment

value: Alive and disease free


title: Mouse_kidney_3month_rep3 [SN7640244]

description:
Mouse_kidney_3month_rep3
Replicate 3

value: kidney

tag: age

value: 3 months

tag: sexe

tag: feeding

tag: genotype


title: Mouse_hypothalamus_26month_rep4

description:
Mouse_hypothalamus_26month_rep4
Replicate 4

tag: tissue


title: xenopus tropicalis sperm-H2AZ_rep2

tag: antibody


title: Pituitary neuroendocrine tumors (PitNETs)-018

description:
Tumor DNA from Pituitary neuroendocrine tumors (PitNETs)_018
PitNET018

tag: methylation group

tag: gender

value: Female

tag: clinical presentation

value: Non-functioning PitNET

tag: ihc

value: All negative

tag: tumor size

tag: invasion

value: No

tag: surgery number

tag: age years

tag: mutations

value: Gonadotroph

value: pituitary tumor

tag: disease state

value: PitNETs

tag: subtypes

value: NS


title: Tumor DNA from Pediatric Adrenocortical Tumor_070

source_name: Pediatric Adrenocortical Tumor 070

value: Male

tag: age (years)

tag: reference center

tag: tumor steroid-secretion

tag: tumor stage

value: I

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

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

tag: disease-free survival (years)

tag: overall survival (years)

tag: outcome


title: xenopus tropicalis sperm-H3K9me2_rep1

tag: tissue

value: sperm

tag: antibody


title: Mouse_kidney_3month_rep2 [SN7640244]

description:
Mouse_kidney_3month_rep2
Replicate 2

tag: age

tag: sexe

tag: feeding

value: AL

tag: genotype