title: Patient 103_lh 143

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 143


title: Patient 104_lh 144

status: Public on Jan 11 2023

type: RNA

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 144

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (SF3A3, GUSB, G6PD). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

molecule: total RNA

organism: Homo sapiens

source_name: Classical Hodgkin Lymphoma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of classical Hodgkin Lymphoma were reviewed by three different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 773 genes by NanoString using the PanCancer Immune Profiling Panel (NanoString Technologies).

treatment_protocol: Pretreatment diagnostic biopsies from ABVD-treated classical Hodgkin Lymphoma patients

tag: tissue

value: tumor

tag: patient diagnosis

value: Classical Hodgkin Lymphoma

tag: gender

value: F

tag: age

tag: Stage

value: II

value: yes


title: Patient 109_lh 153

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 153

value: M

value: IV

value: no


title: Patient 117_lh 181

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 181


title: Patient 100_lh 140

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 140


title: Patient 101_lh 141

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 141


title: Patient 98_lh 135

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 135

value: III


title: Patient 102_lh 142

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 142


title: Patient 99_lh 139

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 139


title: Patient 107_lh 149

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 149


title: Patient 105_lh 145

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 145


title: Patient 91_lh 123

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 123


title: Patient 89_lh 121

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 121


title: Patient 96_lh 133

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 133


title: Patient 83_lh 115

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 115


title: Patient 88_lh 120

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 120


title: Patient 90_lh 122

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 122


title: Patient 95_lh 130

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 130


title: Patient 87_lh 119

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 119


title: Patient 93_lh 127

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 127


title: Patient 79_lh 110

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 110


title: Patient 80_lh 111

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 111


title: Patient 94_lh 129

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 129


title: Patient 86_lh 118

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 118


title: Patient 85_lh 117

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 117


title: Patient 92_lh 125

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 125


title: Patient 76_lh 107

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 107


title: Patient 81_lh 112

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 112


title: Patient 82_lh 113

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 113


title: Patient 77_lh 108

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 108


title: Patient 75_lh 106

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 106


title: Patient 78_lh 109

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 109


title: Patient 74_lh 104

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 104


title: Patient 72_lh 102

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 102


title: Patient 73_lh 103

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 103


title: Patient 70_lh 99

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 99


title: Patient 71_lh 101

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 101


title: Patient 84_lh 116

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 116


title: Patient 97_lh 134

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 134


title: Patient 68_lh 96

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 96


title: Patient 69_lh 97

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 97


title: Patient 64_lh 92

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 92


title: Patient 60_lh 87

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 87


title: Patient 63_lh 90

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 90


title: Patient 59_lh 86

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 86


title: Patient 62_lh 89

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 89


title: Patient 65_lh 93

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 93


title: Patient 66_lh 94

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 94


title: Patient 67_lh 95

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 95


title: Patient 57_lh 82

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 82


title: Patient 56_lh 81

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 81


title: Patient 51_lh 75

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 75


title: Patient 54_lh 79

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 79


title: Patient 53_lh 77

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 77


title: Patient 58_lh 85

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 85


title: Patient 52_lh 76

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 76


title: Patient 48_lh 71

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 71


title: Patient 50_lh 74

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 74


title: Patient 47_lh 70

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 70


title: Patient 46_lh 66

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 66


title: Patient 45_lh 65

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 65


title: Patient 44_lh 62

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 62


title: Patient 41_lh 58

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 58


title: Patient 43_lh 61

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 61


title: Patient 40_lh 56

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 56


title: Patient 42_lh 60

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 60


title: Patient 39_lh 54

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 54


title: Patient 61_lh 88

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 88


title: Patient 38_lh 52

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 52


title: Patient 55_lh 80

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 80


title: Patient 49_lh 73

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 73


title: Patient 35_lh 48

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 48


title: Patient 31_lh 44

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 44


title: Patient 30_lh 43

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 43


title: Patient 29_lh 42

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 42


title: Patient 32_lh 45

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 45


title: Patient 33_lh 46

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 46


title: Patient 36_lh 50

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 50


title: Patient 34_lh 47

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 47


title: Patient 37_lh 51

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 51


title: Patient 28_lh 41

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 41


title: Patient 24_lh 37

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 37


title: Patient 25_lh 38

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 38


title: Patient 26_lh 39

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 39


title: Patient 23_lh 36

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 36


title: Patient 20_lh 33

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 33


title: Patient 19_lh 32

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 32


title: Patient 22_lh 35

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 35


title: Patient 17_lh 29

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 29


title: Patient 18_lh 30

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 30


title: Patient 27_lh 40

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 40


title: Patient 16_lh 27

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 27


title: Patient 15_lh 26

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 26


title: Patient 13_lh 22

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 22


title: Patient 14_lh 24_2

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 24


title: Patient 10_lh 17

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 17


title: Patient 9_lh 16

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 16


title: Patient 8_lh 15

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 15


title: Patient 11_lh 18

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 18


title: Patient 21_lh 34

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 34


title: Patient 6_lh 11

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 11


title: Patient 3_lh 6

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 6


title: Patient 7_lh 13

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 13


title: Patient 2_lh 4

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 4


title: Patient 12_lh 19

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 19


title: Patient 4_lh 9

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 9


title: A5

type: SRA

city: Montreal

first: Bernard

last: Robaire

state: QC

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Novogene RNA-seq Data Analysis
Quality control analysis processed first through in-house perl scripts.
HiSat2 v2.0.5 was used to build the reference genome and align the paired-end reads.
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene.
Assembly: rn_6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Aged Round Spermatid

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

treatment_protocol:
Rats were aged to 4-6 months, or 18-20 months under normal conditions with food and water ad lib.
Germ cells were separated and collected using germ cell separation via STA-PUT method.

tag: cell type

value: primary round spermatid

tag: genotype

value: WT

tag: time

value: 18-20 months


title: A3


title: A2


title: A1


title: Y3

source_name: Young Round Spermatid

value: 4-6 months


title: A4


title: Y4


title: Patient 1_lh 3

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 3


title: Y1


title: Patient 5_lh 10

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 10


city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

state: PA

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

country: USA

institute: University of Pittsburgh

description: Microarray gene expression data

hyb_protocol: 100ng of purified total RNA underwent transcription in-vitro via the MessageAmp Premier Enhanced assay protocol (Thermo Fisher Scientific). The diversity of cRNA was confirmed by Nanodrop. 15 μg of biotin-labeled cRNA was fragmented and hybridized to the Affymetrix Mouse Clariom STM array in accordance with the manufacturers protocol (ThermoFisher Scientific).

scan_protocol: Scanner 3000

data_processing: Transcriptome analysis software (TAC, ThermoFisher) identified those with a p-value <0.05 using default parameters, considered as having a significant change in expression in Dex-treated groups compared to vehicle controls.

label: biotin

organism: Mus musculus

source_name: SOX2 KO Mouse NSPCs at PO, Dex-treated (4h), biological sample 13

label_protocol: Biotinylated cRNA were prepared from 15ug total RNA in accordance with the manufacturers protocol (ThermoFisher Scientific).

growth_protocol: Cortical NSPC cultures derived from the C57BL/6 mouse embryonic telencephalon (P0) were generated in Neurocult media supplemented with epidermal growth factor (EGF), fibroblast growth factor-1 (FGF-1), penicillin streptomycin, and proliferation growth supplement (StemCell Technologies), in accordance with the technical manual provided by StemCell Technologies and the ethical and Environmental Health & Safety practices required by the University of Pittsburgh IACUC and the National Institutes of Health. Cultures from each animal were kept separate, and fetal sex was determined by digesting tail tissue overnight in 200μl of nonionic detergent buffer with 1.2μl of proteinase K at 56°C. Afterwards, samples were heat inactivated at 95°C for 10 minutes and isolated DNA subjected to PCR analysis to detect the Y chromosome Sry gene.

extract_protocol: The RNeasy micro kit (Qiagen) was used to extract total RNA.

treatment_protocol: After the third passage (P3), 100nM Dexamethasone (Dex) or an ethanol vehicle was added directly to the culture media for 4 hours. Cells were removed from the culture media and collected immediately afterwards for analyses.

value: Postnatal day 0

value: mouse fetal telencephalon-derived

value: SOX2 KO


title: Y5


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, Dex-treated (4h), biological sample 12


title: 5032078

city: Beijing

first: Bo

last: Gao

address: No.11 Xizhimen South Street, Beijing, China

department: Department of General Surgery

country: China

institute: Peking university people's hospital

data_processing:
Basecalls were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
FastQC software performs sequencing quality evaluation on reads after removing the adapter (use cutadapt to remove 3‘ and 5’ adapters). Align to reference genome by Hisat2 software. Use StringTie software to refer to official database annotation information to estimate transcription abundance.
The R software Ballgown was used to calculate the FPKM at the gene level and the transcription level, and to calculate the difference in expression at the gene level and the transcription level respectively.
Use rMATS for alternative splicing time detection, difference calculation and mapping.
Genome_build: hg18
Supplementary_files_format_and_content: txt files include FPKM values for each Sample

source_name: gastric cancer tissue

extract_protocol:
Fresh-frozen cancerous tissue samples of these 13 included patients were collected from the institutional biobank. Total RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit（Illumina） was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary gastric cancer

value: Male

tag: t

tag: n

tag: emvi score

tag: pfs time


title: 4220202


title: 4196273


title: 4193117


title: Y2


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, Dex-treated (4h), biological sample 10


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 12


title: 4189275


title: 4188583


title: 4201362


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 8


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 11


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, Dex-treated (4h), biological sample 9


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 9


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 10


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, Dex-treated (4h), biological sample 6


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, Dex-treated (4h), biological sample 7


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 13


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 7


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, Dex-treated (4h), biological sample 8


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, Dex-treated (4h), biological sample 5


description: Microarray gene expression data

source_name: SOX2 KO Mouse NSPCs at PO, Dex-treated (4h), biological sample 11


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 6


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 4


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 5


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, Dex-treated (4h), biological sample 4


title: 4188368

source_name: gastric cancer tissue


title: 4177665


title: 4179903


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, Dex-treated (4h), biological sample 3


title: 4138800

value: Female


title: Sample 49 GEXSCOPETM

city: Nanjing

first: Ran

last: Wang

state: Jiangsu

address: Guangzhou street No.264

institute: The Affiliated Brain Hospital of Nanjing Medical University

data_processing:
Raw reads were processed to generate gene expression profiles using an internal pipeline. Briefly, after filtering read one without polyT tails, cell barcode and UMI was extracted.
Adapters and polyA tails were trimmed before read two was mapped to GRCh38 with ensemble version 92 gene annotation.
Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell.
Cell number was then determined based on the ‘knee’ method.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include UMI values for each Cell.

source_name: brain

extract_protocol:
Single cell RNA was captured by microfluidic technology using millions of unique Barcode-labeles.
The genomic DNA is subjected to steps of interruption, damage repair and end repair to generate a complete double-stranded DNA after interruption, and a hairpin-like linker with a sequencing primer is ligated to both ends of the double-stranded DNA by a linker, and then subjected to digestion. Screening and other steps to generate circular DNA containing no unligated and redundant linkers, and then repaired and purified to obtain a complete DNA library.

value: male

tag: race

value: Asian

tag: who grade

value: WHO III


title: 252991


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 3


title: Sample 44 GEXSCOPETM


title: Sample 47 GEXSCOPETM

value: female


title: 274781


title: Sample 39 GEXSCOPETM


title: Sample 45 GEXSCOPETM


title: Sample 21 GEXSCOPETM

value: WHO IV


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 2


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, Dex-treated (4h), biological sample 2


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, Dex-treated (4h), biological sample 1


title: CTL_10_2

city: Barcelona

first: Patricia

last: Bogdanov

state: Barcelona, Spain

address: Passeig de la Vall d'Hebron 119-129  Collserola Building. Lab 144

department: Diabetes Research and Metabolism Unit

country: Spain

institute: Vall d'Hebron Research Institute

description: GeneChip 3' IVT Pico Kit. Affymetrix GeneChip System 3000scanned using the scanner GCS3000 (7G with autoloader)

hyb_protocol: Following fragmentation, 5,5ug of ds-cDNA were hybridized for 16 hr at 45C on GeneChip Clariom S mouse array cartridge. Array cartridge was washed and stained in the Affymetrix GeneChip System 3000

scan_protocol: Array cartridge was scanned using the scanner GCS3000 (7G with autoloader)

data_processing: Raw expression values were obtained directly from .CEL files and were processed using the RMA method in oligo R package to get normalized expression values (log2 scale) summarized at the gene level.  Different quality checks (boxplots, hierarchical clustering and principal component analyses (PCAs)) were performed before and after normalization to ensure that samples were suitable for differential expression analysis. A complete quality report was obtained using arrayQualityMetrics R package. One sample was identified as a putative outlier during quality control and was therefore excluded from the analysis prior to normalization. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance. Because batch effects were detected, a batch factor was included in the linear model used for differential expression analysis.  P-values are adjusted to obtain strong control over the false discovery rate using the Benjamini and Hochberg method. Statistical significance was set at 0.05 for adjusted p-values. Statistical language R (version 3.6.1) and Bioconductor associated packages were used to process and analyze the data.

label: Biotinylated ds-cDNA

source_name: neuroretinal homogenate

label_protocol: Biotinylated ds-cDNA were prepared according to the standard Affymetrix (ThermoFisher) protocol from 10 ng total RNA (GeneChip 3' IVT Pico Kit Manual Workflow, user guide).

growth_protocol: Eyes were rapidly enucleated and the neuroretinas were dissected. The neuroretina of each animal was directly stored in an empty tube at -80ºC for transcriptomic experiments.

extract_protocol: The neuroretinas were introduced in individual tubes with 140 µL of TRIzol reagent (15596018, InvitrogenTM, Carlsbad, CA, USA) until RNA extraction. For the RNA extraction, neuroretinas were treated with DNase (18068015, ThermoFisher Scientific, Waltham, MA, USA) to remove genomic contamination and were purified on RNeasy MinElute column (74106, Qiagen, Hilden, Germany). After supernatant elimination, RNA sediment was obtained and resuspended in 30 µL of RNAse free water (AM9937, ThermoFisher Scientific, Waltham, MA, USA). An Agilent 2100 Bioanalyzer and a Nanodrop spectrophotometer were used for samples integrity and quantity respectively.

treatment_protocol: At the age of 10 weeks, sitagliptin [sitagliptin phosphate monohydrate (Y0001812, Merck KGaA, Darmstadt, Germany) eyedrops (10 mg/mL; n=10), and vehicle [phosphate buffered saline (PBS)] eyedrops (n=10) were randomly administered twice per day directly onto the superior corneal surface of each eye of diabetic mice with the aid of a micropipette (5 µL). On day 15, animals (12 weeks of age) received one drop of sitagliptin or vehicle 1h before euthanasia. 10 non-diabetic mice matched by age were used as control group.

value: neuroretinal homogenate

tag: mouse group

value: control non diabetic sample (yellow white)

tag: treatment

value: control non-treatment


title: CTL_7_2


title: LSD1_HCT116_KO

city: Shenzhen

first: Cao

last: Qiang

address: No. 66 Gongchang Road, Guangming District, Shenzhen

department: School of Medicine

institute: Sun Yat-sen University

library_source: genomic

data_processing:
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Filter sequencing adapters and low-quality reads using TrimGalore (v0.6.6).
Cleaned reads were aligned to the hg38 genome with Bismark (v0.19.0)
Assembly: GRCh38/hg38
Supplementary files format and content: Bismark coverage file

molecule: genomic DNA

growth_protocol: Human colorectal carcinoma HCT116 cell line was cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin (Procell, Wuhan, China, CM-0096). Human colonic epithelial cell line NCM460 was cultured in DMEM medium (Gibco, NY, USA, C11965500BT) supplemented with 10% FBS (Lonsera, S712-012S) and 100 U/mL penicillin/streptomycin (Gibco, USA, 15140122).

extract_protocol:
Genomic DNA was extracted with a HiPure Tissue DNA Mini Kit (Magen, D3121-02).
The DNA samples were digested using methylation-insensitive restriction enzyme Mspl. All the cytosines were subjected to methylation-modified sequencing adaptors, DNA fragments with insert lengths within the range of 40-220 base pairs were cut from the gel and bisulfite treatment was carried out using an EZ DNA Methylation Gold Kit (Zymo Research). PCR amplification was then performed to obtain the final DNA library. After quality checks of the DNA library, the samples were sent for Illumina HiSeq 2500/4000 sequencing.

tag: cell line

value: colorectal cancer cell line

value: LSD1 knockout


title: LSD1_HCT116_WT

value: wild-type


title: CTL_9_2

tag: tissue


title: LSD1_NCM460_NC

value: Human colonic epithelial cell line

value: negative control


description: Microarray gene expression data

source_name: WT Mouse NSPCs at PO, vehicle ethanol-treated (4h), biological sample 1

value: Postnatal day 0

value: mouse fetal telencephalon-derived

value: WT


title: CTL_8_2


title: CTL_12_1


title: CTL_3_1


title: LSD1_NCM460_OE

value: LSD1 overexpression


title: CTL_1_1


title: LSD1_NCM460_OE_H3K4me1

data_processing:
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Filter sequencing adapters and low-quality reads using TrimGalore (v0.6.6).
Cleaned reads were aligned to the hg38 genome with bowtie2 (v 2.4.5)
Peaks were called using MACS2 (v 2.2.7.1)
Bigwig files adjusted by input data and enrichment profiles across genomic regions of interest were all generated using deeptools
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig file

extract_protocol:
5x 106 cells were cross-linked with 1% formaldehyde for 10 minutes and quenched by 125mM glycine for 5 minutes at room temperature with gentle shaking, and washed twice with PBS. Cells were then pelleted and lysed in ice-cold lysis buffer1 (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) and lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) supplemented with cOmplete protease inhibitors (Roche) for 10 minutes. The cell lysate was sonicated using Covaris M220 with 5% duty factor for 10min at 4 °C to shear DNA to fragments (200~1000 bp). Soluble chromatin was diluted in shearing buffer (1mM EDTA, 10mM Tris-HCl pH 8.0, 0.1% SDS) with 1% Triton X-100 and 150 mM NaCl and incubated with 3μg ChIP-grade antibody at 4°C overnight with gentle shaking. 5% of input was stored prior to the de-crosslinking procedure. 30μl Protein-G magnetic beads (Thermo Fisher Scientific, 01134323) was used for subsequent pull-down of antibody-chromatin complex by incubatioin for 2 hours at 4°C with gentle shaking. The beads were washed with following buffers for 2 times each: IP buffer (0.1% SDS, 1% Triton X-100, 1mM EDTA, 150mM NaCl, 10mM Tris-HCl pH 8.0), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8.0), LiCl Wash Buffer (250mM LiCl, 1% NP-40, 2mM EDTA, 10mM Tris-HCl pH 8.0), and TE buffer+50mM NaCl (1mM EDTA, 50mM NaCl, 10mM Tris-HCl pH 8.0) 1 times. DNA was eluted with Elution Buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0) at 65℃ for 30 minutes with shaking at 1,400 rpm. The supernatant was then collected and incubated at 65°C for overnight to reverse-crosslink the DNA. The day after, the enriched DNA was treated with 4 µL of 20 mg/mL RNase at 37 °C for 2 h and 4 µL of 20 mg/mL Proteinase K (MIKX, FZ690) at 55°C for 2h. The immunoprecipitation DNA was purified by phenol-chloroform-isoamyl alcohol (Solarbio, P1012-100), washed with ethanol, eluted in nuclease-free water, and used for subsequent experiments. The following antibodies were used in ChIP: H3K4me1 (Abcam, ab8895), H3K4me3 (Abcam, ab8580)
Sequencing libraries were constructed and sequenced by the Novogene Bioinformatics Institute (Novogene, Beijing, China).

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: LSD1_NCM460_OE_H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: LSD1_NCM460_OE_input

value: input


title: LSD1_NCM460_NC_H3K4me3


title: LSD1_NCM460_NC_H3K4me1


title: LSD1_NCM460_NC_input


title: PL.DB_20_2

value: diabetic sample (yellow white)

value: eyedrops with vehicle treatment


title: LSD1_HCT116_KO_H3K4me3_rep2


title: LSD1_HCT116_KO_input_rep2


title: LSD1_HCT116_KO_H3K4me3_rep1


title: PL.DB_16_2

value: neuroretinal homogenate


title: CTL_6_2

value: control non diabetic sample (yellow white)


title: LSD1_HCT116_KO_H3K4me1_rep2


title: PL.DB_14_1


title: LSD1_HCT116_KO_input_rep1


title: LSD1_HCT116_KO_H3K4me1_rep1


title: PL.DB_18_2


title: PL.DB_15_1


title: PL.DB_17_2


title: CTL_5_1

value: control non-treatment


title: PL.DB_13_1


title: PL.DB_11_1


title: PL.DB_19_2


title: SIT.DB_8_2

value: eyedrops with sita treatment


title: SIT.DB_10_2


title: SIT.DB_9_2


title: LSD1_HCT116_WT_H3K4me3_rep1

value: colorectal cancer cell line


title: LSD1_HCT116_WT_H3K4me1_rep1

value: wild-type


title: LSD1_HCT116_WT_H3K4me1_rep2


title: LSD1_HCT116_WT_input_rep2


title: LSD1_HCT116_WT_rep1

data_processing:
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Filter sequencing adapters and low-quality reads using Trimmomatic (v0.39).
The clean reads were mapping to the GENCODE reference trancriptome (GRCh38 v36 release) and quantifying with Salmon (v1.4.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: polyA RNA

extract_protocol:
Cells were used to extract the total RNA using the Total RNA Extraction Kit (Omega).
In brief, a total of 1ug RNA per sample was used as input material, and then sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. All libraries were constructed using the TruSeq SBS v3-HS kit before sequencing to investigate the global transcriptome of the control group using Illumina HiSeq 2500 (Illumina, Inc.).


title: LSD1_HCT116_KO_rep3

value: LSD1 knockout


title: LSD1_HCT116_WT_rep3


title: CTL_2_1


title: LSD1_HCT116_WT_H3K4me3_rep2


title: SIT.DB_7_2


title: HCCLM3 cells, TGF-β1, 4 Hours

city: Nanchang

first: Xiaohua

last: Yan

address: No. 1299, Xuefu Avenue, Honggutan

institute: Nanchang University

data_processing:
Raw single end reads were firstly trimmed of the first 13 bp from each end and mapped to the human genome (hg38) with Tophat2 (v2.1.1).
Gene expression level was estimated and normalized with Cufflinks (v2.2.1) into an FPKM matrix using default parameters for the annotation GTF file downloaded from GENCODE (v24).
Differentially expressed genes (DEGs) were generated with Cuffdiff (v1.3.0) with p-value <0.05, and filtered by a Fold change ≥1.5 or ≤0.6.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: HCCLM3 cells

growth_protocol: MHCC97H/MHCC97L/HCCLM3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method
RNA libraries were prepared for sequencing using standard IIIumina proticols

treatment_protocol: MHCC97H, MHCC97L and HCCLM3 cell lines were treated with 2.5 ng/mL TGF-β1 ligand for 4 h

value: HCCLM3 cells

value: human hepatocellular carcinoma

value: 2.5 ng/mL TGF-β1 ligand for 4 h


title: A375 96h Rep1

city: Paris

first: annie

last: dutriaux

address: 15 rue Hélène Brion

department: Institut Jacques Monod

country: France

institute: Universite Paris Cite

description:
melanoma cells
Ct A375_003

data_processing: Ctvalues were generated by Roche Light Cycler 480 system software

label: SYBR Green

source_name: A375M cells

growth_protocol: Cells were grown in DMEM/F12 Glutamax supplemented with antibiotic penicilin streptomycin and 10 % SVF for 24h, others were left for additional 72h

extract_protocol: RNA extraction using Macherey Nagel purification protocoland reagents

tag: sample type


title: SIT.DB_4_1


title: SIT.DB_5_1


title: SIT.DB_1_1


title: SIT.DB_2_1


title: LSD1_HCT116_WT_input_rep1


title: LSD1_HCT116_KO_rep2


title: A375 24h Rep2

description:
melanoma cells
Ct A375_002


title: A375 24h Rep1

description:
melanoma cells
Ct A375_001


title: SIT.DB_3_1


title: SIT.DB_6_2


title: HCCLM3 cells, Control, 4 Hours

value: control 4hrs


title: FO1 96h Rep2

description:
melanoma cells
Ct FO1_008

source_name: FO1 cells

value: FO1 96h


title: LSD1_HCT116_WT_rep2


title: FO1 96h Rep1

description:
melanoma cells
Ct FO1_007


title: MHCC97H cells, Control, 4 Hours

source_name: MHCC97H cells

value: MHCC97H cells


title: FO1 24h Rep1

description:
melanoma cells
Ct FO1_005

value: FO1 24h


title: FO1 24h Rep2

description:
melanoma cells
Ct FO1_006


title: A375 96h Rep2

description:
melanoma cells
Ct A375_004


title: MHCC97H cells, TGF-β1, 4 Hours


title: LSD1_HCT116_KO_rep1


title: Day16_AM_diff_bulk_RNAseq_rep2

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: UW Medicine at South Lake Union, 850 Republican Street

department: Department of Biochemistry

institute: University of Washington

data_processing:
All libraries were sequenced on one NovaSeq platform (Illumina). The recipe used was: read 1: 34 cycles, read 2: 100 cycles, index 1: 10 cycles, index 2: 10 cycles. Base calls, downstream sequence processing and single-cell digital-expression matrix generation steps were similar to what was described in sci-RNA-seq3 paper17. STAR v.2.5.2b54 aligner used with default settings and gene annotations (GRCh38-primary-assembly, gencode.v27). Uniquely mapping reads were extracted, and duplicates were removed using the UMI sequence, reverse transcription index, hairpin ligation adaptor index and read 2 end-coordinate (that is, reads with identical UMI, reverse transcription index, ligation adaptor index and tagmentation site were considered duplicates).
All low-quality reads were removed from the data (including jaws, tooth germs and salivary glands samples from all time points) by setting UMI cutoff to 100 and removing all mitochondrial reads. Following Monocle3 workflow, data underwent normalization by size factor, preprocessing, dimension reduction (UMAP algorithm), and unsupervised graph-based clustering analysis (Leiden Algorithm). Certain clusters from the initial analysis were selected for further sub-clustering, and the previous analysis repeated. Pseudotime analysis also was done with Monocle3 following the default workflow, which include learning the graph, ordering the cells, and plotting the trajectory over UMAP. Mutual nearest neighbors (MNNs) algorithm was used for patch effect correction only between day10 differentiation sample and day16 sample. PanglaoDB, a curated single cell gene expression database was utilized to explore the consensus of cell type markers used across publicly available single cell datasets.
Genome_build: GRCh38-primary-assembly, gencode.v27
Supplementary_files_format_and_content: processed files contain cluster annotations, gene annotations in csv fromat. And the count matrix is in MatrixMarket format.

source_name: Induced pluripotent stem cells

growth_protocol: cells were grown in mTeSR1 stem cell media

extract_protocol:
Frozen tissues were carefully transferred to a stack of chilled aluminum foil kept on dry ice to prevent thawing. The folded foil encapsulating the tissues were placed on a block of dry ice and the foil was pounded with a pestle to pulverize the tissues into powder. 1mL of lysis buffer that contains nuclei buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH 7.4), 0.1% IGEPAL CA-630, 1% SUPERase In RNase inhibitor (20 U/μL, Thermo), and 1% BSA (20 mg/mL, NEB) were added onto the tissue powder and transferred to a 1.5mL tubes. Samples were incubated in the lysis buffer for 1 hour on ice. The samples were pipetted up and down with pre-cut 1000uL pipette tip to further disassociate the tissue. The dissociated tissues were passed through 70 um cell strainers (Corning) into a 50mL conical tube. The strainers were rinsed with lysis buffer to minimize nuclei loss. The samples were centrifuged to pellet the nuclei at 500g for 5 minutes at 4°C and the supernatant was discarded. The samples resuspended again in 1ml lysis buffer, transferred into new 15mL tubes, pelleted again and supernatant was discarded. The pellets were resuspended in 50ul of nuclei buffer, and 5 mL of 4% Paraformaldehyde (PFA) (EMS) diluted in RNase free PBS, was added to fix the nuclei for 15 minutes on ice. The tubes were flicked gently every 5 minutes to reduce clumping of nuclei. The fixed nuclei were pelleted at 500g for 3 minutes at 4°C and the PFA waste was discarded. The pelleted nuclei washed in nuclei wash buffer (cell lysis buffer without IGEPAL) and then centrifuged again at 500g for 5 minutes 4°C, and the supernatant was discarded. Finally, the pellets were resuspended again in nuclei wash buffer and then flash-frozen in liquid nitrogen before storing in –80°C.
For nuclei extraction from the differentiation culture, the cells were treated with StemPro Accutase (Theromo, #A1110501) for 7min to detach the cells and transfer them into 15mL tube, then incubated in trypsin (Theromo, #25300054) for another 7min to prevent re-clumping. The cells were span down to remove trypsin after inactivation with more media. The pellet was treated with nuclei lysis buffer and the same steps for nuclei extraction protocol were followed.
Single-cell combinatorial-indexing RNA-sequencing (sci-RNA-seq) protocol is described previously and more details can be found in this link (https://github.com/bbi-lab/). sci-RNA-seq relies on the following steps, (i) thawed nuclei were permeabilized with 0.2% TritonX-100 (Sigma, #T9284) (in nuclei wash buffer) for 3 min on ice, and briefly sonicated to reduce nuclei clumping; (ii) nuclei distributed across 96-well plates; (iii) A first molecular index is introduced to the mRNA of cells within each well, with in situ reverse transcription (RT) incorporating the unique molecular identifiers (UMIs); (iv) All cells were pooled and redistributed to multiple 96-well plates in limiting numbers (e.g., 10 to 100 per well) and a second molecular index is introduced by hairpin ligation;(v) Second strand synthesis, tagmentation, purification and indexed PCR; (vi) Library purification and sequencing is performed.

treatment_protocol: Briefly, hiPSCs (WTC-11 human induced pluripotent stem cells) (Coriell, #GM25256) were seeded on 12-well plates coated with growth factor-reduced Matrigel (Corning) and cultured in mTeSR1 stem cell medium (stemcell, #85850) until cells reach confluency with medium changes daily. On the first day of differentiation (deemed Day 0), stem cell media is replaced with a base media consisted of RPMI 1640 Medium (Thermo, #11875093) mixed with EpiLife (Thermo, #MEPI500CA) at 1:1 ratio, supplemented with 0.1x supplement S7 (Thermo, #S0175), 0.1uM β-mercaptoethanol (BME) (Sigma, #M7522) and 400um smoothened agonist (SAG) (Selleckchem, # S7779). At day 3 of differentiation 150pM of bone morphogenic protein-4 (BMP4) (rndsystems, #314-BP-010) is continuously added daily till day 7. At day 8, the base media is supplemented with 1uM of BMP-I inhibitor (LDN-193189)(Tocris, # 6053), 5uM of GSK3-Inhibitor (CHIR99021) (Selleckchem, # 4423), 500pM epidermal growth factor (EGF) (rndsystems, #236-EG) and 3.5μM of Neurotrophin-4 (NT4) (rndsystems, #268-N4). The cultures were then harvested at day 10 at an oral epithelium stage, or extended to day 16 by adding 300pM BMP4, and 800nM transforming growth factor beta 1(TGF-β1) (rndsystems, #7754-BH) for the pre-ameloblast stage at day16.

value: Induced pluripotent stem cell

tag: age group

value: Ameloblast differentation protocol

tag: experiment type

value: bulk RNA-seq


title: MHCC97L cells, Control, 4 Hours

source_name: MHCC97L cells

value: MHCC97L cells

tag: cell type


title: Day16_AM_diff_bulk_RNAseq_rep1


title: Day0_undifferentiated_iPSCs_bulk_RNAseq_rep2

value: No treatment


title: MicroC, C42B, rep8, S2

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description: Micro-C in C42B cells

data_processing:
library strategy: Micro-C
Micro-C data were first aligned with BWA MEM v0.7.17, and the aligned reads were paired, sorted and filtered with Pairtoolsv0.3.0 and converted into pairs files.
Resulting pairs files were used to normalize and generate matrix files with Juicertools for Juicer(v1.5).
Assembly: hg38
Supplementary files format and content: .hic

extract_protocol:
The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) Cells were grown at 37 °C in 5% CO2. It was grown in RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma.
1 x 10^6 cells were harvested, and were cross-linked with formaldehyde for 10 minutes at room temperature. Cells were digested with MNase Enzyme Mix and were lysed with 20% SDS. Lysate was mixed with Chromatin Capture Beads to bind chromatin and incubated at room temperature for 10 minutes. End Polishing Master Mix was added lysate and incubated for 30 minutes at 22*C and 30 minutes at 65*C to end polish. For ligation, 50ul of Bridge Ligation Mix and Bridge Ligase were added and incubated at 22ºC for 30 minutes, and 50ul of Intra-aggregate Ligation Buffer and Intra-aggregate Ligation Enzyme Mix were added and incubated at 22ºC for 1 hours. DNA were isolated by reverse-crosslinking with Proteinase K and Crosslink Reversal Buffer, and incubating at 55ºC for 15 minutes, 68ºC for 45 minutes. DNA was then purified. For library preparation, purified DNA was added with End Repair Master Mix and incubated at 20ºC for 30 minutes and 65ºC for 30 minutes for end repair. adaptor for Illumina, ligation enzyme mix and ligation enhancer were added for adapter ligation, then DNA was purified. Adaptor-ligated DNA was then washed and captured with Streptadvidin beads. PCR was performed, and size range between 350-1,000bp was selected for the library. Prepared libraries were then sequenced with Illumina sequencers in pair-end mode.

value: Human prostate cancer cells


title: MHCC97L cells, TGF-β1, 4 Hours


title: TRF_DDP2

city: chongqing

first: Qianyao

last: Chen

address: No.1 Yixueyuan Rd, Yuzhong District

institute: chongqing medical university

data_processing:
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: Human NCBI genome build 38
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

extract_protocol:
The TRIzol reagent (Takara, Japan) was used to extract RNA from A549 tumor cells using the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cisplatin-resistant human lung adenocarcinoma cell


title: MicroC, C42B, rep5, S2

description: Micro-C in C42B cells

growth_protocol: RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin.


title: TRF_DDP3


title: DDP3


title: TRF2


title: NOMe-seq, C42B

description: NOMe-seq in C42B cells

data_processing:
library strategy: NOMe-seq
The raw sequencing data were aligned to hg38 using biscuit to get vcf and bedGraph file with pileup and vcf2bed functions respectively.
The bedGraph file is then transferred to BigWig using bedGraphToBigWig in UCSC toolkits.
Assembly: hg38
Supplementary files format and content: .bw

extract_protocol:
The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) Cells were grown at 37 °C in 5% CO2. It was grown in RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma.
First chromatin was treated with M.CviPI methyltransferase to methylate GpC dinucleotides. After purifying M.CviPI-treated DNA, sonication was performed. Bisulfite treatment was then performed to convert all unmethylated Cs to Ts. Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit and then sequenced with Illumina HiSeq in paired-end mode


title: TRF_DDP1


title: Cow 3, 24 hours post DEX

city: Davis

first: Russell

last: Hovey

address: 1 Shields Ave

department: Animal Science

institute: University of California Davis

data_processing:
Raw reads were processed with HTStream (https://ibest.github.io/HTStream/) to remove adapter and low-quality sequences. On average, 0.2% of reads were removed.
The trimmed reads were aligned to the Bos taurus UMD3.1 genome with Ensembl gene annotation release 93 using the aligner STAR v. 2.6.0c (Dobin et al., 2013) to generate raw counts per gene
Assembly: Bos taurus UMD3.1 genome Ensembl gene annotation release 93

organism: Bos taurus

source_name: Mammary gland

growth_protocol: Four non-pregnant Holstein cows were used (average 738.2 kg, range 648-838 kg) in their second lactation (average 55 DIM, range 40-64 DIM).

extract_protocol:
Total RNA was isolated from biopsy cores (~10-50 mg tissue) from 4 cows at 0, 12, and 24 h, and from 3 cows at 72 h, using TRIzol (Invitrogen, ThermoFisher, Waltham, MA) according to the manufacturer’s instructions. The integrity of the total RNA and its yield were confirmed by formaldehyde gel electrophoresis with staining (SybrSafe, Invitrogen) and UV visualization, and spectrophotometry (Nanodrop, ThermoScientific), respectively. Total RNA (5 μg) was treated with DNaseI (Zymo Research, Irvine, CA) and analyzed for quality (Experion RNA StdSens, BioRad, Hercules, CA), where all samples had an RNA integrity value greater than 8.3.
Gene expression profiling was performed using 3'Tag-RNA-Seq. Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the manufacturer’s recommendations, using 700 ng input RNA and 13 cycles of PCR for final library amplification. Fragment size distribution of the libraries was verified via microcapillary gel electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The library masses were quantified on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. The final pool was treated with Exonuclease VII followed by bead clean-up to remove free primer. The pool was quantified by qPCR with a Kapa Library Quant kit (Kapa Biosystems, loaction).

treatment_protocol: The study period included an 8 d acclimation prior to the single administration of DEX on day 9. On day 9, each cow was administered a single injection of DEX (40 mg, IM, VetOne, Boise, Idaho) between 19:00 and 21:30, immediately after the first biopsy. One or two cores of tissue were collected from the mammary gland using a needle biopsy tool (16 ga. Magnum, Bard, Covington, GA) that was inserted through a small incision in the skin following local anesthesia (0.125% bupivacaine, SC). The left rear QTR was designated as QTR1, the left front was QTR2, the left right was QTR3, and the right rear was QTR4. 0 h post DEX biopsies were from QTR1, 12 h post DEX were from QTR2, 24 h post DEX were from QTR3, 72 h post DEX were from QTR4. Tissue cores were flash frozen in liquid nitrogen and stored at -80oC. Cows received prophylactic ampicillin (Polyflex, Boehringer Ingelheim, IM) for 3 d spanning the biopsy period.

value: Mammary gland

value: Dexamethasone

value: 24 hours

tag: genotype

value: Cow 3


title: MicroC, C42B, rep6, S2

description: Micro-C in C42B cells


title: DDP1


title: TRF3


title: Cow 3, 12 hours post DEX

tag: time

value: 12 hours


title: Cow 4, 72 hours post DEX

value: 72 hours

value: Cow 4


title: TRF1


title: MicroC, C42B, rep7, S2

description: Micro-C in C42B cells


title: Day0_undifferentiated_iPSCs_bulk_RNAseq_rep1


title: Cow 4, 12 hours post DEX


title: Cow 3, 72 hours post DEX


title: CON3


title: MicroC, C42B, rep3, S2

description: Micro-C in C42B cells


title: MicroC, C42B, rep4, S2

description: Micro-C in C42B cells


title: Cow 4, 24 hours post DEX


title: MicroC, C42B, rep2, S2

description: Micro-C in C42B cells


title: Cow 2, 12 hours post DEX

value: Cow 2


title: MicroC, C42B, rep8, S1

description: Micro-C in C42B cells


title: Cow 2, 72 hours post DEX


title: Cow 2, 0 hours post DEX

value: 0 hours


title: Cow 3, 0 hours post DEX


title: Cow 4, 0 hours post DEX


title: Cow 1, 12 hours post DEX

value: Cow 1


title: iCAR, Propylparaben_1uM, 6h, rep3, H03

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T9_D3

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

source_name: heart

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: heart

value: iCAR

value: Cardiomyocytes

value: 6h exposure of chemical


title: Cow 1, 24 hours post DEX


title: Cow 2, 24 hours post DEX


title: DDP2


title: CON2


title: MicroC, C42B, rep5, S1

description: Micro-C in C42B cells


title: MicroC, C42B, rep6, S1

description: Micro-C in C42B cells


title: 5697_NB [Re-analysis of GSM4943678]

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

institute: University of Alberta

description: Re-analysis of GSM4943678

data_processing:
The raw reads were concatenated as there were two files for each read (run on seperate lanes), then trimmed so those samples with quality scores < 20 were filtered, and  mapped to bovine genome (ARS-UCD1.2.98;https://bovinegenome.elsiklab.missouri.edu/downloads/ARS-UCD1.2 ) using the STAR software. The number of reads uniquely aligned to each gene was calculated using FeatureCounts.
Assembly: ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood

extract_protocol:
Total RNA was extracted from Tempus tubes using a Preserved Blood RNA Purification Kit (Norgen Biotek Corp.,Thorlord ON, ), and the Nanodrop 1000 (Thermo Scientifc, Willmingotn, DE, USA) and 2200 RNA Screentape Tapestation System (Agilent Technologies Inc, Cedar Creek, TX) were used respectively to quantify and measure the RNA integrity Number for each sample.
All samples had RIN values above 8,0 and were all used for library construction and RNA-seq was performed on the Novaseq platform running 50 samples per lane on 2 lanes.
cDNA libraries were prepared for sequencing for each individual animal from the high-quality RNA using the TruSeq RNA Library Preparation kit v2 (Illumina, San Diego, CA, United States) and the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs Ltd., Whitby, ON, Canada).

tag: disease status

value: Healthy penmate


title: CON1


title: 5452_NB [Re-analysis of GSM4943676]

description: Re-analysis of GSM4943676


title: 5528_NB [Re-analysis of GSM4943677]

description: Re-analysis of GSM4943677


title: MicroC, C42B, rep7, S1

description: Micro-C in C42B cells

value: Human prostate cancer cells


title: MicroC, C42B, rep1, S2

description: Micro-C in C42B cells


title: U6450_NB

value: BRD


title: Y3551_NB


title: U6325_NB


title: iCAR, Propylparaben_500uM, 6h, rep3, E09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T9_D1


title: MicroC, C42B, rep4, S1

description: Micro-C in C42B cells


title: iCAR, Methylparaben_1uM, 6h, rep3, F04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T8_D3


title: U6623_NB


title: iCAR, Methylparaben_50uM, 6h, rep3, E12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T8_D2


title: MicroC, C42B, rep2, S1

description: Micro-C in C42B cells


title: iCAR, Propylparaben_50uM, 6h, rep3, A08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T9_D2


title: Cow 1, 0 hours post DEX

value: Mammary gland


title: MicroC, C42B, rep1, S1

description: Micro-C in C42B cells


title: iCAR, Methylparaben_500uM, 6h, rep3, D08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T8_D1


title: 5783_NB [Re-analysis of GSM4943674]

description: Re-analysis of GSM4943674


title: 5564_NB [Re-analysis of GSM4943673]

description: Re-analysis of GSM4943673


title: C42B, HiC, rep3

description: Hi-C in C42B cells

data_processing:
Hi-C data were first aligned with BWA MEM v0.7.17, and the aligned reads were paired, sorted and filtered with Pairtoolsv0.3.0 and converted into pairs files.
Resulting pairs files were used to normalize and generate matrix files with Juicertools for Juicer(v1.5).
Assembly: hg38
Supplementary files format and content: .hic

extract_protocol:
The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) Cells were grown at 37 °C in 5% CO2. It was grown in RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma.
In situ Hi-C was performed in duplicate and 5 x 10^6 cells were used for each experiment. MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl). In situ Hi-C ibraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. Library was amplified with PCR and then sequenced using Illumina HiSeq 2000.


title: iCAR, Ethylparaben_1uM, 6h, rep3, D03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T6_D3


title: 5638_NB [Re-analysis of GSM4943675]

description: Re-analysis of GSM4943675


title: 9357_NB [Re-analysis of GSM4943671]

description: Re-analysis of GSM4943671


title: 5291_NB [Re-analysis of GSM4943669]

description: Re-analysis of GSM4943669


title: 5921_NB [Re-analysis of GSM4943668]

description: Re-analysis of GSM4943668


title: C42B, HiC, rep1

description: Hi-C in C42B cells


title: 5644_NB [Re-analysis of GSM4943672]

description: Re-analysis of GSM4943672


title: MicroC, C42B, rep3, S1

description: Micro-C in C42B cells


title: iCAR, Ethylparaben_500uM, 6h, rep3, H09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T6_D1


title: 5764_NB [Re-analysis of GSM4943667]

description: Re-analysis of GSM4943667


title: 9909_NB [Re-analysis of GSM4943665]

description: Re-analysis of GSM4943665


title: 9313_NB [Re-analysis of GSM4943666]

description: Re-analysis of GSM4943666


title: 9819_NB [Re-analysis of GSM4943664]

description: Re-analysis of GSM4943664


title: Promoter Capture Micro-C, C42B, rep8

description: Promoter Capture Micro-C in C42B cells

data_processing:
library strategy: Capture Micro-C
Micro-C data were first aligned with BWA MEM v0.7.17, and the aligned reads were paired, sorted and filtered with Pairtoolsv0.3.0 and converted into pairs files.
Resulting pairs files were used to normalize and generate matrix files with Juicertools for Juicer(v1.5).
Assembly: hg38
Supplementary files format and content: .hic

extract_protocol:
The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) Cells were grown at 37 °C in 5% CO2. It was grown in RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma.
1 x 10^6 cells were harvested, and were cross-linked with formaldehyde for 10 minutes at room temperature. Cells were digested with MNase Enzyme Mix and were lysed with 20% SDS. Lysate was mixed with Chromatin Capture Beads to bind chromatin and incubated at room temperature for 10 minutes. End Polishing Master Mix was added lysate and incubated for 30 minutes at 22*C and 30 minutes at 65*C to end polish. For ligation, 50ul of Bridge Ligation Mix and Bridge Ligase were added and incubated at 22ºC for 30 minutes, and 50ul of Intra-aggregate Ligation Buffer and Intra-aggregate Ligation Enzyme Mix were added and incubated at 22ºC for 1 hours. DNA were isolated by reverse-crosslinking with Proteinase K and Crosslink Reversal Buffer, and incubating at 55ºC for 15 minutes, 68ºC for 45 minutes. DNA was then purified. For library preparation, purified DNA was added with End Repair Master Mix and incubated at 20ºC for 30 minutes and 65ºC for 30 minutes for end repair. adaptor for Illumina, ligation enzyme mix and ligation enhancer were added for adapter ligation, then DNA was purified. Adaptor-ligated DNA was then washed and captured with Streptadvidin beads. PCR was performed, and size range between 350-1,000bp was selected for the library. Prepared libraries were then sequenced with Illumina sequencers in pair-end mode. Micro-C libraries were pooled for hybridization reactions. For hybridization reaction, the probe solution was first heated to 95°C for 2 minutes in a thermal cycler with a lid at 105°C. Library was heated in similar way for 5 minutes. After cooling in ice for 5 minutes, and equilibrating to room temperature for 5 minutes, the probe solution was added to the library. Hybridization Enhancer was then added and the mixed solution was incubated at 70° for 16 hours in a thermal cycler with the lid at 85°C. After hybridization steps, the hybridized targets were washed and captured with Streptavidin beads, amplified with PCR, and then purified. It was sequenced on Illumina platform in pair-end mode.


title: iCAR, Butylparaben_1uM, 6h, rep3, A10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T4_D3


title: Promoter Capture Micro-C, C42B, rep7

description: Promoter Capture Micro-C in C42B cells


title: 9535_NB [Re-analysis of GSM4943663]

description: Re-analysis of GSM4943663


title: iCAR, Butylparaben_50uM, 6h, rep3, F08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T4_D2


title: 9518_NB [Re-analysis of GSM4943661]

description: Re-analysis of GSM4943661


title: Promoter Capture Micro-C, C42B, rep6

description: Promoter Capture Micro-C in C42B cells


title: iCAR, Butylparaben_500uM, 6h, rep3, F10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T4_D1


title: 5700_BRD [Re-analysis of GSM4943662]

description: Re-analysis of GSM4943662


title: iCAR, theophylline_50uM, 6h, rep3, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T27_D3


title: 9362_NB [Re-analysis of GSM4943670]

description: Re-analysis of GSM4943670


title: iCAR, Ethylparaben_50uM, 6h, rep3, F12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T6_D2


title: 9887_BRD [Re-analysis of GSM4943659]

description: Re-analysis of GSM4943659


title: 9777_BRD [Re-analysis of GSM4943658]

description: Re-analysis of GSM4943658


title: Promoter Capture Micro-C, C42B, rep5

description: Promoter Capture Micro-C in C42B cells


title: 5080_BRD [Re-analysis of GSM4943656]

description: Re-analysis of GSM4943656


title: C42B, HiC, rep2

description: Hi-C in C42B cells


title: Promoter Capture Micro-C, C42B, rep3

description: Promoter Capture Micro-C in C42B cells


title: 9436_NB [Re-analysis of GSM4943660]

description: Re-analysis of GSM4943660


title: iCAR, theobromine_50uM, 6h, rep3, C04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T26_D3


title: Promoter Capture Micro-C, C42B, rep1

description: Promoter Capture Micro-C in C42B cells


title: 9900_BRD [Re-analysis of GSM4943657]

description: Re-analysis of GSM4943657


title: Promoter Capture Micro-C, C42B, rep4

description: Promoter Capture Micro-C in C42B cells


title: 9332_BRD [Re-analysis of GSM4943651]

description: Re-analysis of GSM4943651


title: iCAR, theophylline_1000uM, 6h, rep3, C05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T27_D1


title: 5725_BRD [Re-analysis of GSM4943655]

description: Re-analysis of GSM4943655


title: 5242_BRD [Re-analysis of GSM4943654]

description: Re-analysis of GSM4943654


title: iCAR, theobromine_1000uM, 6h, rep3, D09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T26_D1


title: Promoter Capture Micro-C, C42B, rep2

description: Promoter Capture Micro-C in C42B cells


title: 9830_BRD [Re-analysis of GSM4943649]

description: Re-analysis of GSM4943649


title: 5696_BRD [Re-analysis of GSM4943653]

description: Re-analysis of GSM4943653


title: 9986_BRD [Re-analysis of GSM4943648]

description: Re-analysis of GSM4943648


title: 5913_BRD [Re-analysis of GSM4943652]

description: Re-analysis of GSM4943652


title: iCAR, theophylline_500uM, 6h, rep3, D06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T27_D2


title: 9877_BRD [Re-analysis of GSM4943650]

description: Re-analysis of GSM4943650


title: KYSE150 cells, CDCA7SH_2 cells

city: Taiyuan

first: Hongyi

last: Li

address: Xinjian Southroad 56#

institute: Shanxi Medical University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routinesfor determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of  differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species.Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

growth_protocol: KYSE150 and KYSE180 esophageal squamous cell carcinoma cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
The ESCC cells were harvested by digesting with trypsin. The harvested cells were placed on ice and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: KYSE150 cells, CDCA7SH_3 cells

value: esophageal squamous cell carcinoma cells


title: iCAR, paraxanthine_50uM, 6h, rep3, D04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T24_D3


title: KYSE150 cells, CDCA7SH_1 cells


title: iCAR, theobromine_500uM, 6h, rep3, F07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T26_D2


title: 5972_BRD [Re-analysis of GSM4943646]

description: Re-analysis of GSM4943646


title: 9556_BRD [Re-analysis of GSM4943647]

description: Re-analysis of GSM4943647


title: KYSE150_3 cells, Native Control

value: WT


title: 9836_BRD [Re-analysis of GSM4943644]

description: Re-analysis of GSM4943644


title: iCAR, paraxanthine_1000uM, 6h, rep3, A03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T24_D1


title: 5321_BRD [Re-analysis of GSM4943645]

description: Re-analysis of GSM4943645


title: iCAR, 4-Hydroxybenzoic acid_1uM, 6h, rep3, H12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T17_D3


title: 9627_BRD [Re-analysis of GSM4943643]

description: Re-analysis of GSM4943643


title: KYSE150_2 cells, Native Control


title: KYSE150_1 cells, Native Control


title: 9504_BRD [Re-analysis of GSM4943640]

description: Re-analysis of GSM4943640


title: 5979_BRD [Re-analysis of GSM4943639]

description: Re-analysis of GSM4943639


title: iCAR, 4-Hydroxybenzoic acid_50uM, 6h, rep3, A09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T17_D2


title: 5994_BRD [Re-analysis of GSM4943641]

description: Re-analysis of GSM4943641


title: iCAR, 4-Hydroxybenzoic acid_500uM, 6h, rep3, G06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T17_D1


title: 5327_BRD [Re-analysis of GSM4943638]

description: Re-analysis of GSM4943638


title: KYSE180 CDCA7EXP_3 cells

value: CDCA7 overexpression


title: 5969_BRD [Re-analysis of GSM4943637]

description: Re-analysis of GSM4943637


title: 9497_BRD [Re-analysis of GSM4943636]

description: Re-analysis of GSM4943636


title: iCAR, Caffeine_50uM, 6h, rep3, B11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T11_D3


title: KYSE180 CDCA7EXP_1 cells


title: KYSE180 CDCA7EXP_2 cells


title: iCAR, Caffeine_500uM, 6h, rep3, E07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T11_D2


title: KYSE180_3 cells, Native Control


title: iCAR, Caffeine_1000uM, 6h, rep3, A02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T11_D1


title: KYSE180_2 cells, Native Control


title: HDP-005589

city: Lausanne

first: Jean-David

middle: Horacio

last: Morel

state: Vaud

address: Station 15

department: SV/IBI

country: Switzerland

institute: Ecole Ploytechnique Fédérale de Lausanne

description:
A/J  Folic Acid  Week 2
countMatrix_pass.csv

data_processing:
RNA sequencing was performed on a BGISEQ-500. FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed. The STAR aligner48 was used for mapping the RNA-Seq data to the C57BL/6J reference genome and determining gene counts. We did not use distinct genomes for each strain due to various genome quality differences between mouse strains that could create bigger artefacts than mapping all strains on the same reference genome in terms of mapping efficiency and gene count estimation.
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles FASTA_FILE.fa --sjdbGTFfile GTF_FILE.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
Assembly: rnm10
Supplementary files format and content: tab-delimited text file includes mapped read counts per feature, normalized with the TMM (Trimmed Mean of M-values) method (generated by STAR - per strand and combined strands)
Supplementary files format and content: EdgeR-generated fold changes and adj.pvalues for strain by strain comparisons of diet effects, and comparisons between strains.

source_name: kidney

growth_protocol: Mouse strains were imported from Charles River and bred at the École Polytechnique Fédérale de Lausanne (EPFL) animal facility for more than two generations before incorporation into the study. All research was approved by the Swiss cantonal veterinary authorities of Vaud under license 30759.The mice were fed a chow diet (Harlan 2018 (6% kCal of fat, 20% kCal of protein, and 74% kCal of carbohydrates). Mice were housed at 2-4 animals per cage under 12 hours light/dark cycle, with ad libitum access to food and water at all times. Body weight was measured weekly from 8 weeks of age until killing. We examined 7 mouse inbred strains.

extract_protocol:
Mice were sacrificed at week 1,2 and 6 (folic acid treated) or weeks 2 and 6 (controls). The sacrifices took place from 8:30 a.m. until 12 a.m., with isoflurane anesthesia followed by a complete blood draw (~1 mL) from the vena cava, followed by perfusion with phosphate-buffered saline. The left kidney and other organs were flash-frozen in liquid nitrogen and stored at -80°C until processing.For mRNA, liver tissue were crushed in liquid nitrogen and then 10 mg of tissues were suspended in TRIzol (Invitrogen) and homogenized with stainless steel beads using a TissueLyser II (Qiagen) at 30 Hz for 2 min. RNA was extracted and purified using Direct-zol-96 RNA kits (Zymo Research). mRNA concentration was measured for all samples. All samples passed a quality check of purity (NanoDrop) and fragmentation (FragmentAnalyzer).
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: At 9 weeks of age, 3 groups of mice were treated with 125mg/kg of folic acid in 3M sodium bicarbonate and two groups with bicarbonate alone (vehicle controls). Strains were entered into each group randomly, then observed daily to monitor their health.

value: kidney

tag: strain

value: A/J

value: Folic Acid

tag: timepoint

value: Week 2


title: HDP-005415

description:
A/J  Control  Week 2
countMatrix_pass.csv

value: Control


title: HDP-005592


title: HDP-005416


title: HDP-005414


title: HDP-005593


title: HDP-005370


title: 9499_BRD [Re-analysis of GSM4943642]

description: Re-analysis of GSM4943642


title: iCAR, DMSO, 6h, rep3, H08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-H08

value: vehicle control


title: KYSE180_1 cells, Native Control


title: iCAR, DMSO, 6h, rep3, F09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-F09

value: heart


title: HDP-005209

description:
PWK/PhJ  Folic Acid  Week 2
countMatrix_pass.csv

value: PWK/PhJ


title: HDP-005368


title: iCAR, DMSO, 6h, rep3, E05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-E05

value: iCAR

value: Cardiomyocytes


title: HDP-005200

description:
PWK/PhJ  Control  Week 2
countMatrix_pass.csv


title: HDP-005199


title: iCAR, DMSO, 6h, rep3, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-D10


title: HDP-005201


title: HDP-005190

description:
CAST/EiJ  Folic Acid  Week 2
countMatrix_pass.csv

value: CAST/EiJ


title: sV

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
A total of 15 libraries from NS animals (6 for Cow1, 4 for Cow2 and 5 for Cow3) and 30 from S animals (9 for Cow1, 6 for Cow2 and 15 for Cow3) were generated and prepared for 100bp paired-end sequencing on Illumina HiSeq 2000 and sequenced at 1/20th of a lane per sample.
Reads were trimmed in single-end mode, removing adapter read-through contamination as well as poor quality basecalls. In addition, the first 6bp (on the 5'-end) were clipped off to remove the bias introduced by the 6N pulldown oligos.
Trimmed reads were processed using Bismark v0.20.1 (Krueger and Andrews, 2011; parameters: --non_directional) and deduplicated; methylation calls of Read 1 and Read 2 were merged together and analysed using Seqmonk version 1.45.1.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Bismark CpG coverage report files (ending in .cov.gz) are tab-delimited, use 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

source_name: cow oocyte from hormonal stimulated ovary

growth_protocol: oocytes were developed in vivo and collected from preovulatory follicles

extract_protocol:
Oocytes were lysed in 5 µl of RLT Plus buffer (Qiagen, Cat. No 1053393) for 10 min at room temperature and bisulfite conversion was carried out directly on the cell lysate to minimise losses using standard manufacture kit (Zymo Research, D5020).
DNA was eluted in first strand synthesis mix containing oligos with Illumina adaptor sequence at the 5’ end and the random nucleotide sequence at the 3′ end to facilitate binding in all genomic locations
Libraries were purified with AMPure XP beads (Beckman Coulter, cat. no. A 63881) and amplified for 13 PCR cycles.

treatment_protocol: after collection of oocytes in non-treated animals, the same animals were superovulated by administrating GnRH (Dalmarelin®, Fatro, Barcelona, Spain – 25mg/mL, 2mL IM) and FSH/LH (Pluset, Calier, Barcelona, Spain - 500 UI FSHp 500IU LHp) as follows: time 0h GnRH administration; 36h, 3.5mL of FSH/LH (IM) and 4mL FSH/LH (SC) and 60h, 2.5mL of FSH/LH (IM)

value: hormonal stimulated ovary

value: Cow MII oocyte


title: sVI


title: HDP-005188

description:
CAST/EiJ  Control  Week 2
countMatrix_pass.csv


title: sVi


title: sVII


title: iCAR, DMSO, 6h, rep3, B06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-B06


title: iCAR, DMSO, 6h, rep3, D02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-D01


title: sVIII


title: HDP-005186


title: iCAR, DMSO, 6h, rep3, C07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-C07


title: HDP-005187


title: iCAR, DMSO, 6h, rep3, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-DMSO-A11


title: sT


title: HDP-005189


title: sP


title: HDP-005129

description:
C57BL/6J  Control  Week 2
countMatrix_pass.csv


title: iCAR, Propylparaben_50uM, 6h, rep2, H06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T9_D2

value: 6h exposure of chemical


title: HDP-005127


title: HDP-005126

description:
C57BL/6J  Folic Acid  Week 2
countMatrix_pass.csv


title: HDP-005081


title: HDP-005080


title: HDP-004989


title: HDP-004987


title: iCAR, paraxanthine_500uM, 6h, rep3, G09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW913D-T24_D2


title: iCAR, Propylparaben_500uM, 6h, rep2, F07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T9_D1


title: HDP-004988


title: HDP-005128


title: HDP-004986


title: sI


title: HDP-004765

description:
CAST/EiJ  Folic Acid  Week 6
countMatrix_pass.csv

value: Week 6


title: sII