title: PCI_TL3D replicate 1

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

description:
CY-H4
Replicate 1 of library PCI_TL3D

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Peniciullium citrinum with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Screening of differentially expressed genes in paired library (PCI_CK2D/PCI_TL2D; PCI_TL2D/PCI_TL3D). FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Assembly: Penecillium citrinum
Supplementary files format and content: Excel files, including Gene ID, annotation, FPKM values, log2(fold change), FDR-value, regulation (up or down) and significance (yes or no)  for the paired sample.

organism: Penicillium citrinum

source_name: Wild type

growth_protocol: Conidia suspension (100 ul,5X10^6 conidia ml-1) of P. citrinum were inoculated on the Czapek-Dox plates and incubated at 25 °C for 2 day. In addition, conidial suspension was inoculated on the flured tobacco leaves and incubated at 25 °C. At 2 and 3 days post inoculation, the leaves covered with mycelia were sampled for analyses.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates and leaves.

value: 3 days

value: mycelia


title: MYB131_B73

status: Public on May 05 2025

type: SRA

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

country: USA

institute: Rutgers University

library_source: genomic

data_processing:
Illumina reads were mapped using bowtie2 with default parameters. Mapped reads were filtered to retain MAPQ scores greater than 30 using samtools. Peaks were called using GEM3.0 with variable significance thresholds.
Assembly: B73v5 or Mo17_CAU1.0
Supplementary files format and content: narrowPeak format
Library strategy: DAP-seq

molecule: genomic DNA

organism: Zea mays subsp. mays

source_name: seedling leaf

extract_protocol:
genomic DNA was extracted from 14 day-old leaves
genomic DNA was fragmented to 200bp and subjected to standard Illumina library construction prior to incubation with in vitro expressed transcription factor

tag: tissue

value: seedling leaf

tag: genotype

tag: treatment

value: DAP-seq


title: PCI_TL2D replicate 1

country: China

description:
CY-H4
Replicate 1 of library PCI_TL2D

library_source: transcriptomic

molecule: total RNA

tag: time point

value: 2 days

tag: cell type


title: DD_BHLH92_BHLH125_B73

value: doubleDAP-seq


title: PCI_CK2D replicate 1

description:
CY-H4
Replicate 1 of library PCI_CK2D


title: WRKY11_B73


title: peanut-XN_SY01_P1_H06_180926B_SPRI_8_200507

type: genomic

city: Qingdao

first: jing

last: xu

address: 126 Wannianquan Road

institute: Shandong Peanut Research Institute

description:
XN_SY01_P1_H06_180926B_SPRI_8_200507
47K SNPs

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics process, and scanned using the Symbol® Cyclone™ M2000 Scanner.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console® (version 2.0). The raw data CEL files were typed using Axiom Analysis Suite 3.1.51, according to each site A set of indicators assigned to a specified type: PolyHighResolution, NoMinorHom,  MonoHighResolution, OTV,  CallRateBelowThreshold, Other.
Genotype Call (SNP call): AA, AB, BB, NC.

label: biotin

organism: Arachis hypogaea

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Peanuts were grown according to standard conditions

extract_protocol: Young healthy leaves from each accession were collected, with extraction of total genomic DNA via a Plant Genomic DNA Kit (Tiangen Biotech (Beijing) Co., Ltd.). The extracted DNA quality and concentration were determined via 0.8% agarose gel electrophoresis using standard lambda DNA and a NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Wilmington, DE, USA)

tag: tag

value: leaf


title: DD_BHLH61_BHLH125_B73


title: DD_BHLH52_BHLH125_B73


title: peanut-XN_SY01_P1_P24_180926B_SPRI_495_200507

description:
XN_SY01_P1_P24_180926B_SPRI_495_200507
47K SNPs


title: peanut-XN_SY01_P1_P22_180926B_SPRI_493_200507

description:
XN_SY01_P1_P22_180926B_SPRI_493_200507
47K SNPs


title: DD_BHLH135_BHLH125_B73


title: BHLH67_B73


title: BHLH61_B73


title: peanut-XN_SY01_P1_P20_180926B_SPRI_492_200507

description:
XN_SY01_P1_P20_180926B_SPRI_492_200507
47K SNPs


title: BHLH52_B73


title: peanut-XN_SY01_P1_P19_180926A_SPRI_433_200507

description:
XN_SY01_P1_P19_180926A_SPRI_433_200507
47K SNPs


title: PCI_TL3D replicate 2

description:
CY-H4
Replicate 2 of library PCI_TL3D


title: peanut-XN_SY01_P1_P21_180926A_SPRI_435_200507

description:
XN_SY01_P1_P21_180926A_SPRI_435_200507
47K SNPs


title: peanut-XN_SY01_P1_P18_180926B_SPRI_491_200507

description:
XN_SY01_P1_P18_180926B_SPRI_491_200507
47K SNPs


title: BHLH168_B73


title: BHLH150_B73


title: peanut-XN_SY01_P1_P17_180926A_SPRI_426_200507

description:
XN_SY01_P1_P17_180926A_SPRI_426_200507
47K SNPs


title: BHLH14_B73


title: BHLH135_B73


title: PCI_TL2D replicate 2

description:
CY-H4
Replicate 2 of library PCI_TL2D


title: peanut-XN_SY01_P1_P16_180926B_SPRI_488_200507

description:
XN_SY01_P1_P16_180926B_SPRI_488_200507
47K SNPs


title: BHLH113_B73


title: PCI_CK2D replicate 2

description:
CY-H4
Replicate 2 of library PCI_CK2D


title: peanut-XN_SY01_P1_P14_180926B_SPRI_487_200507

description:
XN_SY01_P1_P14_180926B_SPRI_487_200507
47K SNPs


title: peanut-XN_SY01_P1_P15_180926A_SPRI_423_200507

description:
XN_SY01_P1_P15_180926A_SPRI_423_200507
47K SNPs


title: peanut-XN_SY01_P1_P23_180926A_SPRI_436_200507

description:
XN_SY01_P1_P23_180926A_SPRI_436_200507
47K SNPs


title: peanut-XN_SY01_P1_P13_180926A_SPRI_421_200507

description:
XN_SY01_P1_P13_180926A_SPRI_421_200507
47K SNPs


title: LBD37_B73


title: BAF1_B73


title: DD_BHLH113_BHLH125_B73


title: EREB36_B73


title: peanut-XN_SY01_P1_P11_180926A_SPRI_419_200507

description:
XN_SY01_P1_P11_180926A_SPRI_419_200507
47K SNPs


title: peanut-XN_SY01_P1_P12_180926B_SPRI_474_200507

description:
XN_SY01_P1_P12_180926B_SPRI_474_200507
47K SNPs


title: peanut-XN_SY01_P1_P10_180926B_SPRI_462_200507

description:
XN_SY01_P1_P10_180926B_SPRI_462_200507
47K SNPs


title: MYBR17_B73


title: MYBR101_B73


title: MADS73_B73


title: peanut-XN_SY01_P1_P09_180926A_SPRI_417_200507

description:
XN_SY01_P1_P09_180926A_SPRI_417_200507
47K SNPs


title: MADS68_B73


title: peanut-XN_SY01_P1_P08_180926B_SPRI_441_200507

description:
XN_SY01_P1_P08_180926B_SPRI_441_200507
47K SNPs


title: peanut-XN_SY01_P1_P07_180926A_SPRI_410_200507

description:
XN_SY01_P1_P07_180926A_SPRI_410_200507
47K SNPs


title: GRF9_B73


title: peanut-XN_SY01_P1_P05_180926A_SPRI_409_200507

description:
XN_SY01_P1_P05_180926A_SPRI_409_200507
47K SNPs


title: EREB87_B73


title: GLK44_B73


title: peanut-XN_SY01_P1_P04_180926B_SPRI_430_200507

description:
XN_SY01_P1_P04_180926B_SPRI_430_200507
47K SNPs


title: EREB183_B73


title: peanut-XN_SY01_P1_P02_180926B_SPRI_429_200507

description:
XN_SY01_P1_P02_180926B_SPRI_429_200507
47K SNPs


title: EREB149_B73


title: peanut-XN_SY01_P1_P03_180926A_SPRI_407_200507

description:
XN_SY01_P1_P03_180926A_SPRI_407_200507
47K SNPs


title: EREB201_B73


title: BZIP68_B73


title: peanut-XN_SY01_P1_O24_180926A_SPRI_310_200507

description:
XN_SY01_P1_O24_180926A_SPRI_310_200507
47K SNPs


title: BZIP58_B73


title: HSF24_B73


title: peanut-XN_SY01_P1_O23_180926A_SPRI_212_200507

description:
XN_SY01_P1_O23_180926A_SPRI_212_200507
47K SNPs


title: peanut-XN_SY01_P1_P01_180926A_SPRI_406_200507

description:
XN_SY01_P1_P01_180926A_SPRI_406_200507
47K SNPs


title: BZIP39_B73


title: peanut-XN_SY01_P1_O23_180926C_SPRI-427_210107

description:
XN_SY01_P1_O23_180926C_SPRI-427_210107
47K SNPs


title: peanut-XN_SY01_P1_O22_180926A_SPRI_309_200507

description:
XN_SY01_P1_O22_180926A_SPRI_309_200507
47K SNPs


title: peanut-XN_SY01_P1_O21_180926C_SPRI-425_210107

description:
XN_SY01_P1_O21_180926C_SPRI-425_210107
47K SNPs


title: GRF7_B73


title: peanut-XN_SY01_P1_O21_180926A_SPRI_211_200507

description:
XN_SY01_P1_O21_180926A_SPRI_211_200507
47K SNPs


title: GRF2_B73


title: HSF25_B73


title: GRF3_B73


title: peanut-XN_SY01_P1_P06_180926B_SPRI_432_200507

description:
XN_SY01_P1_P06_180926B_SPRI_432_200507
47K SNPs


title: peanut-XN_SY01_P1_O19_180926C_SPRI-424_210107

description:
XN_SY01_P1_O19_180926C_SPRI-424_210107
47K SNPs


title: GLK53_B73


title: peanut-XN_SY01_P1_O19_180926A_SPRI_210_200507

description:
XN_SY01_P1_O19_180926A_SPRI_210_200507
47K SNPs


title: peanut-XN_SY01_P1_O18_180926A_SPRI_306_200507

description:
XN_SY01_P1_O18_180926A_SPRI_306_200507
47K SNPs


title: GLK56_B73


title: GLK17_B73


title: GLK47_B73


title: GBP4_B73


title: GBP11_B73


title: peanut-XN_SY01_P1_O16_180926A_SPRI_305_200507

description:
XN_SY01_P1_O16_180926A_SPRI_305_200507
47K SNPs


title: peanut-XN_SY01_P1_O15_180926C_SPRI-420_210107

description:
XN_SY01_P1_O15_180926C_SPRI-420_210107
47K SNPs


title: BZIP12_B73


title: peanut-XN_SY01_P1_O15_180926A_SPRI_208_200507

description:
XN_SY01_P1_O15_180926A_SPRI_208_200507
47K SNPs


title: peanut-XN_SY01_P1_O14_180926A_SPRI_304_200507

description:
XN_SY01_P1_O14_180926A_SPRI_304_200507
47K SNPs


title: peanut-XN_SY01_P1_O13_180926C_SPRI-418_210107

description:
XN_SY01_P1_O13_180926C_SPRI-418_210107
47K SNPs


title: TCP8_B73


title: TCP5_B73


title: TCP4_B73


title: peanut-XN_SY01_P1_O20_180926A_SPRI_308_200507

description:
XN_SY01_P1_O20_180926A_SPRI_308_200507
47K SNPs


title: peanut-XN_SY01_P1_O12_180926A_SPRI_303_200507

description:
XN_SY01_P1_O12_180926A_SPRI_303_200507
47K SNPs


title: TCP2_B73


title: peanut-XN_SY01_P1_O11_180926C_SPRI-416_210107

description:
XN_SY01_P1_O11_180926C_SPRI-416_210107
47K SNPs


title: BZIP94_B73


title: peanut-XN_SY01_P1_O11_180926A_SPRI_206_200507

description:
XN_SY01_P1_O11_180926A_SPRI_206_200507
47K SNPs


title: HB125_B73


title: peanut-XN_SY01_P1_O17_180926C_SPRI-422_210107

description:
XN_SY01_P1_O17_180926C_SPRI-422_210107
47K SNPs


title: NKD2_B73


title: peanut-XN_SY01_P1_O09_180926C_SPRI-415_210107

description:
XN_SY01_P1_O09_180926C_SPRI-415_210107
47K SNPs


title: peanut-XN_SY01_P1_O17_180926A_SPRI_209_200507

description:
XN_SY01_P1_O17_180926A_SPRI_209_200507
47K SNPs


title: peanut-XN_SY01_P1_O09_180926A_SPRI_205_200507

description:
XN_SY01_P1_O09_180926A_SPRI_205_200507
47K SNPs


title: NKD1_B73


title: peanut-XN_SY01_P1_O08_180926A_SPRI_301_200507

description:
XN_SY01_P1_O08_180926A_SPRI_301_200507
47K SNPs


title: NAC86_B73


title: GBP10_B73


title: peanut-XN_SY01_P1_O07_180926C_SPRI-414_210107

description:
XN_SY01_P1_O07_180926C_SPRI-414_210107
47K SNPs


title: peanut-XN_SY01_P1_O07_180926A_SPRI_204_200507

description:
XN_SY01_P1_O07_180926A_SPRI_204_200507
47K SNPs


title: peanut-XN_SY01_P1_O13_180926A_SPRI_207_200507

description:
XN_SY01_P1_O13_180926A_SPRI_207_200507
47K SNPs


title: peanut-XN_SY01_P1_O05_180926C_SPRI-413_210107

description:
XN_SY01_P1_O05_180926C_SPRI-413_210107
47K SNPs


title: peanut-XN_SY01_P1_O05_180926A_SPRI_203_200507

description:
XN_SY01_P1_O05_180926A_SPRI_203_200507
47K SNPs


title: NAC71_B73


title: NAC42_B73


title: peanut-XN_SY01_P1_O04_180926A_SPRI_299_200507

description:
XN_SY01_P1_O04_180926A_SPRI_299_200507
47K SNPs


title: BZIP1_B73


title: peanut-XN_SY01_P1_O03_180926C_SPRI-412_210107

description:
XN_SY01_P1_O03_180926C_SPRI-412_210107
47K SNPs


title: peanut-XN_SY01_P1_O03_180926A_SPRI_202_200507

description:
XN_SY01_P1_O03_180926A_SPRI_202_200507
47K SNPs


title: peanut-XN_SY01_P1_O10_180926A_SPRI_302_200507

description:
XN_SY01_P1_O10_180926A_SPRI_302_200507
47K SNPs


title: peanut-XN_SY01_P1_O02_180926A_SPRI_298_200507

description:
XN_SY01_P1_O02_180926A_SPRI_298_200507
47K SNPs


title: NAC33_B73


title: peanut-XN_SY01_P1_O01_180926C_SPRI-404_210107

description:
XN_SY01_P1_O01_180926C_SPRI-404_210107
47K SNPs


title: peanut-XN_SY01_P1_N24_180926B_SPRI_411_200507

description:
XN_SY01_P1_N24_180926B_SPRI_411_200507
47K SNPs


title: peanut-XN_SY01_P1_O01_180926A_SPRI_201_200507

description:
XN_SY01_P1_O01_180926A_SPRI_201_200507
47K SNPs


title: A549WT_ctr_3

type: RNA

city: Borstel

first: Doerte

last: Nitschkowski

address: Parkallee 1-40

department: Histology

country: Germany

institute: Research Center Borstel

description: gene expression A549Lsub stimulated with TGFb1-solvent

hyb_protocol: Labeled cRNA was hybridized at 65°C for 17 hours on Agilent Human Gene Expression 4×44k V2 arrays.

scan_protocol: Slides were scanned after washing on the Agilent SureScan Microarray Scanner (G4900DA) using the Feature Extraction (v11.5.1.1) one color protocol (GE1_1105_Oct12_1).

data_processing: Agilent GeneSpring GX software (v13) was used to obtain normalized signal intensities (75th percentile).

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low RNA Input kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: A549 cells (ATCC) were maintained in RPMI-1640 supplemented with 10 % FCS, 1 % penicillin/streptomycin, and 1 % stable glutamine.

extract_protocol: Total RNA was extracted from ≤ 1x107 cells using the RNeasy mini kit (Qiagen), and eluted using 30 µl of RNase-free water. RNA quality was determined using the Bioanalyzer 2100 (Agilent) and the RNA 6000 Nano Kit (Agilent) according to the manufacturer's conditions.

treatment_protocol: 4x106 cells were seeded in T75 flasks with 30 mL RPMI to adhere overnight. The next day, RPMI was replaced with 30 mL of medium supplemented with 5 ng/mL human TGF beta 1 (Thermo Fisher Scientific, PreproTech) and the cells were incubated for 48 hours. For the controls, the cells were stimulated with an equal volume of TGF beta 1 solvent.

tag: disease

value: non-small cell lung cancer

tag: cell line

value: A549 adenocarcinoma cell line

value: WT

value: ctr


title: A549WT_ctr_2


title: NAC27_B73


title: A549WT+TGFb_2

description: gene expression A549Lsub stimulated with human TGFb1 for 48 h

value: TGFb


title: peanut-XN_SY01_P1_N23_180926A_SPRI_405_200507

description:
XN_SY01_P1_N23_180926A_SPRI_405_200507
47K SNPs


title: A549WT_ctr_1


title: A549Lsub+TGFb_3

description: gene expression A549 wild-type stimulated with TGFb1-solvent

value: Lsub


title: A549WT+TGFb_1


title: peanut-XN_SY01_P1_N21_180926A_SPRI_403_200507

description:
XN_SY01_P1_N21_180926A_SPRI_403_200507
47K SNPs


title: peanut-XN_SY01_P1_N20_180926B_SPRI_395_200507

description:
XN_SY01_P1_N20_180926B_SPRI_395_200507
47K SNPs


title: NAC25_B73


title: NAC3_B73


title: NAC20_B73


title: NAC116_B73


title: peanut-XN_SY01_P1_O06_180926A_SPRI_300_200507

description:
XN_SY01_P1_O06_180926A_SPRI_300_200507
47K SNPs


title: peanut-XN_SY01_P1_N19_180926A_SPRI_402_200507

description:
XN_SY01_P1_N19_180926A_SPRI_402_200507
47K SNPs


title: peanut-XN_SY01_P1_N18_180926B_SPRI_393_200507

description:
XN_SY01_P1_N18_180926B_SPRI_393_200507
47K SNPs


title: peanut-XN_SY01_P1_N17_180926A_SPRI_401_200507

description:
XN_SY01_P1_N17_180926A_SPRI_401_200507
47K SNPs


title: peanut-XN_SY01_P1_N16_180926B_SPRI_152_200507

description:
XN_SY01_P1_N16_180926B_SPRI_152_200507
47K SNPs


title: NAC115_B73


title: A549Lsub+TGFb_1


title: NAC28_B73


title: A549Lsub+TGFb_2


title: peanut-XN_SY01_P1_N15_180926A_SPRI_400_200507

description:
XN_SY01_P1_N15_180926A_SPRI_400_200507
47K SNPs


title: peanut-XN_SY01_P1_N22_180926B_SPRI_408_200507

description:
XN_SY01_P1_N22_180926B_SPRI_408_200507
47K SNPs


title: BHLH91_B73


title: peanut-XN_SY01_P1_N14_180926B_SPRI_151_200507

description:
XN_SY01_P1_N14_180926B_SPRI_151_200507
47K SNPs


title: A549Lsub ctr_3

description: gene expression A549 wild-type stimulated with human TGFb1 for 48 h

source_name: A549Lsub ctr


title: peanut-XN_SY01_P1_N13_180926A_SPRI_397_200507

description:
XN_SY01_P1_N13_180926A_SPRI_397_200507
47K SNPs


title: peanut-XN_SY01_P1_N12_180926B_SPRI_149_200507

description:
XN_SY01_P1_N12_180926B_SPRI_149_200507
47K SNPs


title: A549Lsub ctr_2


title: peanut-XN_SY01_P1_N10_180926B_SPRI_148_200507

description:
XN_SY01_P1_N10_180926B_SPRI_148_200507
47K SNPs


title: A549Lsub ctr_1


title: peanut-XN_SY01_P1_N11_180926A_SPRI_396_200507

description:
XN_SY01_P1_N11_180926A_SPRI_396_200507
47K SNPs


title: A549WT+TGFb_3

description: gene expression A549Lsub stimulated with human TGFb1 for 48 h


title: MYB83_B73


title: peanut-XN_SY01_P1_N07_180926A_SPRI_392_200507

description:
XN_SY01_P1_N07_180926A_SPRI_392_200507
47K SNPs


title: MYB40_B73


title: peanut-XN_SY01_P1_N08_180926B_SPRI_147_200507

description:
XN_SY01_P1_N08_180926B_SPRI_147_200507
47K SNPs


title: A549Lsub_3

description: gene expression A549Lsub

treatment_protocol: 4x106 cells were seeded in T75 flasks with 30 ml RPMI to adhere overnight. Next day, cells were harvested using trypsin/EDTA and counted.


title: peanut-XN_SY01_P1_N05_180926A_SPRI_391_200507

description:
XN_SY01_P1_N05_180926A_SPRI_391_200507
47K SNPs


title: peanut-XN_SY01_P1_N03_180926A_SPRI_390_200507

description:
XN_SY01_P1_N03_180926A_SPRI_390_200507
47K SNPs


title: GRF6_B73


title: MADS43_B73


title: peanut-XN_SY01_P1_N04_180926B_SPRI_140_200507

description:
XN_SY01_P1_N04_180926B_SPRI_140_200507
47K SNPs


title: peanut-XN_SY01_P1_N06_180926B_SPRI_146_200507

description:
XN_SY01_P1_N06_180926B_SPRI_146_200507
47K SNPs


title: EREB4_B73


title: A549Lsub_1

description: gene expression A549Lsub


title: peanut-XN_SY01_P1_N01_180926A_SPRI_389_200507

description:
XN_SY01_P1_N01_180926A_SPRI_389_200507
47K SNPs


title: peanut-XN_SY01_P1_N02_180926B_SPRI_138_200507

description:
XN_SY01_P1_N02_180926B_SPRI_138_200507
47K SNPs


title: A549Lsub_2

description: gene expression A549Lsub


title: peanut-XN_SY01_P1_M24_180926A_SPRI_297_200507

description:
XN_SY01_P1_M24_180926A_SPRI_297_200507
47K SNPs


title: MYBR58_B73


title: EREB145_B73


title: peanut-XN_SY01_P1_N09_180926A_SPRI_394_200507

description:
XN_SY01_P1_N09_180926A_SPRI_394_200507
47K SNPs


title: peanut-XN_SY01_P1_M23_180926C_SPRI-399_210107

description:
XN_SY01_P1_M23_180926C_SPRI-399_210107
47K SNPs


title: peanut-XN_SY01_P1_M22_180926A_SPRI_296_200507

description:
XN_SY01_P1_M22_180926A_SPRI_296_200507
47K SNPs


title: peanut-XN_SY01_P1_M23_180926A_SPRI_200_200507

description:
XN_SY01_P1_M23_180926A_SPRI_200_200507
47K SNPs


title: BZIP48_B73


title: peanut-XN_SY01_P1_M21_180926C_SPRI-398_210107

description:
XN_SY01_P1_M21_180926C_SPRI-398_210107
47K SNPs


title: peanut-XN_SY01_P1_M21_180926A_SPRI_199_200507

description:
XN_SY01_P1_M21_180926A_SPRI_199_200507
47K SNPs


title: MADS12_B73


title: peanut-XN_SY01_P1_M20_180926A_SPRI_295_200507

description:
XN_SY01_P1_M20_180926A_SPRI_295_200507
47K SNPs


title: peanut-XN_SY01_P1_M19_180926A_SPRI_198_200507

description:
XN_SY01_P1_M19_180926A_SPRI_198_200507
47K SNPs


title: peanut-XN_SY01_P1_M19_180926C_SPRI-372_210107

description:
XN_SY01_P1_M19_180926C_SPRI-372_210107
47K SNPs


title: DOF1_B73


title: peanut-XN_SY01_P1_M17_180926A_SPRI_197_200507

description:
XN_SY01_P1_M17_180926A_SPRI_197_200507
47K SNPs


title: peanut-XN_SY01_P1_M17_180926C_SPRI-349_210107

description:
XN_SY01_P1_M17_180926C_SPRI-349_210107
47K SNPs


title: DD_BHLH150_BHLH168_B73


title: peanut-XN_SY01_P1_M16_180926A_SPRI_293_200507

description:
XN_SY01_P1_M16_180926A_SPRI_293_200507
47K SNPs


title: peanut-XN_SY01_P1_M15_180926C_SPRI-339_210107

description:
XN_SY01_P1_M15_180926C_SPRI-339_210107
47K SNPs


title: peanut-XN_SY01_P1_M15_180926A_SPRI_196_200507

description:
XN_SY01_P1_M15_180926A_SPRI_196_200507
47K SNPs


title: DOF24_B73


title: peanut-XN_SY01_P1_M14_180926A_SPRI_292_200507

description:
XN_SY01_P1_M14_180926A_SPRI_292_200507
47K SNPs


title: peanut-XN_SY01_P1_M13_180926C_SPRI-330_210107

description:
XN_SY01_P1_M13_180926C_SPRI-330_210107
47K SNPs


title: DD_BHLH150_BHLH125_B73


title: EREB46_B73


title: DD_BHLH14_BHLH168_B73


title: peanut-XN_SY01_P1_M13_180926A_SPRI_195_200507

description:
XN_SY01_P1_M13_180926A_SPRI_195_200507
47K SNPs


title: A549WT_2

description: gene expression A549 wild-type


title: peanut-XN_SY01_P1_M18_180926A_SPRI_294_200507

description:
XN_SY01_P1_M18_180926A_SPRI_294_200507
47K SNPs


title: peanut-XN_SY01_P1_M12_180926A_SPRI_291_200507

description:
XN_SY01_P1_M12_180926A_SPRI_291_200507
47K SNPs


title: DD_BHLH14_BHLH125_B73


title: peanut-XN_SY01_P1_M11_180926C_SPRI-327_210107

description:
XN_SY01_P1_M11_180926C_SPRI-327_210107
47K SNPs


title: A549WT_1

description: gene expression A549 wild-type


title: PIT_Sal_5

city: Krakow

first: Michal

last: Korostynski

state: malopolskie

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Maj Institute of Pharmacology PAS

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were preprocessed using beadarray R package and normalized using quantile normalization.

label: not provided

organism: Mus musculus

source_name: mouse tissues

label_protocol: Biotinylated cRNA were prepared with the labelling kit for Illumina arrays.

extract_protocol: RNA was isolated using RNeasy Mini Kit (Qiagen Inc.) and further purified following the manufacturer's protocol. Total RNA concentration was measured using a NanoDrop ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA). RNA quality was determined by chip-based capillary electrophoresis using RNA 6000 Nano LabChip Kits and an Agilent Bioanalyzer 2100 device (Agilent, Palo Alto, CA, USA). RNA from two mice was randomly pooled to prepare a sample for each microarray.

treatment_protocol: Mice were killed by decapitation 4 h after a single dexamethasone (10 mg/kg) i.p. injection, with a respective saline (10 ml/kg) control group.

tag: strain

value: Pituitary

tag: time

value: Saline


title: PIT_Dex_6

value: Dexamethasone


title: peanut-XN_SY01_P1_M11_180926A_SPRI_194_200507

description:
XN_SY01_P1_M11_180926A_SPRI_194_200507
47K SNPs


title: PIT_Dex_4


title: PIT_Sal_3


title: PIT_Dex_5


title: PIT_Sal_4


title: PIT_Sal_2


title: A549WT_3

description: gene expression A549 wild-type


title: peanut-XN_SY01_P1_M10_180926A_SPRI_290_200507

description:
XN_SY01_P1_M10_180926A_SPRI_290_200507
47K SNPs


title: CCHH2_B73


title: peanut-XN_SY01_P1_M09_180926A_SPRI_193_200507

description:
XN_SY01_P1_M09_180926A_SPRI_193_200507
47K SNPs


title: peanut-XN_SY01_P1_M08_180926A_SPRI_289_200507

description:
XN_SY01_P1_M08_180926A_SPRI_289_200507
47K SNPs


title: CA2P13_CA3P4_CA5P7_B73


title: peanut-XN_SY01_P1_M07_180926A_SPRI_192_200507

description:
XN_SY01_P1_M07_180926A_SPRI_192_200507
47K SNPs


title: peanut-XN_SY01_P1_M07_180926C_SPRI-307_210107

description:
XN_SY01_P1_M07_180926C_SPRI-307_210107
47K SNPs


title: peanut-XN_SY01_P1_M06_180926A_SPRI_288_200507

description:
XN_SY01_P1_M06_180926A_SPRI_288_200507
47K SNPs


title: CA2P13_CA3P1_CA5P7_B73


title: peanut-XN_SY01_P1_M05_180926C_SPRI-247_210107

description:
XN_SY01_P1_M05_180926C_SPRI-247_210107
47K SNPs


title: BZIP99_B73


title: BZIP92_B73


title: PIT_Sal_6


title: peanut-XN_SY01_P1_M05_180926A_SPRI_191_200507

description:
XN_SY01_P1_M05_180926A_SPRI_191_200507
47K SNPs


title: PIT_Sal_1


title: peanut-XN_SY01_P1_M04_180926A_SPRI_287_200507

description:
XN_SY01_P1_M04_180926A_SPRI_287_200507
47K SNPs


title: peanut-XN_SY01_P1_M03_180926A_SPRI_190_200507

description:
XN_SY01_P1_M03_180926A_SPRI_190_200507
47K SNPs


title: peanut-XN_SY01_P1_M09_180926C_SPRI-319_210107

description:
XN_SY01_P1_M09_180926C_SPRI-319_210107
47K SNPs


title: BZIP91_B73


title: BZIP90_B73


title: peanut-XN_SY01_P1_M02_180926A_SPRI_286_200507

description:
XN_SY01_P1_M02_180926A_SPRI_286_200507
47K SNPs


title: peanut-XN_SY01_P1_M01_180926C_SPRI-167_210107

description:
XN_SY01_P1_M01_180926C_SPRI-167_210107
47K SNPs


title: PIT_Dex_1


title: peanut-XN_SY01_P1_M01_180926A_SPRI_189_200507

description:
XN_SY01_P1_M01_180926A_SPRI_189_200507
47K SNPs


title: BZIP87_B73


title: KID_Sal_2

value: Kidney


title: peanut-XN_SY01_P1_L24_180926B_SPRI_136_200507

description:
XN_SY01_P1_L24_180926B_SPRI_136_200507
47K SNPs


title: PIT_Dex_3


title: LIV_Sal_2

value: Liver


title: LIV_Dex_2


title: PIT_Dex_2


title: MUS_Sal_2

value: Muscle


title: BZIP86_B73

value: seedling leaf


title: peanut-XN_SY01_P1_L23_180926A_SPRI_388_200507

description:
XN_SY01_P1_L23_180926A_SPRI_388_200507
47K SNPs


title: KID_Dex_2


title: peanut-XN_SY01_P1_L21_180926A_SPRI_387_200507

description:
XN_SY01_P1_L21_180926A_SPRI_387_200507
47K SNPs


title: peanut-XN_SY01_P1_L20_180926B_SPRI_132_200507

description:
XN_SY01_P1_L20_180926B_SPRI_132_200507
47K SNPs


title: peanut-XN_SY01_P1_M03_180926C_SPRI-174_210107

description:
XN_SY01_P1_M03_180926C_SPRI-174_210107
47K SNPs


title: BZIP84_B73

value: DAP-seq


title: MUS_Dex_2


title: peanut-XN_SY01_P1_L19_180926A_SPRI_386_200507

description:
XN_SY01_P1_L19_180926A_SPRI_386_200507
47K SNPs


title: peanut-XN_SY01_P1_L17_180926A_SPRI_385_200507

description:
XN_SY01_P1_L17_180926A_SPRI_385_200507
47K SNPs


title: KID_Dex_1


title: peanut-XN_SY01_P1_L18_180926B_SPRI_118_200507

description:
XN_SY01_P1_L18_180926B_SPRI_118_200507
47K SNPs


title: BZIP70_B73


title: peanut-XN_SY01_P1_L16_180926B_SPRI_114_200507

description:
XN_SY01_P1_L16_180926B_SPRI_114_200507
47K SNPs


title: peanut-XN_SY01_P1_L15_180926A_SPRI_384_200507

description:
XN_SY01_P1_L15_180926A_SPRI_384_200507
47K SNPs


title: BZIP62_B73


title: peanut-XN_SY01_P1_L22_180926B_SPRI_134_200507

description:
XN_SY01_P1_L22_180926B_SPRI_134_200507
47K SNPs


title: LIV_Sal_1


title: peanut-XN_SY01_P1_L14_180926B_SPRI_95_200507

description:
XN_SY01_P1_L14_180926B_SPRI_95_200507
47K SNPs


title: BZIP61_B73


title: peanut-XN_SY01_P1_L12_180926B_SPRI_93_200507

description:
XN_SY01_P1_L12_180926B_SPRI_93_200507
47K SNPs


title: MUS_Sal_1


title: peanut-XN_SY01_P1_L13_180926A_SPRI_383_200507

description:
XN_SY01_P1_L13_180926A_SPRI_383_200507
47K SNPs


title: peanut-XN_SY01_P1_L11_180926A_SPRI_382_200507

description:
XN_SY01_P1_L11_180926A_SPRI_382_200507
47K SNPs


title: BZIP41_B73


title: KID_Sal_1


title: BZIP52_B73


title: BZIP79_B73


title: peanut-XN_SY01_P1_L09_180926A_SPRI_381_200507

description:
XN_SY01_P1_L09_180926A_SPRI_381_200507
47K SNPs


title: peanut-XN_SY01_P1_L10_180926B_SPRI_92_200507

description:
XN_SY01_P1_L10_180926B_SPRI_92_200507
47K SNPs


title: LIV_Dex_1


title: peanut-XN_SY01_P1_L07_180926A_SPRI_380_200507

description:
XN_SY01_P1_L07_180926A_SPRI_380_200507
47K SNPs


title: BZIP40_B73


title: peanut-XN_SY01_P1_L06_180926B_SPRI_86_200507

description:
XN_SY01_P1_L06_180926B_SPRI_86_200507
47K SNPs


title: MUS_Dex_1


title: peanut-XN_SY01_P1_L05_180926A_SPRI_379_200507

description:
XN_SY01_P1_L05_180926A_SPRI_379_200507
47K SNPs


title: KID_Sal_5


title: BZIP34_B73


title: peanut-XN_SY01_P1_L04_180926B_SPRI_78_200507

description:
XN_SY01_P1_L04_180926B_SPRI_78_200507
47K SNPs


title: peanut-XN_SY01_P1_L08_180926B_SPRI_87_200507

description:
XN_SY01_P1_L08_180926B_SPRI_87_200507
47K SNPs


title: BZIP25_B73


title: KID_Dex_5


title: peanut-XN_SY01_P1_L03_180926A_SPRI_378_200507

description:
XN_SY01_P1_L03_180926A_SPRI_378_200507
47K SNPs


title: peanut-XN_SY01_P1_L02_180926B_SPRI_77_200507

description:
XN_SY01_P1_L02_180926B_SPRI_77_200507
47K SNPs


title: peanut-XN_SY01_P1_L01_180926A_SPRI_377_200507

description:
XN_SY01_P1_L01_180926A_SPRI_377_200507
47K SNPs


title: BZIP23_B73


title: peanut-XN_SY01_P1_K24_180926A_SPRI_285_200507

description:
XN_SY01_P1_K24_180926A_SPRI_285_200507
47K SNPs


title: peanut-XN_SY01_P1_K23_180926C_SPRI-154_210107

description:
XN_SY01_P1_K23_180926C_SPRI-154_210107
47K SNPs


title: BZIP21_B73


title: peanut-XN_SY01_P1_K22_180926A_SPRI_284_200507

description:
XN_SY01_P1_K22_180926A_SPRI_284_200507
47K SNPs


title: LIV_Dex_5


title: LIV_Sal_5


title: MUS_Sal_5


title: peanut-XN_SY01_P1_K21_180926C_SPRI-153_210107

description:
XN_SY01_P1_K21_180926C_SPRI-153_210107
47K SNPs


title: BZIP160_B73


title: MUS_Dex_5


title: peanut-XN_SY01_P1_K21_180926A_SPRI_187_200507

description:
XN_SY01_P1_K21_180926A_SPRI_187_200507
47K SNPs


title: BZIP13_B73


title: peanut-XN_SY01_P1_K23_180926A_SPRI_188_200507

description:
XN_SY01_P1_K23_180926A_SPRI_188_200507
47K SNPs


title: peanut-XN_SY01_P1_K20_180926A_SPRI_283_200507

description:
XN_SY01_P1_K20_180926A_SPRI_283_200507
47K SNPs


title: BZIP128_B73


title: peanut-XN_SY01_P1_K19_180926A_SPRI_186_200507

description:
XN_SY01_P1_K19_180926A_SPRI_186_200507
47K SNPs


title: peanut-XN_SY01_P1_K19_180926C_SPRI-150_210107

description:
XN_SY01_P1_K19_180926C_SPRI-150_210107
47K SNPs


title: peanut-XN_SY01_P1_K18_180926A_SPRI_282_200507

description:
XN_SY01_P1_K18_180926A_SPRI_282_200507
47K SNPs


title: BZIP124_B73


title: SPL_Dex_5

value: Spleen


title: peanut-XN_SY01_P1_K17_180926A_SPRI_185_200507

description:
XN_SY01_P1_K17_180926A_SPRI_185_200507
47K SNPs


title: BZIP115_B73


title: peanut-XN_SY01_P1_K16_180926A_SPRI_281_200507

description:
XN_SY01_P1_K16_180926A_SPRI_281_200507
47K SNPs


title: peanut-XN_SY01_P1_K15_180926A_SPRI_184_200507

description:
XN_SY01_P1_K15_180926A_SPRI_184_200507
47K SNPs


title: peanut-XN_SY01_P1_K14_180926A_SPRI_280_200507

description:
XN_SY01_P1_K14_180926A_SPRI_280_200507
47K SNPs


title: SPL_Sal_5


title: BZIP112_B73


title: HTH_Sal_5

value: Hypothalamus


title: peanut-XN_SY01_P1_K13_180926A_SPRI_183_200507

description:
XN_SY01_P1_K13_180926A_SPRI_183_200507
47K SNPs

value: leaf


title: UNG_Sal_5

value: Lung


title: peanut-XN_SY01_P1_K12_180926A_SPRI_279_200507

description:
XN_SY01_P1_K12_180926A_SPRI_279_200507
47K SNPs


title: peanut-XN_SY01_P1_K11_180926A_SPRI_182_200507

description:
XN_SY01_P1_K11_180926A_SPRI_182_200507
47K SNPs


title: KID_Dex_4


title: peanut-XN_SY01_P1_K13_180926C_SPRI-143_210107

description:
XN_SY01_P1_K13_180926C_SPRI-143_210107
47K SNPs


title: peanut-XN_SY01_P1_K17_180926C_SPRI-145_210107

description:
XN_SY01_P1_K17_180926C_SPRI-145_210107
47K SNPs


title: BZIP105_B73


title: peanut-XN_SY01_P1_K11_180926C_SPRI-142_210107

description:
XN_SY01_P1_K11_180926C_SPRI-142_210107
47K SNPs


title: BHLH99_B73


title: KID_Sal_4


title: LIV_Sal_4


title: HTH_Dex_5


title: peanut-XN_SY01_P1_K09_180926C_SPRI-141_210107

description:
XN_SY01_P1_K09_180926C_SPRI-141_210107
47K SNPs


title: peanut-XN_SY01_P1_K15_180926C_SPRI-144_210107

description:
XN_SY01_P1_K15_180926C_SPRI-144_210107
47K SNPs


title: peanut-XN_SY01_P1_K08_180926A_SPRI_277_200507

description:
XN_SY01_P1_K08_180926A_SPRI_277_200507
47K SNPs


title: BZIP106_B73


title: BHLH57_B73


title: peanut-XN_SY01_P1_K07_180926A_SPRI_180_200507

description:
XN_SY01_P1_K07_180926A_SPRI_180_200507
47K SNPs


title: BHLH17_B73


title: MUS_Dex_4


title: peanut-XN_SY01_P1_K06_180926A_SPRI_276_200507

description:
XN_SY01_P1_K06_180926A_SPRI_276_200507
47K SNPs


title: peanut-XN_SY01_P1_K05_180926C_SPRI-137_210107

description:
XN_SY01_P1_K05_180926C_SPRI-137_210107
47K SNPs


title: peanut-XN_SY01_P1_K05_180926A_SPRI_179_200507

description:
XN_SY01_P1_K05_180926A_SPRI_179_200507
47K SNPs


title: peanut-XN_SY01_P1_K04_180926A_SPRI_275_200507

description:
XN_SY01_P1_K04_180926A_SPRI_275_200507
47K SNPs


title: peanut-XN_SY01_P1_K03_180926C_SPRI-135_210107

description:
XN_SY01_P1_K03_180926C_SPRI-135_210107
47K SNPs


title: BHLH125_B73


title: ABI8_B73


title: SPL_Dex_4


title: peanut-XN_SY01_P1_K09_180926A_SPRI_181_200507

description:
XN_SY01_P1_K09_180926A_SPRI_181_200507
47K SNPs


title: ABI34_B73


title: peanut-XN_SY01_P1_K03_180926A_SPRI_178_200507

description:
XN_SY01_P1_K03_180926A_SPRI_178_200507
47K SNPs


title: peanut-XN_SY01_P1_K02_180926A_SPRI_274_200507

description:
XN_SY01_P1_K02_180926A_SPRI_274_200507
47K SNPs


title: peanut-XN_SY01_P1_K01_180926C_SPRI-133_210107

description:
XN_SY01_P1_K01_180926C_SPRI-133_210107
47K SNPs


title: peanut-XN_SY01_P1_K01_180926A_SPRI_177_200507

description:
XN_SY01_P1_K01_180926A_SPRI_177_200507
47K SNPs


title: ABI19_B73


title: peanut-XN_SY01_P1_J24_180926B_SPRI_75_200507

description:
XN_SY01_P1_J24_180926B_SPRI_75_200507
47K SNPs


title: UNG_SAL_6


title: SPL_DEX_7


title: 231JAG1KO-R tumor 6

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

description:
Library name: KW1312_2j
KW1312_2J_1

data_processing:
data was provided by Novogene as .fq.gz files
data was analyzed using Genialis software and the standard RNA-seq pipeling
Assembly: homo sapiens star index (ENSEMBL 109)
Supplementary files format and content: xlsx file containing featurecounts data

source_name: mammary tumor

growth_protocol: tumor cells were injected into the 4th mammary gland of NCG mice

extract_protocol:
Total RNA was extracted using the miRVana miRNA extraction kit from Thermo Fisher Scientific
libraries were created by Novogene using Illumina kits

treatment_protocol: no treatment

value: mammary tumor

value: human TNBC

value: JAG1 knockout


title: peanut-XN_SY01_P1_J23_180926A_SPRI_376_200507

description:
XN_SY01_P1_J23_180926A_SPRI_376_200507
47K SNPs


title: peanut-XN_SY01_P1_J20_180926B_SPRI_68_200507

description:
XN_SY01_P1_J20_180926B_SPRI_68_200507
47K SNPs


title: HTH_DEX_6


title: peanut-XN_SY01_P1_J19_180926A_SPRI_374_200507

description:
XN_SY01_P1_J19_180926A_SPRI_374_200507
47K SNPs


title: peanut-XN_SY01_P1_J18_180926B_SPRI_67_200507

description:
XN_SY01_P1_J18_180926B_SPRI_67_200507
47K SNPs


title: peanut-XN_SY01_P1_J21_180926A_SPRI_375_200507

description:
XN_SY01_P1_J21_180926A_SPRI_375_200507
47K SNPs


title: KID_Sal_3


title: peanut-XN_SY01_P1_J17_180926A_SPRI_373_200507

description:
XN_SY01_P1_J17_180926A_SPRI_373_200507
47K SNPs


title: HTH_SAL_6


title: 231JAG1KO-R tumor 4

description:
Library name: KW1310_5J
KW1310_5J_1


title: peanut-XN_SY01_P1_K10_180926A_SPRI_278_200507

description:
XN_SY01_P1_K10_180926A_SPRI_278_200507
47K SNPs


title: LIV_Sal_3


title: KID_Dex_3


title: 231JAG1KO-R tumor 3

description:
Library name: KW1308_2J
KW1308_2J_1


title: MUS_Sal_4


title: peanut-XN_SY01_P1_J15_180926A_SPRI_371_200507

description:
XN_SY01_P1_J15_180926A_SPRI_371_200507
47K SNPs


title: peanut-XN_SY01_P1_J22_180926B_SPRI_74_200507

description:
XN_SY01_P1_J22_180926B_SPRI_74_200507
47K SNPs


title: 231JAG1KO-R tumor 2

description:
Library name: KW1307_5J
KW1307_5J_1


title: peanut-XN_SY01_P1_J14_180926B_SPRI_63_200507

description:
XN_SY01_P1_J14_180926B_SPRI_63_200507
47K SNPs


title: 231JAG1KO-R tumor 1

description:
Library name: KS1306_2J
KW1306_2J_1


title: peanut-XN_SY01_P1_J13_180926A_SPRI_370_200507

description:
XN_SY01_P1_J13_180926A_SPRI_370_200507
47K SNPs


title: peanut-XN_SY01_P1_J12_180926B_SPRI_61_200507

description:
XN_SY01_P1_J12_180926B_SPRI_61_200507
47K SNPs


title: LIV_Dex_3


title: peanut-XN_SY01_P1_J11_180926A_SPRI_369_200507

description:
XN_SY01_P1_J11_180926A_SPRI_369_200507
47K SNPs


title: MUS_Sal_3


title: 231JAG1KOCon tumor 4

description:
Library name: KW1301_2C
KW1301_2C_1

value: empty vector


title: MUS_Dex_3


title: peanut-XN_SY01_P1_J08_180926B_SPRI_51_200507

description:
XN_SY01_P1_J08_180926B_SPRI_51_200507
47K SNPs


title: peanut-XN_SY01_P1_J10_180926B_SPRI_54_200507

description:
XN_SY01_P1_J10_180926B_SPRI_54_200507
47K SNPs


title: peanut-XN_SY01_P1_J09_180926A_SPRI_368_200507

description:
XN_SY01_P1_J09_180926A_SPRI_368_200507
47K SNPs


title: 231JAG1KOCon tumor 3

description:
Library name: KW1300_5C
KW1300_5C_1


title: peanut-XN_SY01_P1_J05_180926A_SPRI_366_200507

description:
XN_SY01_P1_J05_180926A_SPRI_366_200507
47K SNPs


title: peanut-XN_SY01_P1_J07_180926A_SPRI_367_200507

description:
XN_SY01_P1_J07_180926A_SPRI_367_200507
47K SNPs


title: peanut-XN_SY01_P1_J04_180926B_SPRI_42_200507

description:
XN_SY01_P1_J04_180926B_SPRI_42_200507
47K SNPs


title: peanut-XN_SY01_P1_J03_180926A_SPRI_365_200507

description:
XN_SY01_P1_J03_180926A_SPRI_365_200507
47K SNPs


title: peanut-XN_SY01_P1_J06_180926B_SPRI_50_200507

description:
XN_SY01_P1_J06_180926B_SPRI_50_200507
47K SNPs


title: SPL_SAL_8


title: HTH_Dex_3


title: peanut-XN_SY01_P1_J02_180926B_SPRI_41_200507

description:
XN_SY01_P1_J02_180926B_SPRI_41_200507
47K SNPs


title: SPL_DEX_6


title: 231JAG1KOCon tumor 1

description:
Library name: KW1295_2C
KW1295_2C_1


title: LIV_Dex_4


title: UNG_Sal_3


title: UBS_KO1_2

city: shanghai

first: Li

last: Cai-tao

state: shanghai

address: 393 Middle Huaxia Road, Pudong New Area, Shanghai

institute: Shanghaitech University

data_processing:
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Assembly: hg38
Supplementary files format and content: CSV files recording the coverage, m5C level, P-value for m5C sites
Library strategy: ultrafast bisulfite-seq

molecule: polyA RNA

source_name: Cell Line

extract_protocol:
Total RNA was extracted using TRIzol reagent (TIANGEN).Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).Bisulfite treatment was performed using UBS-2.In brief, 45 µL of UBS-2 reagent was preheated to 98 °C for 5 min in a PCR instrument, and then approximately 100 ng of poly(A) RNA in 5 µL of water was added and mixed well. The mixture was incubated at 98 °C for 9 min with the lid temperature set to 105 °C. After cooling to room temperature, desulphonation was accomplished on the Zymo-Spin IC columns following the manufacturer’s protocol
The quantity of the converted RNA was determined using the Qubit. Libraries were then constructed using the Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal).

value: Cell Line

value: breast cancer cell line


title: UBS_KO2_2


title: UBS_KO2_1


title: peanut-XN_SY01_P1_I24_180926A_SPRI_273_200507

description:
XN_SY01_P1_I24_180926A_SPRI_273_200507
47K SNPs


title: peanut-XN_SY01_P1_J01_180926A_SPRI_364_200507

description:
XN_SY01_P1_J01_180926A_SPRI_364_200507
47K SNPs


title: UNG_Dex_3


title: UBS_KO1_1


title: peanut-XN_SY01_P1_I23_180926C_SPRI-131_210107

description:
XN_SY01_P1_I23_180926C_SPRI-131_210107
47K SNPs


title: peanut-XN_SY01_P1_I19_180926C_SPRI-123_210107

description:
XN_SY01_P1_I19_180926C_SPRI-123_210107
47K SNPs


title: UBS_WT_1

value: WT


title: SPL_DEX_8

value: Dexamethasone


title: peanut-XN_SY01_P1_I23_180926A_SPRI_176_200507

description:
XN_SY01_P1_I23_180926A_SPRI_176_200507
47K SNPs


title: SPL_SAL_9

value: Saline


title: peanut-XN_SY01_P1_I21_180926C_SPRI-126_210107

description:
XN_SY01_P1_I21_180926C_SPRI-126_210107
47K SNPs


title: UBS_WT_2


title: peanut-XN_SY01_P1_I20_180926A_SPRI_271_200507

description:
XN_SY01_P1_I20_180926A_SPRI_271_200507
47K SNPs


title: HTH_Dex_2


title: BHLH85_B73


title: HTH_Sal_2


title: peanut-XN_SY01_P1_I19_180926A_SPRI_173_200507

description:
XN_SY01_P1_I19_180926A_SPRI_173_200507
47K SNPs


title: peanut-XN_SY01_P1_I22_180926A_SPRI_272_200507

description:
XN_SY01_P1_I22_180926A_SPRI_272_200507
47K SNPs


title: peanut-XN_SY01_P1_I17_180926A_SPRI_172_200507

description:
XN_SY01_P1_I17_180926A_SPRI_172_200507
47K SNPs


title: peanut-XN_SY01_P1_I21_180926A_SPRI_175_200507

description:
XN_SY01_P1_I21_180926A_SPRI_175_200507
47K SNPs


title: RNA-NSun-MDA-MB-231_KD2_19R484_

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Paired-end 150-cycle sequencing was performed on HiSeq X, per the manufacturer’s directions (Illumina).
After adapter trimming by cutadapt RNA-Seq was mapped to human genome hg38(Gencode) by STAR(version 2.7.1a, parameters “--outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS nM XS --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --twopassMode Basic”) and HTSeq(version 0.11.2) were used to count the gene-based reads using gene annotation from GENCODE(v31).
For differential expression analysis, we performed trimmed mean normalization then Voom was used to identify differential expressed genes, two additional negative control samples from GSE166276 were used with batch effect correction.
Assembly: hg38(Gencode)
Supplementary files format and content: txt file with FPKM
Supplementary files format and content: txt file with abuabundance measurements

extract_protocol:
Total RNA was extracted using TRIzol reagent (TIANGEN)
NEBNext Ultra RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA-NSun-MDA-MB-231_KD3_19R483_


title: peanut-XN_SY01_P1_J16_180926B_SPRI_65_200507

description:
XN_SY01_P1_J16_180926B_SPRI_65_200507
47K SNPs


title: RNA-NSun-MDA-MB-231_Negative_control_19R481_


title: peanut-XN_SY01_P1_I15_180926C_SPRI-108_210107

description:
XN_SY01_P1_I15_180926C_SPRI-108_210107
47K SNPs


title: peanut-XN_SY01_P1_I18_180926A_SPRI_270_200507

description:
XN_SY01_P1_I18_180926A_SPRI_270_200507
47K SNPs


title: peanut-XN_SY01_P1_I15_180926A_SPRI_171_200507

description:
XN_SY01_P1_I15_180926A_SPRI_171_200507
47K SNPs


title: RNA-NSun-MDA-MB-231_KD1_19R482_


title: peanut-XN_SY01_P1_I17_180926C_SPRI-116_210107

description:
XN_SY01_P1_I17_180926C_SPRI-116_210107
47K SNPs


title: peanut-XN_SY01_P1_I13_180926A_SPRI_170_200507

description:
XN_SY01_P1_I13_180926A_SPRI_170_200507
47K SNPs


title: PAA3_Elmo2_ko

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Raw FASTQ reads were quality and adapter trimmed using fastp (version 0.23.2 length cutoff 20, quality cutoff 15). The UMI and complex barcode were extracted and demultiplexed using custom scripts (https://github.com/Bioinformatics-Service-MPI-Munster/scrna-tools; rhapsody-extract-barcode).
We merged the GRCm39 reference genome with the reporter vector sequence to create a custom reference. We then used STAR version 2.7.10a to generate a reference genome index, with reporter features and Gencode annotations vM29, subset to lncRNA and protein-coding genes.
FASTQ reads were mapped against the reference genome index using STAR with the settings “--soloType CB_UMI_Simple --soloCellFilter None --outSAMtype BAM SortedByCoordinate --soloFeatures GeneFull_Ex50pAS --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28 --soloUMIlen 8 --soloCBwhitelist rhapsody_whitelist.txt --runRNGseed 1 --soloMultiMappers EM --readFilesCommand zcat”.
Assembly: mm39
Supplementary files format and content: Tab-separated values files, MatrixMarket files, and AnnData files

source_name: 3rd PAA and surrounding mesenchyme

extract_protocol:
Third pharyngeal arch artery and surrounding mesenchyme was micro dissected from E12.5 embryos and immediately transferred into a 48 well plate prefilled with 25mM HEPES in DMEM. Once all samples were collected, tissues were transferred to 100µl of 50mg/ml Liberase TM, 0.1mg/ml DNAse-1, and 25mM HEPES in DMEM and incubated at 37°C for 15 minutes with occasional mixing (all pipetting steps with tissue were carried out with 200µl sterile filter tips to reduce loss of cells). Digestion was stopped by adding 1ml of 10% fetal calf serum (FCS) in DMEM. The cell suspension was filtered through a 40µm strainer. Samples were centrifuged for 7 minutes at 300g and room temperature (RT). After carefully aspirating the supernatant, 100µl RBC lysis buffer was added to the pellet, mixed gently, and incubated for 1 minute at RT. The reaction was stopped by adding 1.5ml of 2% FCS in sterile PBS. Samples were centrifuged at 300g for 7 minutes at 4°C. Supernatant was carefully aspirated and the cell pellet resuspended in 100µl of FACS buffer by gentle pipetting.
Library construction was performed following manufacturer’s instructions (BD Rhapsody™ system mRNA WTA library preparation protocol).

value: 3rd PAA and surrounding mesenchyme


title: peanut-XN_SY01_P1_I12_180926A_SPRI_267_200507

description:
XN_SY01_P1_I12_180926A_SPRI_267_200507
47K SNPs


title: peanut-XN_SY01_P1_I11_180926C_SPRI-100_210107

description:
XN_SY01_P1_I11_180926C_SPRI-100_210107
47K SNPs


title: SPL_Sal_1


title: UNG_Sal_2


title: HTH_Sal_1


title: peanut-XN_SY01_P1_I16_180926A_SPRI_269_200507

description:
XN_SY01_P1_I16_180926A_SPRI_269_200507
47K SNPs


title: SPL_Dex_1


title: PAA3_Elmo2_het

description: BD Rhapsody


title: peanut-XN_SY01_P1_K07_180926C_SPRI-139_210107

description:
XN_SY01_P1_K07_180926C_SPRI-139_210107
47K SNPs


title: UNG_Dex_2


title: peanut-XN_SY01_P1_I11_180926A_SPRI_169_200507

description:
XN_SY01_P1_I11_180926A_SPRI_169_200507
47K SNPs


title: peanut-XN_SY01_P1_I10_180926A_SPRI_266_200507

description:
XN_SY01_P1_I10_180926A_SPRI_266_200507
47K SNPs


title: HTH_Dex_1


title: peanut-XN_SY01_P1_I14_180926A_SPRI_268_200507

description:
XN_SY01_P1_I14_180926A_SPRI_268_200507
47K SNPs


title: peanut-XN_SY01_P1_I09_180926C_SPRI-099_210107

description:
XN_SY01_P1_I09_180926C_SPRI-099_210107
47K SNPs


title: PAA3_Emo2_ctrl

description: BD Rhapsody


title: peanut-XN_SY01_P1_I09_180926A_SPRI_168_200507

description:
XN_SY01_P1_I09_180926A_SPRI_168_200507
47K SNPs


title: peanut-XN_SY01_P1_I08_180926A_SPRI_265_200507

description:
XN_SY01_P1_I08_180926A_SPRI_265_200507
47K SNPs


title: Heart, XML_RBPMS-2_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome assembly mm10 with STAR 2.4.2a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Gene counts were established with featureCounts 1.5.0 by aggregating reads overlapping exons (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: heart

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, with 1x75bp single end setup.

value: heart

value: RBPMS flox/flox RBPMS2 flox/flox XML Cre pos


title: UNG_Sal_1


title: peanut-XN_SY01_P1_I07_180926A_SPRI_166_200507

description:
XN_SY01_P1_I07_180926A_SPRI_166_200507
47K SNPs


title: UNG_Dex_1


title: Heart, XML_RBPMS-2_2


title: peanut-XN_SY01_P1_I05_180926C_SPRI-094_210107

description:
XN_SY01_P1_I05_180926C_SPRI-094_210107
47K SNPs


title: peanut-XN_SY01_P1_I05_180926A_SPRI_165_200507

description:
XN_SY01_P1_I05_180926A_SPRI_165_200507
47K SNPs


title: ADR_Sal_6

value: Adrenal Gland


title: peanut-XN_SY01_P1_I04_180926A_SPRI_263_200507

description:
XN_SY01_P1_I04_180926A_SPRI_263_200507
47K SNPs


title: peanut-XN_SY01_P1_I03_180926C_SPRI-091_210107

description:
XN_SY01_P1_I03_180926C_SPRI-091_210107
47K SNPs


title: Heart, XML_RBPMS-2_1


title: Heart, XML_Ctrl_3

value: RBPMS flox/flox RBPMS2 flox/flox


title: Heart, XML_Ctrl_2


title: peanut-XN_SY01_P1_I03_180926A_SPRI_164_200507

description:
XN_SY01_P1_I03_180926A_SPRI_164_200507
47K SNPs


title: peanut-XN_SY01_P1_I02_180926A_SPRI_262_200507

description:
XN_SY01_P1_I02_180926A_SPRI_262_200507
47K SNPs


title: Heart, XML_Ctrl_1


title: peanut-XN_SY01_P1_I01_180926C_SPRI-090_210107

description:
XN_SY01_P1_I01_180926C_SPRI-090_210107
47K SNPs


title: ADR_Sal_4


title: peanut-XN_SY01_P1_I01_180926A_SPRI_163_200507

description:
XN_SY01_P1_I01_180926A_SPRI_163_200507
47K SNPs


title: peanut-XN_SY01_P1_I07_180926C_SPRI-096_210107

description:
XN_SY01_P1_I07_180926C_SPRI-096_210107
47K SNPs


title: ADR_Sal_5


title: Heart, aMyHC_RBPMS-2_3

data_processing:
Trimmomatic was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome assembly mm10 with STAR 2.4.2a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Gene counts were established with featureCounts 1.5.0 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). 4µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, with 2x75bp paired end setup.

value: RBPMS flox/flox RBPMS2 flox/flox aMyHC Cre pos


title: peanut-XN_SY01_P1_I06_180926A_SPRI_264_200507

description:
XN_SY01_P1_I06_180926A_SPRI_264_200507
47K SNPs

value: leaf


title: ADR_Dex_5


title: 231JAG1KO-R tumor 5

description:
Library name: KW1311_5J
KW1311_5J_1


title: peanut-XN_SY01_P1_H24_180926B_SPRI_35_200507

description:
XN_SY01_P1_H24_180926B_SPRI_35_200507
47K SNPs


title: ADR_Dex_4


title: peanut-XN_SY01_P1_H23_180926A_SPRI_363_200507

description:
XN_SY01_P1_H23_180926A_SPRI_363_200507
47K SNPs


title: peanut-XN_SY01_P1_H17_180926A_SPRI_360_200507

description:
XN_SY01_P1_H17_180926A_SPRI_360_200507
47K SNPs


title: Heart, aMyHC_RBPMS-2_1


title: peanut-XN_SY01_P1_H16_180926B_SPRI_29_200507

description:
XN_SY01_P1_H16_180926B_SPRI_29_200507
47K SNPs


title: peanut-XN_SY01_P1_H20_180926B_SPRI_32_200507

description:
XN_SY01_P1_H20_180926B_SPRI_32_200507
47K SNPs


title: Heart, aMyHC_RBPMS-2_2


title: peanut-XN_SY01_P1_H22_180926B_SPRI_33_200507

description:
XN_SY01_P1_H22_180926B_SPRI_33_200507
47K SNPs


title: peanut-XN_SY01_P1_H15_180926A_SPRI_359_200507

description:
XN_SY01_P1_H15_180926A_SPRI_359_200507
47K SNPs


title: Heart, aMyHC_Ctrl_2


title: peanut-XN_SY01_P1_H18_180926B_SPRI_31_200507

description:
XN_SY01_P1_H18_180926B_SPRI_31_200507
47K SNPs


title: peanut-XN_SY01_P1_H21_180926A_SPRI_362_200507

description:
XN_SY01_P1_H21_180926A_SPRI_362_200507
47K SNPs


title: peanut-XN_SY01_P1_H14_180926B_SPRI_28_200507

description:
XN_SY01_P1_H14_180926B_SPRI_28_200507
47K SNPs


title: Heart, aMyHC_Ctrl_1


title: peanut-XN_SY01_P1_H13_180926A_SPRI_358_200507

description:
XN_SY01_P1_H13_180926A_SPRI_358_200507
47K SNPs


title: peanut-XN_SY01_P1_H12_180926B_SPRI_20_200507

description:
XN_SY01_P1_H12_180926B_SPRI_20_200507
47K SNPs


title: ND_hypoxia_rep3

city: Syracuse

first: Norifumi

last: Urao

state: New York

address: 750 E. Adams St.

department: Pharmacology

institute: SUNY Upstate Medical University

data_processing:
The fastq files were processed using PartekFlow (Partek Inc., St. Louis, MO, USA).  The raw reads were aligned to reference genome mm10 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using mm10 assembly and Ensemble transcripts release 100_v2 and Partek E/M method. The normalization was performed with median ratio through PartekFlow.
Differential expresison analysis was performed using Partek gene-specific analysis (GSA) and results were filtered with p<0.05 and |Fold change|> 1.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow derived macrophages

growth_protocol: BMDMs were derived from whole bone marrow cells and were cultured in DMEM with 10% FBS, pen/strep and 20ng/ml of M-CSF at 37C at 5% CO2. Media was changed to Macrophage-SFM with 20ng/ml of M-CSF at day4.

extract_protocol:
Cells were lysed with TRI Reagent (Zymo Research), and total RNA was extracted with Direct-zol RNA Miniprep Kit (Zymo Research) according to manufacturer’s instructions. RNA quantity was evaluated with QubitFlex and Qubit broad range RNA assay kit (ThermoFisher). The quality of RNA samples was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies), and all samples showed RNA integrity number > 9.
RNA sequencing libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina). Once prepared indexed cDNA libraries were pooled in equimolar amounts and sequenced with single-end 75bp reads on an Illumina NextSeq500. 100 ng of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Cells were cultured in 1% O2 hypoxia chamber for 1 hour at day7

value: Bone marrow derived macrophages

value: Macrophages

value: Normal diet_hypoxia


title: SPL_Sal_4

value: Spleen


title: ADR_Sal_2


title: ADR_Dex_1


title: UNG_Dex_5

value: Lung


title: peanut-XN_SY01_P1_H19_180926A_SPRI_361_200507

description:
XN_SY01_P1_H19_180926A_SPRI_361_200507
47K SNPs


title: ADR_Dex_2


title: peanut-XN_SY01_P1_H10_180926B_SPRI_16_200507

description:
XN_SY01_P1_H10_180926B_SPRI_16_200507
47K SNPs


title: peanut-XN_SY01_P1_H11_180926A_SPRI_357_200507

description:
XN_SY01_P1_H11_180926A_SPRI_357_200507
47K SNPs


title: peanut-XN_SY01_P1_H09_180926A_SPRI_356_200507

description:
XN_SY01_P1_H09_180926A_SPRI_356_200507
47K SNPs


title: ADR_Dex_3


title: peanut-XN_SY01_P1_H08_180926B_SPRI_13_200507

description:
XN_SY01_P1_H08_180926B_SPRI_13_200507
47K SNPs


title: Heart, aMyHC_Ctrl_3


title: peanut-XN_SY01_P1_H05_180926A_SPRI_354_200507

description:
XN_SY01_P1_H05_180926A_SPRI_354_200507
47K SNPs


title: ND_hypoxia_rep2


title: ADR_Sal_3


title: peanut-XN_SY01_P1_H07_180926A_SPRI_355_200507

description:
XN_SY01_P1_H07_180926A_SPRI_355_200507
47K SNPs


title: ADR_Sal_1


title: HFD_hypoxia_rep3

value: High-fat diet_hypoxia


title: peanut-XN_SY01_P1_H04_180926A_SPRI_497_200507

description:
XN_SY01_P1_H04_180926A_SPRI_497_200507
47K SNPs


title: HFD_hypoxia_rep2


title: peanut-XN_SY01_P1_H03_180926A_SPRI_353_200507

description:
XN_SY01_P1_H03_180926A_SPRI_353_200507
47K SNPs


title: DSS treated littermate control mice-6

city: Chengdu

first: Ming

last: Chen

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

institute: West China Hospital of Sichuan University

description: Library name: WT-6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm39
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: csv fles include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was harvested using Trizol from colon tissues
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: colon

value: 2.5%DSS treated 7 days


title: ND_hypoxia_rep1

value: WT


title: FAT_Sal_5+10

value: Adipose

value: Saline


title: HFD_hypoxia_rep1


title: peanut-XN_SY01_P1_H02_180926A_SPRI_494_200507

description:
XN_SY01_P1_H02_180926A_SPRI_494_200507
47K SNPs


title: FAT_Dex_1+3

value: Dexamethasone


title: peanut-XN_SY01_P1_H01_180926A_SPRI_352_200507

description:
XN_SY01_P1_H01_180926A_SPRI_352_200507
47K SNPs


title: ND_normoxia_rep2

value: Normal diet_normoxia


title: DSS treated littermate control mice-4

description: Library name: WT-4


title: DSS treated littermate control mice-5

description: Library name: WT-5


title: ND_normoxia_rep3


title: peanut-XN_SY01_P1_G24_180926A_SPRI_261_200507

description:
XN_SY01_P1_G24_180926A_SPRI_261_200507
47K SNPs


title: DSS treated littermate control mice-3

description: Library name: WT-3


title: peanut-XN_SY01_P1_G23_180926C_SPRI-089_210107

description:
XN_SY01_P1_G23_180926C_SPRI-089_210107
47K SNPs


title: ND_normoxia_rep1


title: FAT_Sal_11+9


title: FAT_Sal_8+2


title: DSS treated littermate control mice-2

description: Library name: WT-2


title: HFD_normoxia_rep3

value: High-fat diet_normoxia


title: FAT_Dex_9+11


title: FAT_Dex_7+5


title: FAT_Sal_12


title: peanut-XN_SY01_P1_G23_180926A_SPRI_162_200507

description:
XN_SY01_P1_G23_180926A_SPRI_162_200507
47K SNPs


title: FAT_Sal_6


title: FAT_Sal_3


title: peanut-XN_SY01_P1_G22_180926A_SPRI_260_200507

description:
XN_SY01_P1_G22_180926A_SPRI_260_200507
47K SNPs


title: DSS treated littermate control mice-1

description: Library name: WT-1


title: HFD_normoxia_rep2


title: FAT_Dex_10


title: DSS treated PCK1 intestinal epithelial cell-specific knockout mice-6

description: Library name: CKO-6

value: CKO


title: HFD_normoxia_rep1


title: peanut-XN_SY01_P1_G21_180926C_SPRI-088_210107

description:
XN_SY01_P1_G21_180926C_SPRI-088_210107
47K SNPs


title: BZIP111_B73

value: seedling leaf

value: DAP-seq


title: peanut-XN_SY01_P1_G21_180926A_SPRI_161_200507

description:
XN_SY01_P1_G21_180926A_SPRI_161_200507
47K SNPs

value: leaf


title: DSS treated PCK1 intestinal epithelial cell-specific knockout mice-5

description: Library name: CKO-5


title: Hom retina 5 prime

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing: Single-nuclei RNA-seq data was processed using mkfastq and count command from 10X Genomics CellRanger v3.0.1.

source_name: retina

extract_protocol:
Surgically resected cortical or retinal tissues were homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol while single cell rna-seq libraries were prepared using the Chromium Single Cell 5’  kit

tag: source

value: single-nucleus

value: HOM

tag: age

value: 12 months old


title: DSS treated PCK1 intestinal epithelial cell-specific knockout mice-4

description: Library name: CKO-4


title: peanut-XN_SY01_P1_G20_180926A_SPRI_259_200507

description:
XN_SY01_P1_G20_180926A_SPRI_259_200507
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 28, biol rep 3

city: Gainesville

first: Chanhee

last: Kim

state: Florida

address: 2187 Mowry Road

department: Physiological sciences

institute: University of Florida

description: Day 28_3

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Human.GRCh38.p13.annot.tsv.gz, Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: comma-separated csv.file which includes raw_gene counts for each sample

source_name: Liver

growth_protocol: HepG2/C3A human liver cells were maintained in MEM media supplemented with 10 % FBS, 1 % MEM non-essential amino acids, 1 % Antibiotic-Antimycotic in humidified atmosphere with 5 % CO2 at 37C

extract_protocol:
Total RNA was extracted using RNeasy mini plus kit (qiagen). 100 ng of total RNA per sample was used to construct TempO-Seq sequencing libraries.
RNA libraries for TempO-Seq were prepared using TempO-Seq assay kit provided by BioSpyer following the manufacturer's instruction.
TempO-Seq

treatment_protocol: 2D monolayered HepG2/C3A cells were forced to aggregate to form spheroids using ultra-low attachment plates (SP5D) and kept in ClinoReactor (CelVivo) for long-term 3D culture

value: Liver

value: Epithelial-like

value: Spheroid formation, Day 28


title: DSS treated PCK1 intestinal epithelial cell-specific knockout mice-3

description: Library name: CKO-3

value: colon

value: 2.5%DSS treated 7 days


title: WT  retina 5 prime

value: WT


title: peanut-XN_SY01_P1_G19_180926C_SPRI-085_210107

description:
XN_SY01_P1_G19_180926C_SPRI-085_210107
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 28, biol rep 2

description: Day 28_2


title: HepG2/C3A, 3D spheroid, Day 28, biol rep 1

description: Day 28_1


title: FAT_Dex_8

value: Adipose


title: FAT_Dex_9

value: Dexamethasone


title: HepG2/C3A, 3D spheroid, Day 21, biol rep 3

description: Day 21_3

value: Spheroid formation, Day 21


title: DSS treated PCK1 intestinal epithelial cell-specific knockout mice-1

description: Library name: CKO-1


title: peanut-XN_SY01_P1_G18_180926A_SPRI_258_200507

description:
XN_SY01_P1_G18_180926A_SPRI_258_200507
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 21, biol rep 2

description: Day 21_2


title: peanut-XN_SY01_P1_G17_180926C_SPRI-083_210107

description:
XN_SY01_P1_G17_180926C_SPRI-083_210107
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 21, biol rep 1

description: Day 21_1


title: Hom cortex 5 prime

source_name: prefontal Cortex


title: Ex vivo, E4.5 embryo

city: Suita

first: Takehiro

last: Hiraoka

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
Barcode processing, gene counting and aggregation were made using Cell Ranger v8.0.0
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: .tsv.gz/ cell barcode and features, .mtx.gz/ count matrix

source_name: E4.5 embryo (ex vivo)

extract_protocol:
E4.5 in vivo embryos and 24h-cultured ex vivo embryos were microscopically isolated, immediately soaked in Accumax (Nacalai Tesque, Japan) at room temperature, and dissociated with glass capillaries. The capillaries were sequentially changed from thicker to thinner ones, and only dispersed single cells were manually picked up into 0.04% BSA (wt/vol) in PBS(-).
The single-cell suspension from a total of 33 in vivo embryos at E4.5 from 4 mice and 32 ex vivo embryos at 24h from 4 donor mice was immediately processed for RNA sequencing library preparation using Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1 (PN-1000268, 10x genomics, USA), Chromium Next GEM Chip G Single Cell Kit　(PN-1000120, 10x genomics, USA), and Chromium iX (10x genomics, USA).

value: E4.5 embryo (ex vivo)


title: peanut-XN_SY01_P1_G17_180926A_SPRI_159_200507

description:
XN_SY01_P1_G17_180926A_SPRI_159_200507
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 14, biol rep 3

description: Day  14_3

value: Spheroid formation, Day 14


title: Hom retina 3 prime

value: single cell


title: peanut-XN_SY01_P1_G16_180926A_SPRI_257_200507

description:
XN_SY01_P1_G16_180926A_SPRI_257_200507
47K SNPs


title: In vivo, E4.5 embryo

source_name: E4.5 embryo

value: E4.5 embryo


title: WT retina 3 prime


title: HepG2/C3A, 3D spheroid, Day 14, biol rep 2

description: Day  14_2


title: WT cortex 5 prime


title: DSS treated PCK1 intestinal epithelial cell-specific knockout mice-2

description: Library name: CKO-2

value: CKO


title: Mab treated with HC2210, Rep 2

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

description: Library name: Mab_HC2210_Rep2_S96

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5).
The sequencing reads were analyzed using the commercially licensed CLC Genomics Suite
Assembly: M. tuberculosis CDC1551 genome (NCBI accession AE000516), M. abscessus  ATCC 19977 (GCA_000069185.1)
Supplementary files format and content: Processed files are presented as .xlsx spreadsheets and represents the average of 2 biological replicates
Supplementary files format and content: Dataset 1_Mab_HC2210 vs DMSO.xlsx
Supplementary files format and content: Dataset 2_Mtb_HC2210 vs DMSO and PA824 vs DMSO.xlsx

organism: Mycobacteroides abscessus ATCC 19977

source_name: Bacterial Cell

growth_protocol: Mab cultures were cultured for 24 hours in T25 standing flasks in a 37C incubator (without 5% CO2). Mtb cultures were incubated in T25 standing flasks at 37C, 5% CO2 for 24 hours.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: For Mab, cultures were treated with 10 uM HC2210 or an equivalent volume of DMSO for 24 hours. For Mtb, cultures were treated with 2 uM HC2210 or PA824 or equivalent volume of DMSO for 24 hours.

value: Bacterial Cell


title: peanut-XN_SY01_P1_G15_180926C_SPRI-082_210107

description:
XN_SY01_P1_G15_180926C_SPRI-082_210107
47K SNPs

value: leaf


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_72CAG_rep3_1

city: Cambridge

first: Matthew

last: Leventhal

state: MA

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

institute: Massachusetts Institute of Technology

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

data_processing:
We processed the ATAC-seq data using the ENCODE-DCC ATAC-seq pipeline v.1.7.1. Using this pipeline, we identified FASTQ read adaptors with the detect_adapter.py script in GGR_code (https://github.com/nboley/GGR_code). We trimmed read adaptors with the trim_adaptors function in cutadapt 1.9.1. Processed FASTQs, were aligned using Bowtie2 version 2.2.6, requiring SAMtools version 1.7 and SAMstats version 0.2.1. Picard tools version 1.126 MarkDuplicates was used to deduplicate the aligned reads. These tools were used with default parameters except for setting the parameters “atac.auto_adect_adapter” and “atac.enable_xcor” to “true”.
The ChIP-seq data was analyzed using the ENCODE-DCC ChIP-seq pipeline v1.3.6. In this pipeline, FASTQ data were cropped with Trimmomatic 0.39, aligned with Bowtie2 version 2.26 and deduplicated with Picard version 1.126 MarkDuplicates. Default parameters were used for all arguments except for setting “chip.pipeline_type” to “histone”.
From the aligned, deduplicated ATAC-seq data, MACS2 version 2.1.0 was used to identify peaks that had significant local enrichments at a p-value threshold of 0.01. For the aligned, deduplicated ChIP-seq data, peak calling was performed using SPP version 1.14, GEM 2.4.1 and PeakSeq version 1.25. IDR 2.0.4 was run to determine a high-quality set of consensus peaks from the results of the multiple peak callers. Upon identifying peaks, DiffBind version 2.10.0 was used to perform differential analysis between ChIP-seq or ATAC-seq peaks for the following comparisons: HTT knock-out vs. control, HTT HD knockdown vs HTT wild-type HD, 56/22 (adult onset) HD vs control, and 72/20 (expanded repeat length) HD vs control. We refer to the union of peaks found in 20/20 and 22/20 cells as “control” in these comparisons. DiffBind in R version 3.5.2 was used to identify differential peaks as those with an FDR-adjusted p-value less than 0.1
To determine similarities and differences across cortical neuron replicates and genotypes in the ATAC-seq or ChIP-seq data, Principal Component Analysis (PCA) was used as implemented in Scikit-Learn version 0.23.2. To preprocess the data, peaks were limited to those that were within 5kb from a protein-coding gene. The signal of the filtered peaks was standardized before performing PCA with 10 principal components. Replicates were removed from the analysis if they failed the ATAC-seq or ChIP-seq ENCODE benchmarks determined from FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with peaks quantified with MACS2

source_name: Human pluripotent stem cell line

extract_protocol:
For Atac-seq, We used 50,000 nuclei for the transposase reaction, following the method described previously. Subsequently, samples were purified with the DNA Clean & Concentrator–5 Kit (Zymo Research), and then PCR-amplified using Nextera indexing primers (Illumina). The number of PCR cycles were optimized by qPCR to avoid over amplification of the libraries. The final libraries were purified using 1x PCRClean DX beads (Aline Biosciences). The enrichment of accessible chromatin regions in the libraries were assessed by qPCR using primers mapped to open chromatin region and gene desert regions. For ChIP-seq data 1X106 cells were incubated in lysis buffer (50 mM Tris-HCL pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% Na- deoxycholate, and 5 mM CaCl2 supplemented with protease inhibitors and 10 mM sodium butyrate for K27ac ChIP) for 20 min on ice. The chromatin was digested to 1-5 nucleosomes using Micrococcal Nuclease (NEB # M0247S), at concentration determined by titration experiments, for 10 min at 37oC. To terminate the digestion, 20 mM EDTA was added to the samples. The antibody was added and incubated overnight at 4oC. On the next day, 25 µl of protein G Dynabeads (Thermo Scientific # 10004D,) was added and the samples rotated for 2 hr at 4oC. The beads were washed 6 times: 2 washes with RIPA buffer (10 mM Tris-HCl pH8, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), 2 washes with high salt buffer (10 mM Tris-HCl pH8, 1 mM EDTA, 360 mM NaCl, 1% Triton X- 100, 0.1% Na-deoxycholate, 0.1% SDS), 2X washes with LiCl buffer (10 mM Tris-HCl pH8, 1  mM EDTA, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% Na-deoxycholate) and 1 wash with TE (10 mM Tris-HCl pH8, 1 mM EDTA). The DNA was eluted by incubation of the beads in elution buffer (10 mM Tris-HCl pH8, 5 mM EDTA, 300 mM NaCl, 0.1% SDS, 50 µg Proteinase K) for 1 hr. at 62 and purified with 1X PCRClean DX beads (Aline Biosciences).
For Atac-seq, samples were purified with the DNA Clean & Concentrator–5 Kit (Zymo Research), and then PCR-amplified using Nextera indexing primers (Illumina). The number of PCR cycles were optimized by qPCR to avoid over amplification of the libraries. For ChIP-seq, The sequencing libraries were constructed using the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina (NEB # E7645S), followed by analysis using Fragment Analyzer™ instrument (Advanced Analytical), and quantification by a qPCR-based method (KAPA Library Quantification Kit for Illumina Sequencing Platforms)

value: Human pluripotent stem cell line


title: 231JAG1KOCon tumor 2

description:
Library name: KW1299_2C
KW1299_2C_1

value: mammary tumor

value: human TNBC

value: empty vector


title: peanut-XN_SY01_P1_G19_180926A_SPRI_160_200507

description:
XN_SY01_P1_G19_180926A_SPRI_160_200507
47K SNPs


title: Het retina 3 prime

value: HET

value: 12 months old


title: HepG2/C3A, 3D spheroid, Day 14, biol rep 1

description: Day  14_1

value: Liver

value: Epithelial-like

value: WT


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_72CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: Mab treated with HC2210, Rep 1

description: Library name: Mab_HC2210_Rep_1_S95


title: peanut-XN_SY01_P1_G15_180926A_SPRI_158_200507

description:
XN_SY01_P1_G15_180926A_SPRI_158_200507
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 10, biol rep 3

description: Day  10_3

value: Spheroid formation, Day 10


title: Mab treated with DMSO, Rep 2

description: Library name: Mab_DMSO_Rep_2_S94


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_72CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: mixed library for mouse endometrial tissues from IS in vivo, I-IS in vivo, IS ex vivo, and I-IS ex vivo, dpc 4.5

description: 10x Genomics

library_source: other

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger v8.0.0
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: .tsv.gz/ cell barcode and features, .mtx.gz/ count matrix

molecule: other

source_name: Endometrium, dpc 4.5

extract_protocol:
Dpc 4.5 uterine lumen was gently flushed with 10% neutral buffered formalin (Nacalai Tesque, Japan) immediately after sacrifice, and implantation sites (ISs) and inter-implantation sites (I-ISs) were microscopically excised into approximately 500 μm size. Finally, a total of 66 ISs and 70 I-ISs from 7 mice were isolated. Similarly, 24h ex vivo ISs and I-ISs were microscopically collected after 10% NBF fixation. A total of 56 ISs and 81 I-ISs from 3 recipient mice were obtained. Isolated samples were processed using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (PN-1000414, 10x genomics, USA), and tissue dissociation was performed with Liberase TL (Roche, Switzerland) in RPMI1640 (Thermo Fisher Scientific, USA) using gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotech, Germany).
After cell counting, the single-cell suspension was treated for RNA sequencing library preparation with Chromium Fixed RNA Kit, Mouse Transcriptome (PN-1000496, 10x genomics, USA), Chromium Mouse Transcriptome Probe Set v1.0.1 (10x genomics, USA), and Chromium X (10x genomics, USA). Samples derived from four different conditions (IS in vivo, interIS in vivo, IS ex vivo, and interIS ex vivo) were mixed.

value: Endometrium, dpc 4.5

value: mixed sample (IS in vivo, I-IS in vivo, IS in vitro, I-IS in vitro)


title: peanut-XN_SY01_P1_G14_180926A_SPRI_256_200507

description:
XN_SY01_P1_G14_180926A_SPRI_256_200507
47K SNPs

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console® (version 2.0). The raw data CEL files were typed using Axiom Analysis Suite 3.1.51, according to each site A set of indicators assigned to a specified type: PolyHighResolution, NoMinorHom,  MonoHighResolution, OTV,  CallRateBelowThreshold, Other.
Genotype Call (SNP call): AA, AB, BB, NC.

extract_protocol: Young healthy leaves from each accession were collected, with extraction of total genomic DNA via a Plant Genomic DNA Kit (Tiangen Biotech (Beijing) Co., Ltd.). The extracted DNA quality and concentration were determined via 0.8% agarose gel electrophoresis using standard lambda DNA and a NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Wilmington, DE, USA)


title: Mab treated with DMSO, Rep 1

description: Library name: Mab_DMSO_Rep_1_S93


title: HepG2/C3A, 3D spheroid, Day 10, biol rep 2

description: Day  10_2


title: Het cortex 5 prime

value: single-nucleus


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_56CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_G13_180926C_SPRI-081_210107

description:
XN_SY01_P1_G13_180926C_SPRI-081_210107
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 10, biol rep 1

description: Day  10_1


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_56CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Lab, 207810940113_R05C02

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description:
Liver methylome in lab mice
207810940113_R05C02

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings
GEO_processed_matrix_GPL30650.csv (Normalized average Beta)
GEO_signal_intensity_matrix_GPL30650.csv (Unmethylated and methylated signal intensities)

label: Cy5 and Cy3

source_name: primary liver tissue

label_protocol: Standard Illumina Protocol

extract_protocol: A Phenol/Chloroform/Isoamyl alcohol protocol was employed (Molecular cloning: a laboratory manual. No. Ed. 2. Cold Spring Harbor laboratory press, 1989) to extract genomic DNA from mouse liver tissues. The whole liver tissue was homogenized using a tissue homogenizer (OMNI, TH115) in 500 µl of lysis buffer containing 10 mM Tris pH 8.0 (VWR, 97062-674), 300 mM NaCl (VWR, 10128-484), 0.5% SDS (Invitrogen, 15553027), and 5 mM EDTA (VWR, 10128-442). After adding 15 µl of Proteinase K (NEB, P8107S), the solution was incubated at 55°C overnight. Subsequently, 100 µl of the solution was combined with an additional 400 µl of lysis buffer and incubated at 55°C for 2 hours. The 500 µl of the solution was placed into a 5PRIME Phase Lock Gel tube (Quanta bio, 10847-802) pre-centrifuged for 1 minute. 500 µl of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich 77617) was added to the phase Lock Gel tube. The aqueous phase solution was transferred to a new 1.5 mL centrifuge tube (Eppendorf, 05414203). 500 µl of 100% isopropanol (MilliporeSigma, EM1.09634.1011), GlycoBlue (Invitrogen™, AM9515), and Ammonium acetate solution 7.5M (Sigma-Aldrich, A2706) were added to the tube. The solution was vortexed and incubated at -20°C for 30 min up to O/N. Samples were centrifuged at 16,000g for 30 min at 4°C and washed twice by adding 1 ml 70% EtOH (MilliporeSigma, EM1.00983.1011). After the last wash and removal of 70% EtOH, the samples were air-dried for 10 min and resuspended in 200 µl of the Tris buffer pH8.0 (VWR, 97062-674), and incubated at 55°C for 10 min. DNAs that were not completely dissolved were incubated at 4°C for overnight. If the dissolved DNA did not exhibit a transparent color or the DNA quantity was inadequate, an additional bead purification step was carried out. Briefly, 2x volume of AMpure XP (Beckman Coulter, A63881) was added to the DNAs, mixed thoroughly, briefly spun down, incubated the mixture for 5 min at room temperature, placed on a magnet stand, and washed 2 times with 500 μl of freshly made 80% EtOH, allowed to dry for 3 to 5 mins. The final elution was performed using 100 ~ 200 μl autoclaved ultrapure water. DNA amount was measured using the Qubit 4 Fluorometer (Invitrogen) with the dsDNA HS Assay Kit (Invitrogen, Q33231).

tag: Sex

value: male

tag: environment

value: Lab


title: peanut-XN_SY01_P1_G13_180926A_SPRI_157_200507

description:
XN_SY01_P1_G13_180926A_SPRI_157_200507
47K SNPs


title: peanut-XN_SY01_P1_G12_180926A_SPRI_255_200507

description:
XN_SY01_P1_G12_180926A_SPRI_255_200507
47K SNPs


title: liver, Lab, 207810940113_R01C02

description:
Liver methylome in lab mice
207810940113_R01C02


title: liver, Lab, 207810940112_R03C01

description:
Liver methylome in lab mice
207810940112_R03C01


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_56CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_G11_180926C_SPRI-080_210107

description:
XN_SY01_P1_G11_180926C_SPRI-080_210107
47K SNPs


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_22CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: HepG2/C3A, 3D spheroid, Day 7, biol rep 3

description: Day 7_3

value: Spheroid formation, Day 7


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_22CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: HepG2/C3A, 3D spheroid, Day 7, biol rep 2

description: Day 7_2


title: HepG2/C3A, 3D spheroid, Day 7, biol rep 1

description: Day 7_1


title: peanut-XN_SY01_P1_G11_180926A_SPRI_156_200507

description:
XN_SY01_P1_G11_180926A_SPRI_156_200507
47K SNPs

value: leaf


title: HepG2/C3A, 3D spheroid, Day 3, biol rep 3

description: Day 3_3

value: Spheroid formation, Day 3


title: liver, Lab, 207810940109_R01C02

description:
Liver methylome in lab mice
207810940109_R01C02

value: female


title: liver, Lab, 207810940111_R05C01

description:
Liver methylome in lab mice
207810940111_R05C01


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_22CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: UNG_DEX_6

data_processing: The data were preprocessed using beadarray R package and normalized using quantile normalization.

extract_protocol: RNA was isolated using RNeasy Mini Kit (Qiagen Inc.) and further purified following the manufacturer's protocol. Total RNA concentration was measured using a NanoDrop ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA). RNA quality was determined by chip-based capillary electrophoresis using RNA 6000 Nano LabChip Kits and an Agilent Bioanalyzer 2100 device (Agilent, Palo Alto, CA, USA). RNA from two mice was randomly pooled to prepare a sample for each microarray.

value: Lung

value: Dexamethasone


title: peanut-XN_SY01_P1_G10_180926A_SPRI_254_200507

description:
XN_SY01_P1_G10_180926A_SPRI_254_200507
47K SNPs


title: HepG2/C3A, 3D spheroid, Day 3, biol rep 2

description: Day 3_2

value: Liver


title: HepG2/C3A, 3D spheroid, Day 3, biol rep 1

description: Day 3_1

value: Epithelial-like


title: liver, Lab, 207810940109_R01C01

description:
Liver methylome in lab mice
207810940109_R01C01


title: peanut-XN_SY01_P1_G09_180926C_SPRI-079_210107

description:
XN_SY01_P1_G09_180926C_SPRI-079_210107
47K SNPs


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_20CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 20CAG control


title: liver, Lab, 207810940053_R01C01

description:
Liver methylome in lab mice
207810940053_R01C01


title: liver, Field, 207363410108_R06C02

description:
Liver methylome in rewilded mice
207363410108_R06C02

value: Field


title: HepG2/C3A, 2D monolayer, biol rep 2

value: WT

value: monolayer culture (control)


title: HepG2/C3A, 2D monolayer, biol rep 3


title: liver, Lab, 207810940053_R05C02

description:
Liver methylome in lab mice
207810940053_R05C02


title: peanut-XN_SY01_P1_G08_180926A_SPRI_253_200507

description:
XN_SY01_P1_G08_180926A_SPRI_253_200507
47K SNPs


title: peanut-XN_SY01_P1_G09_180926A_SPRI_155_200507

description:
XN_SY01_P1_G09_180926A_SPRI_155_200507
47K SNPs


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_20CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_G07_180926C_SPRI-076_210107

description:
XN_SY01_P1_G07_180926C_SPRI-076_210107
47K SNPs


title: HepG2/C3A, 2D monolayer, biol rep 1


title: peanut-XN_SY01_P1_G07_180926A_SPRI_130_200507

description:
XN_SY01_P1_G07_180926A_SPRI_130_200507
47K SNPs


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: HTT KO


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410108_R05C02

description:
Liver methylome in rewilded mice
207363410108_R05C02


title: 4E-S3

city: Fuzhou

first: Kun

last: Zhang

address: Dadao Street 190

department: General Surgery

institute: Fuzhou First General Hospital affliated with Fujian Medical University

description:
4E-S3_FPKM
all.fpkm_anno.xls

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, orfragments thereof, and quality of bases lower than 20, pass filter data of fastg format were processed byCutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: lbp, min. length: 75, proportion of N:0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloadedfrom genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to indexreference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2(v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexedproperly. Then, with the file as a reference gene file, HTSeg (v0.6.1) estimated gene and isoformexpression levels from the pair-end clean data.
Assembly: hg38
Supplementary files format and content: Excel data sheet file includes raw counts for each Sample
Supplementary files format and content: Excel data sheet files include RPKM values for each Sample

source_name: Colorectal cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Colorectal cancer

value: genetic modification

value: TIPE overexpressed


title: peanut-XN_SY01_P1_G06_180926A_SPRI_252_200507

city: Qingdao

first: jing

last: xu

address: 126 Wannianquan Road

institute: Shandong Peanut Research Institute

description:
XN_SY01_P1_G06_180926A_SPRI_252_200507
47K SNPs


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410108_R05C01

description:
Liver methylome in rewilded mice
207363410108_R05C01


title: 4E-S2

description:
4E-S2_FPKM
all.fpkm_anno.xls


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_72CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410108_R04C02

description:
Liver methylome in rewilded mice
207363410108_R04C02


title: Embryonic_stem_cell_H3K4me1_ChIP_seq_20CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me1_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: 4E-S1

description:
4E-S1_FPKM
all.fpkm_anno.xls


title: peanut-XN_SY01_P1_G05_180926C_SPRI-073_210107

description:
XN_SY01_P1_G05_180926C_SPRI-073_210107
47K SNPs


title: 4v-S3

description:
4v-s3_FPKM
all.fpkm_anno.xls

value: control


title: peanut-XN_SY01_P1_G05_180926A_SPRI_129_200507

description:
XN_SY01_P1_G05_180926A_SPRI_129_200507
47K SNPs


title: liver, Field, 207363410108_R04C01

description:
Liver methylome in rewilded mice
207363410108_R04C01


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_72CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_72CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_G04_180926A_SPRI_251_200507

description:
XN_SY01_P1_G04_180926A_SPRI_251_200507
47K SNPs

value: leaf


title: liver, Field, 207363410108_R06C01

description:
Liver methylome in rewilded mice
207363410108_R06C01


title: liver, Field, 207363410108_R03C02

description:
Liver methylome in rewilded mice
207363410108_R03C02


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_56CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410108_R03C01

description:
Liver methylome in rewilded mice
207363410108_R03C01


title: peanut-XN_SY01_P1_G03_180926C_SPRI-072_210107

description:
XN_SY01_P1_G03_180926C_SPRI-072_210107
47K SNPs


title: liver, Field, 207363410108_R02C02

description:
Liver methylome in rewilded mice
207363410108_R02C02


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_56CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: 4v-S2

description:
4v-s2_FPKM
all.fpkm_anno.xls


title: H1 ESCs，E7+NODAL+2DG3, 24h.2

city: macau

first: Chengcheng

last: SONG

address: universtiy of macau

department: fhs

country: Macau

institute: university of macau

data_processing:
Quality control of RNA-seq raw data was performed using Trimmomatic version 0.36
RNA-seq clean data alignment was conducted using STAR version 020201 with the reference genome hg38.
All genes expression were quantified using FeatureCounts version 1.5.3
Differential expression genes (DEGs) were identified with the criteria of p adjusted value < 0.05 and the absolute value of log2(Fold Change) > 1 after profile normalized using DESeq2 version 1.26.0
DEGs analysis were performed the GO and KEGG enrichment analysis through the R package ClusterProfiler 4.0
Assembly: hg38
Supplementary files format and content: Tab-delimited file reports normalized counts

source_name: E7 treatment with NODAL and 2DG 3mM for 24h in H1 ESCs

growth_protocol: H1 ESCs  was maintained in E8 medium supplemented with  antibiotics  with 5% CO2 at 37C. E8 medium contained DMEM/F12, sodium selenite, ascorbic acid trisodium, transferrin, insulin, FGF2 and TGFβ.

extract_protocol:
Cells was harvested in RNAiso Plus reagent (Takara). The poly(A) mRNA isolation was performed using Oligo(dT) beads according to manufacturer’s instructions
1 μg total RNA was used for following library preparation. The RNA Library were sequenced for paired end reads on Illumina NextSeq 500 (Illumina).

treatment_protocol: 2DG 3mM was treated with E7 medium (E8-TGFb) in H1 ESCs. Nodal 100ng/mL, Activin A 100ng/mL and TGFb 1.74ng/mL were used for treatment with or without 2DG treatment.

value: Human embryonic stem cells

value: E7+NODAL+2DG3, 24h


title: peanut-XN_SY01_P1_G02_180926A_SPRI_250_200507

description:
XN_SY01_P1_G02_180926A_SPRI_250_200507
47K SNPs


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_22CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: liver, Field, 207363410108_R02C01

description:
Liver methylome in rewilded mice
207363410108_R02C01

value: male


title: peanut-XN_SY01_P1_G01_180926C_SPRI-071_210107

description:
XN_SY01_P1_G01_180926C_SPRI-071_210107
47K SNPs


title: H1 ESCs，E7+NODAL+2DG3, 24h.1


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_56CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410108_R01C02

description:
Liver methylome in rewilded mice
207363410108_R01C02

value: female

value: Liver


title: H1 ESCs，E7+NODAL, 24h.2

source_name: E7 treatment with NODAL 100 ng/mL for 24h in H1 ESCs

value: E7+NODAL, 24h


title: peanut-XN_SY01_P1_G01_180926A_SPRI_127_200507

description:
XN_SY01_P1_G01_180926A_SPRI_127_200507
47K SNPs


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_22CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410108_R01C01

description:
Liver methylome in rewilded mice
207363410108_R01C01

value: Field


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_22CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: ADR_Dex_6

city: Krakow

first: Michal

last: Korostynski

address: Smetna 12

institute: Maj Institute of Pharmacology PAS

source_name: mouse tissues

value: Adrenal Gland

value: Dexamethasone


title: peanut-XN_SY01_P1_F24_180926A_SPRI_484_200507

description:
XN_SY01_P1_F24_180926A_SPRI_484_200507
47K SNPs


title: H1 ESCs，E7+NODAL, 24h.1

value: WT


title: H1 ESCs，E7+Activin A+2DG3, 24h.2

source_name: E7 treatment with Activin A and 2DG 3mM for 24h in H1 ESCs

value: E7+Activin A+2DG3, 24h


title: 4v-S1

description:
4v-s1_FPKM
all.fpkm_anno.xls

value: Colorectal cancer

value: genetic modification


title: peanut-XN_SY01_P1_F23_180926A_SPRI_351_200507

description:
XN_SY01_P1_F23_180926A_SPRI_351_200507
47K SNPs


title: H1 ESCs，E7+Activin A+2DG3, 24h.1


title: liver, Field, 207363410095_R05C01

description:
Liver methylome in rewilded mice
207363410095_R05C01


title: peanut-XN_SY01_P1_G03_180926A_SPRI_128_200507

description:
XN_SY01_P1_G03_180926A_SPRI_128_200507
47K SNPs


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_20CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 20CAG control


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_20CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: peanut-XN_SY01_P1_F22_180926A_SPRI_483_200507

description:
XN_SY01_P1_F22_180926A_SPRI_483_200507
47K SNPs

value: leaf


title: liver, Field, 207363410095_R02C02

description:
Liver methylome in rewilded mice
207363410095_R02C02


title: peanut-XN_SY01_P1_F21_180926A_SPRI_350_200507

description:
XN_SY01_P1_F21_180926A_SPRI_350_200507
47K SNPs


title: H1 ESCs，E7+Activin A, 24h.1

source_name: E7 treatment with Activin A 100 ng/mL for 24h in H1 ESCs

value: Human embryonic stem cells

value: E7+Activin A, 24h


title: liver, Field, 207363410095_R01C02

description:
Liver methylome in rewilded mice
207363410095_R01C02