title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_G12_2

status: Public on Jul 27 2024

type: SRA

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: ChEC-SEQ with ARO80-MNase spike in for calibration

library_source: genomic

data_processing:
Demultiplexing with bcl2fastq.
Filtering of adapter dimers using cutadapt and picard.
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d).
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.txt files contain genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome.
Library strategy: ChEC-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae BY4741

source_name: cultured yeast cells

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose.

extract_protocol:
ChEC-seq: phenol chloroform.
One tube library construction based on Skeene et al. 2017 as described in Gera 2021.

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021.

tag: cell type

value: cultured yeast cells

tag: tf

tag: fusion

tag: loci

value: HO

tag: delta native tf

value: TRUE

tag: promoter

value: synthetic

tag: mnase loc

value: on TF


title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_G12_1


title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C12_2


title: Gcn4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_B03_1


title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C12_1


title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C09_1


title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_A02_1


title: A673 ARID1A DD1,2 2 in situ Hi-C

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
RNA-seq reads were aligned to the reference genome (hg38) using STAR software v2.7.8a with default parameters. The gene counts were quantified with RSEM.
The adaptor sequences were trimmed out using Cutadapt. The trimmed paired-end sequences were mapped to the human reference genome hg38 using bowtie 2 with parameters “—very-sensitive –X 1000 –dovetail”. The reads with poor mapping quality (MAPQ < 30) and the reads mapped to the mitochondrial genome were discarded. The potential PCR duplicates were marked using MarkDuplicates of PICARD, and the remaining reads were shifted using the alignmentSieve function of deeptools with the “—ATACshift” parameter. The accessible regions information was obtained using MACS2 narrow callpeak, keeping duplicates with a q-value cutoff of 0.01.
The sequenced reads were mapped to the human reference genome (hg38) using BWA-MEM. Chimeric reads spanning multiple sites of the genome were filtered out. The reads with poor mapping quality (MAPQ < 10) were discarded. Self-ligated reads (genome distance < 15 kb) were also filtered out. Potential PCR duplicates were marked using MarkDuplicates of PICARD. The reads were then assigned into 40 kb genomic bins to generate a 40 kb Hi-C contact map. To consider possible genome-dependent bias, coverage-based contact map normalization was performed with covNorm.
Assembly: GRCh38
Supplementary files format and content: RSEM gene count, MACS2 narrowpeak, covNorm coverage-normalized counts

organism: Homo sapiens

extract_protocol: The harvested 1 million cells were crosslinked with 1% formaldehyde for 9 min at RT in 10 ml PBS and 100 µl FBS. Cells were treated with 250 mM glycine for 5 min at RT and 15 min on ice, to quench the crosslinking. The cells were then lysed with 10 nM Tris-HCl pH 8, 10 mM NaCl, and 0.2% IGEPAL CA630. The crosslinked chromatin was digested with 100 U MboI, labeled with biotin-14-dTCP, and ligated with T4 DNA Ligase. The ligated samples were reverse-crosslinked with 2 µg/µl proteinase K, 1% SDS, and 500 mM NaCl overnight at 65ºC. The DNA fragments were collected with Ampure XP beads (Beckman Coulter, A63881) and sonicated using Covaris S220 into 300~400bp. The biotin-labeled DNA was pulled down with Dynabeads MyOne streptavidin T1 beads (Invitrogen, 65602) with thorough washings. DNA end repair, un-ligated ends removal, adenosine addition at 3’ end (NEB, M0212), ligation of Illumina indexed adapters (NEB, M2200), and PCR amplification was performed to generate Hi-C libraries. The generated libraries were sequenced in 100 bp paired-end mode.

tag: cell line

tag: genotype

value: ARID1A DD1,2


title: Gcn4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C09_2


title: A673 ARID1A WT RE3 in situ Hi-C

value: ARID1A WT


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: A673 ARID1A DD1,2 4 in situ Hi-C


title: A673 ARID1A WT RE2 in situ Hi-C


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_H08_2


title: A673 ARID1A PRLD Y/S ATAC-seq

extract_protocol: ATAC-seq libraries were prepared for sequencing using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (#20034197, Illumina, San Diego, CA, USA) and sequenced in paired-end mode.

value: ARID1A PRLD Y/S


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_H08_1


title: A673 ARID1A DD1,2 5 ATAC-seq


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_H03_2


title: Gcn4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_F09_2


title: A673 ARID1A DD1,2 4 ATAC-seq


title: A673 ARID1A DD1,2 3 ATAC-seq


title: Gcn4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_E06_1


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate1_B07_2


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_H03_1


title: A673 ARID1A DD1,2 2 ATAC-seq


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: A673 ARID1A DD1,2 1 ATAC-seq


title: A673 ARID1A WT RE5 ATAC-seq


title: A673 ARID1A WT RE3 ATAC-seq


title: A673 ARID1A KO ATAC-seq

value: ARID1A KO


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_G05_1


title: A673 ARID1A WT RE4 ATAC-seq


title: Gal4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate1_B07_1


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_F07_2


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_G05_2


title: A673 ARID1A WT RE2 ATAC-seq


title: A673 ARID1A DD1,2 4 RNA-seq

library_source: transcriptomic

molecule: polyA RNA

extract_protocol: RNA was extracted from 1 million harvested cells with a Nucleospin RNA XS kit (Macherey-Nagel, MN740902). RNA-seq libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina, 20020594). RNA-seq libraries were sequenced in a 100bp paired-end mode.


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_F07_1


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_B06_2


title: A673 ARID1A DD1,2 3 RNA-seq


title: A673 ARID1A WT RE1 ATAC-seq


title: A673 WT ATAC-seq

value: WT


title: A673 ARID1A PRLD Y/S RNA-seq


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C02_2


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C02_1


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: A673 ARID1A DD1,2 5 RNA-seq


title: A673 ARID1A DD1,2 1 RNA-seq


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C01_1


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_C01_2


title: A673 ARID1A KO RNA-seq


title: A673 ARID1A WT RE4 RNA-seq


title: Gal4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_B06_1


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_B09_1


title: Gal4_Full_lib_Mnase_HO_loc_del_native_loc_TF_B09_2


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_4

description: ChEC-SEQ

value: FALSE


title: A673 WT RNA-seq

value: WT RNA-seq


title: A673 ARID1A WT RE1 RNA-seq


title: A673 ARID1A WT RE3 RNA-seq


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 464

type: genomic

city: Warsaw

first: Lukasz

middle: Michal

last: Szafron

address: Roentgena 5

country: Poland

institute: The Maria Sklodowska-Curie National Research Institute of Oncology

description:
high-grade serous ovarian carcinoma
205771840024_R04C01

hyb_protocol: Bisulphite-converted DNA (with the EZ DNA Methylation Kit, Zymo Research) was hybridized to Infinium MethylationEPIC Beadchip (Illumina) using the standard Illumina protocol.

scan_protocol: Arrays were imaged with the iScan System (Illumina), using recommended settings.

data_processing:
The data were processed according to protocol published by Maksimovic, J. et al., 2016 (PMID: 27347385), using the R script developed by Szafron LM, available for download from https://github.com/lukszafron/methyl_arrays.r.
Beta values normalized using the normalizeMethyLumiSet function from the methylumi package (DOI: 10.18129/B9.bioc.methylumi)

label: Cy5 and Cy3

source_name: FFPE

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from snap-frozen samples was extracted and purified using the QIAamp DNA Mini Kit (Qiagen) according to the standard instructions. Genomic DNA from FFPE samples was isolated with the use of MagCoreÂ® Genomic DNA FFPE One-Step Kit (RBC Bioscience).

tag: gender

value: Female

value: OvCa


title: 337

description:
high-grade serous ovarian carcinoma
205771840024_R08C01


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: 565

description:
high-grade serous ovarian carcinoma
205771840024_R01C01


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: A673 ARID1A DD1,2 2 RNA-seq


title: B10

description:
serous borderline ovarian tumor without the BRAF V600E mutation
205771840022_R08C01

source_name: Frozen

value: BOT


title: A673 ARID1A WT RE2 RNA-seq


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: B61

description:
serous borderline ovarian tumor without the BRAF V600E mutation
205771840022_R06C01


title: B58

description:
serous borderline ovarian tumor without the BRAF V600E mutation
205771840022_R07C01


title: Yap1DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Yap1DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: B68

description:
serous borderline ovarian tumor without the BRAF V600E mutation
205771840022_R05C01


title: A673 ARID1A WT RE5 RNA-seq


title: 270

description:
low-grade serous ovarian carcinoma
205771840022_R02C01

value: lgOvCa


title: B89

description:
serous borderline ovarian tumor without the BRAF V600E mutation
205771840022_R04C01


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: 500

description:
high-grade serous ovarian carcinoma
205771840024_R02C01


title: 303

description:
low-grade serous ovarian carcinoma
205771840022_R01C01


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Yap1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Yap1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Vhr1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_4

description: ChEC-SEQ


title: 451

description:
high-grade serous ovarian carcinoma
205289440131_R06C01


title: 485

description:
high-grade serous ovarian carcinoma
205289440131_R08C01


title: 475

description:
high-grade serous ovarian carcinoma
205289440131_R07C01


title: Vhr1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 301

description:
high-grade serous ovarian carcinoma
205289440131_R02C01


title: Vhr1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: 289

description:
high-grade serous ovarian carcinoma
205289440131_R01C01


title: Vhr1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: B88

description:
serous borderline ovarian tumor with the BRAF V600E mutation
205289440072_R08C01


title: 571

description:
high-grade serous ovarian carcinoma
205289440072_R07C01


title: Sko1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 545

description:
high-grade serous ovarian carcinoma
205289440072_R05C01


title: Sko1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 530

description:
high-grade serous ovarian carcinoma
205289440072_R04C01


title: 524

description:
high-grade serous ovarian carcinoma
205289440072_R03C01


title: Sko1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Sko1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 438

description:
high-grade serous ovarian carcinoma
205289440131_R05C01


title: Sko1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: B84

description:
serous borderline ovarian tumor with the BRAF V600E mutation
205062740115_R06C01


title: Rpn4DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: B79

description:
serous borderline ovarian tumor without the BRAF V600E mutation
205062740115_R05C01


title: B4

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720089_R06C01


title: 37

description:
low-grade serous ovarian carcinoma
205062740115_R07C01


title: Vhr1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: Rpn4DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_4

description: ChEC-SEQ


title: Vhr1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Sko1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Rpn4DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: B8

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720089_R04C01


title: 437

description:
high-grade serous ovarian carcinoma
205289440131_R04C01


title: B6

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720089_R05C01


title: B3

description:
low-grade serous ovarian carcinoma
204361720089_R07C01


title: Rpn4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: B15

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720089_R03C01


title: Rpn4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Rpn4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Rpn4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: Rpn4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Rpn4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: B19

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720089_R02C01


title: 286

description:
high-grade serous ovarian carcinoma
205062740115_R08C01


title: B33

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720076_R08C01


title: Rpn4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: B37

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720076_R06C01


title: Rpn4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: B35

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720076_R07C01


title: Rpn4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Rpn4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Rpn4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: B60

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720075_R07C01


title: 11

description:
high-grade serous ovarian carcinoma
204361720076_R01C01


title: B59

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720076_R03C01


title: Rpn4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: B64

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720075_R05C01


title: B66

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720075_R03C01


title: B65

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720075_R04C01


title: Reb1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: B62

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720075_R06C01


title: Reb1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_4

description: ChEC-SEQ


title: Reb1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 320

description:
high-grade serous ovarian carcinoma
204361720073_R05C01


title: Reb1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Pdr8DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 312

description:
high-grade serous ovarian carcinoma
204361720073_R08C01


title: 316

description:
high-grade serous ovarian carcinoma
204361720073_R06C01


title: Reb1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: Pdr8DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 314

description:
high-grade serous ovarian carcinoma
204361720073_R07C01


title: Reb1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 322

description:
high-grade serous ovarian carcinoma
204361720073_R04C01


title: Pdr8DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 348

description:
high-grade serous ovarian carcinoma
204361720073_R03C01


title: Pdr8DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 351

description:
high-grade serous ovarian carcinoma
204361720073_R02C01


title: Rpn4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Pdr8_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 352

description:
high-grade serous ovarian carcinoma
204361720073_R01C01


title: B67

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720075_R02C01


title: 455

description:
high-grade serous ovarian carcinoma
204361720060_R06C01


title: Pdr8_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 461

description:
high-grade serous ovarian carcinoma
204361720060_R04C01


title: 459

description:
high-grade serous ovarian carcinoma
204361720060_R05C01


title: 470

description:
high-grade serous ovarian carcinoma
204361720060_R02C01


title: 474

description:
high-grade serous ovarian carcinoma
204361720060_R01C01


title: Nrg2_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: Nrg2DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 493

description:
high-grade serous ovarian carcinoma
204361720058_R08C01


title: Nrg2DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 558

description:
high-grade serous ovarian carcinoma
204361720058_R05C01


title: Nrg2_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Msn2DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 609

description:
high-grade serous ovarian carcinoma
204361720058_R02C01


title: 607

description:
high-grade serous ovarian carcinoma
204361720058_R03C01


title: 610

description:
high-grade serous ovarian carcinoma
204361720058_R01C01


title: 496

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720058_R07C01


title: Msn2DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: 408

description:
high-grade serous ovarian carcinoma
204361720057_R07C01


title: 398

description:
high-grade serous ovarian carcinoma
204361720057_R08C01


title: Msn2DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Nrg2DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 414

description:
high-grade serous ovarian carcinoma
204361720057_R06C01


title: Nrg2_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Msn2DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Nrg2DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 415

description:
high-grade serous ovarian carcinoma
204361720057_R05C01


title: Msn2DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Msn2DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 431

description:
high-grade serous ovarian carcinoma
204361720057_R03C01


title: 439

description:
high-grade serous ovarian carcinoma
204361720057_R02C01


title: Msn2DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: 426

description:
high-grade serous ovarian carcinoma
204361720057_R04C01


title: Msn2DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Msn2DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_4

description: ChEC-SEQ


title: 611

description:
high-grade serous ovarian carcinoma
204361720051_R08C01


title: 569

description:
low-grade serous ovarian carcinoma
204361720057_R01C01


title: Msn2DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Msn2DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Msn2_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: B7

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720051_R06C01


title: Msn2_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Msn2_Full_TEF_Mnase_HO_loc_del_native_loc_TF_4

description: ChEC-SEQ


title: B22

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720051_R05C01


title: B27

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720051_R04C01


title: B31

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720051_R03C01


title: Msn2_Full_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Msn2DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: B32

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720051_R02C01


title: B38

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720051_R01C01


title: B41

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720049_R08C01


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Msn2_Full_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: B48

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720049_R05C01


title: Mig3DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: B54

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720049_R03C01


title: 815

description:
low-grade serous ovarian carcinoma
204361720051_R07C01


title: Mig3DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: B45

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204361720049_R06C01


title: Mig3DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: Mig3DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: 253

description:
high-grade serous ovarian carcinoma
204361720035_R08C01


title: B55

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720049_R02C01


title: B56

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720049_R01C01


title: 257

description:
high-grade serous ovarian carcinoma
204361720035_R07C01


title: Mig3DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Msn2_Full_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: Mig3DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Mig3DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Mig3_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 264

description:
high-grade serous ovarian carcinoma
204361720035_R06C01


title: 266

description:
high-grade serous ovarian carcinoma
204361720035_R05C01


title: B42

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204361720049_R07C01


title: Mig3_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 280

description:
high-grade serous ovarian carcinoma
204361720035_R04C01


title: Mig3_Full_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: Mig3_Full_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Met31DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Met31DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Met31_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 306

description:
high-grade serous ovarian carcinoma
204361720035_R01C01


title: 382

description:
high-grade serous ovarian carcinoma
204361720030_R05C01


title: Met31_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Med15_mnase_native_3

description: ChEC-SEQ

value: mnase

value: native

value: on Med15


title: 355

description:
high-grade serous ovarian carcinoma
204361720030_R08C01


title: 291

description:
high-grade serous ovarian carcinoma
204361720035_R03C01


title: 383

description:
high-grade serous ovarian carcinoma
204361720030_R04C01


title: 394

description:
high-grade serous ovarian carcinoma
204361720030_R02C01


title: 300

description:
high-grade serous ovarian carcinoma
204361720035_R02C01


title: Med15_mnase_native_2

description: ChEC-SEQ

value: cultured yeast cells

value: HO


title: Med15_mnase_native_1

description: ChEC-SEQ


title: 396

description:
high-grade serous ovarian carcinoma
204361720030_R01C01


title: 375

description:
high-grade serous ovarian carcinoma
204361720030_R06C01


title: 387

description:
high-grade serous ovarian carcinoma
204361720030_R03C01


title: Med15_mnase_msn2dbdgal4ad_2

description: ChEC-SEQ

value: delta Msn2


title: Med15_mnase_msn2dbdgal4ad_1

description: ChEC-SEQ


title: Med15_mnase_msn2dbdgal4ad_3

description: ChEC-SEQ


title: B69

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204339390014_R08C01


title: B70

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204339390014_R07C01


title: Med15_mnase_mig3dbdgcn4ad_2

description: ChEC-SEQ

value: delta Mig3


title: B71

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204339390014_R06C01


title: B73

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204339390014_R05C01


title: B74

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204339390014_R04C01


title: B76

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204339390014_R03C01


title: Med15_mnase_mig3dbdgcn4ad_1

description: ChEC-SEQ


title: Med15_mnase_mig3dbdgal4ad_2

description: ChEC-SEQ


title: Med15_mnase_mig3dbdgal4ad_1

description: ChEC-SEQ


title: B83

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204339390014_R01C01


title: 353

description:
low-grade serous ovarian carcinoma
204082600082_R07C01


title: Med15_mnase_gal4dbdgal4ad_1

description: ChEC-SEQ

value: delta Gal4


title: 404

description:
high-grade serous ovarian carcinoma
204082600082_R04C01


title: 360

description:
high-grade serous ovarian carcinoma
204082600082_R06C01


title: Gln3DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ

value: on TF


title: Gln3DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: 369

description:
high-grade serous ovarian carcinoma
204082600082_R05C01


title: B17

description:
serous borderline ovarian tumor without the BRAF V600E mutation
204082600082_R01C01


title: Gln3DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Med15_mnase_gal4dbdgal4ad_2

description: ChEC-SEQ


title: 127

description:
high-grade serous ovarian carcinoma
204082600042_R07C01


title: Gln3_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: 30

description:
low-grade serous ovarian carcinoma
204082600042_R08C01


title: Gln3DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: Gcn4DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Gln3_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Gcn4DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Med15_mnase_gal4dbdgal4ad_3

description: ChEC-SEQ


title: B77

description:
serous borderline ovarian tumor with the BRAF V600E mutation
204339390014_R02C01


title: 192

description:
high-grade serous ovarian carcinoma
204082600042_R04C01


title: 175

description:
high-grade serous ovarian carcinoma
204082600042_R05C01


title: Gcn4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ

value: TRUE


title: 271

description:
high-grade serous ovarian carcinoma
204082600042_R03C01


title: Gcn4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: 421

description:
high-grade serous ovarian carcinoma
204082600082_R03C01


title: Gln3DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 313

description:
high-grade serous ovarian carcinoma
204082600042_R02C01


title: Mixl1 induced D1Dox rep 3 RNA-seq

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

data_processing:
Basecalls were performed using RTA (Illumina) and converted to fastq using bcl2fastq
Paired-end reads were aligned and transcript abundances were quantified using STAR aligner.
Differential expression analysis was done in R Statistics Software using the DESeq2 library. Genes were identified as differentially expressed based on the following criteria: absolute Log2 Fold change > 1 and adjusted P-value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Mixl1_vs_Mixl1KO.tsv.gz: tsv file, Output from DESeq2 analysis; FM1ReadsPerGene.out.tab.gz, FM2ReadsPerGene.out.tab.gz, FM3ReadsPerGene.out.tab.gz. KO1ReadsPerGene.out.tab.gz, KO2ReadsPerGene.out.tab.gz, KO3ReadsPerGene.out.tab.gz: tsv file, Raw gene quantification output from STAR Aligner.

molecule: total RNA

organism: Mus musculus

source_name: Mouse epiblast stem cells

growth_protocol: Mouse epiblast stem cells were routinely cultured on irradiated mouse embryonic fibroblasts in EpiSC medium supplemented with 10ng/mL bFGF and 20ng/mL Activin A.  For embryoid body production, cells were passaged in single cells and aggregated using Aggrewells. Embryoid bodies were transferred to non-tissue culture treated plates after 24h.

extract_protocol:
Total RNA was extracted using the Isolate II RNA Mini Kit (Bioline, BIO-52073)
RNA-seq libraries were prepared from extracted RNA using the TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Triplicates of 2d embryoid bodies from Mixl1 inducible mouse EpiSC lines were treated with 1ug/mL Doxycycline 24h prior to collection.

value: serum differentiated mouse epiblast stem cells


title: 328

description:
high-grade serous ovarian carcinoma
204082600042_R01C01


title: Mixl1 induced D1Dox rep 1 RNA-seq


title: Gln3_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ

value: FALSE


title: Mixl1 KO rep 3 RNA-seq


title: Mixl1 KO rep 1 RNA-seq


title: Gcn4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Gcn4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: 130

description:
low-grade serous ovarian carcinoma
204082600042_R06C01


title: Mixl1 KO rep 2 RNA-seq


title: 281

description:
high-grade serous ovarian carcinoma
203916360006_R07C01


title: Mixl1 D1Dox - Input rep 2

data_processing:
Basecalls were performed with CASAVA(v1.8.2)
Reads were aligned to the mm10 mouse genome using Bowtie2 using the following parameters: -X 2000
Reads with MAPQ < 30 and duplicate reads were filtered using samtools and PicardTools.
Biological replicates were merged for peak calling using MACS2 with the following parameters: : -f BAMPE -g mm -q 0.05 --keep-dup all
Peaks were then filtered to exclude peaks falling within the mm10 blacklist and to include peaks with a pileup value greater than or equal to 40.
Genome_build: mm10
Supplementary_files_format_and_content: MIXL1.peaks.bl.p40.uniq.bed.gz: BED file, MACS2 peaks of Mixl1 ChIP vs Input, filtered for peaks with a pileup value > 40 and peaks residing outside the mm10 blacklist

growth_protocol: Mouse epiblast stem cells were routinely cultured on irradiated mouse embryonic fibroblasts in EpiSC medium supplemented with 10ng/mL bFGF and 20ng/mL Activin A.  For embryoid body production, cells were passaged as colonies using Collagenase IV and transferred to non-tissue culture treated plates

extract_protocol:
Chromatin from 4×10^7  cells per replicate were immunoprecipitated using Anti-FLAG M2 Antibody (Sigma-Aldrich, F1804) bound to Dynabeads Protein G (Thermo Fischer Scientific, 10003D) to pull down chromatin bound by FLAG-MIXL1 protein.
NEBNext Ultra™II DNA Library Prep Kit for Illumina

treatment_protocol: 2 d embryoid bodies from Mixl1 inducible mouse EpiSC lines were treated with 1ug/mL Doxycycline 24h prior to collection.

tag: chip antibody


title: Gcn4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Mixl1 D1Dox - FLAG-Mixl1 ChIP rep 1

value: Monoclonal ANTI-FLAG® M2 antibody (Sigma-Aldrich, F1804)


title: Mixl1 D1Dox - FLAG-Mixl1 ChIP rep 2


title: Gcn4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: Mixl1 D1Dox - Input rep 1


title: Gcn4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Gcn4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Mixl1 induced D1Dox rep 3 ATAC-seq

data_processing:
Basecalls were performed using RTA (Illumina) and converted to fastq using bcl2fastq
Reads were aligned to the mm10 mouse genome using Bowtie2 using the following parameters: -k 4 -X 2000
Reads with MAPQ < 10 and duplicate reads were filtered using samtools and sambamba. Multimapping reads were randomly assigned.
Aligned paired-end reads were converted to pseudo-single-ended reads for subsequent peak calling
Peaks were called using MACS2 using the following parameters: -q 0.05 --shift -100 --ext-size 200 --keep-dup all
Genome_build: mm10
Supplementary_files_format_and_content: FM_peaks.narrowPeak.gz: narrowPeak file, MACS2 peaks. KO_peaks.narrowPeak.gz: narrowPeak file, MACS2 peaks.

extract_protocol:
50,000 cells per replicate were lysed in 10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630. The chromatin within intact nuclei were digested using Tn5 transposase. Digested chromatin was retrieved using MinElute PCR Purification Kit (Qiagen), as per manufacturer specifications.
Eluted chromatin was bacoded and adapter tagged using Nextera compatible sequences. 11 cycles of PCR were used to amplify the library, after which, it was purified with 1.3× and 0.5× SPRI bead selection.


title: 299

description:
high-grade serous ovarian carcinoma
203916360006_R06C01

value: Female


title: 323

description:
high-grade serous ovarian carcinoma
203916360006_R04C01

value: OvCa


title: Mixl1 induced D1Dox rep 2 ATAC-seq


title: Mixl1 KO rep 3 ATAC-seq


title: Mixl1 induced D1Dox rep 2 RNA-seq


title: Gcn4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: 340

description:
high-grade serous ovarian carcinoma
203916360006_R03C01


title: Mixl1 induced D1Dox rep 1 ATAC-seq


title: Gcn4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_4

description: ChEC-SEQ


title: 255

description:
high-grade serous ovarian carcinoma
203916360006_R08C01


title: 319

description:
high-grade serous ovarian carcinoma
203916360006_R05C01


title: Mixl1 KO rep 2 ATAC-seq


title: Mixl1 KO rep 1 ATAC-seq


title: 405

description:
high-grade serous ovarian carcinoma
203916360006_R01C01


title: D3

city: Zheng Zhou

first: Nasir

last: ABDUL

address: Jingba Road

department: The Second Clinical Medical School of Zhengzhou University

country: China

institute: Zhengzhou University

data_processing:
the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China)
For raw pair-end reads, adapters and poor quality bases were trimmed off using Skewer version 0.2.2
The clean reads were aligned to the genome reference genome downloaded from the Ensembl website ( http://ensemblgenomes.org/) using STAR version 2.5.3a and comprehensive gene annotation GTF file from Ensembl website
The mapped reads of each sample were then assembled into transcripts based on reference guided assembly strategy using StringTie version 1.3.1
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM for each Sample

organism: Rattus norvegicus

source_name: Cerebral cortex

extract_protocol:
Total RNA was isolated from each sample using the RNA mini kit ( Qiagen, Germany),1μg of total RNA was used for library construction
Sequencing libraries were generated using VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for  Illumina®

tag: tissue

value: Cerebral cortex


title: D2


title: D1


title: IR3


title: IR2


title: IR1


title: Gcn4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Gcn4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: 67

description:
high-grade serous ovarian carcinoma
203916360004_R07C01


title: S2


title: 70

description:
high-grade serous ovarian carcinoma
203916360004_R06C01


title: 8

description:
high-grade serous ovarian carcinoma
203916360004_R08C01


title: Gcn4_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Gcn4_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: S3


title: S1


title: Endosperm, WT

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The reads were aligned to genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density.
Assembly: Genome built from Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Genome-wide cytosine reports are the output file

organism: Oryza sativa

source_name: Endosperm (20 days after anthesis)

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
The DNA samples were sheared by ultrasonication (Covaris) avarage 350bp. Bisulfite convertion by EZ DNA Methylation-Gold Kit (Catalog no-D5005) as per manufacturer’s protocol. Adapters used: Read1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
xGen™ Methyl-Seq DNA Library Prep Kit (Catalog no. 10009860)

treatment_protocol: Endosperm tissues were handled in the same manner.

value: Endosperm (20 days after anthesis)

tag: subspecies

value: Indica

tag: cultivar

value: Pusa Basmati 1 (PB1)


title: Endosperm, clsy3-kd


title: 389

description:
high-grade serous ovarian carcinoma
203916360006_R02C01


title: Gcn4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: 100

description:
high-grade serous ovarian carcinoma
203916360004_R05C01


title: 160

description:
high-grade serous ovarian carcinoma
203916360004_R03C01


title: clsy4-kd, Leaf

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The reads were aligned to PCR templates as genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density.
Assembly: Custome genome built from Oryza sativa japonica nipponbare genome – IRGSP1 with the PCR amplicon regions as template.
Supplementary files format and content: Processed files contain  cytosine report in text format which generated from Bismark alignment tool.

source_name: Leaf (60 days old)

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
Bisulfite convertion by EZ DNA Methylation-Gold Kit (Catalog no-D5005) as per manufacturer’s protocol. Adapters used: Read1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  and Read 2-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT .
library constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions.

treatment_protocol: WT tissues were handled in the same manner. Treated with Zymo bisulfite reagents

value: Leaf (60 days old)

value: Pusa Basmati1 (PB1)


title: 145

description:
high-grade serous ovarian carcinoma
203916360004_R04C01


title: 174

description:
high-grade serous ovarian carcinoma
203916360004_R02C01


title: Gal4DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ

value: cultured yeast cells

value: HO


title: Gcn4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: WT, Endosperm

source_name: Endosperm ( (20 days after anthesis)


title: Gal4DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 498

description:
high-grade serous ovarian carcinoma
203911080047_R08C01


title: 197

description:
high-grade serous ovarian carcinoma
203916360004_R01C01


title: clsy3-kd, Endosperm


title: poliv-kd, Endosperm


title: Endosperm, CR_CLSY3

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
4000 reads are taken from the adaptor trimmed fastq files
Assembly: Custom genome created from the selected genes
Supplementary files format and content: Fasta files containing 4000 reads used for SNP analysis

source_name: Endosperm (10 days after anthesis)

extract_protocol:
cDNA synthesis and PCR amplification
Adapters used: Read1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Library was prepared as ChIP-seq library. The library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: Endosperm (10 days after anthesis) collected and RNA isolation performed

value: Endosperm (10 days after anthesis)

value: Whiteponni x Pusa Basmati (WP x PB1)


title: Gal4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ

value: on TF


title: 508

description:
high-grade serous ovarian carcinoma
203911080047_R07C01


title: Gln3 DBD-Gcn4AD TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep2

description: ChEC-SEQ

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt and picard
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out file contains  genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
Library strategy: ChEC-seq

organism: Saccharomyces cerevisiae

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose

extract_protocol:
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021

tag: strain

tag: delta native_tf

value: delta Gln3


title: Gln3 DBD-Gcn4AD TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep3

description: ChEC-SEQ


title: Gal4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ

value: TRUE


title: 605

description:
high-grade serous ovarian carcinoma
203911080047_R05C01


title: Gal4DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Gln3 DBD-Gal4AD TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep3

description: ChEC-SEQ


title: Gcn4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Gal4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_4

description: ChEC-SEQ

value: FALSE


title: Gln3 DBD-Gal4AD TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep1

description: ChEC-SEQ


title: 509

description:
high-grade serous ovarian carcinoma
203911080047_R06C01


title: Gln3 TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep3

description: ChEC-SEQ


title: Gln3 TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep2

description: ChEC-SEQ


title: B5

description:
serous borderline ovarian tumor without the BRAF V600E mutation
203911080047_R03C01

value: BOT


title: Gln3 TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep1

description: ChEC-SEQ


title: Gal4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: B2

description:
serous borderline ovarian tumor without the BRAF V600E mutation
203911080047_R04C01

value: Female


title: 410

description:
high-grade serous ovarian carcinoma
203911080046_R08C01

value: OvCa


title: Msn2 DBD -Mnase with deletion of 11 TFs (Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep3

description: ChEC-SEQ

value: native

value: delta 12 TFs


title: Endosperm, CR_ARF22_SHH1

value: Indica


title: Msn2 DBD -Mnase with deletion of 11 TFs (Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep4

description: ChEC-SEQ


title: 416

description:
high-grade serous ovarian carcinoma
203911080046_R07C01


title: Gal4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ


title: Msn2 DBD -Mnase with deletion of 11 TFs (Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep1

description: ChEC-SEQ


title: Gal4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: Gln3 DBD-Gcn4AD TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep1

description: ChEC-SEQ


title: Gal4DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 420

description:
high-grade serous ovarian carcinoma
203911080046_R06C01


title: Gal4DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: Gln3 DBD-Gal4AD TF-Mnase  in HO locus with Tef1 promoter and NLS, deleted of endogenous Gln3, Rep2

description: ChEC-SEQ


title: Gcn4AD-Mnse nls, rep2

description: ChEC-SEQ


title: 430

description:
high-grade serous ovarian carcinoma
203911080046_R05C01


title: Gcn4AD-Mnse nls, rep1

description: ChEC-SEQ


title: Gcn4-DBD PIP2AD -Mnase nls, rep2

description: ChEC-SEQ

value: delta Gcn4


title: Gcn4-DBD PIP2AD -Mnase nls, rep1

description: ChEC-SEQ


title: Gal4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ


title: 452

description:
high-grade serous ovarian carcinoma
203911080046_R04C01


title: 454

description:
high-grade serous ovarian carcinoma
203911080046_R03C01


title: Msn2-DBD -Mnase nls, rep1

description: ChEC-SEQ

value: delta Msn2


title: Msn2-DBD HCM1AD -Mnase nls, rep2

description: ChEC-SEQ


title: Gal4_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Msn2-DBD -Mnase nls, rep2

description: ChEC-SEQ


title: Msn2 DBD -Mnase with deletion of 11 TFs (Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep2

description: ChEC-SEQ


title: Msn2-DBD HCM1AD -Mnase nls, rep1

description: ChEC-SEQ


title: Gal4_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Gcn4AD-Mnse nls, rep3

description: ChEC-SEQ


title: WT_TBI2

city: New Orleans

first: Ning

last: Liu

state: LA

address: 1324 Tulane Ave. JBJ building, School of Medicine, Room 632

department: Neurosurgery

country: USA

institute: Tulane University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Brain tissue was enzymatically digested using collagenase 1 and mechanically ground to obtain a single-cell suspension. The cell suspension was filtered through a 70-micron cell strainer to remove large tissue fragments. The cell suspension was centrifuged (400 g, 10 minutes) to precipitate the cells. The supernatant was removed, and the cells were resuspended in cell separation buffer and repeated 2-3 times. According to the instructions of the magnetic bead supplier, 10 microliters of Cd11b magnetic beads were added to the resuspended cells and incubated at 4°C for 20-30 minutes. The labeled cells were washed with cell separation buffer to remove unbound magnetic beads. The cell suspension was sorted through a magnetic separation column. Cd11b-positive cells were eluted using cell separation buffer. Finally, the sorted Cd11b-positive cells were subjected to single-cell sequencing.
Cell numbers and viabilities were validated by Cellometer prior to single cell RNAseq library preparation. For 10x single cell RNAseq assay,  qualified cells from the sham, TBI, and TBI+4-OI groups, respectively were targeted by using 10x Single Cell 3’ RNAseq technology provided by 10x Genomics (10X Genomics Inc, CA). Briefly, viable single cell suspensions were partitioned into nanoliterscale Gel Beads-In-EMulsion (GEMs). mRNA was extracted from single cell suspension using the 10X Genomics Chromium™ Single Cell G Chip Kit. Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v3.1 protocol. Following enzymatic fragmentation, end-repair, A-tailing, and adaptor ligation, single cell 3’ libraries comprising standard Illumina P5 and P7 paired-end constructs were generated. Library quality controls were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer and quantified by Qubit 2.0 fluorometer. Pooled libraries at a final concentration of 750pM were sequenced with paired end single index configuration by Illumina NextSeq 2000.

value: Brain

tag: Sex

value: Male

value: Cd11b+ cell

tag: treatment

value: 40% cyclodextrin


title: Msn2-DBD Rpn4AD2 -Mnase nls, rep2

description: ChEC-SEQ

tag: tf

value: HO


title: Gal4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ

tag: cell type

value: cultured yeast cells

tag: fusion

value: on TF


title: WT_TBI1

description: 10x Genomics


title: SM treated 30 µM (miRNA)

city: Munich

first: Virginia

last: Egea

state: Bayern

address: Max-Lebsche Platz 30

department: IPEK

country: Germany

institute: LMU

data_processing:
The mRNA and miRNA datasets were demultiplexed by a inhouse demultiplexer. Adapter sequences were removed from the 3’-end using Clip adaptor sequence (version 1.0.0, tggaattc, seed 8, mismatch 0, minimum length after clipping 1).
For mRNA data, 9 nucleotides caused by random priming on the 5’-end of the reads were trimmed using FastqFilter (version 1.0.). Reads passing the filtering were aligned to the human genome (hg38 from GENCODE) with STAR (version 2.4.1b, default options: up to 4% mismatches and no multimapping allowed)
Reads per gene were counted using htseq-count (version 1.0.0) (Anders, Pyl et al., 2015) with default settings and GENCODE gene annotation (hg38).
Differentially expressed genes between SM treated and control samples were detected using DESeq2 (Version 2.11.40.7, significance cutoff, adjusted P value < 0.01, Benjamini-Hochberg correction)
the miRNA reads were mapped to the human genome (hg38 from GENCODE) using MiRDeep2 mapper (Version 2.0.0) (Friedländer, Mackowiak et al., 2012) and the abundant reads were quantified using MiRDeep2 quantifier (Version 2.0.0) (Mackowiak, 2011). Differential gene expression analysis was performed using DESeq2 (Version 2.11.40.6, FDR < 0.05) (Friedländer et al., 2012).
Assembly: DESeq2
Supplementary files format and content: Raw counts FASTTQ datei
Supplementary files format and content: Comparative Analysis data

source_name: Keratinocytes

growth_protocol: Primary normal human epidermal keratinocytes (NHEK) were purchased from Promocell (Heidelberg, Germany) and grown in serum-free keratinocyte growth medium containing 0.1 mM CaCl2 (low calcium conditions) (Promocell).

extract_protocol:
Total RNA was extracted from 300 µl aliquots (0.5 x 106 cells) using the Maxwell® RSC miRNA Tissue Kit (Promega, Madison, WI, USA) on the Maxwell® RSC instrument according to the manufacturer’s instructions.
miRNA sequencing libraries were constructed using the QIAseq® miRNA Library Kit (Qiagen) starting with 100 ng of total RNA following the manufacturer’s instructions.

treatment_protocol: Prior to application in each experiment, pure SM was freshly diluted in ethanol and serum-free medium to minimize hydrolysis. NHEK, were treated with the vehicle control (diluted ethanol) or with SM at the indicated concentration for 30 min at 37°C in a specific incubator with humidified air atmosphere in the presence of 5% CO2.

value: Keratinocytes

value: SM 30µM 24h


title: WT_TBI_OI2

description: 10x Genomics


title: Msn2-DBD SumAD -Mnase nls, rep2

description: ChEC-SEQ

tag: loci


title: SM treated 30 µM (RNA)


title: Msn2-DBD Sum1AD -Mnase nls, rep1

description: ChEC-SEQ

tag: promoter


title: SM treated 10 µM (miRNA)

value: SM 10µM 24h


title: Gal4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ

tag: delta native tf

value: TRUE

tag: mnase loc


title: WT_Sham2

description: 10x Genomics

tag: genotype


title: Gal4_Full_ERV_Mnase_HO_loc_nodel_native_loc_TF_2.gz

description: ChEC-SEQ

value: FALSE


title: SM treated 10 µM (RNA)


title: Gal4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_1

description: ChEC-SEQ


title: WT_Sham1

description: 10x Genomics


title: 495

description:
high-grade serous ovarian carcinoma
203911080046_R01C01

tag: gender

value: Female

value: OvCa


title: Msn2-DBD Rpn4AD1 -Mnase nls, rep1

description: ChEC-SEQ


title: Gal4_Full_ERV_Mnase_HO_loc_nodel_native_loc_TF_1.gz

description: ChEC-SEQ


title: dMsn2_med15mnase_4

description: ChEC-SEQ

value: native

value: on Med15


title: EtOH treated (control for 30µM SM) (miRNA)

value: EtOH treated (control for 30µM SM)


title: Msn2-DBD Rpn4AD1 -Mnase nls, rep2

description: ChEC-SEQ

value: delta Msn2


title: TNFR1KO_DC

city: Frederick

first: Nathan

last: Wong

state: MD

address: 8560 Progress Drive

institute: FNLCR/NCI/NIH

description: 10X Genomics

data_processing:
Base calling was performed using Illumina RTA 3.9.25
Demutliplexing (bcl2fastq 2.20.0), barcode processing, read alignment (STAR 2.7.2a) counting performed via 10X cellranger v7.0.1 against pre-built mm10 reference (refdata-gex-mm10-2020-A)
Assembly: mm10
Supplementary files format and content: .h5 matrix files

source_name: pancreatic tumor

extract_protocol:
Cells from these samples were loaded in the 10X HT chip lanes according to the 10X Chromium Next GEM Single Cell 3’ HT v3.1 gene expression User Guide with one capture lane per sample.
Library preparation and quality control were performed as described in the 10X User Guide (Single Cell HT 3’ v3.1)

treatment_protocol: KPC mice were lethally irradiated (9 Gy) at the age of 7 weeks. Irradiated mice were reconstituted with 10^7 bone marrow cells from either WT or TNFR1 KO bone marrow. Infiltrating cells were collected when pancreatic tumor was detected to approximately 300 mm^3

value: pancreatic tumor

value: tumor infiltrating cells

value: C57BL-6-Tnfr1-knock out


title: WT_DC

description: 10X Genomics


title: 492

description:
high-grade serous ovarian carcinoma
203911080046_R02C01


title: EtOH treated (control for 30µM SM) (RNA)


title: Control (miRNA)

value: untreated


title: Gal4_Full_TEF_Mnase_HO_loc_del_native_loc_TF_2

description: ChEC-SEQ

value: cultured yeast cells

value: HO


title: Msn2-DBD SEF1AD -Mnase nls, rep2

description: ChEC-SEQ

value: on TF


title: WT_TBI_OI1

description: 10x Genomics

value: Brain

value: Male

value: Cd11b+ cell


title: Msn2-DBD RPN4AD2 -Mnase nls, rep1

description: ChEC-SEQ


title: Msn2-DBD SEF1AD -Mnase nls, rep1

description: ChEC-SEQ


title: dMsn2_med15mnase_3

description: ChEC-SEQ


title: dMsn2_med15mnase_2

description: ChEC-SEQ


title: Control (RNA)

value: Keratinocytes


title: TNFR1KO_CD45

description: 10X Genomics


title: Msn2-DBD YKL222CAD -Mnase nls, rep2

description: ChEC-SEQ


title: WT_CD45

description: 10X Genomics


title: Msn2-DBD YKL222CAD -Mnase nls, rep1

description: ChEC-SEQ


title: dMsn2_med15mnase_1

description: ChEC-SEQ


title: S-NP9

city: CHEONAN

first: Hyunkyung

last: Cha

state: Cheonan-si

address: Suncheonhyang 6-gil

department: Department of Otorhinolaryngology-Head and Neck Surgery

institute: Soonchunhyang University Cheonan Hospital

description: The nasopharyngeal swab with severe SARS-CoV2 infection

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: nasopharynx

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: nasopharynx

value: tissue swab

value: Infected


title: dMig3_med15mnase_2

description: ChEC-SEQ

extract_protocol:
ChEC-seq: phenol chloroform.
One tube library construction based on Skeene et al. 2017 as described in Gera 2021.

value: native

value: delta Mig3

value: on Med15


title: Msn2-DBD PIP2AD -Mnase nls, rep2

description: ChEC-SEQ

value: delta Msn2


title: dMig3_med15mnase_1

description: ChEC-SEQ


title: S-NP8


title: S-NP2


title: A-KINACT effector cells, GasR201C+/light+, replicate 3

city: La Jolla

first: Wei

last: Lin

state: CA

address: 9500 Gilman Dr

department: Pharmacology

institute: UC San Diego

data_processing:
Raw data were analyzed using the web-based platform Galaxy (https://usegalaxy.org) and open-source R software (version 4.1.0, https://www.r-project.org). Briefly, high-quality raw reads were mapped to the reference human genome hg38 using HISAT2 (version 2.2.1), and aligned reads were counted using htseq-count (version 0.9.1). The R package DESeq2 (version 1.34.0) was used to conduct differentially expressed gene (DEG) analysis. Genes with fold change (> 2) and P-adj < 0.05 were assigned as significantly altered genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes total raw counts of reads mapped to known genome for each sample.

extract_protocol:
Total RNA was extracted using RNA extraction kit (Zymol).1 µg of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: cell line

value: Human embryonic kidney

value: A-KINACT, TetO-PKI-EGFP

value: OE GasR201C / blue light 20 min


title: A-KINACT effector cells, GasR201C+/light+, replicate 1


title: A-KINACT effector cells, GasR201C+/light+, replicate 2


title: dGal4_med15mnase_2

description: ChEC-SEQ

value: cultured yeast cells

value: delta Gal4


title: Msn2-DBD RDS1AD -Mnase nls, rep2

description: ChEC-SEQ

value: HO

value: on TF


title: M-NP7

description: The nasopharyngeal swab with mild SARS-CoV2 infection

tag: tissue


title: Msn2-DBD RDS1AD -Mnase nls, rep1

description: ChEC-SEQ


title: A-KINACT control cells, GasR201C+/light+, replicate 3

value: A-KINACT, TetO-EGFP


title: A-KINACT control cells, GasR201C+/light+, replicate 2


title: dGal4_med15mnase_1

description: ChEC-SEQ


title: Med15 fused w Gcn4 DBD -Mnase-NLS, rep3

description: ChEC-SEQ

value: delta Gcn4


title: Cst6DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ

value: FALSE


title: M-NP2

value: nasopharynx


title: M-NP1

value: tissue swab


title: A-KINACT control cells, GasR201C+/light+, replicate 1


title: A-KINACT effector cells, GasR201C-/light-, replicate 3

value: No treatment


title: Med15 fused w Gcn4 DBD -Mnase-NLS, rep2

description: ChEC-SEQ

value: native


title: Cont6

description: The nasal tissue without SARS-CoV-2 infection

source_name: middle turbinate

value: middle turbinate

value: Tissue lysate

value: Uninfected


title: A-KINACT effector cells, GasR201C-/light-, replicate 2

value: Human embryonic kidney


title: Med15 fused w Gcn4 DBD -Mnase-NLS, rep1

description: ChEC-SEQ


title: Cst6DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Cont5


title: Cst6DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Msn2-DBD PIP2AD -Mnase nls, rep1

description: ChEC-SEQ

value: delta Msn2


title: Med15 fused w Msn2 DBD -Mnase-NLS, rep3

description: ChEC-SEQ


title: A-KINACT effector cells, GasR201C-/light-, replicate 1

value: A-KINACT, TetO-PKI-EGFP


title: A-KINACT control cells, GasR201C-/light-, replicate 3


title: Gcn4DBD_Gal11_TEF_Mnase_HO_loc_del_native_loc_TF_3

description: ChEC-SEQ

value: cultured yeast cells

value: TRUE


title: Cont4


title: Med15 fused w Msn2 DBD -Mnase-NLS, rep2

description: ChEC-SEQ


title: Crz1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ

value: HO


title: Med15 fused w Msn2 DBD -Mnase-NLS, rep1

description: ChEC-SEQ

value: on TF


title: Cst6DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: Med15 fused w Msn2 DBD -Mnase-NLS w del (Msn2, Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep4

description: ChEC-SEQ

value: delta 12 TFs


title: A-KINACT control cells, GasR201C-/light-, replicate 2

value: A-KINACT, TetO-EGFP


title: A-KINACT control cells, GasR201C-/light-, replicate 1


title: Crz1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ

value: FALSE


title: 272N-LineP3

city: Seattle

first: Yuexin

last: Xu

state: WA

address: 1100 Fairview Ave N, D4-100, Fred Hutchinson Cancer Research Center

institute: Fred Hutchinson Cancer Research Institute

data_processing:
Raw RNAseq data were processed by the nextflow nf-core/rnaseq analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Assembly: hg19
Supplementary files format and content: tsv files of gene expression count matrix

source_name: Kidney

extract_protocol:
RNA samples were extracted using RNeasy plus mini kit (Qiagen, Hilden, Germany) to remove genomic DNA.
50ng RNA samples at 5ng/ul concentration were reverse-transcribed by poly-A selection using oligo dT primer. Clontech SMARTv4 (Takara Bio) and Nextera XT (llumina) kits are used to construct the library according to the manufacture’s protocol. The sample pool was sequenced at 30 million 50PE reads per sample, Nextseq P2 flowcell.

value: Kidney

value: P3 Endo Line

value: Normal kidney digest


title: Crz1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ

data_processing:
Demultiplexing with bcl2fastq.
Filtering of adapter dimers using cutadapt and picard.
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d).
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.txt files contain genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome.
Library strategy: ChEC-seq


title: RAM15_Tumor

description: 10x Genomics

data_processing:
The 10X Chromium scRNA-seq outputs were de-multiplexed, mapped to the human reference genome (hg19, GRCh38) and aggregated to one single cell object through the Cell Ranger V4.0 bioinformatics pipeline. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: tsv files of gene features and barcode; mtx files of gene expression matrix all compressed using gzip (.gz)

extract_protocol:
Single-cell suspensions were prepared from primary tissues using the gentleMACSTM tissue dissociator and tumor dissociation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) using the “soft tissue” setting. PBMC were processed using Lymphocyte Separation Medium (Corning Inc., Corning, NY) density gradient centrifugation or SepMate PBMC Isolation (StemCell Technologies, Vancouver, Canada).
scRNA-seq libraries were constructed according to the manufacturer’s protocol.  Pooled V(D)J, 5’ GEX libraries were sequenced on a NovaSeq 6000 SP100 flowcell (Illumina, San Diego, CA) to obtain 5,000 reads/cell and 20,000 reads/cell depth, respectively.

value: Clear cell renal cell carcinoma digest


title: Med15 fused w Msn2 DBD -Mnase-NLS w del (Msn2, Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep2

description: ChEC-SEQ

value: native


title: 214N-LineP3


title: RAM15_NAT

description: 10x Genomics


title: Abf1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: 214T-LineP3


title: Abf1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 154T-LineP3


title: Cst6_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Med15 fused w Msn2 DBD -Mnase-NLS w del (Msn2, Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep3

description: ChEC-SEQ


title: Med15 fused w Msn2 DBD -Mnase-NLS w del (Msn2, Msn4, Crz1, Skn7, Yap1, Rsf2, Tda9, Asg1, Mss11, Sko1, Hot1, Gis1), rep1

description: ChEC-SEQ


title: RAM13_Tumor

description: 10x Genomics


title: 272T-LineP3


title: PAM22jiedu

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

institute: Zijingang Campus of Zhejiang University

description: infected at MOI=1 and harvested at 24 hour post infection

data_processing:
Poly-N, adapter and low-quality were removed by skewer(v0.2.2) ，Quality control analysis was performed by Fast QC version 0.11.5
Clean reads were aligned to the pig reference genome (version: Sus_scrofa.Sscrofa11.1) using STAR(2.5.3a) with the following configurations two passMode Basic --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 24 --outSAMtype SAM --outSAMstrandField intronMotif.
LncRNAs were identified using four predicted tools including predictor of lncRNAs and mRNAs based on k-mer scheme (PLEK version1.2), Coding-Non-Coding-Index (CNCI version 1.2.2) and Coding Potential Calculator (CPC2-beta) ，Coding Potential Assessment Tool (CPAT version 1.2.2)
StringTie version 1.3.1c was used to calculate the FPKMs of both lncRNAs and mRNAs in each sample
Genome_build: Sus_scrofa.Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited excel files include  normalized  values for each Sample

organism: Sus scrofa

source_name: primary porcine macrophages

extract_protocol:
Total RNA was isolated from infected cells using TRIzol reagent (Vazyme Biotech Company, China) according to the manufacturer.
Ribo-zero-magnetic-kit (Epicentre, USA) was used to remove ribosomal RNA. RNA libraries were prepared using TruSeq® RNA LT Sample Prep Kit v2(illumine, USA). Library sequencing was performed on a Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA) in ShangHai Genergy Biotech (Shanghai, China).

treatment_protocol: primary porcine macrophages were infected with ASFV at a multiplicity of infection (MOI) of 1 and harvested at 24 hour post infection or without, respectively.

value: PAM

value: infected with ASFV


title: RAM13_NAT

description: 10x Genomics


title: Crz1DBD_Gcn4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 272T-Primary

value: Primary


title: PAM21jiedu


title: Abf1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_3

description: ChEC-SEQ


title: 272N-Primary


title: RAM12_Tumor

description: 10x Genomics


title: Abf1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Abf1DBD_Gal4AD_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: 214T-Primary


title: PAM20jiedu


title: RAM12_NAT

description: 10x Genomics


title: RAM5_Tumor

description: 10x Genomics


title: 214N-Primary


title: 154N-LineP3


title: PAM21yinxing

description: control

value: uninfected


title: Abf1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_2

description: ChEC-SEQ


title: Abf1_Full_TEF_Mnase_HO_loc_nodel_native_loc_TF_1

description: ChEC-SEQ


title: PAM20yinxing

description: control


title: Pat022

status: Public on Jul 26 2024

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

data_processing:
Skewer version 0.2.2 was used to perform quality trimming of 3’ end bases less that phred quality score of 20.
BISulfite-seq CUI Toolkit (BISCUIT)  version 1.1.0 was used to map paired reads to the set of reference sequences and generate a pileup.
The pileup file was converted to vcf with BiSCUIT and then converted to a bed file.
In orderto get the bed file to be usable with methylkit, an awk 1 liner was used to rearrange the columns.
Methylkit in R was used to unite the measurements for the 24 samples and provide the beta values for downstream statistical analysis.
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Supplementary files format and content: Each sample has a bed file which provides the proportion of methylation at each site and overall coverage.
Supplementary files format and content: We also provide a table of beta values which can be used to reproduce the statistical analysis.

source_name: omental fat

extract_protocol:
A 100 mg sample of omental adipose tissue was obtained during Caesarean delivery and washed thoroughly in ice-cold PBS to remove any blood. Fifty milligram portions were then transferred into cryotubes, snap-frozen in liquid nitrogen and stored at -80°C until DNA/RNA extraction. Omental adipose tissue DNA was isolated using Qiagen blood and tissue kits.
Bisulfite conversion was performed on 500 ng genomic DNA using the Ez-96 DNA Methylation-Lightning MagPrep kit (Zymo Research). One microlitre of bisulfite converted DNA was used for the first round of polymerase chain reaction (PCR) using FastStart PCR Master (Merck) with gene-specific primers carrying tags for the second PCR. Primers were designed with a maximum amplicon length of 400 bp (Masser et al., 2015). All primers were tested by gradient PCR to achieve optimal conditions for second round PCR. Quality control was performed using a Qubit dsDNA high sensitivity assay kit. A 1.5% agarose gel was used to detect primer dimers and by-products from first-round PCR amplicons. Amplicons were then purified using the bead-based Merck AMPure XP kit  according to the manufacturer's protocol. Five microlitres of each of seven 4 nM amplicons derived from the same participant’s sample were pooled and sample-specific adapter primers (barcodes) were bound to these tag sequences in the second round PCR. Equimolar pooling of libraries was conducted prior to sequencing on the Illumina MiSeq instrument.
Targeted bisulfite amplicon sequencing for regions of the following genes: LEP, POMC, NPY, TNF, SOCS3.

value: omental fat

tag: placental weight_g

tag: height cm

tag: weight initial_kg

tag: bmi initial

tag: weight at_delivery_kg

tag: bmi at_delivery

tag: gwg kg

tag: age years

tag: gravida

tag: foetussex

value: Male

tag: birth wt_grams

tag: gestation weeks

tag: gestation days

tag: fetal length_cm

tag: ponderal index

tag: apgar 5

tag: labor onset


title: Pat023

tag: tissue

tag: placental weight_g


title: Pat021

tag: height cm

tag: weight initial_kg

value: Female


title: Pat024

tag: bmi initial

tag: weight at_delivery_kg


title: Pat020

tag: bmi at_delivery

tag: gwg kg


title: Pat017

tag: age years

tag: gravida


title: Pat018

tag: foetussex

tag: birth wt_grams


title: Pat019

tag: gestation weeks

tag: gestation days


title: Pat015

tag: fetal length_cm

tag: ponderal index


title: Pat014

tag: apgar 5

tag: labor onset


title: Pat016

tag: tissue

tag: placental weight_g


title: Pat011

tag: height cm

tag: weight initial_kg


title: Pat012

tag: bmi initial

tag: weight at_delivery_kg


title: Pat010

tag: bmi at_delivery

tag: gwg kg


title: Pat009

tag: age years

tag: gravida


title: Pat006

tag: foetussex

tag: birth wt_grams


title: Pat013

tag: gestation weeks

tag: gestation days


title: Pat008

tag: fetal length_cm

tag: ponderal index


title: Pat005

tag: apgar 5

tag: labor onset


title: Pat004

tag: tissue

tag: placental weight_g


title: Pat007

tag: height cm

tag: weight initial_kg


title: Pat003

tag: bmi initial

tag: weight at_delivery_kg


title: Pat002

tag: bmi at_delivery

tag: gwg kg


title: 154T-Primary

tag: cell line

tag: cell type


title: RAM5_NAT

description: 10x Genomics


title: Pat001

tag: age years

tag: gravida

tag: foetussex

tag: birth wt_grams


title: C_terminal_Ab42_double_mutants_output3

city: Barcelona

first: Mireia

last: Seuma

state: Barcelona

address: Carrer de Baldiri Reixac, 10, 12

country: Spain

institute: Institute for Bioengineering of Catalonia

description: PCR DNA amplicon from plasmid library

library_source: other

data_processing:
FastQ files from paired-end sequencing of each Aß42 library before (‘input’) and after selection (‘output’) were processed using the DiMSum pipeline (https://github.com/lehner-lab/DiMSum)
Assembly: NA
Supplementary files format and content: Spreadsheet file with columns indicating aa_seq = amino acid sequence of variant, aa_seq_full = full amino acid sequence of AB42 containing the variant (ready to feed in MoCHI), dataset = dataset label (N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants, Combinatorial_1, Combinatorial_2), mean_count= Mean read counts of the input replicates, fitness= Merged fitness, sigma = Merged error over fitness, fAD_category = Associated pathogenicity (non-fAD, fAD).
Library strategy: DNA-seq

molecule: other

source_name: single cell eukaryotic microorganism

growth_protocol: For each Aβ42 plasmid library, yeast cells were transformed in 3 biological replicas (1,2,3), with a minimum of 3, 2.2, 0.99 and 0.43 million transformants for each of the replicate of N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants, Combinatorial_1 and Combinatorial_2 libraries, respectively. Once the culture reached the exponential phase, cells were resuspended in 100-1000mL protein inducing medium (-URA, 20% glucose, 100uM Cu2SO4) at OD600=0.05. Selection was performed for each biological replica. After 24h, 25-50ml of cells were harvested for input pellets and a minimum of 75, 12, 230 and 1.5 million cells / replica (for N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants, Combinatorial_1 and Combinatorial_2 libraries, respectively) were plated on -URA-ADE selection medium plates (145cm2, Nunc, Thermo Scientific) and incubated for 6-7 days at 30C. The number of cells plated ensures a minimum coverage of 10 times each variant in the library. Finally, colonies were scraped off the plates and harvested for output pellets. Inputs and output pellets were stored at -20C and later treated for DNA extraction.

extract_protocol:
Input and output pellets (3 biological replicates each, 6 tubes in total) were resuspended in 2ml extraction buffer (2% Triton-X, 1% SDS, 100 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA pH 8) and subjected to two cycles of freezing-thawing in an ethanol-dry ice bath and water bath at 62C for 10min each. 1.5ml of phenol:chloroform:isoamyl 25:24:1 was then added to the pellets and vortexed for 10min. The aqueous phase was recovered by means of 30min centrifugation at 3000 rpm. DNA was precipitated with 1:10 V NaOAc 3M and 2.2 V of 99% cold ethanol and incubated at -20C for 2h. After centrifugation, pellets were dried overnight at RT. The next day, pellets were resuspended in TE 1X buffer (10mM Tris pH8, 1mM EDTA pH8) and treated with 10ul RNase A (Thermo Scientific) for 1h at 37C. DNA was purified using a silica beads extraction kit (QIAEX II Gel Extraction Kit, Qiagen).
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 50 (for Combinatorial_2) or 100 (for N_terminal_Ab42_double_mutants, C_terminal_Ab42_double_mutants and Combinatorial_1 libraries) million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Illumina sequencing primers. PCR products from the first step were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. The three input samples were pooled together equimolarly, and the same for the three output samples. The two final pools were purified from a 2% agarose gel using a silica beads extraction kit (QIAEX II Gel Extraction Kit, Qiagen).

value: single cell eukaryotic microorganism

tag: genotype

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

tag: treatment

value: protein expression


title: C_terminal_Ab42_double_mutants_output2

description: PCR DNA amplicon from plasmid library


title: C_terminal_Ab42_double_mutants_output1

description: PCR DNA amplicon from plasmid library


title: C_terminal_Ab42_double_mutants_input3

description: PCR DNA amplicon from plasmid library


title: N_terminal_Ab42_double_mutants_output3

description: PCR DNA amplicon from plasmid library


title: C_terminal_Ab42_double_mutants_input2

description: PCR DNA amplicon from plasmid library


title: C_terminal_Ab42_double_mutants_input1

description: PCR DNA amplicon from plasmid library


title: N_terminal_Ab42_double_mutants_output2

description: PCR DNA amplicon from plasmid library


title: N_terminal_Ab42_double_mutants_output1

description: PCR DNA amplicon from plasmid library


title: N_terminal_Ab42_double_mutants_input3

description: PCR DNA amplicon from plasmid library


title: N_terminal_Ab42_double_mutants_input2

description: PCR DNA amplicon from plasmid library


title: N_terminal_Ab42_double_mutants_input1

description: PCR DNA amplicon from plasmid library


title: Serum exosome miRNA, Control, 2022, 20

city: Bunkyo

first: Zhiyang

last: Yu

state: Tokyo to

address: Hongo 2-1-1

department: Department of Neurology

country: Japan

institute: Juntendo University

data_processing:
Generated sequencing data was aligned and mapped to miRBase using the Bowtie2.
Assembly: hg19(whole genome) miRBase(miRNA)
Supplementary files format and content: xlsx file containing raw counts and RPM values for all samples

source_name: Serum exosome

extract_protocol:
Total Exosome RNA and Protein Isolation Kit (Thermo Fisher Scientific, Waltham, MA) was utilised to extract total RNA from serum exosomes, following the manufacturer's instructions.
Small RNA library construction, alignment and mapping were performed by staff at Thermo Fisher Scientific. The small RNA libraries were prepared with the Ion Total RNA-Seq Kit version 2 on the Ion PGM System (Thermo Fisher Scientific, Waltham, MA). Quality control of the generated small RNA library was carried out using the Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Serum samples were collected from participants at the outpatient department of Juntendo University Hospital. Upon collection, the serum samples were immediately stored at −80°C until use.

value: Serum exosome

tag: disease state

value: PD (Baseline)

value: Extracellular vesicles


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 26

description: Dropped out

tag: tissue

value: PD (Dropped out)


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 23

description: Dropped out


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 46

value: PD (Rasagiline Treatment)


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 21

description: Dropped out


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 47


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 22

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 25

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 24

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, 2022, 46


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 45


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 20

description: Dropped out


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 43


title: Serum exosome miRNA, PD, Baseline, 2022, 45


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 44


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 42


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 41


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 40


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 39


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 38


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 37


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 36


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 30


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 29


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 34


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 31


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 24


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 28


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 26


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 21


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 18


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 23


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 19


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 22


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 14


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 27


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 25


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 13


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 16


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 10

description: PD10: Medication discontinued


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 15


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 35


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 09


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 12


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 33


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 32


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 08


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 07


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 06


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 05


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 03


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 04


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 20


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 02


title: PAM22yinxing

description: control

tag: strain


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 11


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 01


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 19

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 13

description: Dropped out


title: Serum exosome miRNA, Rasagiline Treatment, 2022, 17


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 16

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 14

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 15

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 08

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 07

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 10

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 06

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 11

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 04

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 17

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 05

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 03

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, 2022, 44


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 09

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 01

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 02

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, 2022, 42


title: Serum exosome miRNA, PD, Baseline, 2022, 43


title: Serum exosome miRNA, PD, Baseline, 2022, 41


title: Serum exosome miRNA, PD, Baseline, 2022, 40


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 18

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, 2022, 39


title: Serum exosome miRNA, PD, Baseline, 2022, 38


title: Serum exosome miRNA, PD, Baseline, Dropped Out, 2022, 12

description: Dropped out


title: Serum exosome miRNA, PD, Baseline, 2022, 35


title: Serum exosome miRNA, PD, Baseline, 2022, 37


title: Serum exosome miRNA, PD, Baseline, 2022, 36


title: Serum exosome miRNA, PD, Baseline, 2022, 34


title: Serum exosome miRNA, PD, Baseline, 2022, 30


title: Serum exosome miRNA, PD, Baseline, 2022, 32


title: Serum exosome miRNA, PD, Baseline, 2022, 29


title: Serum exosome miRNA, PD, Baseline, 2022, 33


title: Serum exosome miRNA, PD, Baseline, 2022, 26


title: Serum exosome miRNA, PD, Baseline, 2022, 22


title: Serum exosome miRNA, PD, Baseline, 2022, 20


title: Serum exosome miRNA, PD, Baseline, 2022, 17


title: Serum exosome miRNA, PD, Baseline, 2022, 25


title: Serum exosome miRNA, PD, Baseline, 2022, 27


title: Serum exosome miRNA, PD, Baseline, 2022, 19


title: Serum exosome miRNA, PD, Baseline, 2022, 24


title: Serum exosome miRNA, PD, Baseline, 2022, 23


title: Serum exosome miRNA, PD, Baseline, 2022, 28


title: Serum exosome miRNA, PD, Baseline, 2022, 21


title: Serum exosome miRNA, PD, Baseline, 2022, 18


title: Serum exosome miRNA, PD, Baseline, 2022, 16


title: Serum exosome miRNA, PD, Baseline, 2022, 12


title: Serum exosome miRNA, PD, Baseline, 2022, 11


title: Serum exosome miRNA, PD, Baseline, 2022, 13


title: Serum exosome miRNA, PD, Baseline, 2022, 15


title: Serum exosome miRNA, PD, Baseline, 2022, 10

description: PD10: Medication discontinued


title: Serum exosome miRNA, PD, Baseline, 2022, 31


title: Serum exosome miRNA, PD, Baseline, 2022, 09


title: Serum exosome miRNA, PD, Baseline, 2022, 08


title: Serum exosome miRNA, PD, Baseline, 2022, 07


title: Serum exosome miRNA, PD, Baseline, 2022, 03


title: Serum exosome miRNA, PD, Baseline, 2022, 06


title: Serum exosome miRNA, PD, Baseline, 2022, 05


title: Serum exosome miRNA, PD, Baseline, 2022, 02


title: Serum exosome miRNA, PD, Baseline, 2022, 01


title: Serum exosome miRNA, PD, 2021, 45

value: PD


title: Serum exosome miRNA, PD, 2021, 46


title: Serum exosome miRNA, PD, 2021, 44


title: Serum exosome miRNA, PD, 2021, 42


title: Serum exosome miRNA, PD, Baseline, 2022, 14


title: Serum exosome miRNA, PD, 2021, 43


title: Serum exosome miRNA, PD, 2021, 39


title: Serum exosome miRNA, PD, 2021, 38


title: Serum exosome miRNA, PD, 2021, 41


title: Serum exosome miRNA, PD, 2021, 36


title: Serum exosome miRNA, PD, 2021, 31


title: Serum exosome miRNA, PD, 2021, 33


title: Serum exosome miRNA, PD, 2021, 30


title: Serum exosome miRNA, PD, 2021, 34


title: Serum exosome miRNA, PD, 2021, 35


title: Serum exosome miRNA, PD, 2021, 29


title: Serum exosome miRNA, PD, Baseline, 2022, 04


title: Serum exosome miRNA, PD, 2021, 27


title: Serum exosome miRNA, PD, 2021, 28


title: Serum exosome miRNA, PD, 2021, 26


title: Serum exosome miRNA, PD, 2021, 25


title: Serum exosome miRNA, PD, 2021, 23


title: Serum exosome miRNA, PD, 2021, 21


title: Serum exosome miRNA, PD, 2021, 20


title: Serum exosome miRNA, PD, 2021, 22


title: Serum exosome miRNA, PD, 2021, 19


title: Serum exosome miRNA, PD, 2021, 40


title: Serum exosome miRNA, PD, 2021, 37


title: Serum exosome miRNA, PD, 2021, 17


title: Serum exosome miRNA, PD, 2021, 18


title: Serum exosome miRNA, PD, 2021, 16


title: Serum exosome miRNA, PD, 2021, 15


title: Serum exosome miRNA, PD, 2021, 14


title: Serum exosome miRNA, PD, 2021, 12


title: Serum exosome miRNA, PD, 2021, 10


title: Serum exosome miRNA, PD, 2021, 13


title: Serum exosome miRNA, PD, 2021, 32


title: Serum exosome miRNA, PD, 2021, 08


title: Serum exosome miRNA, PD, 2021, 05


title: Serum exosome miRNA, PD, 2021, 06


title: Serum exosome miRNA, PD, 2021, 07


title: Serum exosome miRNA, PD, 2021, 03


title: Serum exosome miRNA, PD, 2021, 24


title: Serum exosome miRNA, PD, 2021, 04


title: Serum exosome miRNA, PD, 2021, 01


title: Serum exosome miRNA, Control, 2021, 34

value: Control


title: Serum exosome miRNA, Control, 2021, 32


title: Serum exosome miRNA, PD, 2021, 02


title: Serum exosome miRNA, Control, 2021, 31


title: Serum exosome miRNA, Control, 2021, 30


title: Serum exosome miRNA, Control, 2021, 28


title: Serum exosome miRNA, PD, 2021, 11


title: Serum exosome miRNA, Control, 2021, 26


title: Serum exosome miRNA, Control, 2021, 23


title: Serum exosome miRNA, Control, 2021, 24


title: Serum exosome miRNA, PD, 2021, 09


title: Serum exosome miRNA, Control, 2021, 25


title: Serum exosome miRNA, Control, 2021, 29


title: Serum exosome miRNA, Control, 2021, 21


title: Serum exosome miRNA, Control, 2021, 20


title: Serum exosome miRNA, Control, 2021, 19


title: Serum exosome miRNA, Control, 2021, 15


title: Serum exosome miRNA, Control, 2021, 13

description: QC Failed, retained for data integrity


title: Serum exosome miRNA, Control, 2021, 16


title: Serum exosome miRNA, Control, 2021, 33


title: Serum exosome miRNA, Control, 2021, 14


title: Serum exosome miRNA, Control, 2021, 12

description: QC Failed, retained for data integrity


title: Serum exosome miRNA, Control, 2021, 11


title: Serum exosome miRNA, Control, 2021, 10


title: Serum exosome miRNA, Control, 2021, 08


title: Serum exosome miRNA, Control, 2021, 05


title: Serum exosome miRNA, Control, 2021, 06


title: Serum exosome miRNA, Control, 2021, 04


title: Serum exosome miRNA, Control, 2021, 09


title: Serum exosome miRNA, Control, 2021, 02


title: Serum exosome miRNA, Control, 2021, 27


title: Serum exosome miRNA, Control, 2021, 03


title: Serum exosome miRNA, Control, 2021, 01


title: Serum exosome miRNA, Control, 2020, 50


title: Serum exosome miRNA, Control, 2020, 49


title: Serum exosome miRNA, Control, 2021, 22


title: Serum exosome miRNA, Control, 2020, 48


title: Serum exosome miRNA, Control, 2020, 47


title: Serum exosome miRNA, Control, 2020, 44


title: Serum exosome miRNA, Control, 2020, 46


title: Serum exosome miRNA, Control, 2020, 45


title: Serum exosome miRNA, Control, 2020, 41


title: Serum exosome miRNA, Control, 2020, 43


title: Serum exosome miRNA, Control, 2020, 40


title: Serum exosome miRNA, Control, 2021, 07


title: Serum exosome miRNA, Control, 2020, 37


title: Serum exosome miRNA, Control, 2020, 38


title: Serum exosome miRNA, Control, 2020, 35


title: Serum exosome miRNA, Control, 2020, 32


title: Serum exosome miRNA, Control, 2020, 34


title: Serum exosome miRNA, Control, 2020, 33


title: Serum exosome miRNA, Control, 2020, 36


title: Serum exosome miRNA, Control, 2020, 29


title: Serum exosome miRNA, Control, 2020, 30


title: Serum exosome miRNA, Control, 2020, 28


title: Serum exosome miRNA, Control, 2020, 24


title: Serum exosome miRNA, Control, 2020, 27


title: Serum exosome miRNA, Control, 2020, 39


title: Serum exosome miRNA, Control, 2020, 23


title: Serum exosome miRNA, Control, 2020, 22


title: Serum exosome miRNA, Control, 2020, 21


title: Serum exosome miRNA, Control, 2020, 20


title: Serum exosome miRNA, Control, 2020, 42


title: Serum exosome miRNA, Control, 2020, 18


title: Serum exosome miRNA, Control, 2020, 31


title: Serum exosome miRNA, Control, 2020, 19


title: Serum exosome miRNA, Control, 2020, 14


title: Serum exosome miRNA, Control, 2020, 16


title: Serum exosome miRNA, Control, 2020, 13


title: Serum exosome miRNA, Control, 2020, 17


title: Serum exosome miRNA, Control, 2020, 15


title: Serum exosome miRNA, Control, 2020, 12


title: Serum exosome miRNA, Control, 2020, 11


title: Serum exosome miRNA, Control, 2020, 09


title: Serum exosome miRNA, Control, 2020, 26


title: Serum exosome miRNA, Control, 2020, 06


title: Serum exosome miRNA, Control, 2020, 03


title: Serum exosome miRNA, Control, 2020, 01


title: Serum exosome miRNA, Control, 2020, 02


title: Serum exosome miRNA, Control, 2020, 10


title: Serum exosome miRNA, Control, 2020, 04


title: Serum exosome miRNA, PD, 2020, 50


title: Serum exosome miRNA, PD, 2020, 48


title: Serum exosome miRNA, PD, 2020, 46


title: Serum exosome miRNA, Control, 2020, 08


title: Serum exosome miRNA, PD, 2020, 45


title: Serum exosome miRNA, PD, 2020, 41


title: Serum exosome miRNA, PD, 2020, 42


title: Serum exosome miRNA, PD, 2020, 43


title: Serum exosome miRNA, PD, 2020, 47


title: Serum exosome miRNA, PD, 2020, 44


title: Serum exosome miRNA, PD, 2020, 40


title: Serum exosome miRNA, PD, 2020, 39


title: Serum exosome miRNA, Control, 2020, 05


title: Serum exosome miRNA, PD, 2020, 37


title: Serum exosome miRNA, PD, 2020, 34


title: Serum exosome miRNA, Control, 2020, 07


title: Serum exosome miRNA, PD, 2020, 36


title: Serum exosome miRNA, PD, 2020, 33


title: Serum exosome miRNA, PD, 2020, 35


title: Serum exosome miRNA, PD, 2020, 32


title: Melanoma human, transfection control, dabrafenib+trametinib, 24h, rep1

city: Bonn

first: Thais

middle: Marina

last: Schlee-Guimarães

address: Venusberg-Campus 1

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital, University of Bonn

data_processing:
Next, sequencing reads were aligned to the human reference genome using STAR (Dobin et al., 2013).
Quantifying  with HTSeq (G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analysing high-throughput sequencing data in Python with HTSeq 2.0 ).
Gene expression analysis was performed with the statical R-package edgeR (Robinson MD, McCarthy DJ, Smyth GK (2010).
Assembly: GRCh38.109
Supplementary files format and content: counts csv files

growth_protocol: Kept at 37°C 5% CO2  A375 cell line was cultured in DMEM  with 10 % (v/v) fetal calf serum (FCS) and 100 units penicillin and 100µg streptomycin per mL Media (p/s).

extract_protocol:
Qiagen, RNeasy Mini Kit, accodring to manufacturers recomandation
mRNA was purified by poly-A enrichment using NEBNext® Poly(A) mRNA Magnetic Isolation Module. For library preparation NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads with NEBNext® Multiplex Oligos for Illumina® were used.

treatment_protocol: For RIG-I stimulation a chemically synthesized dsRNA with a 3p end was used. CA21 control RNA (5’-CACACACACACACACACACAC-3’) was used als transfection control. For transfection RNA was complexed to Lipofectamine 2000 (Invitrogen) according to the manufactures protocol. Dabrafenib and Trametinib were dissolved in Dimethylsulfoxid (DMSO) and added at indicated concentrations. DMSO at highest used concentration served as vehicle control.

value: melanoma

value: BRAF mut

tag: group

value: transfection control

value: dabrafenib 1000 nM + trametinib 100 nM


title: Serum exosome miRNA, PD, 2020, 49


title: Serum exosome miRNA, PD, 2020, 30