title: M67, M68 CD5hi + M67, M68 CD5lo + M67 CD4+

description: Barcodes: I1:M67 CD5hi, I2:M67 CD5lo, I3:M67 CD4+, I4:M68 CD5hi, I5:M68 CD5lo, I6:M68 CD4+

tag: tissue

value: spleen and peripheral lymph nodes (inguinal, axillary, brachial, superficial cervical, and mesenteric)

tag: strain

tag: cell type

value: CD5hi/CD5lo/CD4+ T cells

tag: genotype

value: WT

tag: treatment

value: not applicable


title: HippoCells_DIV11_shctrl_TSA_1

status: Public on Jan 09 2023

type: SRA

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

library_source: transcriptomic

data_processing:
Fastq Quality Control using FastQC.
Adapter trimming and quality filtering was done using Cutadapt 2.1 with Python 3.6.7 with the following configurations: -j 8 -e 0.1 -q 16 -O 3 --trim-n --minimum-length 25 -a AGATCGGAAGAGC
Trimmed and quality filtered RNA-Seq reads were aligned to mm10 genome assembly using STAR_2.6.1d with the following configurations: STAR --runThreadN 20 --sjdbOverhang 100 --readFilesCommand zcat --outSAMunmapped Within --outSAMtype BAM Unsorted --outStd BAM_Unsorted --sjdbGTFfile
Coverage of bam files was calculated with bamCoverage and RPKM normalised: binLength: 25, numberOfSamples: None blackListFileName: None, defaultFragmentLength: read length, numberOfProcessors: 8, verbose: False, region: None, bedFile: None, minMappingQuality: None, ignoreDuplicates: False  chrsToSkip: [] stepSize: 25, center_read: False ,samFlag_include: None, samFlag_exclude: None, minFragmentLength: 0, maxFragmentLength: 0, zerosToNans: False  smoothLength: None, save_data: False, out_file_for_raw_data: None, maxPairedFragmentLength: 1000
Gene level counts were obtained by running featurecounts. featurecounts options: -C -Q 10 --primary fragmentLength: 200 libraryType: 2 salmonIndexOptions: --type puff -k 31 dnaContam: False
DESeq2 (v. 1.22.1) on count matrices output from snakePipes (featureCounts, v. 1.6.4). A linear model controlling for batch effects (e.g., ∼batch + treatment or ∼ batch + condition) was used and apeglm log2(Fold Change) shrinkage was applied.
Genome_build: mm10
Supplementary_files_format_and_content: tsv, gene counts, DESEQ2 results tables

molecule: total RNA

organism: Mus musculus

source_name: Primary Hippocampal Neurons

growth_protocol: Primary hippocampal tissue isolation and culture was done following a protocol modified after Brewer et al., 1993. Hippocampal tissue was isolated from E18.5 mouse embryos and dissociated by trypsinisation and trituration. Cells were counted and seeded 150,000/well in 24 well-plates and were grown in Neurobasal medium with B27 supplement (DIV0). Half-volume medium change was done every 48 hours.

extract_protocol:
RNA was extracted using Qiagen Rneasy kit following the manufacturer's instructions.
Library Prep was performed with NEBNext E7530S following the manual, 11 cycles of PCR were performed for amplification. NEBNext E7335L was used for multiplexing. Quality control: the size and distribution were controlled on gel. RNA-Seq libraries were sequenced on Illumina HiSeq 3000 as 100-nt paired end reads.

treatment_protocol:
Cells were treated with lentivirus on DIV1 for shRNA expression in neuronal cells. The viral plasmid was in plKO.1 backbone and had the reporter turboGFP, shRNA, and puromycin resistance casette. Cells were divided into 2 groups for the treatment of shFoxg1, or shLuciferase expressing viruses. After the half-volume media change, 300 microliters of media was removed from each well (500 microliters total volume). 50 microliters of virus mix with a MOI of 1.5 was added in each well and left to incubate overnight. On DIV2, 200 microliters of medium was added back into each well. On DIV4, puromycin (final: 0.3 ug/ul) and cytosine arabinoside (Ara-C, final: 2mM) were added for selection of shRNA expressing cells, and to stop the proliferation of non-neuronal cells, respectively.
On DIV10 cells were treated with 0,5 uM HDAC inhibitor TSA (trichostatin A) or DMSO as control. Cells were harvested on DIV11 for subsequent RNA extraction.

tag: days in vitro(div)

value: TSA

tag: knockdown

value: shControl

value: hippocampus

tag: dissection age


title: 66-11

city: Stanford

first: Myung Chang

last: Lee

state: CA

address: 265 Campus Drive, G2065

department: Pediatrics and Genetics

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Library strategy: Tuba-seq
Each read is expected to contain an 8-nucleotide sgID region followed by a 30-nucleotide barcode (BC) region (GCNNNNNTANNNNNGCNNNNNTANNNNNGC), and each of the 20 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
We kept only the sgID-BC reads with perfect match between forward and reverse sequences, and we calculated the overall counts of sgID-BC to determine enrichment or depletion in the tumor samples.
Abundance of each barcode was calculated by aggregating the frequencies of each barcode per sample.
Assembly: sgID-BC reference (8N followed by GCNNNNNTANNNNNGCNNNNNTANNNNNGC)

molecule: genomic DNA

source_name: Transformed lung epithelial cell

extract_protocol:
Genomic DNA was isolated from formalin-fixed paraffin-embedded mouse lung tumor tissue sections using laser capture microdissection. Q5 High-Fidelity 2X Master Mix (New England Biolabs M0494X) was used to amplify the sgID-BC region using unique dual-indexed primers.
For sgID-BC amplicon libraries, we performed PCR with dual-indexed primers and purified the amplicon using MinElute kit as well as two-sided bead purification with Ampure XP beads.

value: Lung

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTsc1/PGK-Cre


title: HippoCells_DIV11_shctrl_TSA_2


title: input DNA_Foxg1KD_n1

data_processing:
Sequencing data were processed with snakePipes (v. 1.1.1).
Fastq Quality Control using FastQC.
 high quality and uniquely mapping reads were retained (mapq > 5). RELACS custom barcodes were designed with integrated UMI, so duplicate removal was performed using UMITools.
Adapter trimming and quality filtering was done using Cutadapt 2.1 with Python 3.6.7 with the following configurations: -j 8 -e 0.1 -q 16 -O 3 --trim-n --minimum-length 25 -a AGATCGGAAGAGC
Trimmed and quality filtered reads were aligned to mm10 genome assembly using STAR_2.6.1d with the following configurations: STAR --runThreadN 20 --sjdbOverhang 100 --readFilesCommand zcat --outSAMunmapped Within --outSAMtype BAM Unsorted --outStd BAM_Unsorted --sjdbGTFfile
Peaks were called using MACS2 ( v. 2.2.6) using default parameters from filtered BAM files.
Genome_build: mm10
Supplementary_files_format_and_content: bw and narrowpeak

extract_protocol:
Restriction enzyme-based labeling of chromatin in situ (RELACS) was used for H3K27ac and H3K4me3 ChIP-sequencing (25). DIV11 primary hippocampal neurons with FOXG1 or luciferase KD were fixed in 1% formaldehyde for 15 min. The reaction was stopped with 125 mM glycine for 5 min, followed by two-time DPBS +PIC washes. Cell nuclei were isolated following the NEXSON protocol (treatment time 20 s) and permeabilized with 0.5% SDS (26). Chromatin was digested in situ using five units of restriction enzyme CviKI-1 (NEB, R0710S) every 100.000 nuclei and RELACS custom barcodes (4 bp UMI + 8 bp RELACS barcode) were ligated to end-repaired and A-tailed chromatin using components from NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) (25).
The barcoded chromatin fragments were extracted by sonication for 5 min using these parameters: peak power 105 W, 2% duty factor, 200 cycles/burst (Covaris microtubes (520185), Covaris E220 Focused-ultrasonicator). A single immunoprecipitation (IP) reaction for all pooled samples was carried out on SX-8G Compact IP-Star platform (Diagenode) following Arrigoni et al. (25). Immunoprecipitated chromatin was used for NGS library preparation (NEBNext Ultra II DNA Library Prep Kit for Illumina, NEB). Libraries were sequenced at the Max Planck Institute of Immunology and Epigenetics using HiSeq 3000 (Illumina) as 75 bp reads.
Sequencing was performed at the Max Planck Institute of Immunology and Epigenetics, Bioinformatics Core Facility (Freiburg).

treatment_protocol: Cells were treated with lentivirus on DIV1 for shRNA expression in neuronal cells. The viral plasmid was in plKO.1 backbone and had the reporter turboGFP, shRNA, and puromycin resistance casette. Cells were divided into 2 groups for the treatment of shFoxg1 or shLuciferase expressing viruses. After the half-volume media change, 300 microliters of media was removed from each well (500 microliters total volume). 50 microliters of virus mix with a MOI of 1.5 was added in each well and left to incubate overnight. On DIV2, 200 microliters of medium was added back into each well. On DIV4, puromycin (final: 0.3 ug/ul) and cytosine arabinoside (Ara-C, final: 2mM) were added for selection of shRNA expressing cells, and to stop the proliferation of non-neuronal cells, respectively. Half-volume medium changes were continued every 48 hours until DIV11.

tag: antibody


title: Patient sample 075A (re-analysis)

city: Los Angeles

first: Matthew

middle: A

last: Fischer

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

institute: University of California, Los Angeles

description: re-analysis of GSM5829634

data_processing:
BS-Seeker2 (PMID 24206606) was used to align the reads to hg38, allowing for up to 10 mismatches, and methylation was called for CpGs and then processed using MethylKit in R as described in previous publications (PMIDs 29566149 and 26838786)
We removed from analysis CpGs with less than 10x coverage. Additionally, CpGs were removed from the cohort if they were located at SNPs with minor allele frequency greater than 1% in humans (dbSNP build 150 common SNPs: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/snp150Common.txt.gz) or not present in at least 50% of the cohort after filtering for coverage.
Assembly: Hg38
Supplementary files format and content: Each patient's methylation call file contains the chromosome and base pair location of each CpG and each CpG's coverage and percent methylation data.

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Genomic DNA was isolated (PureLink Genomic DNA Kit, K1820-01) from whole blood (separately we biobanked buffy coat containing leukocytes and platelets at -80ºC), subjected to enzymatic digestion with MspI (NEB, R0106S) and bisulfite converted (EpiTect Fast. DNA Bisulfite Kit, Qiagen, 59824).
Libraries were prepared using Illumina TruSeq kit, size-selected for 330 bp with AMPure XP beads and subjected to 100 bp, single-end sequencing on HiSeq instruments.

tag: individual

value: Patient 075

value: Whole blood

tag: time

value: pre-operative

tag: Sex

value: Male

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

value: Yes

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: input DNA_Foxg1KD_n2

tag: days in vitro(div)

tag: tissue

tag: dissection age

tag: strain

tag: antibody

tag: knockdown


title: H3K27ac_Control_n2

value: Rb, polyclonal, H3K27ac (Diagenode)

value: Control


title: H3K27ac_Foxg1KD_n2


title: Patient sample 071A (re-analysis)

description: re-analysis of GSM5829632

tag: individual

value: Patient 071

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery


title: 66-10

tag: tissue

tag: genotype

tag: treatment


title: 66-9


title: H3K27ac_Foxg1KD_n1

tag: days in vitro(div)

tag: dissection age

tag: strain

tag: antibody


title: HippoCells_DIV11_shFoxg1_TSA_1

tag: knockdown


title: Patient sample 070A (re-analysis)

description: re-analysis of GSM5829631

tag: individual

value: Patient 070

tag: time

tag: Sex

value: Female

tag: age

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: H3K4me3_Control_n2

tag: days in vitro(div)

tag: tissue

tag: dissection age

tag: strain

value: Rb, polyclonal, H3K4me3 (Diagenode)


title: 66-6

tag: genotype

tag: treatment


title: 66-7


title: 66-8


title: Patient sample 066A (re-analysis)

description: re-analysis of GSM5829629

tag: individual

value: Patient 066

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery


title: ATAC_Foxg1KD_n2

data_processing:
All sequencing data were processed with snakePipes (v. 1.1.1).
Fastq Quality Control using FastQC.
 high quality and uniquely mapping reads were retained (mapq > 5).  Standard deduplication was applied for ATAC-seq reads.
Adapter trimming and quality filtering was done using Cutadapt 2.1 with Python 3.6.7 with the following configurations: -j 8 -e 0.1 -q 16 -O 3 --trim-n --minimum-length 25 -a AGATCGGAAGAGC
Trimmed and quality filtered reads were aligned to mm10 genome assembly using STAR_2.6.1d with the following configurations: STAR --runThreadN 20 --sjdbOverhang 100 --readFilesCommand zcat --outSAMunmapped Within --outSAMtype BAM Unsorted --outStd BAM_Unsorted --sjdbGTFfile
Peaks were called using MACS2 ( v. 2.2.6) using default parameters from filtered BAM files.
Genome_build: mm10
Supplementary_files_format_and_content: bw and narrow peak

extract_protocol:
ATAC-seq was performed on DIV11 primary hippocampal neurons after Foxg1 or luciferase KD following the protocol of Buenrostro et al., 2015 [41]. Briefly, cells were washed with PBS and detached by 5 minute 0.05% trypsin incubation. Dissociation was stopped with 10% FBS and cells were collected and centrifuged for 5 minutes at 500xg 4°C. After one time wash with ice-cold PBS, cells were counted and separated into 5x105cells/replicate/condition. Cells were resuspended in lysis buffer ( 10mM Tris-HCl pH=7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal Ca-630) and immediately centrifuged for 10 minutes at 500xg 4°C.
Transposition, PCR amplification and DNA library preparation were done using Nextera DNA library prep kit according to the manufacturer’s instructions (Illumina). DNA was purified and eluted using MinElute PCR purification kit (Qiagen).
Paired end sequencing was performed at the Max Planck Institute of Immunology and Epigenetics, Bioinformatics Core Facility (Freiburg).

tag: days in vitro(div)

tag: tissue

tag: knockdown


title: ATAC_Control_n2

tag: dissection age

tag: strain

value: shLuciferase


title: ATAC_Control_n1

value: hippocampus


title: H3K27ac_Control_n1

tag: antibody


title: 66-4

value: Lung

tag: genotype

tag: treatment


title: 66-5

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTsc1/PGK-Cre


title: Patient sample 064A (re-analysis)

description: re-analysis of GSM5829627

tag: individual

value: Patient 064

tag: time

tag: Sex

tag: age

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 063A (re-analysis)

description: re-analysis of GSM5829626

value: Patient 063

tag: tissue

value: Whole blood

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery


title: Siha cell 1

city: Guangzhou

first: Chenfei

last: Zhou

state: Guangdong

address: No.151, Yanjiang Road, Yuexiu District, Guangzhou

department: Obstetrics and Gynecology

country: China

institute: The First Affiliated Hospital of Guangzhou Medical University

description: total cellular small RNA isolated from Siha

data_processing:
bowtie for mapping
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Siha cell

growth_protocol: hCEp cells were cultured in Cervical Epithelial Cell Medium (ScienCell) with 5% FBS (Gibco) ; SiHa cells were cultured in DMEM (Gibco) supplemented with 10%  FBS  (Gibco)

extract_protocol:
Exosomes were purified from hCEp or Siha-derived supernatant  by ultracentrifugation, exosomal and cellular small RNA was harvested using miRNeasy Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cellular supernatant was first prepared by incubating cells grown at sub-confluence in growth media containing exosome-depleted FBS (prepared by overnight ultracentrifugation of medium-diluted FBS at 100,000g at 4 °C) for 48 h

tag: cell type

value: Siha

tag: passages

tag: molecule subtype

value: total cellular small RNA


title: Siha cell 3


title: Patient sample 062A (re-analysis)

description: re-analysis of GSM5829625

tag: individual

value: Patient 062

tag: time

value: pre-operative

tag: Sex

value: Male

tag: age

value: No

tag: isolated valve surgery

tag: combined surgery

value: Yes

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: H3K4me3_Control_n1

tag: days in vitro(div)

tag: tissue

tag: dissection age

tag: strain

tag: antibody

tag: knockdown

value: Control


title: Siha exo 3

description: total exosomal small RNA isolated from Siha

source_name: Siha exosome

tag: cell type

tag: passages

tag: molecule subtype

value: total exosomal small RNA


title: 66-2

tag: genotype

tag: treatment


title: 66-12


title: Siha exo 2


title: Siha exo 1


title: Patient sample 067A (re-analysis)

description: re-analysis of GSM5829630

tag: individual

value: Patient 067

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 061A (re-analysis)

description: re-analysis of GSM5829624

tag: individual

value: Patient 061

tag: tissue

value: Female

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: 66-3

value: Lung

tag: genotype

tag: treatment


title: hCEp cell 3

description: total cellular small RNA isolated from hCEp

source_name: hCEp cell

tag: cell type

value: hCEp (Human Cervical Epithelia Cells)

tag: passages

tag: molecule subtype


title: ATAC_Foxg1KD_n1

tag: days in vitro(div)

value: hippocampus

tag: dissection age

tag: strain

tag: knockdown


title: H3K4me3_Foxg1KD_n2

tag: antibody

value: Rb, polyclonal, H3K4me3 (Diagenode)


title: 66-1

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTsc1/PGK-Cre


title: H3K4me3_Foxg1KD_n1


title: HCT116-TEAD4KR-2

city: shanghai

first: Zhenyu

last: Huang

address: NO. 1665 kongjiang RD.

institute: Colorectal Cancer Research Center of Shanghai

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GR38p7
Supplementary_files_format_and_content: abundance measurements

source_name: HCT116 CELL LINE

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: TEAD4 K178R


title: hCEp cell 1

value: total cellular small RNA


title: Siha cell 2

value: Siha


title: Patient sample 059A (re-analysis)

description: re-analysis of GSM5829622

tag: individual

value: Patient 059

tag: tissue

value: Whole blood

tag: time

value: pre-operative

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: hCEp exo 3

description: total exosomal small RNA isolated from hCEp

source_name: hCEp exosome

tag: cell type

tag: passages

tag: molecule subtype


title: hCEp exo 2


title: Patient sample 065A (re-analysis)

description: re-analysis of GSM5829628

tag: individual

value: Patient 065

tag: tissue

tag: time

tag: Sex

value: Male

tag: age

value: No

value: Yes

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: hCEp exo 1

value: total exosomal small RNA


title: HCT116-TEAD4KR-1

tag: cell line

tag: genotype


title: HCT116-TEAD4WT-2

value: TEAD5 wild type


title: Patient sample 058A (re-analysis)

description: re-analysis of GSM5829621

value: Patient 058

value: Female

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: hCEp cell 2

tag: cell type

value: hCEp (Human Cervical Epithelia Cells)

tag: passages

tag: molecule subtype


title: TCF 7-3

city: Daejeon

first: Jaeeun

last: Jung

address: 125 Gwahak-ro, Youseong-gu

country: South Korea

institute: KRIBB

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 mm10 whole genome using Tophat
FPKM calculation using Cufflink
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: mouse liver

extract_protocol:
Liver tissues were removed, flash frozen in liquid nitrogen. Total RNA from mouse livers was extracted using the easy-spin Total RNA Extraction Kit (iNtRON Biotechnology, Cat#17221).
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: mice were fasted for 24 h and refed a normal-chow diet (NCD) for 24 h

tag: strain

tag: tissue

value: Liver

tag: age

value: 12 week old

value: TCF7L2 liver specific knockout

tag: treatment

value: Refeeding a NCD for 24 h


title: TCF 8-3

tag: genotype


title: TCF 7-2


title: WT 8-3

value: wild type


title: Patient sample 057A (re-analysis)

description: re-analysis of GSM5829620

tag: individual

value: Patient 057

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: post-operative atrial fibrillation


title: HCT116-PQ-2

tag: cell line

value: control


title: HCT116-TEAD4WT-1

value: TEAD4 wild type


title: WT 8-1

tag: strain

tag: tissue

tag: age


title: Patient sample 056A (re-analysis)

description: re-analysis of GSM5829619

tag: individual

value: Patient 056

value: Whole blood

value: pre-operative

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: WT 7-2

tag: genotype

tag: treatment


title: Patient sample 055A (re-analysis)

description: re-analysis of GSM5829618

value: Patient 055

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

value: Yes

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: linc-133(aqz 3)_3

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

institute: Henan university

data_processing:
Illumina Casava1.7 software used for base-calling
Sequenced reads were trimmed for adaptor sequence. and masked for low-complexity or low-quality sequence. then mapped to WBcel235 whole genome using bowtie v0.12.2 with parameters
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level was calculated through a protocol from Chepelev et al., Nucleic Acids Research,2009.
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: C. elegans genome version WBcel235 was used as the reference.
Supplementary files format and content: The txt format file contains the FPKM value of  expression gene

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Mix stage worms were harvested and synchronized to collect the eggs. Eggs were cultured in M9  and incubated at 20°C for 3 days. The L1 arrest worms were collected to be used for RNA preparation.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Synchronized eggs of N2 and linc-133 (aqz 3) mutants were cultured in M9 for 3 days to L1 arrest stage at 20°C days.

tag: strain

value: linc-133(aqz 3)

tag: developmental stage

value: L1 arrest larvae

tag: tissue

value: whole body


title: Patient sample 060A (re-analysis)

description: re-analysis of GSM5829623

tag: individual

value: Patient 060

value: Female

tag: age

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: NL04_22 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

data_processing:
Library strategy: Tuba-seq
Illumina RTA software was used for basecalling, fastq files were generated by bcl2fastq software
Each read is expected to contain an 8-nucleotide sgID region followed by a 30-nucleotide barcode (BC) region (GCNNNNNTANNNNNGCNNNNNTANNNNNGC), and each of the 20 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
We kept only the sgID-BC reads with perfect match between forward and reverese sequences, and we calculated the overall counts of sgID-BC to determine enrichment or depletion in the tumor samples.
Tumor size (number of neoplastic cells) is calculated by normalizing the number of reads to the three benchmark cell lines (1 * 10^5 cells for each) added to each sample.
Assembly: sgID-BC reference (8N followed by GCNNNNNTANNNNNGCNNNNNTANNNNNGC)

extract_protocol:
Genomic DNA isolation from tumor-bearing mouse lung was performed via phenol:chloroform isolation and ethanol precipitation. Three benchmark control cell lines (1 * 10^5 cells per control) were added to correlate sgID-BC reads with cell number. Q5 High-Fidelity 2X Master Mix (New England Biolabs M0494X) was used to amplify the sgID-BC region using unique dual-indexed primers.
For sgID-BC amplicon libraries, we performed PCR with dual-indexed primers and purified the amplicon using MinElute kit as well as two-sided bead purification with Sera-Mag Select beads or Ampure XP beads.

value: Lung

tag: genotype

tag: treatment

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: N2_3


title: Patient sample 053A (re-analysis)

description: re-analysis of GSM5829617

value: Patient 053

tag: time

tag: Sex

value: Male

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: NL04_21 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: tissue


title: Patient sample 051A (re-analysis)

description: re-analysis of GSM5829616

tag: individual

value: Patient 051

tag: age

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition


title: N2_2

tag: strain

tag: developmental stage


title: HCT116-PQ-1

tag: cell line

tag: genotype

value: control


title: linc-133(aqz 3)_2


title: Patient sample 050A (re-analysis)

description: re-analysis of GSM5829615

value: Patient 050

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: NL04_20 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: tissue

tag: treatment


title: NL04_19 [Pool #2]

description:
Pool #2
Raw data lost to disk failure


title: Patient sample 049A (re-analysis)

description: re-analysis of GSM5829614

tag: individual

value: Patient 049

value: Whole blood

tag: age

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition


title: NL04_18 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: genotype


title: Patient sample 045A (re-analysis)

description: re-analysis of GSM5829612

value: Patient 045

tag: time

value: pre-operative

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: combined surgery

tag: current smoker

tag: b cells composition


title: Patient sample 047A (re-analysis)

description: re-analysis of GSM5829613

tag: individual

value: Patient 047

tag: tissue

tag: age

value: No

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

value: Yes

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: NL04_17 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: genotype

tag: treatment


title: linc-133(aqz 3)_1

tag: strain

value: linc-133(aqz 3)

tag: developmental stage

value: L1 arrest larvae

value: whole body


title: NL04_16 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

value: Lung


title: Patient sample 044A (re-analysis)

description: re-analysis of GSM5829611

value: Patient 044

tag: time

tag: Sex

value: Female

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition


title: N2_1

tag: tissue


title: NL04_14 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: T73

city: Newcastle upon Tyne

first: Laura

last: Sabater

state: Newcastle Upon Tyne

address: 4th Floor, William Leech Building

department: Biosciences institute

country: United Kingdom

institute: Newcastle University

data_processing:
Chimira (release 1.0, last accessed 24.03.2020) software was used to trim and align sequences.
Matrix with raw miRNA counts was obtained from Chimira (release 1.0, last accessed 24.03.2020).
Normalization and differential expression analysis was done with DESeq2 R package (v 1.36.0).
Assembly: miRBase
Supplementary files format and content: Count file with raw miRNA counts

source_name: Lung

extract_protocol:
For IPF fibrotic foci, Laser Capture Microdissection was used to isolate fibrotic foci from formalin embedded IPF tissue. RNA was isolated from LCM cut tissue and whole IPF formalin embedded tissue using FFPE RNeasy extraction kit (Qiagen). Lung fibroblasts were isolated from IPF lung tissue and normal human lungs. The cells were grown to 90% confluence, then serum starved for 24h in media containing 0.4% foetal calf serum. After the 24h perios, the cells were incubated for 48h with complete media only or media supplemented with 3ng/ml TGFβ1. The cells were harvested at 48h and total RNA extracted using an RNeasy mini kit (Qiagen).
NEBNext small RNA libraries (New England BioLabs Inc.) were prepared from total RNA.

tag: tissue type

value: Fibrotic Foci cut with LCM from FFPE IPF lung tissue

tag: molecule subtype

value: miRNA


title: T91


title: 91IPF

value: FFPE whole IPF lung


title: T37


title: 88IPF


title: 80IPF


title: 90IPF


title: T88


title: T80IPF


title: T90


title: T45


title: T27


title: 73IPF


title: Patient sample 043A (re-analysis)

description: re-analysis of GSM5829610

tag: individual

value: Patient 043

tag: age

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: T70


title: NL04_13 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: genotype

tag: treatment


title: 70IPF


title: Patient sample 040A (re-analysis)

description: re-analysis of GSM5829607

value: Patient 040

value: Whole blood

tag: time

tag: Sex

value: Male

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition


title: 45IPF

tag: tissue

tag: tissue type

tag: molecule subtype


title: Patient sample 042A (re-analysis)

description: re-analysis of GSM5829609

tag: individual

value: Patient 042

value: pre-operative

tag: age

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 039A (re-analysis)

description: re-analysis of GSM5829606

value: Patient 039

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: anesthesia time

value: Yes

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: 37IPF

tag: tissue

tag: tissue type

tag: molecule subtype


title: NL04_12 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: genotype

tag: treatment


title: 27IPF


title: NL04_10 [Pool #2]

description:
Pool #2
Raw data lost to disk failure


title: Patient sample 038A (re-analysis)

description: re-analysis of GSM5829605

tag: individual

value: Patient 038

tag: age

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: monocyte composition

tag: natural killer cell composition


title: CNCLL8B1

value: Lung

tag: cell type

value: Fibroblasts isolated from IPF tissue


title: NL04_15 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: tissue


title: CNCLL8


title: Patient sample 037A (re-analysis)

description: re-analysis of GSM5829604

value: Patient 037

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: NL04_7 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: genotype

tag: treatment

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: NL04_8 [Pool #2]

description:
Pool #2
Raw data lost to disk failure


title: CNCL26

tag: molecule subtype


title: Patient sample 035A (re-analysis)

description: re-analysis of GSM5829602

tag: individual

value: Patient 035

tag: age

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: monocyte composition

tag: natural killer cell composition


title: CNCL24B1

tag: tissue

tag: cell type

value: miRNA


title: CNCL15B1


title: Patient sample 029A (re-analysis)

description: re-analysis of GSM5829600

value: Patient 029

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: C91IPFB1

tag: treatment

tag: molecule subtype


title: CNCL22


title: CNCL24


title: NL04_4 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: genotype


title: CNCL26B1


title: CNCL22B1


title: NL04_3 [Pool #2]

description:
Pool #2
Raw data lost to disk failure


title: C90IPFB1


title: C90IPF


title: Patient sample 036A (re-analysis)

description: re-analysis of GSM5829603

tag: individual

value: Patient 036

tag: age

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: monocyte composition

tag: natural killer cell composition


title: MIBG alone, Day 3, 72 hours rep 5

city: Livermore

last: Coleman

address: 7000 East Avenue

institute: Lawrence Livermore National Laboratory

description: MIBG alone, Day 3, 72 hours

data_processing:
Read quality was assessed using FastQC
Read counts were aligned to the human reference genome GRCh38 with STAR
Samtools was utilized to sort the STAR output, and gene-wise read counts were calculated using ‘featureCounts’ with GRCh38 gene annotation
DESeq2 was utilized to identify differentially expressed genes
Assembly: hg38
Supplementary files format and content: Excel file containing raw counts from featurecounts output.

source_name: peripheral blood

extract_protocol:
RNA was harvested with MagMAX RNA Isolation kit compatible with PAXgene tubes (Thermo Fisher)
Libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer using both the UDI-adapter and UMI Second-Strand Synthesis modules (Lexogen), as well as the Homo sapiens RS-Globin Block module for globin depletion (Lexogen). The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA).   The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. The library pool was Exonuclease VII (NEB, Ipswich, MA) treated, SPRI-bead purified with KapaPure beads (Kapa Biosystems / Roche, Basel, Switzerland) , and quantified via qPCR with a Kapa Library Quant kit (Kapa Biosystems) on a QuantStudio 5 RT-PCR system (Applied Biosystems, Foster City, CA). Up to forty-eight libraries were sequenced per lane on a HiSeq 4000 sequencer (Illumina, San Diego, CA) with single-end 85 bp reads.

tag: tissue

value: peripheral blood


title: NL04_2 [Pool #2]

description:
Pool #2
Raw data lost to disk failure


title: Patient sample 028A (re-analysis)

description: re-analysis of GSM5829599

value: Patient 028

value: Whole blood

tag: time

tag: Sex

value: Female

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: neutrophil composition


title: C88IPFB1

tag: cell type

tag: treatment

tag: molecule subtype


title: MIBG alone, Day 3, 72 hours rep 4

description: MIBG alone, Day 3, 72 hours


title: C80IPFB1


title: NL04_6 [Pool #2]

description:
Pool #2
Raw data lost to disk failure

tag: genotype


title: NL04_1 [Pool #2]

description:
Pool #2
Raw data lost to disk failure


title: Patient sample 034A (re-analysis)

description: re-analysis of GSM5829601

tag: individual

value: Patient 034

value: pre-operative

value: Male

tag: age

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: monocyte composition

tag: post-operative atrial fibrillation


title: C80IPF

tag: tissue


title: NL04_9 [Pool #2]

description:
Pool #2
Raw data lost to disk failure


title: MIBG alone, Day 3, 72 hours rep 3

description: MIBG alone, Day 3, 72 hours


title: MIBG alone, Day 3, 72 hours rep 2

description: MIBG alone, Day 3, 72 hours


title: NL01_14 [Pool #1]

description: Pool #1


title: C27IPFb1


title: NL01_13 [Pool #1]

description: Pool #1


title: MIBG alone, Day 3, 72 hours rep 1

description: MIBG alone, Day 3, 72 hours


title: rat high dose didymin rep1

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

data_processing:
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: mm9

organism: Rattus norvegicus

source_name: liver

growth_protocol: model group and didymin group were induced non-alcoholic fatty liver disease by High-fat-diet,normal group were given same dose normal saline

extract_protocol:
Total RNA was extracted from liver tissues with Trizol reagent
NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）,AMPure XP system

treatment_protocol: didymin group were treated with didymin

value: liver

tag: strain

value: Sprague Dawley


title: C27IPF

value: Lung

tag: cell type


title: C88IPF

value: Fibroblasts isolated from IPF tissue


title: MIBG alone, Day 0, baseline rep 5

description: MIBG alone, Day 0, baseline

tag: treatment

value: Untreated


title: CNCL15

tag: molecule subtype


title: rat  low dose didymin rep2


title: MIBG alone, Day 0, baseline rep 4

description: MIBG alone, Day 0, baseline


title: rat  low dose didymin rep3


title: rat model rep3


title: rat  low dose didymin rep1


title: MIBG alone, Day 0, baseline rep 3

description: MIBG alone, Day 0, baseline


title: rat model rep2


title: rat wt rep3


title: NL01_5 [Pool #1]

description: Pool #1

tag: genotype

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: MIBG alone, Day 0, baseline rep 2

description: MIBG alone, Day 0, baseline


title: rat wt rep2


title: rat high dose didymin rep3


title: rat model rep1


title: rat high dose didymin rep2


title: NL01_12 [Pool #1]

description: Pool #1


title: rat wt rep1


title: NL01_2 [Pool #1]

description: Pool #1


title: MIBG alone, Day 0, baseline rep 1

description: MIBG alone, Day 0, baseline


title: MIBG+Irinotecan, Day 3, 72 hours rep 4

description: MIBG+Irinotecan, Day 3, 72 hours


title: NL01_1 [Pool #1]

description: Pool #1


title: NL01_10 [Pool #1]

description: Pool #1


title: MIBG+Irinotecan, Day 3, 72 hours rep 3

description: MIBG+Irinotecan, Day 3, 72 hours


title: NL01_7 [Pool #1]

description: Pool #1


title: HeLa-scrambled3

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
Reads were aligned to the human genome sequences (build GRCh38.p7) using the STAR aligner v. 2.7.5a (Dobin et al., 2013).
Quality control (QC) of the reads was inspected using the multiqc reporting tool (Ewels, Magnusson, Lundin, & Kaller, 2016), including fastqc (available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc), dupradar (Sayols, Scherzinger, & Klein, 2016), qualimap (Garcia-Alcalde et al., 2012), and RNA-SeqC (DeLuca et al., 2012).
Raw counts were extracted using the STAR program.
Assembly: GRCh38.p7
Supplementary files format and content: count extracted using the STAR program and feature annotations

source_name: HeLa

extract_protocol:
Total RNA was extracted from HeLa cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
500 - 1,000 ng total RNA of transfected cell cultures were sequenced with 16 million reads (75 bp single end) on a NextSeq 500 using the NextSeq 500/550 High Output Kit v2.5 (75 cycles).

tag: cell line

value: HeLa

value: scrambled


title: HPL-2-Dam_intestine_rep2

city: Seville

first: Patricia

last: De La Cruz Ruiz

address: Ctra. de Utrera, km 1

country: Spain

institute: 1Andalusian Centre for Developmental Biology. Universidad Pablo de Olavide

data_processing:
The quality control of the DamID technique was performed by damid.seq.r pipeline version 0.1.3 in Rstudio (R version 3.4.3) (available at github.com/damidseq/rDamlDSeq) (Sharma, Ritler, and Meister 2016). From FastQ files, the pipeline detects and maps reads containing the DamID adapters (adapt.seq="CGCGGCCGAG”) and match them to genomic regions flanked by GATCs sites (restr.seq = "GATC") to obtain Bam Files. The Bam files were used to generate the normalized log2 HPL::Dam/GFP::Dam ratio scores per GATC fragments, using perl script damidseq_pipeline v1.4.5 (Marshall and Brand 2015) (available at https://github.com/owenjm/damidseq_pipeline). The pipeline integrates a Bowtie 2 v2.3.4 (Langmead and Salzberg 2012) calling to map reads on C. elegans bowtie indexes from assembly WBcel235 (available in Illumina iGenomes webpage; identical to ce11). In addition, it includes also Samtools v1.9 (Li et al. 2009) for alignment guidance, and a GFF file containing all GATC sites in the C. elegans genome. Last GATC coordinates file was built by gatc.track.maker.pl tool provided by the same pipeline script using WBcel235 FASTA file for C. elegans (available at https:// ensembl.org/Caenorhabditis_elegans/Info/Index. Final bedgraph files for each replica was averaged using average_tracks perl script included in damid_misc (available at https://github.com/owenjm/damid_misc).
The selection of statistically significant peaks for every HP1 sample was done by find_peaks perl script (available at https://github.com/owenjm/find_ peaks) with a false discovery rate (FDR) lower than 0.05 using as input averaged bedgraph files containing normalized log2 HPL::Dam/GFP::Dam ratio scores per GATC fragment.
Assembly: ce11
Supplementary files format and content: bedgraph files from damidseq_pipeline script; 1 file per replica and 1 file with combined data; contain log2 scores for each GATC fragment.
Supplementary files format and content: gff file from find_peaks script, 1 file per combined data that contains all peaks with an FDR less than 0.05.
Library strategy: DamID-seq

source_name: intestine

growth_protocol: For synchronization of nematodes by hypochlorite treatment (“bleaching”), a mixed-stage population with many gravid adults was washed off an NGM plate with M9 into a 15 mL tube and centrifuged at 500g during 2 min. The supernatant was aspirated and the animals resuspended in 15 mL M9 buffer and centrifuged again at 500  g for 2 min. The washing was repeated and the supernatant aspirated as much as possible without disturbing the pellet of worms. Two mL of hypochlorite solution was added and shaken. The animals were monitored under a stereoscope until the majority were broken up (this depends on the concentration of the hypochlorite; should not be more than 5–6 min) and the tubes were filled immediately with sterile M9 and centrifuged at 800  g for 1 min. The supernatant was aspirated and the embryos resuspended in 15 mL M9 buffer and centrifuged again at 800  g for 1 min. The washes were repeated ten times (in sterile conditions) and left in a suitable volume of M9 to reach ~20 embryos/μL. Animals were incubated for 48h at 20°C until L4 stage. Larvae were harvested by centrifugation, washed with M9 10 times and distributed in aliquots of 30 μL. Excess liquid was removed and aliquots were snap-frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Genomic DNA (gDNA) extraction from ~30 μl L4s was performed by 5 rounds of rapid freeze/thaw cycles in liquid nitrogen and 37°C water bath to break the worm cuticle followed by purification using a DNeasy Blood and Tissue Kit (QIAGEN #69504). gDNA was eluted in two rounds in a total volume of 300 μl and precipitated using 0.1x volume NaAc 3M and 2.5x volume 96% ethanol. The final concentration after resuspension in 10 μl of 10mM Tris-Cl was measured by QUBIT.
To prepare the libraries, 200 ng gDNA were digested using 10 units DpnI (NEB #R0176S; cuts methylated GATC) in 10 μl for 6 hours at 37°C in a thermocycler. Next, DpnI was inactivated by heating to 80°C for 20 min. Double-stranded adaptors were prepared by heating a mixture of 50 μl primer AdRt (5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA, 100 μM) and 50 μl AdRb (5’-TCCTCGGCCGCG; 100 μM) to 95°C and cooling slowly to room temperature. Next, 0.8 μl of the double-stranded adapters were ligated to the DpnI-digested gDNA in a volume of 20 μl at 16°C in a thermocycler overnight using T4 DNA ligase (Roche #10799009001), which later was inactivated by incubation for 10 min at 65°C. The ligated gDNA was purified with 1.8x volume Agencourt AMPure XP® beads (Beckman Coulter; #A63880) using a magnetic particle concentrator, washed with 180 μl of freshly prepared 70% ethanol and eluted in 20 μl elution buffer (EB; 10 mM Tris-Cl, pH 8.5). Unmethylated GATC sites were digested with 10 units of DpnII (NEB #R0543S) in a volume of 50 μl for 1 h at 37°C. Next, DpnII was inactivated by heating to 80°C for 20 min. The digested gDNA was re-purified with AMPure XP® beads as above and eluted in 25 μl. Methylated gDNA fragments were amplified using Taq DNA polymerase with ThermoPol buffer (NEB #M0267) in 50 μl reactions containing 5 μl 10x PCR reaction buffer, 25 μl DpnII digested DNA, 1.25 μl primer AdR (5’-NNNNGTGGTCGCGGCCGAGGATC; 50 μM), 4 μl dNTP mix (each 2.5 mM), 1 μl polymerase. PCR parameters were 1) 68°C 10 min; 2) 94°C 1 min; 3) 65°C 5 min; 4) 68°C 15 min; 5) 94°C 1 min; 6) 65°C 1 min; 7) 68°C 10 min; 8) Go to step 5 and repeat three times; 9) 94°C 1 min; 10) 65°C 1 min; 11) 68°C 2 min; 12) Go to step 9 and repeat 19 times. Five μl of each PCR reaction were analyzed by agarose gel electrophoresis: successful amplification of methylated DNA was confirmed by the presence of a 400–1000 bp smear which was not observed in controls without DpnI or T4 DNA ligase. Finally, the PCR products were purified using QIAquick PCR Purification Kit (QIAGEN #28104), eluted in 30 μl EB and their concentration was measured using QUBIT. 400 ng of PCR fragments were used as input in the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370). The manufacturer’s instructions were used with the following conditions. Size selection was performed by first adding 30 μl of resuspended SpeedBead Magnetic Carboxylate Modified Particles, Azide 0.05% (GE65152105050250) to the 100 μl ligation reaction. The beads were discarded and the supernatant was mixed with 60 μl resuspended SpeedBeads. Then, the supernatant was discarded and the beads were washed with ethanol and DNA was eluted in 17 μl of 10mM Tris. Eight PCR cycles were performed to amplify the samples. The quality of the samples was verified by agarose gel electrophoresis and QUBIT analysis as above.

value: intestine

tag: developmental stage

value: L4 larvae

value: MRS580 (HPL-2::Dam in intestine)


title: HPL-1-Dam_intestine_rep2

value: MRS579 (HPL-1::Dam in intestine)


title: HPL-2-Dam_hypodermis_rep2

source_name: hypodermis

value: hypodermis

value: MRS578 (HPL-2::Dam in hypodermis)


title: HPL-1-Dam_intestine_rep1


title: HPL-2-Dam_intestine_rep1


title: HeLa-scrambled1


title: GFP-Dam_intestine_rep2

value: BN1051 (GFP::Dam in intestine)


title: GFP-Dam_intestine_rep1


title: MIBG+Irinotecan, Day 3, 72 hours rep 5

description: MIBG+Irinotecan, Day 3, 72 hours

value: peripheral blood


title: GFP-Dam_hypodermis_rep1

value: BN561 (GFP::Dam in hypodermis)


title: HeLa-RSPO4-Promoter-3


title: HeLa-RSPO4-Promoter-1


title: GFP-Dam_hypodermis_rep2


title: MIBG+Irinotecan, Day 3, 72 hours rep 2

description: MIBG+Irinotecan, Day 3, 72 hours


title: HeLa-scrambled2


title: MIBG+Irinotecan, Day 0, baseline rep 5

description: MIBG+Irinotecan, Day 0, baseline


title: MIBG+Irinotecan, Day 3, 72 hours rep 1

description: MIBG+Irinotecan, Day 3, 72 hours


title: MIBG+Irinotecan, Day 0, baseline rep 4

description: MIBG+Irinotecan, Day 0, baseline


title: HeLa-RSPO4-Promoter-2


title: HPL-2-Dam_hypodermis_rep1


title: MIBG+Irinotecan, Day 0, baseline rep 3

description: MIBG+Irinotecan, Day 0, baseline


title: LINC00607-KO 3 [RNA-seq]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC .
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (release 99) using STAR 2.7.3a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.26.0. Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: library size normalized counts

source_name: human umbilical vein endothelial cells

growth_protocol: HUVEC p1 were transduced with lentiviral CRISPR/Cas9 construct. 7 days of Puromycin/Hygromycin selection, cultivated until p3 for RNA isolation

extract_protocol:
Total RNA Isolation was performed using the RNA Mini Kit (Bio&Sell).
900ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

treatment_protocol: no treatment or stimulation after antibiotic selection

value: HUVEC

value: human umbilical vein endothelial cells

value: LINC00607 CRISPR/Cas9 knock-out (KO)


title: LINC00607-KO 2 [RNA-seq]


title: MIBG+Irinotecan, Day 0, baseline rep 2

description: MIBG+Irinotecan, Day 0, baseline


title: MIBG+Irinotecan, Day 0, baseline rep 1

description: MIBG+Irinotecan, Day 0, baseline


title: LINC00607-KO 1 [RNA-seq]


title: C. elegans CRT-1(KO), biological rep2

type: RNA

city: Pamplona

first: José Luis

last: Vizmanos

state: Navarra

address: Irunlarrea, 1

department: Department of Biochemistry and Genetics

institute: University of Navarra

description: Gene expression data from C. elegans calreticulin knockout worms at late L4 after 56 h of incubation at 20 ºC on NGM plates

hyb_protocol: Fragmented cDNA preparations were hybridized for 16-18 h at 45 ºC on genome oligonucleotide array C. elegans Gene 1.0 ST (Thermo Fisher Scientific-Affymetrix, Santa Clara, CA, USA) with the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System.

data_processing: The data were analyzed with Affymetrix® Transcriptome Analysis Console (TAC) 4.0 using Affymetrix default analysis settings and the RMA alforithm (Robust Multiarray Analysis)

label: Biotin

source_name: C. elegans calreticulin knockout worms at late L4 stage

label_protocol: Biotinylated single-stranded DNA was prepared from the 100 ng of total RNA using the GeneChip WT PLUS Reagent kit according to manufacturer's instructions.

growth_protocol: Animals were age-synchronized by standard hypochlorite treatment of gravid nematodes to obtain eggs that were allowed to hatch in M9 medium during 48 h. Approximately 4 000 age synchronized L1 nematodes per strain were grown in triplicate on a total of 8 NGM plates (~500 nematodes per plate) at 20 °C until they reached the L4 stage. Wild-type worms, type 1/type 2-like mutants and calreticulin knockout nematodes were collected and washed after 44, 51 and 56 hours, respectively.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The RNA was purified from TRIzol® using the Qiagen RNeasy® Mini Kit (Qiagen, Hilden, Germany) following the recommended protocol for RNA cleanup.

value: Late L4

tag: gender

value: Hermaphrodite


title: C. elegans WT, biological rep1

description: Gene expression data from C. elegans wild-type worms at late L4 after 44 h of incubation at 20 ºC on NGM plates

source_name: C. elegans wild-type worms at late L4 stage

value: N2 Bristol


title: C. elegans CRT-1(mut2), biological rep3

description: Gene expression data from C. elegans worms harboring type 2-like calreticulin mutations at late L4 after 51 h of incubation at 20 ºC on NGM plates

source_name: C. elegans worms with type 2-like calreticulin mutations at late L4 stage


title: C. elegans CRT-1(KO), biological rep1


title: MIBG+Vorinostat, Day 3, 72 hours rep 5

description: MIBG+Vorinostat, Day 3, 72 hours


title: Slamseq_xrn1_P_t0_r2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description: xrn1∆ parental strain background: BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)

data_processing:
F SLAMseq data was anaysed with slamdunk provided by nextflow pipeline(v 1.0.0). https://nf-co.re/slamseq . As stranded library was prepared with dUTP method and fastq files were first converted to reverse complementary reads to feed into slamdunk nf core pipeline.  Adapter contamination and low quality region was trimmed with TrimGalore, trim length 30bp was used instead of default value. When aligned to genome, transcript annotation downloaded from SGD database (version 64-1-1) (Xu et al., 2009) were first converted into bed file and then used as input for parameter utrbed. At least 2 conversions cooccur in one reads is regarded as a confident call for nascent RNA. SNP masking was employed to uncouple Single Nucletide Polymorphism from converted nucleotides.
Assembly: V64-1-1
Supplementary files format and content: bigwig format of spike in normalised reads
Supplementary files format and content: bigwig format of spike in normalised nascent  reads
Library strategy: SLAMseq

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: S. cerevisiae grown in YPD at 30°C

extract_protocol:
RNA was extracted with MasterPure RNA extraction kit from Lucigene  The DNA was purified with phenol, precipitated with ethanol and sodium acetate at -20 °C, washed with cold 70% ethanol, and resuspended in 30 µl TE buffer.
SLAMSeq: Metabolic labeling of newly synthesized RNA molecules was done as previously described (Voichek et al., 2016). Briefly, 4-thiouracil (4tU) (Sigma) was dissolved in NaOH(83mM), Newly synthesized RNA was labeled for indicated  time  spans  (10  min)  at  a  final  concentration  of  5mM  4-thiouridine  (4sU,  Carbosynth). MES buffer with a final concentration 10mM PH 5.9 was added to media to avoid pH change as a result of NaOH addition. At each time points before harvesting, 4tU was added to media for ten minutes ahead of desired time point.  cells were snap frozen in liquid nitrogen immediately at the time point required.     Pulse and Chase: briefly, 4-thiouracil (4tU) (Sigma) was prepared as explained above. Prewarmed 4tU was added to culture media (YPD with MES buffer) containing wild-type cells. After 1 hour labelling with 4tU, cells were washed and resuspend in YPGal media and time points were collected at 0, 10 and 30 minutes (t0, t10, t30, t0’, t10’, t30’) by centrifugation and snap frozen in liquid nitrogen immediately. Between the first and second exposure to YPGal, cells were cultured for 3 hours in YPD.     RNA purification was done with MasterPure Yeast RNA Purification Kit. Total RNA was subjected to thiol(SH)-linked alkylation by iodoacetamide (Sigma, 10 mM) at 50C for 15 minutes (Herzog et al., 2017), the reaction was stopped by 20 mM DTT and RNA  was  re-purified by ethanol precipitation. After rRNA depletion with RiboPool Depletion Kit, library was prepared by Ultra™ II Directional RNA Library Prep Kit for Illumina® and sequenced single end with read length 150bp on Nextseq 500 Illumina sequencer.

treatment_protocol: Cells were shifted to pre-warmed YPGal and then grown at 30°C for 3 hours (naïve). After this, cells are put in YPD for resting for 3 hours, cells were shifted back to prewarmed YPG for second induction (primed).

value: yeast cells


title: Non-Target Control 2 [RNA-seq]

value: non-target control (CTL)


title: MIBG+Vorinostat, Day 3, 72 hours rep 4

description: MIBG+Vorinostat, Day 3, 72 hours


title: C. elegans WT, biological rep2


title: MIBG+Vorinostat, Day 3, 72 hours rep 3

description: MIBG+Vorinostat, Day 3, 72 hours


title: Slamseq_xrn1_P_t0_r1


title: Slamseq_xrn1_N_t0_r2


title: HUVEC LINC00607 CRISPR/Cas9 knock-out (KO) 3

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nt.
Only reads above 15 nt were cleared for further analyses. These were mapped versus the hg38 version (emsambl release 101) of the human genome with STAR 2.7.7a using only unique alignments to exclude reads with uncertain arrangement.
Reads were further deduplicated using Picard 2.21.7 to avoid PCR artefacts leading to multiple copies of the same original fragment.
The Macs2 peak caller version 2.1.1 was employed to accommodate for the range of peak widths typically expected for ATAC-Seq (Zhang et al., Model-based Analysis of ChIP-Seq). Minimum qvalue was set to -4 and FDR was changed to 0.0001. Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
In order to be able to compare peaks in different samples, the resulting lists of significant peaks were overlapped and unified to represent identical regions. The counts per unified peak per sample were computed with BigWigAverageOverBed (UCSC Genome Browser Utilities, http://hgdownload.cse.ucsc.edu/downloads.html). Raw counts for unified peaks were submitted to DESeq2 (version 1.20.0) for normalization.
Peaks were annotated with the promoter of the nearest gene in range (TSS +- 5000 nt) based on reference data of GENCODE vM15. Peaks were deemed to have significantly different counts between conditions at an average score of 20, and a log2 transformed fold change of < -0.59 or >0.59.
Assembly: hg38
Supplementary files format and content: library and background normalized counts in unified peaks

extract_protocol:
50.000 HUVEC were used for ATAC library preparation using llumina Tagment DNA Enzyme and Buffer Kit (Illumina). The cell pellet was resuspended in 50 µL of the lysis/transposition reaction mix (25 µL TD-Buffer, 2.5 µL Nextera Tn5 Transposase, 0.5 µL 10% NP-40 and 32 µL H2O) and incubated at 37°C for 30 min followed by immediate purification of DNA fragments with the MinElute PCR Purification Kit (Qiagen).
Purification of DNA fragments was done with the MinElute PCR Purification Kit (Qiagen).
Amplification of Library and Indexing was performed as descried elsewhere (Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015).


title: Slamseq_xrn1_N_t0_r3


title: C. elegans WT, biological rep3


title: C. elegans CRT-1(mut1), biological rep1

description: Gene expression data from C. elegans worms harboring type 1-like calreticulin mutations at late L4 after 51 h of incubation at 20 ºC on NGM plates

source_name: C. elegans worms with type 1-like calreticulin mutations at late L4 stage


title: Slamseq_xrn1_N_t0_r1


title: Slamseq_ski2_P_t0_r3

description: ski2∆ parental strain background: BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)


title: C. elegans CRT-1(mut2), biological rep2


title: HUVEC LINC00607 CRISPR/Cas9 knock-out (KO) 2


title: MIBG+Vorinostat, Day 3, 72 hours rep 2

description: MIBG+Vorinostat, Day 3, 72 hours


title: Non-Target Control 3 [RNA-seq]


title: MIBG+Vorinostat, Day 3, 72 hours rep 1

description: MIBG+Vorinostat, Day 3, 72 hours


title: Slamseq_ski2_P_t0_r2


title: Slamseq_ski2_N_t0_r3


title: Slamseq_ski2_P_t0_r1


title: Slamseq_xrn1_P_t0_r3


title: C. elegans CRT-1(mut1), biological rep2


title: C91IPF

value: Lung

value: Fibroblasts isolated from IPF tissue

value: miRNA


title: Non-Target Control 1  [RNA-seq]


title: HUVEC LINC00607 CRISPR/Cas9 knock-out (KO) 1


title: MIBG+vorinostat, Day 0, baseline  rep 5

description: MIBG+vorinostat, Day 0, baseline

value: Untreated


title: Slamseq_ski2_N_t0_r2


title: Slamseq_by_Pulse_Chase_P_t30_r3

description: BY4741 (MAT a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)


title: HUVEC non-target control (CTL) 3


title: Slamseq_by_Pulse_Chase_P_t30_r2


title: C. elegans CRT-1(mut2), biological rep1


title: MIBG+vorinostat, Day 0, baseline  rep 4

description: MIBG+vorinostat, Day 0, baseline


title: HUVEC non-target control (CTL) 2


title: MIBG+vorinostat, Day 0, baseline  rep 2

description: MIBG+vorinostat, Day 0, baseline


title: HUVEC non-target control (CTL) 1


title: Slamseq_ski2_N_t0_r1


title: MIBG+vorinostat, Day 0, baseline  rep 3

description: MIBG+vorinostat, Day 0, baseline


title: Slamseq_by_Pulse_Chase_P_t10_r3


title: Slamseq_by_Pulse_Chase_P_t10_r2


title: Slamseq_by_Pulse_Chase_P_t30_r1


title: Slamseq_by_Pulse_Chase_P_t0_r3


title: MIBG+vorinostat, Day 0, baseline  rep 1

description: MIBG+vorinostat, Day 0, baseline


title: Slamseq_by_Pulse_Chase_N_t30_r2


title: Slamseq_by_Pulse_Chase_N_t30_r1


title: Slamseq_by_Pulse_Chase_N_t30_r3


title: Slamseq_by_Pulse_Chase_P_t0_r2


title: ATAC-seq_P50

city: Koto-ku

first: Reo

last: Maruyama

state: Tokyo

department: Cancer Institute

country: Japan

institute: Japanese Foundation For Cancer Research

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to hg38 genome by bowtie2
PCR de-duplicate was performed by Picard
Peak call was performed by MACS2
Assembly: hg38
Supplementary files format and content: Browser Extensible Data format for peak summit data
Supplementary files format and content: Comma-Separated Values format for count matrix

source_name: Breast Cancer

extract_protocol:
Breast cancer specimens were obtained by core needle biopsy of surgically removed tumors. Specimens were dissociated into single cells using a MACS Tumor Dissociation Kit and a gentle MACS dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Single cells were cryopreserved using the Banbanker.
Libraries were prepared with the Omni-ATAC protocol.

value: Breast Cancer

tag: subtype

tag: ctmn

tag: histology

value: IDC


title: shGPC_rep3

city: Marseille

first: Thomas

last: Vannier

address: Campus de Luminy, 163 Av. de Luminy

country: France

institute: Aix-Marseille University

description: down-regulated for GPC4

data_processing:
The quality of the raw reads was assessed using FastQC v0.11.9 toolkit.
Adapters and low-quality reads were trimmed using Trimmomatic v0.39
The reads were aligned with HiSat2 v2.2.1 using default options.
Gene counts were quantified using feature Counts from the Subread v2.0.1 package
Gene counts were normalized and used for differential expression testing using DESeq2 v1.28.0
Assembly: GRCh38.p13 (Ensembl release 101)
Supplementary files format and content: xlsx files include counts and normalized counts value from DESeq2 of each Sample

source_name: human induced pluripotent cell (hiPSC) line

extract_protocol:
Total RNA was isolated with RNeasy Min Elute clean-up kit (Qiagen, ref. 74204), according to the manufacturer’s protocol. Concentration and RNA quality were evaluated by NanoDrop (ND-1000 Spectrophotometer; Thermofisher Scientific).
1 μg of RNA per sample at the Concentration: > 20 ng/μl dissolved in RNase-, DNase- and protease-free molecular grade water was sent to GATC Biotech. The RNA-sequencing was performed by using Illumina HiSeq 2500 technology.


title: Slamseq_by_Pulse_Chase_N_t10_r2


title: ATAC-seq_P54

value: ILC


title: shGPC_rep1

description: down-regulated for GPC4


title: Slamseq_by_Pulse_Chase_N_t10_r1


title: Slamseq_by_Pulse_Chase_P_t10_r1


title: Slamseq_by_Pulse_Chase_N_t0_r3


title: Slamseq_by_Pulse_Chase_N_t10_r3


title: ATAC-seq_P44

value: TNBC


title: ATAC-seq_P65

value: DCIS


title: ATAC-seq_P64

value: Mucinous


title: shGPC_rep2

description: down-regulated for GPC4


title: Slamseq_by_Pulse_Chase_P_t0_r1


title: shCTRL_rep1

description: control line

value: shCTRL


title: ATAC-seq_P39


title: ATAC-seq_P41


title: shCTRL_rep2

description: control line


title: WT_rep3

description: control line

value: WT


title: Slamseq_by_Pulse_Chase_N_t0_r2


title: WT_rep2

description: control line


title: ATAC-seq_P38


title: ATAC-seq_P37


title: ATAC-seq_P36


title: ATAC-seq_P35


title: WT_rep1

description: control line


title: shCTRL_rep3

description: control line


title: ATAC-seq_P34


title: ATAC-seq_P49


title: RRP6-batch3-2nd-30min

description: rRNA depleted RNA

data_processing:
For RNASEQ. The genome assembly and annotation for the RNA-Seq data analysis was downloaded from SGD database (version 64-1-1) (Xu et al., 2009). The quality of the RNA-Seq data was assessed with FastQC (Andrews, 2010). The reads were aligned to the genome with STAR and parameters --outFilterMismatchNmax 4 --alignIntronMin 13 --alignIntronMax 2482.  Read counts were then summarised using featurecounts with parameter -s 2 -C . chimeric fragments was excluded from fragment counting.  MultiQC was used to assess the performance of the preprocessing steps (Ewels et al., 2016). Differential gene expression analysis was perfomed with DESEQ2 package in R. The counts were normalized by coding transcriptome.   For ChIPseq and MNase-seq Illumina adptor was detected and trimmed by TrimGalore. Trimmed reads were then alignment with BWA to Saccharomyces_cerevisiae genome assembly R64-1-1. High repetitive Ribosome DNA region was provided as blacklist and removed from alignment.  PCR duplicates were marked with Picard MarkDuplicates and then removed for subsequent analysis. Deduplicted reads from biological replicates were then merged together. Bigwig files were then generated from merged bam files by deeptools bamcoverage command. Parameter --binSize 1 --MNase --minFragmentLength 100 --maxFragmentLength 200 --normalizeUsing CPM were used to take only mononucleosome, deconvolute and take only the center dyad genomic coordinate of each nucleosome. Bed files contains gene groups gerenerated from RNAseq data were provided to deepltools computatematrix command to extract the nucleosome occupancy and histone modification level of each gene within particular group. Deeptools plotProfile tool were then used to summarise above matrix into metagene plot with parameter –perGroup.  SLAMseq: SLAMseq data was anaysed with slamdunk provided by nextflow pipeline(v 1.0.0). https://nf-co.re/slamseq . As stranded library was prepared with dUTP method and fastq files were first converted to reverse complementary reads to feed into slamdunk nf core pipeline.  Adapter contamination and low quality region was trimmed with TrimGalore, trim length 30bp was used instead of default value. When aligned to genome, transcript annotation downloaded from SGD database (version 64-1-1) (Xu et al., 2009) were first converted into bed file and then used as input for parameter utrbed. At least 2 conversions cooccur in one reads is regarded as a confident call for nascent RNA. SNP masking was employed to uncouple Single Nucletide Polymorphism from converted nucleotides.
Assembly: V64-1-1
Supplementary files format and content: bigwig for ChIP-seq, txt files of normalised RNASEQdata and slamseq data

extract_protocol:
RNA was extracted with MasterPure RNA extraction kit from Lucigene  The DNA was purified with phenol, precipitated with ethanol and sodium acetate at -20 °C, washed with cold 70% ethanol, and resuspended in 30 µl TE buffer.
RNA-Seq: First rRNA was depleted  from total RNA with Illumina ribozero Gold kit. Then stranded RNA library was generated with NEBnext Ultra Directional RNA Library Prep kit for illumina.  MNase and ChIPSeq-Seq:  100 ml culture per S. cerevisiae sample and 30 ml of S. pombe culture was crosslinked using 1% formaldehyde for 15 minutes at room temperature. Formaldehyde was quenched by 0.125 M glycine for 5 minutes. Then cells were washed three times with cold TBS, flash-frozen in liquid nitrogen and stored at -80 °C.  Frozen cell pellets were resuspended in zymolyase solution (1 M sorbitol, 50 mM Tris-HCl pH 7.5, 1% beta-mercaptoethanol, 0.1 U/µl zymolyase). The zymolyase digestion proceeded at +37 °C for 30 min (S. cerevisiae) or 90 min (S. pombe). Spheroplasts were isolated by centrifugation at 6000xg for 10 minutes at +4 °C. Spheroplasts were resuspended in NP buffer (10 mM Tris-HCl pH 7.5, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40 (Tergitol), 1% beta-mercaptoethanol, 0.5 mM spermidine, 1% yeast protease inhibitor cocktail). The suspensions were pre-warmed and then 0.5 U/µl of MNase for S. cerevisiae and 2 U/µl for S. pombe was added per sample. MNase digestion proceeded at 37 °C for 40 min (S. cerevisiae) or 30 min (S. pombe) and stopped by addition of EGTA. The supernatants containing chromatin fragments were collected and  diluted with 1 ml RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate) with 1% yeast protease inhibitor cocktail. Equal volumes of S. pombe chromatin were spiked in to S. cerevisiae chromatin samples at this point, corresponding to around 3% of S. cerevisiae DNA.  Each sample was immunoprecipitated with anti-H3K4me3 (Abcam ab8580) and anti-H3K4me2 (Abcam ab7766) antibodies. Protein A/G beads (Pierce) were coupled to antibodies and resuspended in diluted chromatin and rotated o/n at 4 °C.  The next day, beads were washed with RIPA buffer, RIPA-500 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% v/v NP-40, 0.5% w/v sodium deoxycholate), and TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8). Volume of each wash was 150 µl. Chromatin was eluted from beads in 2x10 µl ChIP elution buffer (Tris-HCl pH 8 50 mM, 1% SDS, 10 mM EDTA pH 8). The immunoprecipitated chromatin as well as a 20 µl sample of input chromatin were decrosslinked by TE, RNase cocktail, Proteinase K and 6 µl SDS (10% w/v), incubating overnight at 65 °C. DNA was purified by ethanol precipitation. Illumina sequencing libraries were prepared from the DNA using the NEBNext Ultra II kit without dual size selection and using 1.4X volume of AMPure XP beads for the purification steps. The libraries were sequenced on Illumina’s NextSeq 500, paired-end, 39 bases from each end     SLAMSeq: Metabolic labeling of newly synthesized RNA molecules was done as previously described (Voichek et al., 2016). Briefly, 4-thiouracil (4tU) (Sigma) was dissolved in NaOH(83mM), Newly synthesized RNA was labeled for indicated  time  spans  (10  min)  at  a  final  concentration  of  5mM  4-thiouridine  (4sU,  Carbosynth). MES buffer with a final concentration 10mM PH 5.9 was added to media to avoid pH change as a result of NaOH addition. At each time points before harvesting, 4tU was added to media for ten minutes ahead of desired time point.  cells were snap frozen in liquid nitrogen immediately at the time point required and RNA purification was done with MasterPure Yeast RNA Purification Kit. Total RNA was subjected to thiol(SH)-linked alkylation by iodoacetamide (Sigma, 10 mM) at 50C for 15 minutes (Herzog et al., 2017), the reaction was stopped by 20 mM DTT and RNA  was  re-purified by ethanol precipitation. After rRNA depletion with RiboPool Depletion Kit, library was prepared by Ultra™ II Directional RNA Library Prep Kit for Illumina® and sequenced single end with read length 150bp on Nextseq 500 Illumina sequencer.

treatment_protocol: cells were shifted to pre-warmed YPG and then grown at 30°C for 3 hours harvesting at time point 0min, 30 min, 60min and 180 min for the first Galactose treatment. After put in YPD for middle resting for 3 hours, cells were shifted back to prewarmed YPG for second induction and harvested at 0min, 15min, 30min and 60 min.

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 30 minutes  of SECOND Galactose treatment


title: ATAC-seq_P31


title: ATAC-seq_P32


title: RRP6-batch3-2nd-15min

description: rRNA depleted RNA

value: time 15 minutes of SECOND Galactose treatment


title: RRP6-batch3-2nd-1h

description: rRNA depleted RNA

value: time 1 hour of SECOND Galactose treatment


title: ATAC-seq_P30


title: Slamseq_by_Pulse_Chase_N_t0_r1

value: yeast cells


title: ATAC-seq_P29


title: ATAC-seq_P28


title: RRP6-batch3-2nd-000

description: rRNA depleted RNA

value: time 0 of SECOND Galactose treatment


title: RRP6-batch3-1st-3h

description: rRNA depleted RNA

value: time 3 hour of FIRST Galactose treatment


title: ATAC-seq_P27


title: RRP6-batch3-1st-1h

description: rRNA depleted RNA

value: time 1 hour of FIRST Galactose treatment


title: RRP6-batch3-1st-30min

description: rRNA depleted RNA

value: time 30 minutes  of FIRST Galactose treatment


title: ATAC-seq_P33

value: Breast Cancer


title: ATAC-seq_P24R

value: Mixed


title: ATAC-seq_P21

value: IDC


title: ATAC-seq_P22


title: ATAC-seq_P23


title: ATAC-seq_P26


title: ATAC-seq_P24L


title: ATAC-seq_P19


title: ATAC-seq_P20

value: TNBC

value: Metaplastic


title: ATAC-seq_P18


title: RRP6-batch1-2nd-1h

description: rRNA depleted RNA


title: RRP6-batch1-2nd-15min

description: rRNA depleted RNA


title: ATAC-seq_P17


title: ATAC-seq_P15


title: ATAC-seq_P14


title: RRP6-batch1-2nd-30min

description: rRNA depleted RNA


title: RRP6-batch2-1st-3h

description: rRNA depleted RNA


title: RRP6-batch2-1st-30min

description: rRNA depleted RNA


title: RRP6-batch2-1st-000

description: rRNA depleted RNA

value: time 0 of FIRST Galactose treatment


title: RRP6-batch3-1st-000

description: rRNA depleted RNA


title: RRP6-batch2-1st-1h

description: rRNA depleted RNA


title: RRP6-batch2-2nd-000

description: rRNA depleted RNA


title: RRP6-batch2-2nd-15min

description: rRNA depleted RNA


title: RRP6-batch2-2nd-1h

description: rRNA depleted RNA


title: RRP6-batch2-2nd-30min

description: rRNA depleted RNA


title: RRP6-batch1-2nd-000

description: rRNA depleted RNA


title: SNP_screen_RBBP5_SKMEL28_rep2

type: other

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

hyb_protocol: Microarray DNA double stranding and PBM protocols are as previously described (Berger et al. PMID: 19265799, Mohaghegh et al. PMID: 30657937)

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner and fluorescence was quantified using GenePix Pro 7.2

data_processing: Exported fluorescence data from GenePix Pro 7.2 were normalized with MicroArrary LINEar Regression (Berger et al, 2006). Processed data corresponds to z-scores normalized against the fluorescence distribution obtained at sets of random background probes

label: Alexa fluor conjugated antibody

molecule: other

source_name: Sk-mel-28 cells, rep2

label_protocol: PBM experiments using cell extracts were performed following the protocols previously described (Berger et al. PMID: 19265799, Mohaghegh et al. PMID: 30657937) and outlined here. The double-stranded microarray was pre-wetted in HBS+TX-100 (20mM HEPES, 150mM NaCl, 0.01% Triton X-100) for 5 min and then de-wetted in an HBS bath. Each of the microarray chambers were then incubated with 180 mL of nuclear extract binding mixture for 1 h in the dark. Nuclear extract binding mixture (per chamber): 400-600 mg of nuclear extract; 20mM HEPES (pH 7.9); 100mM NaCl; 1mM DTT; 0.2mg/mL BSA; 0.02% Triton X-100; 0.4mg/mL salmon testes DNA (Sigma-Aldrich, Catalog #D7656)). The microarray was then rinsed in an HBS bath containing 0.1% Tween-20 and subsequently de-wetted in an HBS bath. After the nuclear extract incubation, the microarray was incubated for 20 min in the dark with 20mg/mL primary antibody for the TF or COF of interest. The primary antibody was diluted in 180 mL of 2% milk in HBS. The array was then rinsed in an HBS bath containing 0.1% Tween-20, de-wetted in an HBS bath, and incubated with 10mg/mL of either Alexa488- or Alexa647-conjugated secondary antibody for 20 min in the dark. The secondary antibody was diluted in 180 mL of 2% milk in HBS. Excess antibody was removed by washing the array twice for 3 min in 0.05% Tween-20 in HBS and once for 2 min in HBS in Coplin jars as described above. After the washes, the microarray was de-wetted in an HBS bath and scanned

growth_protocol: Jurkat cells were grown in suspension in RPMI 1640 Glutamax media (Thermofisher Scientific, Catalog #72400120) with 10% heat-inactivated fetal bovine serum (FBS) (Thermofisher Scientific, Catalog #132903). Cells were grown in 50mL of media in T175 (Thermofisher Scientific, Catalogue #132903) non-treated flasks. SK-MEL-28 cells were grown in EMEM media (ATCC, Catalog #30-2003) with 10% heat-inactivated FBS (Thermofisher Scientific, Catalog #132903). Cells were grown in 30mL of media in T225 flasks for adherent cells (Corning, Catalog #35138).

extract_protocol: Nuclear extracts were obtained as previously described (Bray et al. PMID: 35252945, Mohaghegh et al. PMID: 30657937) with modifications detailed below. To harvest nuclear extracts from Jurkat cells, the cells were collected in a 15 ml falcon tube and placed on ice. To harvest nuclear extracts from SK-MEL-28 cells, the media was aspirated off and the cells were washed once with 1X PBS (Thermofisher Scientific, Catalog #100010049). Once the 1X PBS used to wash the cells was aspirated off, enough 1X PBS was mixed with 0.1mM Protease Inhibitor (Sigma-Aldrich, Catalogue #P8340) to cover the cells was added to each flask. A cell scraper was used to dislodge the cells from the flask, and cells were collected in a 15 ml falcon tube and placed on ice. Jurkat and SK-MEL28 cells were pelleted by centrifugation at 500xg for 5 min at 4˚C. Both pellets were washed with 2mL of 1X PBS with Protease Inhibitor and pelleted again at 500xg for 2 min at 4˚C. To lyse the plasma membrane, the cells were resuspended in Buffer A (1 mL Buffer A for Jurkat cells, 1.5 mL Buffer A for SK-MEL28 cells) (10mM HEPES, pH 7.9, 1.5mM MgCl, 10mM KCl, 0.1mM Protease Inhibitor, Phosphatase Inhibitor (Santa-Cruz Biotechnology, Catalog #sc-45044), 0.5mM DTT (Sigma-Aldrich, Catalog #4315) and incubated for 10 min on ice. After the 10 min incubation, Igepal detergent (final concentration of 0.1%) was added to the cell and Buffer A mixture and vortexed for 10 s. To separate the cytosolic fraction from the nuclei, the sample was centrifuged at 500xg for 5 min at 4˚C to pellet the nuclei. The cytosolic fraction was collected into a separate microcentrifuge tube. The pelleted nuclei were then resuspended in Buffer C (100 µL for Jurkat nuclei and 150 µL for SK-MEL-28 nuclei) (20mM HEPES, pH 7.9, 25% glycerol, 1.5mM MgCl, 0.2mM EDTA, 0.1mM Protease Inhibitor, Phosphatase Inhibitor, 0.5mM DTT, and 420mM NaCl) and then vortexed for 30 s. To extract the nuclear proteins (i.e., the nuclear extract), the nuclei were incubated in Buffer C for 1 h while mixing at 4˚C. To separate the nuclear extract from the nuclear debris, the mixture was centrifuged at 21,000xg for 20 min at 4˚C. The nuclear extract was collected in a separate microcentrifuge tube and flash frozen using liquid nitrogen. Nuclear extracts were stored at -80˚C

treatment_protocol: Jurkat and SK-MEL-28 cells were untreated. For each condition, nuclear lysates were harvested. For all nuclear lysates assayed using PBM experiments.

value: untreated

tag: target protein

tag: primary antibody

tag: primary antibody concentration

value: 20 mg/mL

tag: secondary antibody

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)

tag: secondary antibody concentration

value: 10 mg/mL

tag: molecule type

value: Nuclear extract


title: SNP_screen_MOF_SKMEL28_rep1

source_name: Sk-mel-28 cells, rep1

value: MOF


title: SNP_screen_TBL1XR1_SKMEL28_rep2

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: ATAC-seq_P11

tag: tissue


title: ATAC-seq_P13


title: ATAC-seq_P9


title: SNP_screen_BRD4_SKMEL28_rep2


title: RRP6-batch1-1st-30min

description: rRNA depleted RNA

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: RRP6-batch1-1st-3h

description: rRNA depleted RNA

value: time 3 hour of FIRST Galactose treatment


title: SNP_screen_BRD4_SKMEL28_rep1


title: SNP_screen_TBL1XR1_SKMEL28_rep1


title: RRP6-batch1-1st-1h

description: rRNA depleted RNA

value: time 1 hour of FIRST Galactose treatment


title: RRP6-batch1-1st-000

description: rRNA depleted RNA


title: SNP_screen_SRC1_SKMEL28_rep2


title: SNP_screen_SRC1_SKMEL28_rep1


title: ATAC-seq_P8

value: Microinvasive


title: ATAC-seq_P7

value: Breast Cancer


title: BY-batch3-2nd-30min

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 30 minutes  of SECOND Galactose treatment


title: SNP_screen_RBBP5_SKMEL28_rep1


title: ATAC-seq_P5

value: TNBC

value: IDC


title: BY-batch3-2nd-1h

description: rRNA depleted RNA

value: time 1 hour of SECOND Galactose treatment


title: ATAC-seq_P4


title: SNP_screen_MOF_SKMEL28_rep2

value: untreated


title: BY-batch3-2nd-15min

description: rRNA depleted RNA

value: time 15 minutes of SECOND Galactose treatment


title: ATAC-seq_P3


title: SNP_screen_RBBP5_JURKAT_rep2

source_name: Jurkat cells, rep2

value: 20 mg/mL

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: SNP_screen_MOF_JURKAT_rep1

source_name: Jurkat cells, rep1

value: 10 mg/mL

value: Nuclear extract


title: BY-batch3-1st-3h

description: rRNA depleted RNA


title: ATAC-seq_P1


title: SNP_screen_NCOR1_JURKAT_rep1


title: rectal adjacent normal tissue, rep1

city: Shanghai

first: Xin

last: Hu

address: 688 Hongqu Road

department: Precision Medicine

institute: Fudan University Shanghai Cancer Center

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 40%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCh38Ensembl91
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: rectum normal tissue

growth_protocol: Miltenyi Tissue Storage Solution

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: endoscopy

value: rectum normal tissue

tag: disease state

value: complete response

tag: Sex

value: male

value: MSI-high/TIB-high

value: anti-PD1 (pembrolizumab)


title: SNP_screen_NCOR1_JURKAT_rep2

tag: treatment


title: sigmoid cancer, PD, POLE-mutant/TMB-UH, rep1

description: 10X Genomics

source_name: sigmoid cancer

value: sigmoid cancer

value: progressive disease

tag: genotype

value: POLE-mutant/TMB-UH


title: BY-batch3-1st-30min

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 30 minutes  of FIRST Galactose treatment


title: rectal cancer, CR, MSI-high/TIB-high, rep1

description: 10X Genomics

source_name: rectal cancer

value: rectal cancer


title: SNP_screen_RBBP5_JURKAT_rep1

value: untreated


title: SNP_screen_SRC1_JURKAT_rep1

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: SNP_screen_MOF_JURKAT_rep2

value: MOF

value: 20 mg/mL


title: SNP_screen_SRC1_JURKAT_rep2

value: 10 mg/mL


title: BY-batch3-1st-1h

description: rRNA depleted RNA

value: time 1 hour of FIRST Galactose treatment


title: ATAC-seq_P12

value: Breast Cancer

value: IDC


title: SNP_screen_TBL1XR1_JURKAT_rep2

value: Nuclear extract


title: 43A

city: Athens

first: Ioanna

last: Papadatou

state: Greece

address: Thivon & Papadiamantopoulou 1

department: "Agia Sophia" Children's Hospital

country: Greece

institute: National and Kapodistrian University of Athens

description: Healthy, before 2nd dose

data_processing:
Basecalling on Illumina NextSeq550
Alignement with STAR on hg38 with pipeline provided by Lexogen and BlueBee
Bam used for bedgraph construction
bigWig constructed through bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Whole Blood

extract_protocol:
Total RNA was isolated from whole blood, stored in paxgene, using the ExtractionMonarch® Total  RNA Miniprep Kit (NEB #T2010). Upon blood isolation, Monarch DNA/RNA Protection Reagent  (supplied as a 2x concentrate) was added undiluted to an equal volume of blood. Addition of the  protection reagent and the following RNA isolation was performed as described in the Kit's manual  for Total RNA Purification from Mammalian Whole Blood Samples.
After quantification on a NanoDrop ND-1000 (Thermofisher) and Bioanalyzer RNA 6000 Nano  assay (Agilent), 140-300ng of total RNA from samples passing quality control were processed  using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, 015.96) for library  preparation. Libraries were assessed for molarity and median library size using Bioanalyzer High  Sensitivity DNA Analysis (Agilent, 5067-4626)
RNA sequencing. The kit creates Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA.

value: Blood

tag: age

value: Female

tag: status

value: Pre


title: RNA-seq_97L_R2

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

data_processing:
SOAP nuke software (v2.1.0) was used to remove reads with unknown bases more than 10% and low-quality reads (the ratio of the bases with quality value Q ≤ 15 greater than 50%).
Bowtie2 and HISAT (v2.1.0) were used to align clean reads to the reference genome hg19.
RSEM (v1.2.4) was then used to quantify the gene-expression level through the fragments per kilobase of transcript per million mapped reads (FPKM) method.
The differentially expressed genes (DEGs) were determined by DESeq2 (v1.18.1, fold change ≥ 2 and p value ≤ 0.05).
Assembly: hg19
Supplementary files format and content: TXT

source_name: liver

growth_protocol: DMEM medium with 10% fetal calf serum.

extract_protocol:
MHCC-97H and MHCC-97L cells were maintained in DMEM medium with 10% fetal calf serum. Approximately 2 x 10e7 cells were used for ChIP-seq assay. For Flag-OGT ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-Flag-magnetic beads. For ZNF263, H3K4me3, or H3K27ac ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-ZNF263, anti-H3K4me3, or anti-H3K27ac antibody.  For HA-ZNF263-WT and HA-ZNF263-S662A ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-HA-magnetic beads. For RNA-seq, total RNA was extracted from the Flag-OGT expressing cells using Trizol reagent (Invitrogen). RNA quality was checked by Hiseq 2000 instrument (Illumina). RNA libraries were prepared for sequencing using standard protocols.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit.

treatment_protocol: The sequence coding human full-length (1-1036aa) wild type (WT) human OGT were subcloned into lentiviral luciferase expressing pLVX-IRES-Luc-G418 vector containing an C-terminal 3 × Flag tag. ZNF263 was transiently knockdown by ZNF263 shRNA. The sequence coding human full-length (1-683aa) wild type (WT) human ZNF263 and O-GlcNAcylation site mutants (Ser662 → Ala) ZNF263 were subcloned into lentiviral luciferase expressing pLVX-IRES-Luc-Hygro vector containing an C-terminal HA tag.  Transfection of the MHCC-97H and MHCC-97L cells were performed with geneticin  according to the manufacturer’s instructions. The stably transfected cells were then selected by the addition of neomycin or hygro to the medium.  ~2x10e7 cells were used as a unit of cells for each experiment.

value: liver

tag: cell line

tag: cell type

value: hepatocellular carcinoma


title: 43B

description: Healthy, after 2nd dose

tag: gender

value: Post


title: SNP_screen_TBL1XR1_JURKAT_rep1


title: BY-batch3-1st-000

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 0 of FIRST Galactose treatment


title: 41B

description: Healthy, after 2nd dose


title: RNA-seq_97L_R1


title: 41A

description: Healthy, before 2nd dose


title: SNP_screen_BRD4_JURKAT_rep2

value: untreated

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: BY-batch2-2nd-30min

description: rRNA depleted RNA

value: time 30 minutes  of SECOND Galactose treatment


title: BY-batch3-2nd-000

description: rRNA depleted RNA

value: time 0 of SECOND Galactose treatment


title: 40B

description: Healthy, after 2nd dose

value: Male


title: BY-batch2-2nd-1h

description: rRNA depleted RNA

value: time 1 hour of SECOND Galactose treatment


title: BY-batch2-2nd-15min

description: rRNA depleted RNA

value: time 15 minutes of SECOND Galactose treatment


title: control-3

city: Shaanxi

first: Xueni

last: You

state: 陕西省

address: 22 Xi-nong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

data_processing:
none provided by the submitter
Supplementary files format and content: FPKM

organism: Sus scrofa

source_name: testis

extract_protocol: none provided by the submitter

value: testis

value: porcine primitive spermatogonia

value: 0.1% ethanol in place of retinoic acid was applied


title: RA-3

value: 2 umol/L all-trans-retinoic acid


title: CASCADE_NCOR1_JURKAT_rep1

value: 20 mg/mL

value: 10 mg/mL

value: Nuclear extract


title: 40A

description: Healthy, before 2nd dose

value: Blood

value: Pre


title: RNA-seq_97L_OGT_R2

value: liver

value: hepatocellular carcinoma

value: Flag-OGT expressed


title: RNA-seq_97L_OGT_R1