title: spcing1, H3K9Ac, rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
MACS2 was used to identify GFP ChIP-enriched peaks. SICER2 was used to identify H3K9Ac ChIP-enriched peaks.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis seedlings

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with GFP or H3K9Ac antibodies.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

tag: tag

value: spcing1 mutant

value: anti-H3K9Ac (Millipore, 07-352)


title: Col-0, H3K9Ac, rep1

status: Public on Jan 09 2023

type: SRA

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

tag: tissue

value: seedlings

tag: genotype

value: WT

tag: chip antibody


title: ada2a, H3K9Ac, rep2

value: ada2a mutant


title: spcing1, H3K9Ac, rep1


title: Col-0_12d_rep3

library_source: transcriptomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

molecule: total RNA

source_name: seedlings

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

value: wild type


title: input_H3K14Ac_rep1

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
SICER2 was used to identify H3K14Ac ChIP-enriched peaks.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with H3K14Ac antibodies.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

tag: antibody


title: ING1-GFP, IP, rep1

value: GFP

value: anti-GFP (Abcam, ab290)


title: Col-0, H3K9Ac, rep2


title: GCN5-GFP, IP, rep1


title: ING1-GFP, input


title: GCN5-GFP, IP, rep2


title: GCN5-GFP, input


title: ADA2B-GFP, IP, rep1


title: ADA2B-GFP, IP, rep2


title: ADA2A-GFP, IP, rep1


title: ADA2A-GFP, input


title: ADA2A-GFP, IP, rep2


title: PFC_MK-801_5

city: Yangzhou

first: Bo

last: Pan

state: Jiangsu

address: No.136, JiangYangZhongLu

department: Department of Pharmacy

institute: Yangzhou University Medical College

data_processing:
Reads were aligned to the genome using HISAT2 (Version 2.2.1) and SAMtools (Version 1.15.1) with referencing the gene annotation file mRatBN7.2 from Ensembl (Release 105).
FeatureCounts (Subread package Version 2.0.1) was employed to count the reads and then to create the expression matrix
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Rattus norvegicus

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The RNA-seq library for sequencing was prepared by Novogene following the standard Illumina protocols.

value: brain

tag: strain

value: SD

tag: Sex

value: male

tag: treatment


title: ada2a, H3K9Ac, rep1


title: PFC_MK-801_2


title: PFC_MK-801_4


title: PFC_MK-801_3


title: PFC_MK-801_1


title: PFC_Control_4

value: saline (0.9%)


title: PFC_Control_2


title: PFC_Control_3


title: PFC_Control_1


title: Patient sample 219B

city: Los Angeles

first: Matthew

middle: A

last: Fischer

state: CA

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

country: USA

institute: University of California, Los Angeles

description: Postoperative sample from patient 219

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 219

value: Whole blood

tag: time

value: post-operative

value: Female

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

tag: isolated aortic surgery

tag: isolated myomectomy surgery

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

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Col-0_12d_rep2

tag: tissue

tag: genotype


title: PFC_Control_5

tag: strain

tag: Sex

tag: treatment


title: Patient sample 215B

description: Postoperative sample from patient 215

tag: individual

value: Patient 215

tag: time

value: Male

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


title: Patient sample 217B

description: Postoperative sample from patient 217

value: Patient 217

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


title: Patient sample 218B

description: Postoperative sample from patient 218

tag: individual

value: Patient 218

tag: tissue

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: post-operative atrial fibrillation


title: ING1-GFP, IP, rep2

value: seedlings

tag: tag

tag: chip antibody


title: Patient sample 208B

description: Postoperative sample from patient 208

value: Patient 208

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: combined surgery


title: Patient sample 200B

description: Postoperative sample from patient 200

tag: individual

value: Patient 200

tag: tissue

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


title: Patient sample 193B

description: Postoperative sample from patient 193

value: Patient 193

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: post-operative atrial fibrillation


title: Patient sample 202B

description: Postoperative sample from patient 202

value: Patient 202

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: combined surgery


title: Patient sample 209B

description: Postoperative sample from patient 209

tag: individual

value: Patient 209

tag: tissue

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 207B

description: Postoperative sample from patient 207

value: Patient 207

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 191B

description: Postoperative sample from patient 191

value: Patient 191

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: post-operative atrial fibrillation


title: Patient sample 168B

description: Postoperative sample from patient 168

tag: individual

value: Patient 168

tag: tissue

value: Whole blood

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: ADA2B-GFP, input

tag: tag

value: GFP

tag: chip antibody


title: Patient sample 160B

description: Postoperative sample from patient 160

value: Patient 160

tag: time

value: post-operative

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 158B

description: Postoperative sample from patient 158

tag: individual

value: Patient 158

tag: tissue

value: Male

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

value: Yes

tag: post-operative atrial fibrillation


title: Patient sample 149B

description: Postoperative sample from patient 149

value: Patient 149

tag: time

tag: Sex

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: Patient sample 129B

description: Postoperative sample from patient 129

value: Patient 129

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 146B

description: Postoperative sample from patient 146

tag: individual

value: Patient 146

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery


title: Patient sample 131B

description: Postoperative sample from patient 131

value: Patient 131

tag: time

tag: Sex

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: post-operative atrial fibrillation


title: Patient sample 124B

description: Postoperative sample from patient 124

value: Patient 124

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 130B

description: Postoperative sample from patient 130

tag: individual

value: Patient 130

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 125B

description: Postoperative sample from patient 125

value: Patient 125

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery


title: Patient sample 119B

description: Postoperative sample from patient 119

value: Patient 119

value: Female

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 121BB

description: Postoperative sample from patient 121

tag: individual

value: Patient 121

tag: tissue

value: Whole blood

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 128B

description: Postoperative sample from patient 128

value: Patient 128

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 120BB

description: Postoperative sample from patient 120

value: Patient 120

value: post-operative

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition


title: Patient sample 115B

description: Postoperative sample from patient 115

tag: individual

value: Patient 115

tag: tissue

value: No

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 118B

description: Postoperative sample from patient 118

value: Patient 118

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

value: Yes

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 117BB

description: Postoperative sample from patient 117

value: Patient 117

value: Male

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 122BB

description: Postoperative sample from patient 122

tag: individual

value: Patient 122

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: current smoker

tag: b cells composition


title: Patient sample 123BB

description: Postoperative sample from patient 123

value: Patient 123

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 112B

description: Postoperative sample from patient 112

value: Patient 112

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 111B

description: Postoperative sample from patient 111

tag: individual

value: Patient 111

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 113B

description: Postoperative sample from patient 113

value: Patient 113

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: current smoker

tag: b cells composition


title: Patient sample 109B

description: Postoperative sample from patient 109

value: Patient 109

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 116BB

description: Postoperative sample from patient 116

tag: individual

value: Patient 116

tag: tissue

value: Female

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 107B

description: Postoperative sample from patient 107

value: Patient 107

value: Whole blood

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 108B

description: Postoperative sample from patient 108

value: Patient 108

value: post-operative

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition


title: Patient sample 167B

description: Postoperative sample from patient 167

tag: individual

value: Patient 167

tag: tissue

value: No

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 105B

description: Postoperative sample from patient 105

value: Patient 105

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

value: Yes

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 110B

description: Postoperative sample from patient 110

value: Patient 110

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 104B

description: Postoperative sample from patient 104

tag: individual

value: Patient 104

tag: tissue

value: Male

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: current smoker

tag: b cells composition


title: Patient sample 127B

description: Postoperative sample from patient 127

value: Patient 127

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 099B

description: Postoperative sample from patient 099

value: Patient 099

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 102B

description: Postoperative sample from patient 102

tag: individual

value: Patient 102

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 114B

description: Postoperative sample from patient 114

value: Patient 114

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: current smoker

tag: b cells composition


title: Patient sample 103B

description: Postoperative sample from patient 103

value: Patient 103

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 097B

description: Postoperative sample from patient 097

tag: individual

value: Patient 097

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 090B

description: Postoperative sample from patient 090

value: Patient 090

tag: time

tag: Sex

value: Female

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 089B

description: Postoperative sample from patient 089

value: Patient 089

value: Whole blood

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition


title: Patient sample 084B

description: Postoperative sample from patient 084

tag: individual

value: Patient 084

tag: tissue

value: post-operative

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 085B

description: Postoperative sample from patient 085

value: Patient 085

tag: time

tag: Sex

value: No

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 079B

description: Postoperative sample from patient 079

value: Patient 079

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

value: Yes

tag: combined surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 088B

description: Postoperative sample from patient 088

tag: individual

value: Patient 088

tag: tissue

value: Male

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: current smoker

tag: b cells composition


title: Patient sample 078B

description: Postoperative sample from patient 078

value: Patient 078

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 080B

description: Postoperative sample from patient 080

value: Patient 080

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 070B

description: Postoperative sample from patient 070

tag: individual

value: Patient 070

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 083B

description: Postoperative sample from patient 083

value: Patient 083

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: current smoker

tag: b cells composition


title: Patient sample 076B

description: Postoperative sample from patient 076

value: Patient 076

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 081B

description: Postoperative sample from patient 081

tag: individual

value: Patient 081

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 075B

description: Postoperative sample from patient 075

value: Patient 075

tag: time

tag: Sex

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 077B

description: Postoperative sample from patient 077

value: Patient 077

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition


title: Patient sample 065B

description: Postoperative sample from patient 065

tag: individual

value: Patient 065

tag: tissue

value: Whole blood

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: Patient sample 064B

description: Postoperative sample from patient 064

value: Patient 064

tag: time

value: post-operative

tag: Sex

value: Female

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 067B

description: Postoperative sample from patient 067

value: Patient 067

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 063B

description: Postoperative sample from patient 063

tag: individual

value: Patient 063

tag: tissue

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

value: Yes

tag: current smoker

tag: b cells composition


title: Patient sample 062B

description: Postoperative sample from patient 062

value: Patient 062

tag: time

tag: Sex

value: Male

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: cd4+ t cell composition

tag: post-operative atrial fibrillation


title: 5194

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: mice with 28-day Angiotensin-II (500ng/kg/min) infusion and VAL (10.4mg/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: GCRmm38/mm10(UCSC)
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

organism: Mus

source_name: cardiac tissue

extract_protocol:
The cardiac tissues were dissected and  stored in RNA later and stored in -20℃.Total RNA was extracted with TRIzol® Reagent (Cat.15596-026, Ambion, Austin, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

tag: strain

value: cardiac tissue

tag: genotype

tag: treatment

value: Angiotensin-II

value: Valsartan

tag: group

value: AngII+VAL


title: Patient sample 060B

description: Postoperative sample from patient 060

tag: individual

value: Patient 060

tag: tissue

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 059B

description: Postoperative sample from patient 059

value: Patient 059

tag: time

tag: Sex

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: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: 5121

tag: strain

tag: tissue

tag: genotype

tag: treatment

tag: group


title: Patient sample 071B

description: Postoperative sample from patient 071

tag: individual

value: Patient 071

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 057B

description: Postoperative sample from patient 057

value: Patient 057

value: Whole blood

tag: time

tag: Sex

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: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: Patient sample 098B

description: Postoperative sample from patient 098

tag: individual

value: Patient 098

tag: tissue

value: post-operative

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated valve surgery

tag: combined surgery


title: 5131

tag: strain

tag: genotype

tag: treatment

tag: group


title: 5163

description: mice with 28-day Angiotensin-II (500ng/kg/min) infusion and GAS (5mg/kg/d) treatment

value: Gastrodin

value: AngII+GAS


title: Patient sample 056B

description: Postoperative sample from patient 056

value: Patient 056

tag: time

tag: Sex

value: No

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: 5112

tag: tissue


title: 5158


title: Patient sample 091B

description: Postoperative sample from patient 091

tag: individual

value: Patient 091

value: Female

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

value: Yes

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: 5148

tag: strain

value: cardiac tissue

tag: genotype

tag: treatment

value: Angiotensin-II

tag: group


title: 5135


title: Patient sample 051B

description: Postoperative sample from patient 051

value: Patient 051

tag: time

tag: Sex

value: Male

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 053B

description: Postoperative sample from patient 053

tag: individual

value: Patient 053

tag: tissue

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition


title: Patient sample 050B

description: Postoperative sample from patient 050

value: Patient 050

tag: time

tag: Sex

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: cd4+ t cell composition


title: Patient sample 066B

description: Postoperative sample from patient 066

tag: individual

value: Patient 066

tag: tissue

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: 5133

description: mice with 28-day Angiotensin-II (500ng/kg/min) infusion and BAI (5mg/kg/d) treatment

tag: strain

tag: genotype

tag: treatment

value: Baicalin

tag: group

value: AngII+BAI


title: Patient sample 058B

description: Postoperative sample from patient 058

value: Patient 058

value: Whole blood

tag: time

value: post-operative

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition


title: 5140

tag: tissue


title: Patient sample 061B

description: Postoperative sample from patient 061

tag: individual

value: Patient 061

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

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 096B

description: Postoperative sample from patient 096

value: Patient 096

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery


title: Patient sample 055B

description: Postoperative sample from patient 055

tag: individual

value: Patient 055

tag: tissue

value: Female

tag: anesthesia time

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition


title: 5124

tag: strain

value: cardiac tissue

tag: genotype

tag: treatment

value: Valsartan

tag: group

value: AngII+VAL


title: Patient sample 049B

description: Postoperative sample from patient 049

value: Patient 049

tag: time

tag: Sex

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

value: Yes

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 047B

description: Postoperative sample from patient 047

tag: individual

value: Patient 047

tag: tissue

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker


title: Patient sample 045B

description: Postoperative sample from patient 045

value: Patient 045

tag: time

tag: Sex

value: Male

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: b cells composition

tag: cd4+ t cell composition


title: 5154

tag: strain

tag: tissue

tag: genotype

tag: treatment

value: Angiotensin-II

value: Baicalin

tag: group

value: AngII+BAI


title: Patient sample 044B

description: Postoperative sample from patient 044

tag: individual

value: Patient 044

value: Whole blood

value: post-operative

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 043B

description: Postoperative sample from patient 043

value: Patient 043

tag: time

tag: Sex

value: No

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: 5120

tag: strain

tag: tissue

tag: genotype

tag: treatment

value: Gastrodin

tag: group

value: AngII+GAS


title: Patient sample 042B

description: Postoperative sample from patient 042

tag: individual

value: Patient 042

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: 5125

description: mice with 28-day Angiotensin-II (500ng/kg/min) infusion and ETH (5mg/kg/d) treatment

value: cardiac tissue

value: Ethoxysanguinarine

value: AngII+ETH


title: Patient sample 040B

description: Postoperative sample from patient 040

value: Patient 040

tag: time

tag: Sex

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

value: Yes

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: 5123

tag: strain

tag: tissue

tag: genotype

tag: treatment

tag: group


title: 5113


title: Patient sample 038B

description: Postoperative sample from patient 038

tag: individual

value: Patient 038

value: Male

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 036B

description: Postoperative sample from patient 036

value: Patient 036

tag: time

tag: Sex

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: Patient sample 039B

description: Postoperative sample from patient 039

tag: individual

value: Patient 039

tag: tissue

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery


title: 5141

tag: strain

tag: genotype

tag: treatment

value: Angiotensin-II

tag: group


title: Patient sample 034B

description: Postoperative sample from patient 034

value: Patient 034

value: Whole blood

tag: time

tag: Sex

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: 5128

description: mice with 28-day Angiotensin-II (500ng/kg/min) infusion and Saline treatment

tag: tissue

value: Saline

value: AngII


title: 5153

description: mice with 28-day Saline infusion and Saline treatment

value: Control


title: 5156


title: 5143


title: 5161


title: 5130


title: Patient sample 037B

description: Postoperative sample from patient 037

tag: individual

value: Patient 037

value: post-operative

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

value: No

tag: isolated aortic surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition


title: Patient sample 029B

description: Postoperative sample from patient 029

value: Patient 029

tag: time

tag: Sex

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: cd8+ t cell composition


title: 5138

tag: strain

tag: tissue

value: cardiac tissue

tag: genotype

tag: treatment

value: Baicalin

tag: group

value: AngII+BAI


title: 5193


title: Patient sample 035B

description: Postoperative sample from patient 035

tag: individual

value: Patient 035

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

value: Yes

tag: isolated aortic surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 219A (re-analysis)

description: re-analysis of GSM5829708

value: Patient 219

tag: time

value: pre-operative

tag: Sex

value: Female

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: 5116

tag: strain

tag: tissue

tag: genotype

tag: treatment

tag: group


title: Patient sample 217A (re-analysis)

description: re-analysis of GSM5829706

tag: individual

value: Patient 217

value: Male

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 218A (re-analysis)

description: re-analysis of GSM5829707

value: Patient 218

value: Whole blood

tag: time

tag: Sex

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: 5155

tag: strain

tag: tissue

tag: genotype

tag: treatment

value: Saline

tag: group

value: Control


title: Patient sample 215A (re-analysis)

description: re-analysis of GSM5829704

tag: individual

value: Patient 215

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery

tag: isolated valve surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: 5118

value: Angiotensin-II

value: Ethoxysanguinarine

value: AngII+ETH


title: 5164

value: cardiac tissue


title: 5114


title: Patient sample 209A (re-analysis)

description: re-analysis of GSM5829702

value: Patient 209

tag: time

tag: Sex

value: No

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Mab Control Rep 2

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude.
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Mycobacterium abscessus ATCC19977 genome (Genome accession: NC_010397) using STAR2.7.1 and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 in the R statistical computing environment.
Assembly: Mycobacterium abscessus ATCC19977 genome (Genome accession: NC_010397)
Supplementary files format and content: tab-delimited text file includes raw counts table used for differential expression analysis.

organism: Mycobacteroides abscessus ATCC 19977

source_name: Planktonic cells

growth_protocol: Mycobacteria abscessus ATCC 19977 was grown in 5mL of Mueller Hinton broth II (MHB II) to log phase O.D.600 0.4-0.8.

extract_protocol:
RNA was harvested through the addition of 2 volumes of RNA protect (Qiagen), then centrifuged for 4 minutes at 10,000xg at 4C. Supernatant was poured off and pellets stored at -80°C. Next day samples were thawed out and re-suspended in 500µL RLT + 1% betamercaptoethanol and transferred to Lysing Matrix B (VWR, Pittsburgh PA). Samples were placed into a Bead Mill 4 homogenizer (Fisher Scientific, Atlanta GA) and homogenized 4 times for 40 sec at 4.5m/s with 1 min of wet ice cooling between each round of homogenization. Lysate was spun down at 8000g for 2 minutes and supernatant removed to clean centrifuge tube. Subsequent extraction of RNA was performed according to the RNAeasy extraction kit (Qiagen). RNA was eluted in 40µL of elution buffer yielding a typical concentration of 400-500ng/µL. RNA samples were then DNase treated to remove residual genomic DNA from samples. This was performed using the Genomic DNA Clean and Concentrator Kit (Zymo Research, Irvine CA). Samples were eluted in 30-45µL of RNase free water, yields ranging from 100-250ng/µL.
Libraries were prepared from total RNA with the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020595). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) and by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina) or HiSeq 2500 by the St. Jude Children's Research Hospital sequencing core at a depth of 100M reads/sample.

treatment_protocol: Samples were exposed to 1µg/mL or 10µg/mL  of spectinomycin or 2694, 1µg/mL of 2593, or equal volumes of vehicle control (DMSO) for 3 hours.

tag: cell type

value: Planktonic cells

tag: treatment

value: DMSO

value: 3 hour


title: Mab Control Rep 3


title: Patient sample 028B

description: Postoperative sample from patient 028

tag: individual

value: Patient 028

tag: tissue

value: post-operative

value: Female

tag: age

tag: paroxysmal atrial fibrillation

value: Yes

tag: asa class

tag: anesthesia time

tag: isolated aortic surgery

tag: isolated valve surgery

tag: monocyte composition


title: Mab Control Rep 1

tag: time


title: Patient sample 207A (re-analysis)

description: re-analysis of GSM5829700

value: Patient 207

value: Whole blood

value: pre-operative

tag: Sex

value: Male

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: combined surgery

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 200A (re-analysis)

description: re-analysis of GSM5829697

tag: individual

value: Patient 200

tag: tissue

tag: age

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: bran_4

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

description: Branaplam

data_processing:
Reads were mapped to the human genome hg38 using Ensembl v103 transcriptome annotation using STAR v.2.7.8a
rMATS v4.1.0 was used to define simple alternative splicing events and count the number of reads supporting each processing variant for each sample
Assembly: hg38
Supplementary files format and content: tab-delimited text files including PSI and reads for each exon cassette event as reported by rMATS
Supplementary files format and content: csv file with inferred PSIs and credible intervales for each treatment group

molecule: polyA RNA

source_name: HeLa

growth_protocol: HeLa cells were seeded at 5x10^5 cells on 150 mm plates, cultured under 37C 5% CO2 for 24 hrs, applied drug treatment and further cultured for 48 hours.

extract_protocol:
Total RNA was extracted by Trizol following the manufacturer's protocol.
RNA-seq libraries were prepared using KAPA mRNA HyperPrep kits (Roche)

treatment_protocol: HeLa cells were treated with 140 nM risdiplam, 70 nM branaplam, or solvent DMSO.

tag: cell line

value: HeLa

tag: strain

value: CSHL cell line repository

tag: treatment

value: Branaplam


title: bran_5

description: Branaplam


title: bran_2

description: Branaplam


title: Patient sample 168A (re-analysis)

description: re-analysis of GSM5829693

value: Patient 168

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated aortic surgery

tag: isolated valve surgery

tag: monocyte composition


title: Patient sample 202A (re-analysis)

description: re-analysis of GSM5829698

tag: individual

value: Patient 202

tag: tissue

tag: age

value: No

tag: isolated cabg surgery

tag: isolated myomectomy surgery

tag: combined surgery

tag: current smoker

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: bran_3

description: Branaplam

tag: cell line

tag: strain

tag: treatment


title: ris_5

description: Risdiplam

value: Risdiplam


title: Patient sample 191A (re-analysis)

description: re-analysis of GSM5829694

value: Patient 191

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: bran_1

description: Branaplam


title: Patient sample 193A (re-analysis)

description: re-analysis of GSM5829696

tag: individual

value: Patient 193

tag: tissue

tag: age

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: monocyte composition


title: ris_3

description: Risdiplam

tag: cell line

tag: strain

tag: treatment


title: Patient sample 158A (re-analysis)

description: re-analysis of GSM5829690

value: Patient 158

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: ris_2

description: Risdiplam


title: Patient sample 160A (re-analysis)

description: re-analysis of GSM5829691

tag: individual

value: Patient 160

tag: tissue

tag: age

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 149A (re-analysis)

description: re-analysis of GSM5829687

value: Patient 149

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

value: Yes

tag: asa class

tag: combined surgery

tag: current smoker

tag: monocyte composition


title: ris_1

description: Risdiplam

tag: cell line

tag: strain

tag: treatment


title: Patient sample 131A (re-analysis)

description: re-analysis of GSM5829682

tag: individual

value: Patient 131

tag: tissue

value: Whole blood

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: dmso_5

description: DMSO

value: DMSO


title: Patient sample 146A (re-analysis)

description: re-analysis of GSM5829684

value: Patient 146

tag: time

value: pre-operative

tag: Sex

value: Male

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 208A (re-analysis)

description: re-analysis of GSM5829701

tag: individual

value: Patient 208

tag: tissue

value: Female

tag: age

tag: anesthesia time

tag: combined surgery

tag: current smoker

tag: monocyte composition


title: Patient sample 130A (re-analysis)

description: re-analysis of GSM5829681

value: Patient 130

tag: time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: dmso_4

description: DMSO

tag: cell line

value: HeLa

tag: strain

value: CSHL cell line repository

tag: treatment


title: dmso_3

description: DMSO


title: Patient sample 128A (re-analysis)

description: re-analysis of GSM5829679

tag: individual

value: Patient 128

tag: Sex

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 129A (re-analysis)

description: re-analysis of GSM5829680

value: Patient 129

tag: tissue

tag: time

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: combined surgery

tag: current smoker

tag: monocyte composition


title: dmso_2

description: DMSO

tag: cell line

tag: strain

tag: treatment


title: Patient sample 167A (re-analysis)

description: re-analysis of GSM5829692

tag: individual

value: Patient 167

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 127A (re-analysis)

description: re-analysis of GSM5829678

value: Patient 127

tag: tissue

tag: time

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: ris_4

description: Risdiplam

tag: cell line

tag: strain

tag: treatment

value: Risdiplam


title: Patient sample 123AA (re-analysis)

description: re-analysis of GSM5829675

tag: individual

value: Patient 123

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

value: Yes

tag: current smoker

tag: monocyte composition


title: dmso_1

description: DMSO

value: DMSO


title: NTC 1

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main

description: HUVEC with non-targeting control gRNA

data_processing:
FastQC
Read trimming (Trim Galore!)
Alignment (Bowtie2 )
Peak calling (MACS3)
Normalisation (DeepTools, bamCoverage)
Assembly: hg38
Supplementary files format and content: bigwig, normalised read depth per position (RPKM)
Library strategy: CUT&RUN

source_name: HUVEC

growth_protocol: Pooled human umbilical vein endothelial cells (HUVEC) were purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) and cultured at 37°C with 5% CO2 in a humidified incubator. Gelatin-coated dishes (356009, Corning Incorporated, USA) were used to culture the cells. Endothelial growth medium (EGM), consisting of endothelial basal medium (EBM) supplemented with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (15140-122, Gibco/ Lifetechnologies, USA) was used.

extract_protocol:
BRG1 Cleavage Under Targets & Release Using Nuclease (CUT&RUN), a method established by Skene and Henikoff in 2017, was performed similarly as described in the EpiCypher CUT&RUN Protocol v2.0, but with minor modifications for the cell-type and antibody used. Briefly, 500,000 NTC or BRG1 knockout HUVEC were washed with wash buffer (20 mM HEPES knockoutH pH 7.9, 150 mM NaCl, 500 nM spermidine, 1X Roche Protein Inhibitor Cocktail) at RT. Cells were resuspended in wash buffer and 10 µL BioMag®Plus Concanavalin A (ConA) beads (86057-3, Polysciences) added for 10 min at RT. Beads were separated on a magnetic rack and washed once before being resuspended in 100 µL antibody buffer (wash buffer, 0.25% Digitonin and 2 mM EDTA) and 1 µL BRG1 antibody (ab110641, Abcam). Beads were incubated with the antibody overnight with gentle shaking at 4 °C. The next day, beads were washed twice with 200 µL 0.25 % Digitonin wash buffer and resuspended in Digitonin wash buffer containing 2 µL CUTANA™ pAG-MNase (15-1016, EpiCypher) and incubated on ice for 30 min. Samples were washed twice and then resuspended in 100 µL Digitonin wash buffer containing 2 µL CaCl2 at a final concentration of 100 mM and incubated for 2 h at 4 °C with gentle shaking. 33 µL of 2X “stop solution” (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.25 % Digitonin, 100 µg/mL RNase A, 50 µg/mL Glycoblue) was added to the beads and incubated at 37 °C for 10 min. Samples were placed on a magnetic rack and the supernatant removed and kept for DNA purification. Briefly, 5X volume of binding buffer (20 mM HEPES knockoutH pH 7.9, 20 mM KCl, 1 mM CaCl2, 1 mM MnCl2) was added to the samples and the pH adjusted with sodium acetate before being transferred to a purification column (58002, ActiveMotif) and centrifuged at 11,000 g for 30 sec. The column was then washed with 750 µL wash buffer and dried by centrifugation for 2 min. DNA was eluted with 25 µL elution buffer and the DNA concentration measured with a Qubit 3.0 Fluorometer (life technologies).
DNA libraries were prepared according to the manufacturer’s protocol (NEBNext® Ultra II, NEB) with some minor adjustments for CUT&RUN samples. Briefly, samples were brought to 50 µL with 0.1X TE buffer and DNA end preparation performed as instructed but with incubation at 20 °C for 20 min and then 58 °C for 45 min. Adaptor ligation was performed with a 1:10 dilution of adaptor (E6440S, NEB). For DNA purification, 0.9X Volume AMPure XP beads (A63881, Beckman Coulter) was added to the samples and incubated for 5 min at RT. Beads were washed twice with 200 µL 80 % ethanol and DNA eluted with 17 µL 0.1X TE buffer for 2 min at RT. PCR amplification of the eluted DNA was performed as described in the manufacturer’s protocol but with the addition of 2.5 µL Evagreen (20X) for visualization of the amplification curves on an AriaMx Real-time PCR system (Agilent). The denaturation and annealing/extension steps of the PCR amplifaction were performed for around 12 cycles and stopped before the curves plateaued. A cleanup of the PCR reaction was performed twice with 1.1X Ampure beads and eluted each time in 33 µL 0.1X TE buffer. DNA concentrations were measured with a Qubit and size distributions measured on a Bioanalyzer (Agilent).
Sequencing was performed on the NextSeq2000 (Illumina) using a P2 flowcell at a depth of around 10M reads per library with 1x75bp paired-end setup. The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC. Trim Galore! (Krueger, F. (2021). Trim Galore. GitHub repository. Version 0.6.7. Retrieved from https://https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye) was used to trim reads before alignment to the Ensembl human genome version hg38 (ensembl release 104) using Bowtie2. Duplicate reads were removed with rmdup and coverage tracks generated with bamCoverage (deepTools Version 3.5.1). ComputeMatrix and plotHeatmap (deepTools Version 3.5.1) were used on the coverage tracks to generate heatmaps of BRG1 binding across the genome. Peaks were called on the aligned data using MACS2 and annotatePeaks (HOMER) was used to identify the nearest genes to called peaks.

treatment_protocol: BRG1 knockout was performed using a single gRNA approach. The gRNAs were cloned into lentiCRISPRv2 vector backbone with Esp3I (ThermoFisher #FD0454) according to the standard protocol. lentiCRISPRv2 was a gift from Feng Zhang (Addgene plasmid #52961; http://n2t.net/addgene:52961; RRID:Addgene_52961)). The modification of the lentiviral CRISPR/Cas9 v2 plasmid with hygromycin resistance was provided by Frank Schnütgen (Dept. of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University).

tag: cell type

value: HUVEC

tag: knockout

value: NTC

tag: antibody

value: BRG1 antibody (ab110641, Abcam)


title: BRG1 KO 1

description: HUVEC with CRISPR-Cas9 mediated knockout of BRG1

value: BRG1 KO


title: Patient sample 122AA (re-analysis)

description: re-analysis of GSM5829674

value: Patient 122

tag: tissue

value: Whole blood

tag: time

value: pre-operative

value: Male

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: S759C-2

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

description: thr-1 araD139 Δ(argF-lac) 169tsx-33 supE44 galK2 hisG4 rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211 Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan dnaE S759C zae502::Tn10

data_processing:
Library strategy: HydEn-seq
Trimming for quality and adaptor sequence of all reads was performed with cutadapt 1.12 (2). Pairs containing one or both reads shorter than 15 nt were discarded. Bowtie 1.2 (3) was used to align Mate 1 of all remaining pairs to the list of index primers used to prepare the libraries; all matching pairs were discarded. All remaining pairs were aligned with bowtie (-v2 –X2000-best) to the E. coli K12, DH10B reference genome build 2008-03-17 from NCBI. Single-end alignments were then performed for mate 1 of all unaligned pairs (-m1, -v2). The count of 5´-ends of all unique paired-end and single-end alignments was determined for all samples and shifted one base upstream to the location of the hydrolyzed ribonucleotide.
Genome_build: E. coli K12, DH10B reference genome build 2008-03-17 from NCBI
Supplementary_files_format_and_content: bedGraph files

organism: Escherichia coli K-12

source_name: isolate

growth_protocol: The E. coli K-12 strains used in this study are listed in Table 1 of the manuscript. The cells were thawed from frozen stocks, and streaked out on LB agar plates containing 50 μg/ml kanamycin, 25 μg/ml spectinomycin, and 25 μg/ml zeosin. Next day, 5-6 colonies were picked up to be diluted in 2-3 ml LB media supplemented with the mentioned antibiotics to incubate at 37°C overnight. The culture was diluted to OD600=0.05 in 25 ml LB with the above-mentioned antibiotics. After 2-3 hours, the cells reached to exponential growth (OD600=0.4-0.6). The cells were centrifuged to pellet and used for the next step.

extract_protocol: HydEn-seq method has been previously described. Briefly, DNA extraction was performed using MasterPure™ Complete DNA and RNA Purification Kit (Lucigen, Epicentre, MC85200). After measuring the DNA concentration using Qubit® dsDNA BR Assay Kit (Life Technologies, molecular probes, Q32853), 1 µg DNA was hydrolyzed using 0.3 M KOH by incubation at 55°C for 2 hours. Ethanol-precipitated DNA was denatured by 3 minutes incubation at 85°C. The single strand DNA containing 5´-OH ends was phosphorylated using 3´-phosphatase minus T4 polynucleotide kinase (BioLabs, M0236L), incubated at 65°C for 20 min, washed with beads (GC biotech, CPCR-0050), denatured, ligated to ARC140 adaptor using T4 RNA Ligase 1 (BioLabs, M0204S), denatured, polymerized using T7 DNA Polymerase (BioLabs, M0274L) and ARC76/77 oligos, and bead-washed. KAPA HiFi hotstart readymix (2X) kit (KAPA biosystems, 07958935001) was used to amplify the libraries. Paired-end sequencing was performed using Illumina NextSeq 500 system.

tag: strain/background

tag: genotype/variation

value: thr-1 araD139 <delta>(argF-lac) 169tsx-33 supE44 galK2 hisG4 rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211 <delta>( umuDC)596::ermGT <delta>dinB61::ble <delta>polB::<omega>Spc <delta>rnhB782::kan dnaE S759C zae502::Tn10


title: S759C-3


title: Patient sample 120AA (re-analysis)

description: re-analysis of GSM5829672

tag: individual

value: Patient 120

tag: Sex

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: monocyte composition


title: Patient sample 118A (re-analysis)

description: re-analysis of GSM5829670

value: Patient 118

tag: tissue

tag: time

value: Female

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: b cells composition

tag: cd4+ t cell composition


title: Patient sample 119A (re-analysis)

description: re-analysis of GSM5829671

tag: individual

value: Patient 119

tag: Sex

tag: paroxysmal atrial fibrillation

tag: cd8+ t cell composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 116AA (re-analysis)

description: re-analysis of GSM5829668

value: Patient 116

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: monocyte composition


title: S759N-2

description: thr-l araD139 Δ(argF -lac)169 tsx-33 supE44 galK2 hisG4rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211Δ(umuDC)596::ermGTΔdinB61::bleΔpolB::ΩSpcΔrnhB782::kan dnaE S759NyafC::Tn l0

tag: strain/background

tag: genotype/variation

value: thr-l araD139 <delta>(argF -lac)169 tsx-33 supE44 galK2 hisG4rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211<delta>(umuDC)596::ermGT<delta>dinB61::ble<delta>polB::<omega>Spc<delta>rnhB782::kan dnaE S759NyafC::Tn l0


title: S759N-3


title: Patient sample 117AA (re-analysis)

description: re-analysis of GSM5829669

value: Patient 117

tag: tissue

tag: time

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: b cells composition

tag: cd4+ t cell composition


title: S759T-3

description: thr-1 araD139 Δ(argF-lac)169 tsx-33 supE44 galK2 hisG4 rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211 Δ(umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782 KanS dnaE(S759T) yafC::kan

value: thr-1 araD139 <delta>(argF-lac)169 tsx-33 supE44 galK2 hisG4 rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211 <delta>(umuDC)596::ermGT <delta>dinB61::ble <delta>polB::<omega>Spc <delta>rnhB782 KanS dnaE(S759T) yafC::kan


title: S759N-1


title: S759T-2


title: Patient sample 124A (re-analysis)

description: re-analysis of GSM5829676

tag: individual

value: Patient 124

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

value: Yes

tag: isolated aortic surgery

tag: cd8+ t cell composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 112A (re-analysis)

description: re-analysis of GSM5829664

value: Patient 112

tag: tissue

tag: time

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: current smoker

tag: monocyte composition


title: Patient sample 125A (re-analysis)

description: re-analysis of GSM5829677

value: Patient 125

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: b cells composition

tag: cd4+ t cell composition


title: Patient sample 114A (re-analysis)

description: re-analysis of GSM5829666

tag: individual

value: Patient 114

value: Whole blood

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: cd8+ t cell composition

tag: natural killer cell composition


title: Patient sample 113A (re-analysis)

description: re-analysis of GSM5829665

value: Patient 113

tag: tissue

tag: time

value: pre-operative

value: Male

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: NTC 2

description: HUVEC with non-targeting control gRNA

tag: cell type

value: HUVEC

tag: knockout

value: NTC

tag: antibody

value: BRG1 antibody (ab110641, Abcam)


title: Patient sample 121AA (re-analysis)

description: re-analysis of GSM5829673

tag: individual

value: Patient 121

value: Female

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

value: No

tag: isolated cabg surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: monocyte composition


title: S759T-1

tag: strain/background

tag: genotype/variation


title: Patient sample 108A (re-analysis)

description: re-analysis of GSM5829660

value: Patient 108

tag: tissue

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: cd8+ t cell composition

tag: natural killer cell composition

tag: neutrophil composition


title: S759C-1

value: thr-1 araD139 <delta>(argF-lac) 169tsx-33 supE44 galK2 hisG4 rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211 <delta>( umuDC)596::ermGT <delta>dinB61::ble <delta>polB::<omega>Spc <delta>rnhB782::kan dnaE S759C zae502::Tn10


title: Patient sample 110A (re-analysis)

description: re-analysis of GSM5829662

tag: individual

value: Patient 110

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: current smoker

tag: b cells composition

tag: post-operative atrial fibrillation


title: M65, M66 CD5hi + M65, M66 CD5lo + M65, M66 CD4+

city: Nijmegen

first: Franka

last: Buytenhuijs

state: Please select your county

address: Toernooiveld 200

country: Netherlands

institute: Radboud University

description: Barcodes: I1:M65 CD5hi, I2:M65 CD5lo, I3:M65 CD4+, I4:M66 CD5hi, I5:M66 CD5lo, I6:M66 CD4+

data_processing:
none provided
Supplementary files format and content: Comma-delimited text

organism: Mus musculus

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

extract_protocol:
RNA from sorted populations was extracted using innuPREP RNA Mini Kit (Analytik Jena, Hildesheim, Germany). cDNA  synthesis, amplification of TCRβ-chain transcripts.
library preparation was performed with the arm-PCR (ampliconrescued multiplex PCR) technology (iRepertoire Inc. Huntsville, USA) using the Qiagen OneStep RT-PCR Kit and Qiagen Multiplex PCR Kit (both Qiagen) according to the manufacturer’s protocols.

tag: tissue

tag: strain

tag: cell type

value: CD5hi/CD5lo/CD4+ T cells

tag: genotype

value: WT

tag: treatment

value: not applicable


title: M71, M72 CD5hi + M71, M72 CD5lo + M71, M72 CD4+

description: Barcodes: I7:M71 CD5hi, I8:M71 CD5lo, I9:M71 CD5hi, I10:M72 CD5hi, I11:M72 CD5lo, I12:M72 CD4+

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


title: M73, M74 CD5hi + M73, M74 CD5lo + M73, M74 CD4+

description: Barcodes: I7:M73 CD5hi, I8:M73 CD5lo, I9:M73 CD4+, I16:M74 CD5hi, I17:M74 CD5lo, I18:M74 CD4+


title: Patient sample 103A (re-analysis)

description: re-analysis of GSM5829656

value: Patient 103

value: Whole blood

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

value: Yes

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition


title: Patient sample 111A (re-analysis)

description: re-analysis of GSM5829663

tag: individual

value: Patient 111

value: pre-operative

value: Male

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: current smoker

tag: b cells composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 115A (re-analysis)

description: re-analysis of GSM5829667

value: Patient 115

tag: tissue

tag: time

tag: Sex

tag: paroxysmal atrial fibrillation

tag: asa class

tag: isolated aortic surgery

tag: isolated myomectomy surgery


title: WT-1

description: thr-1 araD139 Δ(argF -lac) l69tsx-33 supE44 galK2 hisG4rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211Δ(umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpcΔrnhB782::kan

tag: strain/background

tag: genotype/variation

value: thr-1 araD139 <delta>(argF -lac) l69tsx-33 supE44 galK2 hisG4rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211<delta>(umuDC)596::ermGT <delta>dinB61::ble <delta>polB::<omega>Spc<delta>rnhB782::kan


title: Patient sample 109A (re-analysis)

description: re-analysis of GSM5829661

tag: individual

value: Patient 109

tag: age

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: isolated valve surgery

tag: combined surgery

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition


title: WT-2


title: Patient sample 107A (re-analysis)

description: re-analysis of GSM5829659

value: Patient 107

tag: tissue

tag: time

value: No

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: current smoker

tag: b cells composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: M70, M71, M72, M73, M74 CD4+

description: Barcodes: I8:M71 CD4+, I9:M71 CD4+, I10:M72 CD4+, I11:M73 CD4+, I12:M74 CD4+

tag: strain

tag: cell type

value: CD4+ T cells

tag: genotype

tag: treatment


title: Patient sample 104A (re-analysis)

description: re-analysis of GSM5829657

tag: individual

value: Patient 104

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery


title: Patient sample 105A (re-analysis)

description: re-analysis of GSM5829658

value: Patient 105

tag: tissue

tag: time

tag: deep hyperthermic circulatory arrest

tag: isolated cabg 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


title: Patient sample 097A (re-analysis)

description: re-analysis of GSM5829651

tag: individual

value: Patient 097

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: post-operative atrial fibrillation


title: Patient sample 091A (re-analysis)

description: re-analysis of GSM5829648

value: Patient 091

tag: tissue

tag: time

value: Female

tag: cardiopulmonary bypass time

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery


title: M69, M70 CD5hi + M69, M70 CD5lo + M69, M70 CD4+

description: Barcodes: I7:M69 CD5hi, I8:M69 CD5lo, I9:M69 CD4+, I10:M70 CD5hi, I11:M70 CD5lo, I12:M70 CD4+

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: M22, M37, M38, M39 CD5lo + M26, M27 CD4+ TdTKO

description: Barcodes: I5: M26 CD4+, I6:M27 CD4+, I9:M22 CD5lo, I10:M37 CD5lo, I11:M38 CD5lo, I12:M39 CD5lo

value: C57BL/6 + TdTKO

value: CD5lo/CD4+ TdTKO T cells

value: WT/TdTKO


title: Patient sample 102A (re-analysis)

description: re-analysis of GSM5829655

tag: individual

value: Patient 102

value: Whole blood

value: pre-operative

tag: Sex

value: Male

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

value: Yes

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


title: WT-3

tag: strain/background

tag: genotype/variation

value: thr-1 araD139 <delta>(argF -lac) l69tsx-33 supE44 galK2 hisG4rpsL31 xyl-5 mtl-1 argE3 thi-1 sulA211<delta>(umuDC)596::ermGT <delta>dinB61::ble <delta>polB::<omega>Spc<delta>rnhB782::kan


title: M1, M2, M3 CD4SP

description: Barcodes: I1:M1 CD4SP, I2:M2 CD4SP, I3:M3 CD4SP

source_name: thymus

tag: tissue

value: thymus

tag: strain

value: CD4SP T cells


title: M1, M2, M3, M4 CD4DP + M4, M5 CD4SP

description: Barcodes: I1:M2 CD4DP, I2:M3 CD4DP, I3:M4 CD4P, I4:M4 CD4SP, I5:M5 CD4SP, I6:M1 CD4DP

tag: cell type

value: CD4DP/SP T cells

tag: genotype


title: M1, M2, M3, M4, M5 CD5lo + M6, M7 CD4SP

description: Barcodes: I1:M4 CD5lo, I2:M5 CD5lo, I4:M1 CD5lo, I5:M2 CD5lo, I6:M3 CD5lo, I7:M6 CD4SP, I8:M7 CD4SP

source_name: spleen and peripheral lymph nodes (inguinal, axillary, brachial, superficial cervical, and mesenteric) (CD5lo) + thymus (CD4SP)

value: CD5lo/CD4SP T cells

tag: treatment


title: Patient sample 096A (re-analysis)

description: re-analysis of GSM5829650

tag: individual

value: Patient 096

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time

tag: isolated aortic surgery

tag: isolated myomectomy surgery

tag: isolated valve surgery

tag: combined surgery

tag: post-operative atrial fibrillation


title: M7, M8, M9, M10, M17, M18 CD5hi + M14 CD4+ TdTKO

description: Barcodes: I1:M14 CD4+, I7:M17 CD5hi, I8:M18 CD5hi, I10:M7 CD5hi, I11:M8 CD5hi, I12:M9 CD5hi, I13:M10 CD5hi

tag: tissue

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

tag: strain

value: CD5hi/CD4+ TdTKO T cells


title: Patient sample 098A (re-analysis)

description: re-analysis of GSM5829652

value: Patient 098

tag: deep hyperthermic circulatory arrest

tag: isolated cabg 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


title: Patient sample 099A (re-analysis)

description: re-analysis of GSM5829653

tag: individual

value: Patient 099

tag: time

tag: Sex

value: Female

tag: age

tag: paroxysmal atrial fibrillation

tag: asa class

tag: anesthesia time

tag: cardiopulmonary bypass time


title: M6 CD5hi + M15, M16 CD4+ TdTKO

description: Barcodes: I2:M15 CD4+, I3:M16 CD4+, I9:M6 CD5hi

tag: tissue

tag: strain

value: C57BL/6 + TdTKO

tag: cell type

tag: genotype

value: WT/TdTKO

tag: treatment

value: not applicable


title: 377_Foxg1_PlusPlus_hippoc

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

institute: University of Freiburg

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
Genome_build: mm10

source_name: hippocampus of 6-week old male Foxg1+/+ mouse (control)

growth_protocol: 6-week old male mice of Foxg1cre/+ and Foxg1+/+ genotype were sacrificed, hippocampi were isolated and snap frozen in liquid nitrogen.

extract_protocol:
RNA was extracted using Qiagen Rneasy kit.
Library Prep was performed with NEBNext E7530S following the manual, 11 cycles of PCR were performed for amplification. Multiplexing was done with NEBNext E7335L. 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.

value: 6 weeks

value: hippocampus

value: male

value: control


title: 374_Foxg1_crePlus_hippoc

source_name: hippocampus of 6-week old male Foxg1cre/+ mouse

value: Foxg1 haploinsufficiency


title: 373_Foxg1_PlusPlus_hippoc


title: 378_Foxg1_crePlus_hippoc


title: Patient sample 088A (re-analysis)

description: re-analysis of GSM5829645

value: Patient 088

value: Whole blood

value: pre-operative

value: Male

tag: deep hyperthermic circulatory arrest

tag: isolated cabg surgery

tag: isolated aortic surgery

tag: isolated myomectomy surgery

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

tag: post-operative atrial fibrillation


title: HippoCells_DIV11_shctrl_DMSO_4

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

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: DMSO

tag: knockdown

value: shControl

tag: dissection age


title: HippoCells_DIV11_shFoxg1_TSA_4

value: TSA

tag: tissue

tag: strain


title: M20, M21 CD5hi

description: Barcodes: I1:M3 CD5hi, I2:M4 CD5hi, I3:M5 CD5hi, I4:M5CD4DP, I5:M1 CD5hi, I6:M2 CD5hi

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

tag: cell type

value: CD5hi T cells

tag: genotype

value: WT

tag: treatment


title: Patient sample 089A (re-analysis)

description: re-analysis of GSM5829646

tag: individual

value: Patient 089

tag: time

tag: Sex

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

tag: isolated aortic surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 090A (re-analysis)

description: re-analysis of GSM5829647

value: Patient 090

tag: tissue

value: Female

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: post-operative atrial fibrillation


title: M17, M18, M19 CD5lo + M12, M13 CD4+ TdTKO

description: Barcodes: I8:M17 CD5lo, I9:M18 CD5lo, I10:M19 CD5lo, I11:M12 CD4+, I13:M13 CD4+

tag: strain

value: C57BL/6 + TdTKO

tag: cell type

value: CD5lo/CD4+ TdTKO T cells

tag: genotype

value: WT/TdTKO

tag: treatment

value: not applicable


title: HippoCells_DIV11_shFoxg1_DMSO_4

tag: days in vitro(div)

tag: knockdown

value: hippocampus

tag: dissection age


title: Patient sample 085A (re-analysis)

description: re-analysis of GSM5829643

tag: individual

value: Patient 085

value: Whole blood

tag: time

value: pre-operative

tag: Sex

value: Male

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: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: M7, M8, M9, M10, M17, M18, M19 CD4DP

description: Barcodes: I7:M18 CD4DP, I8:M19 CD4DP, I9:M7 CD5lo, I10:M8 CD4DP, I11:M9 CD4DP, I12:M10 CD4DP, I13:M17 CD4DP

tag: tissue

value: thymus

tag: strain

tag: cell type

value: CD4DP T cells

tag: genotype

tag: treatment


title: M1, M2, M3, M4, M5 CD5hi + M5 CD4DP

source_name: spleen and peripheral lymph nodes (inguinal, axillary, brachial, superficial cervical, and mesenteric) (CD5hi) + thymus (CD4DP)

value: CD5hi/CD4DP T cells


title: HippoCells_DIV11_shctrl_DMSO_3

tag: days in vitro(div)

value: DMSO

tag: knockdown

value: shControl

tag: dissection age


title: HippoCells_DIV11_shctrl_TSA_3

value: TSA


title: HippoCells_DIV11_shFoxg1_TSA_3


title: M6, M7, M8, M9, M10 CD5lo + M19 CD5hi

description: Barcodes: I7:M10 CD5lo,  I9: M19 CD5hi, I10:M6 CD5lo, I11:M7 CD5lo, I12:M8 CD5lo, I13:M9 CD5lo

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

value: CD5hi/CD5lo T cells

value: WT


title: M8, M9, M10, M17, M18, M19 CD4SP + M6 CD4DP

description: Barcodes: I7:M19 CD4SP, I8:M6 CD4SP, I9:M8 CD4SP, I10:M9 CD4SP, I11:M10 CD4SP, I12:M17 CD4SP, I13:M18 CD4SP

value: CD4SP/DP T cells


title: Patient sample 081A (re-analysis)

description: re-analysis of GSM5829640

tag: individual

value: Patient 081

tag: time

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: asa class

tag: isolated myomectomy surgery

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

tag: post-operative atrial fibrillation


title: HippoCells_DIV11_shFoxg1_DMSO_3

tag: days in vitro(div)

tag: treatment

tag: tissue

value: hippocampus

tag: strain


title: M28, M30, M31, M32, M34, M35 CD4+

description: Barcodes: I7:M28 CD4+, I8:M30 CD4+, I9:M31 CD4+, I10:M32 CD4+, I11:M34 CD4+, I12:M35 CD4+

value: TdTKO

tag: cell type

value: CD4+ TdTKO T cells

tag: genotype

value: not applicable


title: HippoCells_DIV11_shctrl_DMSO_2

tag: knockdown

tag: dissection age


title: M22, M37, M38, M39 CD5hi + M20, M21 CD5lo

description: Barcodes: I7:M20 CD5lo, I8:M21 CD5lo, I9:M22 CD5hi, I10:M37 CD5lo, I11:M38 CD5lo, I12:M39 CD5lo


title: HippoCells_DIV11_shctrl_TSA_4


title: Patient sample 080A (re-analysis)

description: re-analysis of GSM5829639

tag: individual

value: Patient 080

value: Whole blood

tag: time

value: pre-operative

tag: Sex

value: Male

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: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: Patient sample 083A (re-analysis)

description: re-analysis of GSM5829641

value: Patient 083

tag: tissue

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: post-operative atrial fibrillation


title: HippoCells_DIV11_shFoxg1_TSA_2

tag: days in vitro(div)

tag: treatment

value: TSA

tag: knockdown

tag: dissection age

tag: strain


title: Patient sample 084A (re-analysis)

description: re-analysis of GSM5829642

tag: individual

value: Patient 084

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: monocyte composition


title: HippoCells_DIV11_shctrl_DMSO_1

tag: days in vitro(div)

value: DMSO

value: shControl

tag: tissue


title: input DNA_control_n2

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

tag: knockdown

value: Control


title: HippoCells_DIV11_shFoxg1_DMSO_1

tag: treatment

tag: dissection age

tag: strain


title: Patient sample 079A (re-analysis)

description: re-analysis of GSM5829638

tag: individual

value: Patient 079

tag: time

tag: Sex

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: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 078A (re-analysis)

description: re-analysis of GSM5829637

value: Patient 078

tag: tissue

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

tag: isolated aortic surgery

tag: monocyte composition


title: HippoCells_DIV11_shFoxg1_DMSO_2

tag: days in vitro(div)

tag: treatment

tag: knockdown

value: hippocampus

tag: dissection age

tag: strain


title: Patient sample 077A (re-analysis)

description: re-analysis of GSM5829636

tag: individual

value: Patient 077

tag: time

tag: Sex

tag: isolated myomectomy surgery

tag: isolated valve surgery

value: Yes

tag: combined surgery

tag: current smoker

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: natural killer cell composition

tag: neutrophil composition


title: 66-14

city: Stanford

first: Myung Chang

address: 265 Campus Drive, G2065

department: Pediatrics and Genetics

institute: Stanford University

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)

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.

tag: tissue

value: Lung

tag: genotype

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


title: 66-13

tag: treatment


title: input DNA_control_n1

tag: days in vitro(div)

tag: dissection age

tag: antibody

tag: knockdown


title: BRG1 KO 2

description: HUVEC with CRISPR-Cas9 mediated knockout of BRG1

tag: cell type

value: HUVEC

tag: knockout

value: BRG1 KO

value: BRG1 antibody (ab110641, Abcam)


title: Patient sample 076A (re-analysis)

description: re-analysis of GSM5829635

tag: individual

value: Patient 076

value: Whole blood

tag: time

value: pre-operative

tag: Sex

value: Male

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: post-operative atrial fibrillation