title: 200379120058_R05C02: genomic DNA from whole Blood


title: RNAseq_03519

status: Public on Dec 31 2020

type: SRA

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

country: USA

institute: Brigham and Women's Hospital

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

library_source: transcriptomic

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: genomic DNA from adult cancer survivor_EP7

type: genomic

city: Newcastle

first: Gordon

last: Strathdee

address: Framlington Place

country: United Kingdom

institute: Newcastle University

description: Normal PBL sample from adult cancer survivor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: tissue

value: peripheral blood

tag: disease state

value: Normal

tag: developmental stage

value: adult


title: genomic DNA from adult cancer survivor_EP9

value: Male


title: 200379120082_R05C01: genomic DNA from whole Blood

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

source_name: Blood - buffy coat

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol:
DNA from a Control extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

tag: Sex

value: M

value: Control

tag: status


title: 200379120058_R04C02: genomic DNA from whole Blood

value: F


title: 200379120058_R03C02: genomic DNA from whole Blood


title: 200379120058_R02C02: genomic DNA from whole Blood

source_name: Blood - EDTA tube

extract_protocol:
DNA from a Case extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: Schizophrenia

value: Case


title: 200379120058_R01C02: genomic DNA from whole Blood


title: RNAseq_22429

tag: batch

tag: current smoker


title: RNAseq_83198

tag: pack years

tag: age


title: 200379120058_R06C01: genomic DNA from whole Blood

value: Schizoaffective Disorder


title: RNAseq_73875

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_48141

tag: fev1 % predicted

tag: neutrophil percent


title: genomic DNA from patient post therapy_32B

description: Normal sample - solid tumour, i.e., sampled tissue is not cancerous although subject is a cancer patient with a solid tumour


title: RNAseq_00535

tag: lymphocyte percent

tag: eosinophil percent


title: genomic DNA from adult cancer survivor_EP10


title: 200379120058_R04C01: genomic DNA from whole Blood


title: RNAseq_63323

tag: monocyte percent

tag: basophil percent


title: 200379120058_R03C01: genomic DNA from whole Blood


title: 200379120058_R02C01: genomic DNA from whole Blood


title: 200379120058_R05C01: genomic DNA from whole Blood

description: Sample was excluded from the final analysis due to low quality


title: RNAseq_33958


title: RNAseq_07107


title: genomic DNA from patient post therapy_31B

tag: gender

tag: tissue


title: 200379120058_R01C01: genomic DNA from whole Blood


title: genomic DNA from adult cancer survivor_EP8

tag: disease state

tag: developmental stage


title: genomic DNA from patient undergoing therapy_29A

description: Remission - ALL

value: Remission


title: RNAseq_32624


title: 200379120013_R06C02: genomic DNA from whole Blood

tag: Sex

tag: status


title: genomic DNA from patient post therapy_30B


title: genomic DNA from patient undergoing therapy_31A


title: RNAseq_79372

tag: batch

tag: current smoker


title: RNAseq_65650

tag: pack years

tag: age


title: genomic DNA from patient undergoing therapy_30A


title: genomic DNA from patient undergoing therapy_27A

description: Remission - ALL

value: Bone marrow


title: 200379120013_R04C02: genomic DNA from whole Blood


title: RNAseq_15644

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_19719

tag: fev1 % predicted

tag: neutrophil percent


title: genomic DNA from patient undergoing therapy_32A


title: RNAseq_93397

tag: lymphocyte percent

tag: eosinophil percent


title: 200379120013_R03C02: genomic DNA from whole Blood


title: genomic DNA from adult cancer survivor_EP4


title: genomic DNA from patient post therapy_29B

description: Remission - ALL


title: RNAseq_31287

tag: monocyte percent

tag: basophil percent


title: RNAseq_52406


title: 200379120013_R05C02: genomic DNA from whole Blood


title: 200379120013_R01C02: genomic DNA from whole Blood


title: genomic DNA from patient post therapy_27B

description: Remission - ALL

tag: gender

tag: tissue


title: genomic DNA from patient post therapy_26B

tag: disease state


title: 200379120013_R06C01: genomic DNA from whole Blood

tag: Sex


title: RNAseq_25945


title: RNAseq_80194


title: genomic DNA from patient undergoing therapy_26A


title: 200379120013_R02C02: genomic DNA from whole Blood

tag: status


title: RNAseq_66672

tag: batch


title: genomic DNA from adult cancer survivor_EP2

tag: developmental stage


title: genomic DNA from patient undergoing therapy_28A


title: RNAseq_21989

tag: current smoker

tag: pack years


title: 200379120013_R02C01: genomic DNA from whole Blood

tag: age


title: RNAseq_08500

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: genomic DNA from patient post therapy_24B


title: genomic DNA from adult cancer survivor_EP3


title: genomic DNA from patient undergoing therapy_25A

description: Remission - AML


title: genomic DNA from patient post therapy_25B

description: Remission - AML


title: genomic DNA from patient post therapy_23B

description: Remission - ALL


title: 200379120013_R01C01: genomic DNA from whole Blood


title: 200379120129_R06C02: genomic DNA from whole Blood

extract_protocol:
DNA from a Case extracted using Phenol-Chloroform method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.


title: genomic DNA from patient undergoing therapy_24A


title: RNAseq_89618

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_15582

tag: lymphocyte percent

tag: eosinophil percent


title: genomic DNA from patient post therapy_22B

description: Remission - ALL


title: 200379120013_R05C01: genomic DNA from whole Blood

extract_protocol:
DNA from a case extracted using Phenol-Chloroform method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: case


title: 200379120129_R05C02: genomic DNA from whole Blood


title: RNAseq_56674

tag: monocyte percent

tag: basophil percent


title: genomic DNA from patient undergoing therapy_23A

description: Remission - ALL

tag: gender

tag: tissue


title: RNAseq_74742


title: 200379120129_R04C02: genomic DNA from whole Blood

tag: Sex


title: genomic DNA from patient post therapy_21B

description: Remission - ALL

tag: disease state


title: RNAseq_01626

tag: batch


title: RNAseq_34402


title: genomic DNA from patient post therapy_20B


title: 200379120129_R02C02: genomic DNA from whole Blood

tag: status


title: 200379120013_R04C01: genomic DNA from whole Blood


title: RNAseq_09475

tag: current smoker


title: 200379120129_R01C02: genomic DNA from whole Blood


title: 200379120129_R06C01: genomic DNA from whole Blood


title: RNAseq_62317

tag: pack years


title: 200379120129_R05C01: genomic DNA from whole Blood

tag: age


title: 200379120013_R03C01: genomic DNA from whole Blood


title: RNAseq_46215

tag: gender (1=male, 2=female)


title: 200379120129_R04C01: Meth Control

source_name: Meth control

extract_protocol:
Fully methylated control sample
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.


title: genomic DNA from adult cancer survivor_EP1

tag: developmental stage


title: 200379120129_R03C02: genomic DNA from whole Blood


title: RNAseq_98809

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: genomic DNA from patient undergoing therapy_20A


title: 200379120129_R03C01: genomic DNA from whole Blood


title: RNAseq_03890

tag: neutrophil percent

tag: lymphocyte percent


title: 200379120129_R02C01: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_19A

description: Remission - ALL


title: RNAseq_74926

tag: eosinophil percent

tag: monocyte percent


title: 200379120129_R01C01: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_21A

description: Remission - ALL

tag: gender


title: genomic DNA from patient undergoing therapy_22A

description: Remission - ALL

tag: tissue


title: 200049730149_R06C02: genomic DNA from whole Blood

tag: Sex


title: RNAseq_81873

tag: basophil percent


title: 200049730149_R05C02: genomic DNA from whole Blood


title: 200049730149_R04C02: genomic DNA from whole Blood


title: RNAseq_53674

tag: batch


title: genomic DNA from patient post therapy_18B

description: Remission - ALL

tag: disease state


title: genomic DNA from patient post therapy_19B

description: Remission - ALL


title: RNAseq_56459

tag: current smoker


title: RNAseq_31638

tag: pack years


title: 200049730149_R03C02: genomic DNA from whole Blood

tag: status

tag: age


title: RNAseq_67062

tag: gender (1=male, 2=female)


title: genomic DNA from patient post therapy_28B


title: RNAseq_76507

tag: race (1=white, 2=black)


title: 200049730149_R01C02: genomic DNA from whole Blood


title: 200049730149_R02C02: genomic DNA from whole Blood


title: RNAseq_01374

tag: fev1 % predicted


title: genomic DNA from patient post therapy_17B

description: Remission - ALL


title: 200049730149_R06C01: genomic DNA from whole Blood


title: 200049730149_R05C01: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_18A

description: Remission - ALL


title: RNAseq_21651

tag: neutrophil percent


title: RNAseq_98616

tag: lymphocyte percent


title: RNAseq_40409

tag: eosinophil percent


title: 200049730149_R04C01: genomic DNA from whole Blood


title: 200049730149_R03C01: genomic DNA from whole Blood


title: genomic DNA from patient post therapy_14B

description: Remission - ALL


title: genomic DNA from patient undergoing therapy_16A

description: Remission - Lymphoma


title: RNAseq_78751

tag: monocyte percent


title: genomic DNA from patient post therapy_15B

description: Remission - ALL

tag: gender


title: RNAseq_56610


title: genomic DNA from patient undergoing therapy_17A

description: Remission - ALL

tag: tissue


title: genomic DNA from patient undergoing therapy_15A

description: Remission - ALL


title: 200049730149_R01C01: genomic DNA from whole Blood

tag: Sex


title: genomic DNA from patient undergoing therapy_14A

description: Remission - ALL


title: RNAseq_83210

tag: basophil percent


title: RNAseq_69105

tag: batch


title: 200049730085_R06C02: genomic DNA from whole Blood


title: genomic DNA from patient post therapy_16B

description: Remission - Lymphoma

tag: disease state


title: RNAseq_93918

tag: current smoker


title: 200049730085_R05C02: genomic DNA from whole Blood


title: RNAseq_52155

tag: pack years


title: 200049730085_R04C02: genomic DNA from whole Blood

tag: status


title: RNAseq_10057

tag: age


title: genomic DNA from patient post therapy_12B

description: Remission - ALL


title: 200049730085_R03C02: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_11A

description: Remission - ALL


title: RNAseq_58245

tag: gender (1=male, 2=female)


title: 200049730085_R02C02: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_13A

description: Remission - ALL


title: 200049730149_R02C01: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_12A

description: Remission - ALL


title: genomic DNA from patient post therapy_13B

description: Remission - ALL


title: RNAseq_29292

tag: race (1=white, 2=black)


title: 200049730085_R06C01: genomic DNA from whole Blood


title: RNAseq_94690

tag: fev1 % predicted


title: 200049730085_R01C02: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_10A

description: Remission - ALL


title: 200049730085_R05C01: genomic DNA from whole Blood


title: RNAseq_34259

tag: neutrophil percent


title: RNAseq_71257

tag: lymphocyte percent


title: 200049730085_R04C01: genomic DNA from whole Blood


title: 200049730085_R03C01: genomic DNA from whole Blood


title: RNAseq_37366

tag: eosinophil percent


title: 200049730085_R02C01: genomic DNA from whole Blood


title: RNAseq_86283

tag: monocyte percent


title: 200049730087_R06C02: genomic DNA from whole Blood


title: RNAseq_08523


title: 200049730087_R04C02: genomic DNA from whole Blood


title: genomic DNA from patient post therapy_8B

description: Remission - AML

tag: gender


title: 200049730087_R05C02: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_8A

description: Remission - AML

tag: tissue


title: genomic DNA from patient post therapy_10B

description: Remission - ALL


title: genomic DNA from patient post therapy_11B

description: Remission - ALL


title: RNAseq_42302


title: RNAseq_89907


title: genomic DNA from patient post therapy_7B

description: Remission - ALL


title: genomic DNA from patient post therapy_6B

description: Remission - ALL


title: 200049730087_R06C01: genomic DNA from whole Blood

tag: Sex


title: 200049730087_R01C02: genomic DNA from whole Blood


title: RNAseq_03210

tag: basophil percent


title: RNAseq_65958

tag: batch


title: 200049730087_R02C02: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_7A

description: Remission - ALL

tag: disease state


title: genomic DNA from patient undergoing therapy_5A

description: Remission - ALL


title: genomic DNA from patient post therapy_5B

description: Remission - ALL


title: RNAseq_02087

tag: current smoker


title: RNAseq_92100

tag: pack years


title: 200049730087_R04C01: genomic DNA from whole Blood

tag: status


title: meCLIP_HEK293_rep2_INPUT

city: Mobile

first: Justin

last: Roberts

state: AL

address: 5851 USA Drive North, MSB 3370

department: Pharmacology

institute: University of South Alabama

data_processing:
The resulting reads are analyzed via a modified computational pipeline based on the original eCLIP strategy that has been converted into a Snakemake workflow.
Briefly, the reads are initially inspected for appropriate quality using FastQC (v. 0.11.7).
The in-line unique molecular identifier (UMI) located within the ssDNA adapter (rand3Tr3) at the beginning of read 2 is extracted using UMI-tools (v. 1.0.0) to prepare the reads for downstream de-duplication.
The remaining non-random ssDNA adapter and indexed RNA adapters are then removed using Cutadapt (v. 2.4), with any reads less than 18bp being discarded. The trimmed reads are then briefly analyzed visually once more with FastQC to ensure all adapters are successfully removed.
Two mapping steps are then performed using the splicing-aware RNA aligner STAR (v. 2.7.1a). First the reads are mapped to the species appropriate version of RepBase (v18.05) with any successfully mapped reads being removed from further analysis. The remaining reads are then mapped to the full species appropriate genome with only uniquely mapping reads being included in final alignment. Subsequent removal of PCR duplicates is performed with UMI-tools using the previously extracted UMIs.
The final alignment file is sorted and indexed using samtools (v. 1.9) and variations from the reference genome are identified using the 'mpileup' command of samtools. An internally developed Java package is then employed to identify C-to-T mutations occurring within the m6A consensus motif at a set frequency threshold of greater than or equal to 2.5% and less than or equal to 50% of the total reads at a given position (with a minimum of 3 C-to-T mutations at a single site). The resulting m6A sites are then automatically compared to those identified in the corresponding input sample and any sites occurring in both are removed from the final list of m6As.
Genome_build: hg19
Supplementary_files_format_and_content: XLS files consisting of a list of annoated m6As and corresponding BED files (categorized by confidence) were generate using custom Java package. Indexed BAM files consisting of reads (read2) that were successfully mapped to the genome are supplied for visualization of overall library quality and C-to-T conversion frequencies relative to identified m6A sites.

source_name: embryonic kidney cells

extract_protocol:
Cells were cultured in appropriate media and total RNA was isolated using the Trizol (15596018, Invitrogen). Poly(A) selection was performed using the Magnosphere® Ultrapure mRNA Purification Kit (9186, Takara). RNA was fragemented at 70C for ~3min using RNA Fragmentation Reagents (AM8740, Ambion). A small amount (~500ng) of fragmented RNA was saved for use as the input sample.
Library was prepared using eCLIP-seq protocol with minor modifications. Briefly, the fragmented poly(A) RNA was incubated with anti-m6A antibody (Abcam Ab151230) and then crosslinked twice at 150 mJ/cm2 (254nm wavelength) using a Stratalinker UV Crosslinker. The RNA:antibody sample was incubated with Protein A/G Magnetic Beads (88803, Pierce) overnight at 4C and then a RNA adapter is ligated on the 3' end of the sample. The RNA:antibody complex is then ran on an SDS-PAGE gel and transferred to a nitrocellulose membrane to remove any non-crosslinked RNA. Following treatment with Proteinase K to remove nearly all of the antibody except the crosslinked amino acid, the RNA is isolated, one adapter is ligated, and the RNA is converted into cDNA for full library amplification. Sequencing of the cDNA libraries was primarily performed using an Illumina NovaSEQ 6000 to generate 2x150bp paired-end runs consisting of 40 million raw reads per sample.

tag: cell line

tag: cell type

value: embryonic kidney cells

tag: genotype

value: overexpressing lncRNA HOTAIR

tag: rip antibody


title: 200049730087_R03C01: genomic DNA from whole Blood

tag: age


title: meCLIP_HEK293_rep3_INPUT


title: genomic DNA from patient post therapy_3B

description: Remission - ALL


title: 200049730087_R02C01: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_9A

description: Remission - ALL


title: RNAseq_43849

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: genomic DNA from patient undergoing therapy_6A

description: Remission - ALL

tag: gender

tag: tissue


title: RNAseq_79002

tag: batch

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_84816

tag: current smoker

tag: pack years


title: genomic DNA from patient undergoing therapy_4A

description: Remission - ALL

tag: disease state


title: RNAseq_63102


title: 200049730087_R01C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: genomic DNA from patient post therapy_4B

description: Remission - ALL


title: RNAseq_37231

tag: age


title: 200049730138_R05C02: genomic DNA from whole Blood


title: 200049730138_R06C02: genomic DNA from whole Blood


title: genomic DNA from patient post therapy_9B

description: Remission - ALL


title: RNAseq_28590

tag: gender (1=male, 2=female)


title: meCLIP_MDAMB231_rep2_INPUT

source_name: breast cancer cell

tag: cell line

tag: cell type

value: breast cancer cell

tag: genotype

tag: rip antibody


title: 200049730085_R01C01: genomic DNA from whole Blood


title: meCLIP_MDAMB231_rep3_INPUT


title: 200049730138_R03C02: genomic DNA from whole Blood


title: 200049730138_R02C02: genomic DNA from whole Blood


title: 200049730138_R01C02: genomic DNA from whole Blood


title: RNAseq_96788

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_18998

tag: batch

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_34310

tag: current smoker

tag: pack years

tag: basophil percent


title: genomic DNA from patient post therapy_2B

description: Remission - ALL

tag: gender

value: Female

tag: tissue

tag: disease state


title: RNAseq_28484

tag: age

tag: gender (1=male, 2=female)


title: meCLIP_MCF7_rep3_INPUT

tag: cell line

tag: cell type


title: RNAseq_24633

tag: race (1=white, 2=black)


title: 200049730138_R04C02: genomic DNA from whole Blood

tag: Sex

tag: status


title: RNAseq_53092

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: meCLIP_HEK293_rep1_INPUT

tag: genotype

tag: rip antibody


title: 200049730138_R06C01: genomic DNA from whole Blood


title: meCLIP_MDAMB231_rep1_INPUT


title: 200049730138_R05C01: genomic DNA from whole Blood


title: meCLIP_MCF7_rep2_INPUT


title: genomic DNA from patient undergoing therapy_2A

description: Remission - ALL

value: peripheral blood


title: RNAseq_33408

tag: batch

tag: current smoker

tag: pack years

tag: eosinophil percent

tag: monocyte percent


title: genomic DNA from patient post therapy_1B

description: Remission - ALL

tag: gender

tag: tissue

tag: disease state


title: RNAseq_93810

tag: age

tag: gender (1=male, 2=female)

tag: basophil percent


title: 200049730138_R04C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: RNAseq_99334

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: genomic DNA from patient undergoing therapy_1A

description: Remission - ALL


title: 200049730138_R02C01: genomic DNA from whole Blood


title: 200049730138_R03C01: genomic DNA from whole Blood


title: RNAseq_81360

tag: lymphocyte percent


title: 200049730087_R03C02: genomic DNA from whole Blood


title: 200049730138_R01C01: genomic DNA from whole Blood


title: 200049730097_R06C02: genomic DNA from whole Blood


title: 200049730097_R05C02: genomic DNA from whole Blood


title: genomic DNA from patient undergoing therapy_3A

description: Remission - ALL


title: RNAseq_46281

tag: batch


title: RNAseq_72949

tag: current smoker


title: RNAseq_36170

tag: pack years


title: RNAseq_06466

tag: eosinophil percent


title: 200049730097_R04C02: genomic DNA from whole Blood


title: 200049730097_R03C02: genomic DNA from whole Blood


title: 200049730097_R02C02: genomic DNA from whole Blood


title: R10 tumor post

city: Houston

first: Moran

last: Amit

state: TX

address: 1515 Holcombe Blvd

department: Head & Neck Surgery - Research

institute: The University of Texas MD Anderson Cancer Center

data_processing:
aligning against the genome
gene count
differential expression
Genome_build: hg38
Supplementary_files_format_and_content: The matrices were created after reads with Counts Per Million (CPM) values of 2 or less and reads that appeared in only one sample were filtered out. Normalization was performed by the Trimmed Mean of M-values (TMM) method.
Supplementary_files_format_and_content: GO enrichment analysis

source_name: Metastatic melanoma tumor

extract_protocol:
RNA sequencing analysis was based on FFPE material from the recipient patient biopsies. Prior to each biopsy block sectioning, the microtome was meticulously cleaned using a 70% ethanol solution followed by RNAase AWAY™ spray (Thermo Fischer, USA), and the water in the water plate were replaced. The FFPE materials were sectioned into sterile 1.5mL vials. A separate vial was used for each of the samples. The vials were sealed with parafilm and were kept in -80C until RNA extraction and sequencing
FFPE samples were shipped in -80C packages to Otogenetics Corporation (Georgia, USA). Extraction of RNA from FFPE was conducted using RNeasy FFPE kit (Qiagen, The Netherlands).
cDNA library was generated using Illumina truseq stranded cDNA library preparation kit (Illumina, USA, Cat# 20020594) using 500ng of total RNA.

treatment_protocol: fecal microbiota transplantation (FMT) and re-induction of anti-PD-1 immunotherapy in patients with anti-PD-1-refractory metastatic melanoma.

value: Metastatic melanoma tumor

tag: per vs post treatment

value: post

tag: recipient patient diagnosis

tag: recipient patient clinical response status

value: Non-responder

tag: recipient subject id

tag: donor group


title: R8 tumor pre

tag: tissue

value: pre


title: R9 tumor pre


title: R9 tumor post


title: R10 tumor pre


title: R8 tumor post


title: RNAseq_74677

tag: age

tag: gender (1=male, 2=female)

tag: monocyte percent

tag: basophil percent


title: R7 tumor post

value: Responder


title: RNAseq_86993

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_71012

tag: neutrophil percent

tag: lymphocyte percent


title: R7 tumor pre


title: RNAseq_54576

tag: batch

tag: current smoker


title: 200049730097_R06C01: genomic DNA from whole Blood

tag: Sex

value: M

value: Control

tag: status


title: 200049730097_R01C02: genomic DNA from whole Blood

extract_protocol:
DNA from a control extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: control


title: R6 tumor post

tag: per vs post treatment

tag: recipient patient diagnosis


title: RNAseq_33493

tag: pack years

tag: eosinophil percent


title: R6 tumor pre

tag: tissue

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: RNAseq_44979

tag: age

tag: gender (1=male, 2=female)

tag: monocyte percent

tag: basophil percent


title: 200049730097_R04C01: genomic DNA from whole Blood

value: Schizoaffective Disorder

value: Case


title: RNAseq_73329

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_06944

tag: batch

tag: current smoker


title: R4 tumor post

tag: per vs post treatment

tag: recipient patient diagnosis


title: R5 tumor pre


title: RNAseq_49664

tag: pack years

tag: eosinophil percent


title: 200049730097_R01C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: R5 tumor post

tag: tissue

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: R4 tumor pre


title: 200049730097_R02C01: genomic DNA from whole Blood

tag: age


title: RNAseq_43139

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: monocyte percent

tag: basophil percent


title: RNAseq_00980

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: 200049730046_R06C02: genomic DNA from whole Blood


title: RNAseq_18641

tag: current smoker

tag: pack years


title: 200049730097_R05C01: genomic DNA from whole Blood

tag: Sex

value: F


title: R3 tumor post

tag: per vs post treatment

tag: recipient patient diagnosis


title: RNAseq_41346

tag: eosinophil percent


title: 200049730046_R04C02: genomic DNA from whole Blood

tag: status


title: 200049730046_R03C02: genomic DNA from whole Blood

value: Schizophrenia


title: R1 tumor pre

tag: tissue

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: R1 tumor post


title: 200049730046_R02C02: genomic DNA from whole Blood

tag: age


title: RNAseq_34461

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: monocyte percent

tag: basophil percent


title: 200049730046_R01C02: genomic DNA from whole Blood


title: R10 gut post

source_name: Sigmoid colon

value: Sigmoid colon


title: 200049730097_R03C01: genomic DNA from whole Blood


title: R10 gut pre


title: RNAseq_01347

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: 200049730046_R05C02: genomic DNA from whole Blood

tag: Sex


title: R3 tumor pre

tag: per vs post treatment

tag: recipient patient diagnosis


title: RNAseq_85605

tag: current smoker

tag: pack years

tag: eosinophil percent


title: 200049730046_R06C01: genomic DNA from whole Blood

tag: status


title: RNAseq_76074


title: 200049730046_R03C01: genomic DNA from whole Blood


title: 200049730046_R05C01: genomic DNA from whole Blood

value: Schizophrenia (Galway CP)


title: R9 gut pre

tag: tissue

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: R8 gut post


title: RNAseq_92744

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: monocyte percent


title: R8 gut pre


title: R9 gut post


title: 200049730046_R04C01: genomic DNA from whole Blood


title: 200049730046_R02C01: genomic DNA from whole Blood


title: 200049730046_R01C01: genomic DNA from whole Blood


title: RNAseq_59512

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: basophil percent


title: 200049730089_R06C02: genomic DNA from whole Blood

tag: Sex


title: RNAseq_92636

tag: current smoker

tag: lymphocyte percent


title: R7 gut pre

tag: per vs post treatment

tag: recipient patient diagnosis


title: RNAseq_96464

tag: pack years

tag: eosinophil percent


title: RNAseq_67453


title: 200049730089_R05C02: genomic DNA from whole Blood

tag: status


title: R6 gut post

tag: tissue

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: RNAseq_59731

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: monocyte percent


title: RNAseq_76698

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: basophil percent


title: R6 gut pre

tag: per vs post treatment


title: RNAseq_57333

tag: current smoker

tag: lymphocyte percent


title: 200049730089_R04C02: genomic DNA from whole Blood

tag: Sex


title: 200049730087_R05C01: genomic DNA from whole Blood

value: Schizoaffective Disorder (Galway SZ)

tag: status


title: R5 gut post

tag: tissue

tag: recipient patient diagnosis


title: RNAseq_24798

tag: pack years

tag: eosinophil percent


title: 200049730089_R02C02: genomic DNA from whole Blood

tag: age


title: RNAseq_32043

tag: gender (1=male, 2=female)


title: 200049730089_R03C02: genomic DNA from whole Blood


title: 200049730089_R01C02: genomic DNA from whole Blood


title: RNAseq_31947

tag: race (1=white, 2=black)


title: R4 gut post

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: 200049730089_R06C01: genomic DNA from whole Blood


title: R7 gut post


title: RNAseq_62582

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: monocyte percent


title: R3 gut post

tag: per vs post treatment


title: R3 gut pre


title: RNAseq_68997

tag: current smoker

tag: lymphocyte percent

tag: basophil percent


title: R4 gut pre

tag: tissue

tag: recipient patient diagnosis


title: 200049730089_R04C01: genomic DNA from whole Blood

tag: Sex

tag: status


title: 200049730089_R05C01: genomic DNA from whole Blood

tag: age


title: RNAseq_28949

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: eosinophil percent


title: 200049730089_R03C01: genomic DNA from whole Blood


title: R1 gut post

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: RNAseq_47760

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: monocyte percent


title: 200049730089_R02C01: genomic DNA from whole Blood


title: MM_72 (RNA-seq)

city: Seoul

first: Sungyoung

last: Lee

address: 101 Daehak-ro

department: Center for Precision Medicine

country: South Korea

institute: Seoul National University Hospital

data_processing:
detected TCR sequences were aligned to the human reference V, D, J and C genes of TCRs using MiXCR version 2.1.9
Overlapping fragmented sequencing reads that were partially aligned were assembled into CDR3-containing contigs
clonotypes and then extracted after sequencing quality score filtering and error correction
TCR repertoires from bulk transcriptome sequencing data were also determined using MiXCR, which uses parameters specifically optimized for RNA-seq to detect sequences with small parts of the TCR region in detail
Genome_build: human reference V, D, J and C genes of TCRs
Supplementary_files_format_and_content: TCR repertoire analysis result files conducted with RNA-Seq data were named starting with "RNA-neg" and "MM-rep" for IR-Seq.

source_name: Bone Marrow (BM)

extract_protocol:
For the isolation of CD138- cells directly from whole BM samples, the mononuclear cell (MNC) layer was first depleted and separated MNCs were then released with MACS buffer followed by incubation with 20 µl of CD138 magnetically labeled microbeads.
RNA libraries were prepared for sequencing using standard Illumina protocols. TCR libraries with molecular barcoded (MBC) adaptors to amplify the T-cell receptor alpha/delta and beta/gamma chains were constructed using the Immunoverse™ kit (ArcherDX) after PCR amplification.

tag: disease state

value: multiple myeloma

tag: sample

value: male

value: BM

tag: cell sorting

value: 138 negative


title: RNAseq_74746

tag: current smoker

tag: lymphocyte percent

tag: basophil percent


title: 200049730089_R01C01: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: MM_71 (RNA-seq)

tag: tissue


title: RNAseq_17054

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: eosinophil percent


title: 200049730086_R06C02: genomic DNA from whole Blood


title: R5 gut pre

tag: per vs post treatment

tag: recipient patient diagnosis

tag: recipient patient clinical response status

tag: recipient subject id

tag: donor group


title: 200049730086_R05C02: genomic DNA from whole Blood


title: RNAseq_63543

tag: batch

tag: fev1 % predicted

tag: neutrophil percent

tag: monocyte percent


title: RNAseq_21593

tag: current smoker

tag: lymphocyte percent

tag: basophil percent


title: RNAseq_10115

tag: age


title: 200049730086_R04C02: genomic DNA from whole Blood

tag: Sex

tag: status


title: MM_68 (RNA-seq)

tag: disease state

tag: sample

value: female

tag: tissue

tag: cell sorting


title: MM_7 (RNA-seq)


title: RNAseq_43919

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: eosinophil percent


title: RNAseq_21166

tag: batch

tag: fev1 % predicted


title: MM_70 (RNA-seq)


title: 200049730086_R03C02: genomic DNA from whole Blood


title: R1 gut pre

tag: per vs post treatment

value: pre

tag: recipient patient diagnosis

tag: recipient patient clinical response status

value: Non-responder

tag: recipient subject id

tag: donor group


title: MM_61 (RNA-seq)

tag: age

tag: Sex


title: MM_67 (RNA-seq)

tag: disease state


title: MM_66 (RNA-seq)

tag: sample


title: MM_6 (RNA-seq)

tag: tissue


title: RNAseq_42963

tag: current smoker

tag: neutrophil percent

tag: lymphocyte percent

tag: monocyte percent

tag: basophil percent


title: 200049730086_R02C02: genomic DNA from whole Blood

value: M

tag: status


title: 200049730086_R06C01: genomic DNA from whole Blood


title: RNAseq_74174

tag: batch

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: 200049730086_R05C01: genomic DNA from whole Blood

value: Control

tag: age


title: RNAseq_82999


title: 200049730086_R04C01: genomic DNA from whole Blood

tag: Sex


title: MM_5 (RNA-seq)

tag: disease state

tag: cell sorting


title: 200049730086_R03C01: genomic DNA from whole Blood


title: RNAseq_59578


title: MM_49 (RNA-seq)

tag: sample

tag: tissue


title: RNAseq_57368

tag: current smoker

tag: neutrophil percent


title: 200049730086_R02C01: genomic DNA from whole Blood


title: 200049730086_R01C01: genomic DNA from whole Blood


title: 200049730086_R01C02: Meth Control


title: RNAseq_50329

tag: lymphocyte percent

tag: monocyte percent


title: MM_48 (RNA-seq)


title: MM_47 (RNA-seq)


title: RNAseq_70515

tag: basophil percent


title: RNAseq_20988

tag: batch


title: 200049730101_R05C02: genomic DNA from whole Blood

tag: status


title: MM_46 (RNA-seq)


title: 200049730101_R06C02: genomic DNA from whole Blood


title: MM_44 (RNA-seq)


title: RNAseq_68509

tag: pack years

tag: gender (1=male, 2=female)


title: RNAseq_10551

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: MM_50 (RNA-seq)

tag: age


title: MM_41 (RNA-seq)

tag: Sex


title: MM_42 (RNA-seq)

tag: disease state


title: MM_40 (RNA-seq)

tag: cell sorting


title: RNAseq_86461

tag: eosinophil percent


title: RNAseq_16913


title: 200049730101_R03C02: genomic DNA from whole Blood


title: 200049730101_R04C02: genomic DNA from whole Blood


title: 200049730101_R01C02: genomic DNA from whole Blood


title: MM_4 (RNA-seq)

tag: sample

tag: tissue


title: 200049730101_R06C01: genomic DNA from whole Blood


title: RNAseq_15433

tag: current smoker

tag: neutrophil percent


title: MM_39 (RNA-seq)


title: RNAseq_35677

tag: lymphocyte percent

tag: monocyte percent


title: 200049730101_R05C01: genomic DNA from whole Blood

extract_protocol:
DNA from a case extracted using Gentra Autopure method
Genomic DNA was extracted from frozen  blood samples using either Gentra Autopure or Phenol-Chloroform method.

value: case


title: RNAseq_57527

tag: batch

tag: basophil percent


title: MM_38 (RNA-seq)


title: RNAseq_70160

tag: pack years


title: 200049730101_R02C02: genomic DNA from whole Blood

tag: status


title: MM_36 (RNA-seq)


title: RNAseq_17560

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: RNAseq_47782

tag: age

tag: fev1 % predicted


title: MM_34 (RNA-seq)

tag: disease state

tag: Sex


title: MM_31 (RNA-seq)

tag: cell sorting


title: RNAseq_73410

tag: eosinophil percent


title: MM_35 (RNA-seq)

tag: sample

tag: tissue


title: RNAseq_02645

tag: current smoker

tag: neutrophil percent


title: 200049730098_R05C02: genomic DNA from whole Blood


title: 200049730101_R04C01: genomic DNA from whole Blood


title: 200049730098_R06C02: genomic DNA from whole Blood


title: 200049730098_R03C02: genomic DNA from whole Blood

value: Schizoaffective Disorder


title: 200049730101_R03C01: genomic DNA from whole Blood


title: 200049730098_R04C02: genomic DNA from whole Blood

value: Case


title: 200049730101_R02C01: genomic DNA from whole Blood


title: RNAseq_37054

tag: lymphocyte percent

tag: monocyte percent


title: RNAseq_95538

tag: batch

tag: basophil percent


title: RNAseq_33591

tag: pack years


title: MM_29 (RNA-seq)


title: 200049730098_R02C02: genomic DNA from whole Blood

value: F

tag: status


title: MM_10 (RNA-seq)


title: RNAseq_66736

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: MM_37 (RNA-seq)

tag: age


title: MM_1 (RNA-seq)

tag: disease state


title: RNAseq_09916

tag: fev1 % predicted


title: 200049730098_R01C02: genomic DNA from whole Blood

tag: Sex

value: Schizophrenia


title: 200049730101_R01C01: genomic DNA from whole Blood


title: RNAseq_64127

tag: eosinophil percent


title: RNAseq_96283


title: 200049730098_R06C01: genomic DNA from whole Blood


title: 200049730098_R05C01: genomic DNA from whole Blood


title: RNAseq_32438


title: 200049730098_R04C01: genomic DNA from whole Blood


title: MM_19 (RNA-seq)

tag: sample

tag: cell sorting


title: CD34_HSPC_AE-FKBP(+)dTAG_anti-HA-2

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

library_source: genomic

data_processing:
Library strategy: CUT&RUN
For Cut&Run: adaptor trimming with Trimmomatic-0.32
alignment to hg19+scer genome with bowtie2
high quality reads (F4q10) were filtered using samtools
peaks called with MACS2 (narrowPeak, q=0.001)
for HA cut&run +/-dTAG, differential peaks were identified by Diffbind/DESeq2
bigwig files were generated using deepTools
For ChIP-seq: adaptor trimming with Trimmomatic-0.32
alignment to hg19+dm3 genome with bowtie2
high quality reads (F4q10) were filtered using samtools
normalized bigwig files were generated with deepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, MACS2 peak files, differential peak files generated by Diffbind+DESeq2

growth_protocol: Kasumi-1 cells were grown in RPMI +15% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. CD34+ cells were cultured in IMDM + 20% FBS, 55 μM BME, 50 U/ml penicillin, 50 μg/ml streptomycin, 2mM L-glutamine, and 10 ng/mL SCF, Flt3-L, TPO, IL-3, and IL-6

extract_protocol:
For Cut&Run, released DNA fragments were extracted using phenol:chloroform:IAA and ethanol precipitation. For ChIP-seq, after cross-link reversal, immunoprecipitated DNA was purified by ampure beads
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: for H3K27ac, cells were treated with dTAG for 24 hours. For HA, cells were treated with dTAG for 18 hours.

tag: antibody

value: HA

tag: antibody manufacturer;cat#

value: Cell Signaling Technology; 3724


title: CD34_HSPC_AE-FKBP(-)dTAG_anti-HA-1


title: CD34_HSPC_AE-FKBP(-)dTAG_anti-HA-2


title: CD34_HSPC_AE-FKBP(+)dTAG_anti-HA-1


title: 200049730098_R03C01: genomic DNA from whole Blood


title: 200049730098_R01C01: genomic DNA from whole Blood


title: 200049730098_R02C01: genomic DNA from whole Blood


title: RNAseq_12870

tag: current smoker

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_26908

tag: batch

tag: monocyte percent

tag: basophil percent


title: 200049730104_R06C02: genomic DNA from whole Blood

tag: status


title: Kasumi-1_(-)dTAG_anti-LSD1-1

value: Abcam; ab17721


title: Kasumi-1_(-)dTAG_anti-LSD1-2


title: Kasumi-1_(+)dTAG_anti-LSD1-2


title: RNAseq_37473

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: Kasumi-1_(+)dTAG-6hr_anti-H3K27ac

data_processing:
For Cut&Run: adaptor trimming with Trimmomatic-0.32
alignment to hg19+scer genome with bowtie2
high quality reads (F4q10) were filtered using samtools
peaks called with MACS2 (narrowPeak, q=0.001)
for HA cut&run +/-dTAG, differential peaks were identified by Diffbind/DESeq2
bigwig files were generated using deepTools
For ChIP-seq: adaptor trimming with Trimmomatic-0.32
alignment to hg19+dm3 genome with bowtie2
high quality reads (F4q10) were filtered using samtools
normalized bigwig files were generated with deepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, MACS2 peak files, differential peak files generated by Diffbind+DESeq2

value: Abcam; ab4729


title: 200049730104_R05C02: genomic DNA from whole Blood

tag: age


title: RNAseq_22603

tag: fev1 % predicted


title: Kasumi-1_(+)dTAG-2hr_anti-H3K27ac


title: 200049730104_R03C02: genomic DNA from whole Blood

tag: Sex


title: 200049730104_R04C02: genomic DNA from whole Blood


title: RNAseq_96340

tag: eosinophil percent


title: Kasumi-1_parental_anti-H3K27ac


title: RNAseq_45829


title: 200049730104_R01C02: genomic DNA from whole Blood


title: CD34_HSPC_AE-FKBP(+)dTAG_anti-H3K27me3-2

value: Cell Signaling Technology; 9733


title: RNAseq_10229


title: 200049730104_R06C01: genomic DNA from whole Blood


title: RNAseq_65305


title: RNAseq_13126


title: CD34_HSPC_AE-FKBP(+)dTAG_anti-H3K27me3-1


title: CD34_HSPC_AE-FKBP(-)dTAG_anti-H3K27me3-2


title: Kasumi-1_(+)dTAG_anti-LSD1-1


title: 200049730104_R05C01: genomic DNA from whole Blood


title: RNAseq_49766


title: 200049730104_R04C01: genomic DNA from whole Blood


title: 200049730104_R03C01: genomic DNA from whole Blood


title: CD34_HSPC_AE-FKBP(-)dTAG_anti-H3K27me3-1


title: 200049730104_R02C01: genomic DNA from whole Blood


title: Kasumi-1_(+)dTAG_anti-H3K27me3-1


title: RNAseq_17157


title: Kasumi-1_(+)dTAG_anti-H3K27me3-2


title: RNAseq_42242


title: 200049730104_R01C01: genomic DNA from whole Blood


title: RNAseq_42790


title: RNAseq_33924


title: RNAseq_20465


title: 200049730104_R02C02: genomic DNA from whole Blood


title: Kasumi-1_(-)dTAG_anti-H3K27me3-2


title: 200049730116_R06C02: genomic DNA from whole Blood


title: RNAseq_04473


title: Kasumi-1_(-)dTAG_anti-H3K27me3-1


title: 200049730116_R05C02: genomic DNA from whole Blood


title: Kasumi-1_(+)dTAG_anti-H3K4me3-2

value: Abcam; ab12209


title: RNAseq_63275


title: Kasumi-1_(+)dTAG_anti-H3K4me3-1


title: 200049730116_R04C02: genomic DNA from whole Blood


title: 200049730116_R03C02: genomic DNA from whole Blood


title: RNAseq_31965


title: Kasumi-1_(-)dTAG_anti-H3K4me3-2


title: 200049730116_R02C02: genomic DNA from whole Blood


title: RNAseq_71063


title: RNAseq_90623


title: Kasumi-1(+)6hr_dTAG_anti-PU.1-2

value: Santa Cruz; sc-390405


title: 200049730116_R01C02: genomic DNA from whole Blood


title: Kasumi-1_(-)dTAG_anti-H3K4me3-1


title: RNAseq_58253


title: RNAseq_18587


title: Kasumi-1(+)6hr_dTAG_anti-PU.1-1


title: 200049730116_R06C01: genomic DNA from whole Blood


title: Kasumi-1_(-)dTAG_anti-PU.1-2


title: RNAseq_09015


title: RNAseq_20601


title: 200049730116_R05C01: genomic DNA from whole Blood


title: 200049730116_R04C01: genomic DNA from whole Blood


title: 200049730116_R03C01: genomic DNA from whole Blood


title: RNAseq_70615


title: Kasumi-1(+)6hr_dTAG_anti-RUNX1-2

value: Santa Cruz; sc-365644


title: 200049730116_R02C01: genomic DNA from whole Blood


title: RNAseq_29123


title: RNAseq_40380


title: Kasumi-1(-)dTAG_anti-RUNX1-2


title: Kasumi-1(+)6hr_dTAG_anti-RUNX1-1


title: Kasumi-1_(-)dTAG_anti-RUNX1-1


title: RNAseq_56987


title: 200049730102_R05C02: genomic DNA from whole Blood


title: 200049730102_R06C02: genomic DNA from whole Blood


title: RNAseq_34105


title: RNAseq_10864


title: 200049730102_R02C02: genomic DNA from whole Blood


title: Kasumi-1_(-)dTAG_anti-PU.1-1


title: RNAseq_43699


title: JA1_monolayer_Un_S73_L004

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. A custom python script was used to organize the data and log reduced using log2(TPM) if TPM > 1 and TPM - 1 if TPM <= 1.
Genome_build: Genome assembly: GRCh38.p12, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text files include log2(TPM) if TPM > 1 else TPM - 1 values for each Sample.

source_name: Lung

growth_protocol: Stem cells were isolated from human lung tissue and cultured as 3D organoids. The organoids were broken into single cells and seeded as a monolayer in a 384-well plate.

extract_protocol:
All monolayers were lysed using TRI-Reagent and RNA was isolated using Zymo Research: Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: The lung cells were infected by SARS-CoV2 for 48h and 72h timepoints and uninfected wells were kept as a control.

tag: condition

value: Monolayer

tag: infection

value: Uninfected


title: 200049730102_R01C02: genomic DNA from whole Blood

value: M


title: 200049730102_R06C01: genomic DNA from whole Blood

value: Control


title: JA1_monolayer_72h_S75_L004


title: RNAseq_19657


title: JA1_ALI_72h_2_S81_L004

value: Air Liquid Interface


title: 200049730102_R04C01: genomic DNA from whole Blood


title: RNAseq_50585


title: 200049730116_R01C01: genomic DNA from whole Blood


title: JA1_ALI_48h_2_S79_L004


title: 200049730102_R03C01: genomic DNA from whole Blood


title: JA1_ALI_72h_1_S80_L004


title: JA1_ALI_48h_1_S78_L004


title: 200049730102_R02C01: genomic DNA from whole Blood


title: RNAseq_27080


title: RNAseq_23642


title: RNAseq_25338


title: RNAseq_90498


title: JA1_ALI_UN_2_S77_L004


title: 200049730102_R04C02: genomic DNA from whole Blood


title: RNAseq_15280


title: RNAseq_17758


title: 200049730102_R01C01: genomic DNA from whole Blood


title: JA1_ALI_UN_1_S76_L004


title: 200049730102_R03C02: genomic DNA from whole Blood


title: RNAseq_91714


title: JA1_2E4_48h_2_S72_L004


title: RNAseq_71459


title: 200049730105_R05C02: genomic DNA from whole Blood


title: RNAseq_55358


title: 200049730105_R04C02: genomic DNA from whole Blood


title: JA1_2E4_48h_1_S71_L004


title: JA1_2E4_UN_2_S70_L004


title: 200049730105_R03C02: genomic DNA from whole Blood


title: JA1_2E4_UN_1_S69_L004


title: 200049730105_R06C02: genomic DNA from whole Blood


title: RNAseq_13976


title: 200049730105_R02C02: genomic DNA from whole Blood


title: JA1_1E4_48h_2_S68_L004


title: RNAseq_72220


title: RNAseq_88622


title: RNAseq_32274


title: JA1_1E4_48h_1_S67_L004


title: RNAseq_56685


title: 200049730105_R05C01: genomic DNA from whole Blood


title: JA1_1E4_UN_2_S66_L004


title: JA1_1E4_UN_1_S65_L004


title: RNAseq_71559


title: 200049730105_R03C01: genomic DNA from whole Blood


title: 200049730105_R02C01: genomic DNA from whole Blood

value: Schizoaffective Disorder


title: RNAseq_79490


title: RNAseq_31553


title: RNAseq_57174


title: RNAseq_23462


title: 200049730117_R06C02: genomic DNA from whole Blood


title: RNAseq_34666


title: 200049730105_R01C02: genomic DNA from whole Blood


title: 200049730105_R04C01: genomic DNA from whole Blood


title: 200049730117_R03C02: genomic DNA from whole Blood

value: Case


title: 200049730117_R04C02: genomic DNA from whole Blood


title: 200049730105_R06C01: genomic DNA from whole Blood

value: F


title: 200049730117_R02C02: genomic DNA from whole Blood


title: 200049730117_R01C02: genomic DNA from whole Blood

value: Schizophrenia


title: RNAseq_03266


title: CD34_AML1-ETO-FKBP-dTAG_4hr-2 [RNA-seq]

description:
4hr_500 nM dTAG-47
processed data file: CD34_DMSO_v_dTAG-4hr_gene_exp.diff

data_processing:
Adaptors were trimmed using trimmomatic (SE for Kasumi-1 cells, PE for CD34+ cells).
Trimmed reads were aligned to the human genome (hg19) with TopHat v2.0.11.
Differential gene expression was determined using Cuffdiff v.2.1.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_gene_exp.diff: Cuffdiff differential gene expression output; tab delimited text file.

molecule: polyA RNA

source_name: CD34+ human cord blood

growth_protocol: Kasumi-1 cells were grown in RPMI +15% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. CD34+ cells were cultured in IMDM + 20% FBS, 55 μM BME, 50 U/ml penicillin, 50 μg/ml streptomycin, 2mM L-glutamine, and 10 ng/mL SCF, Flt3-L, TPO, IL-3, and IL-6.

extract_protocol:
Total RNA was extracted by Trizol according to the manufacturer's protocol and precipitated with isopropanol.
Libraries were constructed on polyA selected transcript using standard Illumina protocol.

treatment_protocol: Cells were treated with 500 nM dTAG-47 for the indicated timepoints.

tag: cell type

value: CD34+ cord blood cells

tag: genotype/variation

tag: treatment

value: 500 nM dTAG-47

tag: time point


title: RNAseq_53074

tag: batch

tag: current smoker

tag: neutrophil percent

tag: lymphocyte percent


title: 200049730117_R06C01: genomic DNA from whole Blood

tag: status


title: RNAseq_26726

tag: pack years

tag: gender (1=male, 2=female)

tag: monocyte percent

tag: basophil percent


title: CD34_AML1-ETO-FKBP-dTAG_4hr-1 [RNA-seq]


title: 200049730117_R05C01: genomic DNA from whole Blood

tag: Sex

tag: age


title: RNAseq_90160

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: CD34_AML1-ETO-FKBP-DMSO_4hr-2 [RNA-seq]

description:
4hr_DMSO
processed data file: CD34_DMSO_v_dTAG-4hr_gene_exp.diff

tag: cell type

tag: genotype/variation

value: DMSO


title: RNAseq_29158


title: 200049730105_R01C01: genomic DNA from whole Blood


title: RNAseq_83881


title: 200049730117_R05C02: genomic DNA from whole Blood


title: 200049730117_R03C01: genomic DNA from whole Blood


title: 200049730117_R02C01: genomic DNA from whole Blood


title: RNAseq_06215


title: RNAseq_33526


title: 200049730117_R01C01: genomic DNA from whole Blood


title: RNAseq_83230


title: RNAseq_76538


title: 200049730099_R05C02: genomic DNA from whole Blood


title: RNAseq_78938


title: 200049730099_R06C02: genomic DNA from whole Blood


title: 200049730099_R04C02: Meth Control


title: RNAseq_14816


title: RNAseq_76718


title: 200049730099_R02C02: genomic DNA from whole Blood


title: 200049730099_R03C02: genomic DNA from whole Blood


title: RNAseq_07214


title: 200049730117_R04C01: genomic DNA from whole Blood


title: 200049730099_R01C02: genomic DNA from whole Blood


title: RNAseq_74240


title: 200049730099_R05C01: genomic DNA from whole Blood


title: 200049730099_R06C01: genomic DNA from whole Blood


title: RNAseq_75215


title: CD34_AML1-ETO-FKBP-DMSO_4hr-1 [RNA-seq]

tag: treatment

tag: time point


title: 200049730099_R04C01: genomic DNA from whole Blood


title: RNAseq_74936

tag: batch

tag: current smoker


title: RNAseq_11795

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_68048

tag: pack years


title: 200049730099_R03C01: genomic DNA from whole Blood

tag: status


title: 200049730099_R01C01: genomic DNA from whole Blood


title: RNAseq_72569

tag: gender (1=male, 2=female)

tag: monocyte percent


title: 200090280030_R05C02: genomic DNA from whole Blood

tag: Sex


title: RNAseq_00227

tag: age

tag: basophil percent


title: 200090280030_R04C02: genomic DNA from whole Blood


title: 200090280030_R03C02: genomic DNA from whole Blood


title: RNAseq_52675

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_65873

tag: eosinophil percent


title: RNAseq_46307


title: 200090280030_R02C02: genomic DNA from whole Blood


title: 200090280030_R06C01: genomic DNA from whole Blood


title: 200090280030_R05C01: genomic DNA from whole Blood


title: RNAseq_28876


title: RNAseq_93357


title: RNAseq_37743


title: 200090280030_R01C02: genomic DNA from whole Blood


title: RNAseq_39474


title: RNAseq_74776


title: RNAseq_57411


title: 200049730099_R02C01: genomic DNA from whole Blood


title: 200090280030_R04C01: genomic DNA from whole Blood


title: 200090280030_R03C01: genomic DNA from whole Blood


title: 200049730102_R05C01: genomic DNA from whole Blood


title: 200090280030_R02C01: genomic DNA from whole Blood


title: 200090280030_R06C02: genomic DNA from whole Blood


title: 200090280030_R01C01: genomic DNA from whole Blood


title: RNAseq_35364


title: RNAseq_89426


title: RNAseq_78266


title: RNAseq_36996


title: RNAseq_20086


title: 200090280119_R06C02: genomic DNA from whole Blood


title: 200090280119_R05C02: genomic DNA from whole Blood


title: RNAseq_68677


title: 200090280119_R04C02: genomic DNA from whole Blood


title: 200090280119_R03C02: genomic DNA from whole Blood

value: case


title: RNAseq_43742


title: RNAseq_48044


title: 200090280119_R02C02: genomic DNA from whole Blood


title: RNAseq_37278


title: 200090280119_R06C01: genomic DNA from whole Blood


title: RNAseq_31313


title: 200090280119_R05C01: genomic DNA from whole Blood


title: RNAseq_17675


title: RNAseq_10614


title: RNAseq_20129


title: 200090280119_R02C01: genomic DNA from whole Blood


title: RNAseq_09554


title: JA1_monolayer_48h_S74_L004

tag: condition

tag: infection


title: RNAseq_39667


title: 200090280119_R03C01: genomic DNA from whole Blood


title: RNAseq_20272


title: 200090280119_R01C01: genomic DNA from whole Blood


title: RNAseq_26783


title: 200090280066_R05C02: genomic DNA from whole Blood


title: 200090280066_R04C02: genomic DNA from whole Blood


title: RNAseq_96840


title: 200090280119_R01C02: genomic DNA from whole Blood


title: RNAseq_91633


title: 200090280066_R06C02: genomic DNA from whole Blood


title: RNAseq_88493


title: 200090280119_R04C01: genomic DNA from whole Blood


title: 200090280066_R02C02: genomic DNA from whole Blood


title: RNAseq_70616


title: 200090280066_R01C02: genomic DNA from whole Blood


title: 200090280066_R06C01: genomic DNA from whole Blood


title: LMyc-overexpressed with MYC gRNA 3 NCI-H82 cells_2 [ATAC-seq]

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ATAC-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option and filtered off an ATAC blacklist (Buenrostro et al., 2013) for mitochondrial DNA and homologous sequences.
Both fragment ends were shifted +4 nucleotides for positive strand and -5 for negative strand.
Peak were called with MACS2 with parameters --nomodel --extsize 100 --shift 50 --nolambda --keep-dup all
Peaks were filtered by MYC motif using findMotifsGenome function in Homer using four motif matrices MA0058.2 (MAX), MA0059.1 (MAX::MYC), MA0104.4 (MYCN), and MA0147.3 (MYC
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bed

source_name: small cell lung cancer

growth_protocol: Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Five thousand cells were harvested and pre-treated with DNase I. Nuclei were isolated and resuspended in transposase reaction mixture carried out at 37C for 30 minutes followed by DNA purification with DNA Clean and Concentrator-25 (Zymo Research) according to manufacturer’s recommendation.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000 or Illumina NextSeq500 with paired-end 75bp reads.

tag: cell line

tag: cell type

value: small cell lung cancer cell line

tag: overexpression vector

tag: grna vector

tag: cas9 vector


title: 200090280066_R05C01: genomic DNA from whole Blood


title: LMyc-overexpressed with MYC gRNA 1 NCI-H82 cells_2 [ATAC-seq]


title: 200090280066_R04C01: genomic DNA from whole Blood


title: 200090280066_R02C01: genomic DNA from whole Blood


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_3 [ATAC-seq]


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_2 [ATAC-seq]


title: 200090280066_R01C01: genomic DNA from whole Blood


title: LacZ-overexpressed NCI-H82 cells_1 [ATAC-seq]


title: 200090280066_R03C01: genomic DNA from whole Blood


title: RNAseq_34597

tag: batch

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent


title: 200090280126_R04C02: genomic DNA from whole Blood

tag: Sex

tag: status

tag: age


title: 200090280066_R03C02: genomic DNA from whole Blood


title: 200090280126_R05C02: genomic DNA from whole Blood


title: 200090280126_R06C02: genomic DNA from whole Blood


title: 200090280126_R03C02: genomic DNA from whole Blood


title: OMM1.3 TRAM 24hr R1

first: Tyler

last: Hitchman

address: 417 E 68th Street

department: HOPP

institute: MSKCC

data_processing:
The sequenced reads from fastq files were mapped to mm9 (melan-a) and hg19 using STAR version 2.330
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks suite v2.2.1 (Trapnell Nature biotechnology). We ran cuffquant on each BAM file and then Cuffnorm using upper quartile normalization. Genes were mapped to Ensembl  mm9 or Hg19 genome
Please note the RPKM of the same cell type, including duplicates, were combined into a single file.
Genome_build: mm9/hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: OMM1.3 Human Uveal Melanoma Cells

growth_protocol: Cells were grown in 10% FBS

extract_protocol:
RNA was purified using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq per manufacturer's protocol

treatment_protocol: Cells were treated with the indicated drug(s) for indicated times

tag: treatment

value: 30nM Trametinib


title: OMM1.3 Combo 24hr R1

value: 100nM YM-254890 and 30nM Trametinib


title: OMM1.3 Combo 24hr R2


title: OMM1.3 TRAM 24hr R2


title: OMM1.3 YM 24hr R2


title: OMM1.3 YM 24hr R1


title: 200090280126_R01C02: genomic DNA from whole Blood


title: 200090280126_R02C02: genomic DNA from whole Blood


title: 200090280126_R05C01: genomic DNA from whole Blood


title: 200090280126_R04C01: genomic DNA from whole Blood


title: LMyc-overexpressed with MYC gRNA 2 NCI-H82 cells_2 [ATAC-seq]


title: Mel202 Combo 24hr R2

source_name: Mel202 Human Uveal Melanoma Cells

value: 30nM YM-254890 and 10nM Trametinib


title: 200090280126_R03C01: genomic DNA from whole Blood


title: OMM1.3 VEH 24hr R1


title: Mel202 TRAM 24hr R2

value: 10nM Trametinib


title: 200090280126_R02C01: genomic DNA from whole Blood


title: Mel202 TRAM 24hr R1


title: Mel202 YM 24hr R2


title: 200090280129_R06C02: genomic DNA from whole Blood


title: Mel202 YM 24hr R1


title: 200090280126_R01C01: genomic DNA from whole Blood


title: 200090280129_R05C02: genomic DNA from whole Blood


title: 200090280129_R04C02: genomic DNA from whole Blood


title: Mel202 VEH 24hr R1


title: Mel202 VEH 24hr R2


title: 200090280129_R02C02: genomic DNA from whole Blood


title: 200090280129_R05C01: genomic DNA from whole Blood


title: 200090280129_R01C02: genomic DNA from whole Blood


title: 200090280129_R06C01: genomic DNA from whole Blood


title: 200090280129_R03C01: genomic DNA from whole Blood


title: OMM1.3 VEH 24hr R2


title: 200090280129_R04C01: genomic DNA from whole Blood


title: 200090280129_R01C01: genomic DNA from whole Blood


title: 200090280129_R03C02: genomic DNA from whole Blood


title: 200090280129_R02C01: genomic DNA from whole Blood


title: 200090280126_R06C01: genomic DNA from whole Blood


title: 200090280128_R06C02: genomic DNA from whole Blood


title: Mel202 Combo 24hr R1


title: 200090280128_R05C02: genomic DNA from whole Blood


title: SU_9h_B

city: Zurich

first: Constance

last: Ciaudo

state: Zurich

address: Otto-Stern-Weg 7, HPL G.31

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description:
reverse-stranded protocol
20151223.B-SU_9h_B

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.5.0c allowing up to 2 mismatches
FeatureCounts V1.4.5-p1 was used to summarize reads for each gene, using -s 2 (reversely stranded) and ignoring multiple-hit reads
Genome_build: hg38.83
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts

growth_protocol: cells were grown to ~80% confluency on Matrigrel in mTeSR medium in Falcon 6well plates, medium was replenished 2h before pathway inhibition

extract_protocol:
Total RNA from untreated (0 and 9 hours) and treated cells (3,6,9 hours) was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 10µM SB431542 for TGF-ß inhibtion and 10µM SU5402 for FGF inhibition or an equal amount of DMSO as control, treatment lasted for 3,6 and 9 hours.

value: SU5402 (FGF pathway) 9h

value: Embyronic stem cells

tag: gender

value: male

tag: passages

value: Passage 25

tag: genotype

value: wild type cells


title: SU_6h_B

description:
reverse-stranded protocol
20151223.B-SU_6h_B

value: SU5402 (FGF pathway) 6h

tag: cell line


title: 200090280128_R02C02: genomic DNA from whole Blood

value: M

value: Schizoaffective Disorder

value: Case


title: SU_9h_A

description:
reverse-stranded protocol
20151223.B-SU_9h_A

tag: cell type


title: 200090280128_R03C02: genomic DNA from whole Blood

value: Control


title: SU_9h_C

description:
reverse-stranded protocol
20151223.B-SU_9h_C


title: SU_6h_A

description:
reverse-stranded protocol
20151223.B-SU_6h_A


title: SU_3h_C

description:
reverse-stranded protocol
20151223.B-SU_3h_C

value: SU5402 (FGF pathway) 3h


title: 200090280128_R01C02: genomic DNA from whole Blood

value: F

value: Schizophrenia


title: 200090280128_R05C01: genomic DNA from whole Blood


title: 200090280128_R04C01: genomic DNA from whole Blood


title: 200090280128_R03C01: genomic DNA from whole Blood


title: SU_3h_A

description:
reverse-stranded protocol
20151223.B-SU_3h_A


title: SB_9h_C

description:
reverse-stranded protocol
20151223.B-SB_9h_C

value: SB431542 (TGF-ß pathway) 9h


title: SU_3h_B

description:
reverse-stranded protocol
20151223.B-SU_3h_B


title: 200090280090_R06C02: genomic DNA from whole Blood


title: 200090280090_R05C02: genomic DNA from whole Blood


title: 200090280128_R01C01: genomic DNA from whole Blood


title: SB_6h_C

description:
reverse-stranded protocol
20151223.B-SB_6h_C

value: SB431542 (TGF-ß pathway) 6h


title: SB_9h_A

description:
reverse-stranded protocol
20151223.B-SB_9h_A


title: SB_9h_B

description:
reverse-stranded protocol
20151223.B-SB_9h_B


title: SB_6h_A

description:
reverse-stranded protocol
20151223.B-SB_6h_A


title: 200090280090_R03C02: genomic DNA from whole Blood


title: SB_6h_B

description:
reverse-stranded protocol
20151223.B-SB_6h_B


title: SB_3h_C

description:
reverse-stranded protocol
20151223.B-SB_3h_C

value: SB431542 (TGF-ß pathway) 3h


title: 200090280128_R06C01: genomic DNA from whole Blood


title: SU_6h_C

description:
reverse-stranded protocol
20151223.B-SU_6h_C


title: 200090280128_R04C02: genomic DNA from whole Blood


title: 200090280090_R01C02: genomic DNA from whole Blood

description: Sample was excluded from the final analysis due to low quality


title: SB_3h_B

description:
reverse-stranded protocol
20151223.B-SB_3h_B


title: 200090280090_R06C01: genomic DNA from whole Blood


title: SB_3h_A

description:
reverse-stranded protocol
20151223.B-SB_3h_A


title: 200090280090_R05C01: genomic DNA from whole Blood


title: not_treated_9h_B

description:
reverse-stranded protocol
20151223.B-not_treated_9h_B

value: not treated 9h


title: not_treated_9h_A

description:
reverse-stranded protocol
20151223.B-not_treated_9h_A


title: 200090280128_R02C01: genomic DNA from whole Blood


title: 200090280090_R04C01: genomic DNA from whole Blood


title: not_treated_0h_C

description:
reverse-stranded protocol
20151223.B-not_treated_0h_C

value: not treated 0h


title: 200090280090_R03C01: genomic DNA from whole Blood


title: 200090280090_R02C01: genomic DNA from whole Blood


title: not_treated_0h_B

description:
reverse-stranded protocol
20151223.B-not_treated_0h_B

value: Embyronic stem cells


title: 200090280090_R01C01: genomic DNA from whole Blood


title: not_treated_0h_A

description:
reverse-stranded protocol
20151223.B-not_treated_0h_A

value: male


title: DMSO_9h_C

description:
reverse-stranded protocol
20151223.B-DMSO_9h_C

value: DMSO 9h

value: Passage 25


title: 200090280090_R04C02: genomic DNA from whole Blood


title: 200090280120_R06C02: genomic DNA from whole Blood


title: 200090280120_R04C02: genomic DNA from whole Blood


title: DMSO_9h_A

description:
reverse-stranded protocol
20151223.B-DMSO_9h_A

value: wild type cells


title: 200090280120_R02C02: genomic DNA from whole Blood

value: M


title: DMSO_9h_B

description:
reverse-stranded protocol
20151223.B-DMSO_9h_B


title: 200090280120_R03C02: Meth Control


title: 200090280090_R02C02: genomic DNA from whole Blood


title: DMSO_6h_B

description:
reverse-stranded protocol
20151223.B-DMSO_6h_B

value: DMSO 6h


title: DMSO_6h_C

description:
reverse-stranded protocol
20151223.B-DMSO_6h_C


title: 200090280120_R01C02: genomic DNA from whole Blood


title: 200090280120_R05C01: genomic DNA from whole Blood


title: DMSO_6h_A

description:
reverse-stranded protocol
20151223.B-DMSO_6h_A


title: 200090280120_R06C01: genomic DNA from whole Blood


title: 200090280120_R04C01: genomic DNA from whole Blood


title: DMSO_3h_C

description:
reverse-stranded protocol
20151223.B-DMSO_3h_C

value: DMSO 3h


title: DMSO_3h_B

description:
reverse-stranded protocol
20151223.B-DMSO_3h_B


title: DMSO_3h_A

description:
reverse-stranded protocol
20151223.B-DMSO_3h_A


title: 200090280120_R02C01: genomic DNA from whole Blood

value: Control


title: not_treated_9h_C

description:
reverse-stranded protocol
20151223.B-not_treated_9h_C


title: 200090280120_R03C01: genomic DNA from whole Blood

value: Case


title: 200090280120_R01C01: genomic DNA from whole Blood

value: Schizoaffective Disorder


title: 200379120002_R06C02: genomic DNA from whole Blood

value: F

value: Schizophrenia


title: 200379120002_R05C02: genomic DNA from whole Blood

label: Cy3, Cy99


title: 200379120002_R04C02: genomic DNA from whole Blood

label: Cy3, Cy98


title: 200379120002_R01C02: genomic DNA from whole Blood

label: Cy3, Cy95


title: 200379120002_R06C01: genomic DNA from whole Blood

description: Sample was excluded from the final analysis due to low quality

label: Cy3, Cy94


title: 200379120002_R05C01: genomic DNA from whole Blood

label: Cy3, Cy93


title: 200090280120_R05C02: genomic DNA from whole Blood


title: 200379120002_R03C02: genomic DNA from whole Blood

label: Cy3, Cy97


title: 200379120002_R04C01: genomic DNA from whole Blood

label: Cy3, Cy92


title: 200379120002_R03C01: genomic DNA from whole Blood

label: Cy3, Cy91


title: 200379120083_R05C02: genomic DNA from whole Blood

label: Cy3, Cy87


title: 200379120083_R06C02: genomic DNA from whole Blood

label: Cy3, Cy88


title: 200379120083_R03C02: genomic DNA from whole Blood

label: Cy3, Cy85


title: 200379120083_R04C02: genomic DNA from whole Blood

label: Cy3, Cy86


title: 200379120083_R02C02: genomic DNA from whole Blood

label: Cy3, Cy84


title: 200379120002_R02C01: genomic DNA from whole Blood

label: Cy3, Cy90


title: 200379120002_R01C01: genomic DNA from whole Blood

label: Cy3, Cy89


title: 200379120083_R01C02: genomic DNA from whole Blood

label: Cy3, Cy83


title: 200379120083_R05C01: genomic DNA from whole Blood

label: Cy3, Cy81


title: 200379120083_R03C01: genomic DNA from whole Blood

label: Cy3, Cy79


title: 200379120083_R06C01: genomic DNA from whole Blood

label: Cy3, Cy82


title: 200379120155_R06C02: genomic DNA from whole Blood

label: Cy3, Cy76


title: 200379120155_R03C02: genomic DNA from whole Blood

label: Cy3, Cy73

value: Schizoid PD

value: case


title: 200379120155_R04C02: genomic DNA from whole Blood

label: Cy3, Cy74


title: 200379120155_R05C02: genomic DNA from whole Blood

label: Cy3, Cy75


title: 200379120155_R02C02: genomic DNA from whole Blood

label: Cy3, Cy72


title: 200379120155_R01C02: genomic DNA from whole Blood

label: Cy3, Cy71


title: 200379120155_R06C01: genomic DNA from whole Blood

label: Cy3, Cy70


title: 200379120002_R02C02: genomic DNA from whole Blood

label: Cy3, Cy96


title: 200379120155_R05C01: genomic DNA from whole Blood

label: Cy3, Cy69


title: 200379120057_R06C02: genomic DNA from whole Blood

label: Cy3, Cy64


title: 200379120155_R02C01: genomic DNA from whole Blood

label: Cy3, Cy66


title: 200379120155_R03C01: genomic DNA from whole Blood

label: Cy3, Cy67


title: 200379120155_R01C01: genomic DNA from whole Blood

label: Cy3, Cy65


title: 200379120057_R05C02: genomic DNA from whole Blood

label: Cy3, Cy63


title: 200379120155_R04C01: genomic DNA from whole Blood

label: Cy3, Cy68


title: 200379120057_R04C02: genomic DNA from whole Blood

label: Cy3, Cy62


title: 200379120057_R03C02: genomic DNA from whole Blood

label: Cy3, Cy61


title: 200379120057_R02C02: genomic DNA from whole Blood

label: Cy3, Cy60


title: 200379120057_R01C02: genomic DNA from whole Blood

label: Cy3, Cy59


title: 200379120057_R06C01: genomic DNA from whole Blood

label: Cy3, Cy58


title: 200379120057_R05C01: genomic DNA from whole Blood

label: Cy3, Cy57


title: 200379120083_R01C01: genomic DNA from whole Blood

label: Cy3, Cy77


title: 200379120083_R02C01: genomic DNA from whole Blood

label: Cy3, Cy78


title: 200379120083_R04C01: genomic DNA from whole Blood

label: Cy3, Cy80


title: 200379120057_R04C01: genomic DNA from whole Blood

label: Cy3, Cy56


title: 200379120057_R01C01: genomic DNA from whole Blood

label: Cy3, Cy53


title: 200379120057_R02C01: genomic DNA from whole Blood

label: Cy3, Cy54


title: 200379120057_R03C01: genomic DNA from whole Blood

label: Cy3, Cy55


title: 200379120018_R05C02: genomic DNA from whole Blood

label: Cy3, Cy51


title: 200379120018_R03C02: genomic DNA from whole Blood

label: Cy3, Cy49


title: 200379120018_R01C02: genomic DNA from whole Blood

label: Cy3, Cy47


title: 200379120018_R04C02: genomic DNA from whole Blood

label: Cy3, Cy50


title: 200379120018_R02C02: genomic DNA from whole Blood

label: Cy3, Cy48


title: 200379120018_R06C01: genomic DNA from whole Blood

label: Cy3, Cy46


title: 200379120018_R05C01: genomic DNA from whole Blood

label: Cy3, Cy45


title: 200379120018_R04C01: genomic DNA from whole Blood

label: Cy3, Cy44


title: 200379120018_R02C01: genomic DNA from whole Blood

label: Cy3, Cy42


title: 200379120018_R03C01: genomic DNA from whole Blood

label: Cy3, Cy43


title: 200379120147_R05C02: genomic DNA from whole Blood

label: Cy3, Cy39


title: 200379120147_R06C02: genomic DNA from whole Blood

label: Cy3, Cy40


title: 200379120147_R04C02: genomic DNA from whole Blood

label: Cy3, Cy38


title: 200379120147_R02C02: genomic DNA from whole Blood

label: Cy3, Cy36


title: 200379120018_R01C01: genomic DNA from whole Blood

label: Cy3, Cy41


title: 200379120147_R03C02: genomic DNA from whole Blood

label: Cy3, Cy37


title: 200379120147_R06C01: genomic DNA from whole Blood

label: Cy3, Cy34


title: 200379120147_R01C02: genomic DNA from whole Blood

label: Cy3, Cy35


title: 200379120018_R06C02: genomic DNA from whole Blood

label: Cy3, Cy52


title: 200379120147_R02C01: genomic DNA from whole Blood

label: Cy3, Cy30


title: 200379120147_R04C01: genomic DNA from whole Blood

label: Cy3, Cy32


title: 200379120147_R03C01: genomic DNA from whole Blood

label: Cy3, Cy31


title: 200379120065_R03C02: genomic DNA from whole Blood

label: Cy3, Cy25


title: 200379120065_R06C02: genomic DNA from whole Blood

label: Cy3, Cy28


title: 200379120065_R02C02: genomic DNA from whole Blood

label: Cy3, Cy24


title: 200379120147_R01C01: genomic DNA from whole Blood

label: Cy3, Cy29

value: control


title: 200379120065_R05C02: genomic DNA from whole Blood

label: Cy3, Cy27

value: Schizophrenia (Galway CP)


title: 200379120065_R06C01: genomic DNA from whole Blood

label: Cy3, Cy22


title: 200379120065_R01C02: genomic DNA from whole Blood

label: Cy3, Cy23


title: 200379120065_R01C01: genomic DNA from whole Blood

label: Cy3, Cy17


title: 200379120065_R04C01: genomic DNA from whole Blood

label: Cy3, Cy20


title: 200379120027_R05C02: genomic DNA from whole Blood

label: Cy3, Cy15


title: 200379120027_R03C02: genomic DNA from whole Blood

label: Cy3, Cy13


title: 200379120065_R03C01: genomic DNA from whole Blood

label: Cy3, Cy19


title: 200379120027_R06C02: genomic DNA from whole Blood

label: Cy3, Cy16


title: 200379120065_R02C01: genomic DNA from whole Blood

label: Cy3, Cy18


title: 200379120065_R05C01: genomic DNA from whole Blood

label: Cy3, Cy21


title: 200379120027_R01C02: genomic DNA from whole Blood

label: Cy3, Cy11


title: 200379120027_R06C01: genomic DNA from whole Blood

label: Cy3, Cy10


title: 200379120027_R04C01: Meth Control

label: Cy3, Cy8


title: 200379120027_R05C01: genomic DNA from whole Blood

label: Cy3, Cy9


title: 200379120027_R03C01: genomic DNA from whole Blood

label: Cy3, Cy7


title: 200379120147_R05C01: genomic DNA from whole Blood

label: Cy3, Cy33


title: 200379120027_R01C01: genomic DNA from whole Blood

label: Cy3, Cy5


title: 200379120027_R02C01: genomic DNA from whole Blood

label: Cy3, Cy6


title: 200379120065_R04C02: genomic DNA from whole Blood

label: Cy3, Cy26


title: 200379120027_R04C02: genomic DNA from whole Blood

label: Cy3, Cy14


title: 200379120027_R02C02: genomic DNA from whole Blood

label: Cy3, Cy12


title: FAH-_p53-_100_3

type: RNA

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Drinking water was supplemented with 7.5 mg/L NTBC 14 unless otherwise indicated, and mice had access to food (Altromin1324 M, Altromin, Germany) and water ad libitum. Mice were housed in individually ventilated cages and all experiments were performed during the day time of a 12 hour day/night cycle.

extract_protocol: NucleoSpin RNA #740955, Macherey-Nagel

treatment_protocol: Fah-/-  and Fah/ p53-/-  mice were exposed to a reduced treatment regimen of NTBC (2.5% of the normal dose) 3 months

value: 100% NTBC

tag: tissue

value: liver


title: FAH-_p53-_0_2

value: 0% NTBC


title: FAH-_p53-_0_3


title: FAH-_p53-_25_2

value: 25% NTBC


title: FAH-_25_3

value: Fah -/-


title: FAH-_p21-_0_4


title: FAH-_p53-_100_1


title: FAH-_p21-_0_1


title: FAH-_0_4


title: A9-P7-S1

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

data_processing:
Hisat2 (v2.1.0) was used to aligned the obtained reads to the genome of Macaca mulatta.
Cufflinks (v2.2.1) was used to obtain the genes and transcripts and genes with the Macaca mulatta annotation.
Cuffmerge (v1.0.0) was used to merge the assembled genes and transcripts from individual libraries.
CuffCompare (v2.2.1) was used to compare the merged genes and transcripts to the annotated genes and transcripts in the Macaca mulatta database.
Cuffquant (v2.2.1) was used to quantify the expression levels (FPKM) values of genes and transcripts.
Cuffnorm (v2.2.1) was used to normalize the FPKM values of genes and transcripts.
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: FPKM values of genes

organism: Macaca mulatta

source_name: one of the single-cell formatted colonies from neuroepithelial stem cells at passage 23

growth_protocol: The rhesus monkey fibroblast cells (named as RF-P3) was maintained in high glucose DMEM, 10% FBS and incubated at 37 °C, 5% CO2.

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols with only ribosomal RNA removal.

treatment_protocol: Briefly, ear skin fibroblasts (RF-P3) were obtained from two male rhesus monkey fetuses of embryonic 65 days. The plasmids pMXs-SOX2, pMXsOCT4 and pMXs-KLF4 with rhesus monkey sequences were gifted from Hongkui Deng Lab (Peking University). The three concentrated retroviruses including OCT4/SOX2/KLF4 were mixed to twice infect monkey fibroblasts which were passaged 24 h before at 3*104 cells per 35 mm dish. At the 3rd day after infection, fibroblasts were harvested by trypsin digestion and replated on laminin-coated plates at 1*105 cells in one well of a 6-well-plate pre-coated with 5 ug/ml laminin (Gibco) in 3 ml induction medium (iNSC-M) supplemented with 5 µM Y27632 (StemRD) and 1 mM valproic acid (VPA) (TOCRIS). iNSC-M is composed of Neurobasal media with 1xB27 (Gibco), 1xN2 (Gibco), 1XNEAA (Gibco), 1% Glutmax (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 50 ug/ml Vitamin C (Sigma), 3 µM CHIR99021 (Cellagen technology), 5 µM SB431542 (Cellagen technology) and 10 ng/ml bFGF (Millipore, GF003AF). Y27632 and VPA were removed from the media at 5th (RF-iN-d5) and 7th day, respectively. At 7th day, the confluent fibroblasts were digested into single cells for further passaging at the ratio of 1:3 and cultured in iNSC-M without Y27632 and VPA until 11st day (RF-iN-d11). Induced epithelial cell colonies at 11st were gently detached from the plates with pipette pressure for further passaging and cultured on 5 mg/ml laminin (Gibco) coated plates in iNESC-M culture media. Then, we collected epithelial cell colonies at early passages 6 (CHIR-P6) and later passages 23 (CHIR-P23). The iNESC-M is composed of Neurobasal media with 1xB27, 1xN2, 1XNEAA, 1% Glutmax, 3 µM CHIR99021, 5 µM SB431542, 50 ug/ml Vitamin C, 10 ng/ml bFGF and 1000 U/ml hLIF (Millipore). The Induced epithelial cell colonies at passages 23 were dissociated into single cells with trypsin, and cultured on 5 mg/ml laminin (Gibco) coated 96-well-plates in iNESC-M culture media. Ultimately, we have got two ideal single-cell formated clonies C8-P7 and A9-P7. 0.025% trypsin (Sigma) was used to digest iNESCs for encouraging cell propagation when passaging. The cells were routinely passaged to 1:8 to 1:16 ratios every 3-4 days in the iNESC-M. Two biological replicates were collected for each of the seven cell lines.

tag: passage

value: passage 23


title: A9-P7-S2

value: one of the single-cell formatted colonies from neuroepithelial stem cells


title: FAH-_p53-_0_4


title: FAH-_p21-_0_2


title: FAH-_p53-_100_4


title: FAH-_p53-_25_1


title: FAH-_p53-_25_4


title: FAH-_0_1


title: FAH-_p53-_100_2


title: FAH-_p53-_0_1


title: FAH-_p21-_0_3


title: FAH-_p53-_25_3


title: FAH-_25_4


title: FAH-_0_2


title: FAH-_25_1


title: FAH-_100_1


title: C8-P7-S2


title: FAH-_0_3


title: FAH-_100_4


title: FAH-_100_3


title: C8-P7-S1


title: CHIR-P23-S1

source_name: neuroepithelial stem cells at passage 23

value: neuroepithelial stem cells


title: CHIR-P6-S2

source_name: neuroepithelial stem cells at passage 6

value: passage 6


title: CHIR-P23-S2


title: FAH-_100_2


title: FAH-_25_2


title: CHIR-P6-S1


title: RF-iN-d11-S2

source_name: cells collected on day 11 when converting fibroblast cells to neuroepithelial stem cells


title: RF-iN-d11-S1

value: cells collected on day 11 when converting fibroblast cells to neuroepithelial stem cells


title: RF-iN-d5-S2

source_name: cells collected on day 5 when converting fibroblast cells to neuroepithelial stem cells


title: RF-P3-S2

source_name: fibroblast cells

value: fibroblast cells


title: RF-iN-d5-S1

value: cells collected on day 5 when converting fibroblast cells to neuroepithelial stem cells


title: RF-P3-S1


title: rl-fr_rep1

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the cucumber genome sequence using Hisat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM (Reads per Million) values

organism: Cucumis sativus

source_name: cucumber 649

growth_protocol: All plants were grown in the greenhouse of Xiangyang farm of Northeast Agricultural University, Harbin, China. Pest and water management was carried out according to standard practices.

extract_protocol:
The total RNA was extracted using the Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. Dried RNA samples were dissolved in diethylpyrocarbonate treated H2O, then used for cDNA synthesis by using RevertAidTM First Strand cDNA Synthesis Kit (MBI Fermentas, Canada).
RNA libraries were prepared for sequencing using Illumina HiSeq 2000

treatment_protocol: No treatment

value: Female bud

tag: geographic location

tag: cultivar

value: Southern China type

value: round leaf (rl)


title: WT-fr_rep2

value: wild type


title: WT-fr_rep1


title: single cell RNA-low 96

city: Toronto

first: Alyssa

middle: M

last: Molinaro

state: Ontario

address: 686 Bay Street

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Trimmed reads (3' 15 bp) were aligned to the transcriptome associated with NCBI BioProject PRJNA215411 using the program Bowtie2. Raw counts were extracted from resulting SAM files.
For bulk samples, raw counts were normalized to the number of mapped reads to calculate Reads Per Million (RPM) prior to analysis. For single cell samples, raw counts were log2 normalized with a small pseudocount of +1 prior to analysis.
Genome_build: NCBI BioProject 215411, SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: Excel tab delimited. Raw counts.

organism: Schmidtea mediterranea

source_name: planarian whole body

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.

extract_protocol:
Bulk samples were RNA extracted in Trizol reagent.
Bulk samples were library prepped using Illumina's Truseq Library kits. Single cell samples were prepped using the Smart-seq2 protocol.

treatment_protocol: Animals were dissociated by douncing in cold CMF + 1% BSA and cells were stained with Hoechst and pyrnonin Y prior to FACS.

tag: facs gate

value: RNA-low

tag: sample type

value: single cell

value: Hoechst/pyronin Y stain & FACS

value: sorted cells

tag: strain

value: Asexual CIW4


title: TK3_2_ATAC-seq

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

data_processing:
After removing low quality reads (quality < 15) using Trimmomatic[1], 150 bp paired-end ATAC-seq reads were mapped to the reference human genome build GRCh38/hg38 by using bowtie2 (-sensitive)[2]. Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis. Significant peak regions of each samples were identified using MACS2[3] with parameters "-q 0.05 --nomodel --shift -100 --extsize 200". Viewable TDF files were generated using igvtools[4]. Genomic region of the peak was annotated using the ChIPseeker[5] R package. Compute differentially bound sites from ATAC-seq experiments using affinity (quantitative) data[6].
bowtie2
MACS2
Genome_build: hg38

source_name: ITNK cells

growth_protocol: cells cultured in T551 H3 (Takara, Japan) medium supplemented with 5% heat-inactivated fetal bovine serum (FBS), 1000 IU/ml recombinant human IL-2, 10 mM HEPES, 2 mM glutamine and 1% penicillin/streptomycin.

extract_protocol:
a total of 50,000 cells were washed once with 50 mL of cold PBS and resuspended in 50 mL lysis buffer (10mMTris-HCl pH 7.4, 10mMNaCl, 3 mMMgCl2, 0.2% (v/v) IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10 min at 500 g at 4 oC, followed by the addition of 50 mL transposition reaction mix (25 mL TD buffer, 2.5 mL Tn5 transposase and 22.5 mL nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina, USA). Samples were then PCR amplified and incubated at 37oC for 30 min. DNA was isolated using a MinElute Kit (QIAGEN, Germany).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described (Buenrostro et al., 2015a), and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (QIAGEN, Germany) column. Library concentration was measured using a KAPA Library Quantification kit (KK4824) according to the manufacturer’s instructions

treatment_protocol: Sorted T, ITNK and NK cells was prepared according to the TruSeqTM RNA Sample Preparation Guide

tag: tag

value: Cord blood T

value: ITNK cells


title: rl-fr_rep2


title: single cell RNA-low 95


title: single cell RNA-low 94


title: TK3_1_ATAC-seq


title: TK2_2_ATAC-seq


title: single cell RNA-low 93


title: single cell RNA-low 92


title: TK2_1_ATAC-seq


title: single cell RNA-low 91


title: single cell RNA-low 90


title: DGC_10X1aF GAP6_sh5_rep1

city: Tokyo

first: Masayuki

last: Komatsu

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

description: ARHGAP6 shRNA-expressing cells

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring version 12.6 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

label: biotin

source_name: Diffuse-type gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: Cells were maintained in 10% FBS-containing RPMI-1640 medium under an atmosphere of 5% CO2 and 95% air at 37˚C.

extract_protocol: Cultured cells were resuspended by ISOGEN solution. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 2×105 cells were cultured by collagen-coated dish for 5 days under normal condition.

value: DGC


title: TK1_ATAC-seq

source_name: T cells

value: T cells


title: T3_ATAC-seq


title: DGC_10X1aF Cont_sh_rep2

description: Control shRNA-expressing cells


title: single cell RNA-low 88


title: DGC_10X1aF GAP6_sh3_rep2

description: ARHGAP6 shRNA-expressing cells


title: MDA-MB-231 stably expressing MYOSIN10 shRNA 2

city: Changchun

first: Rangjuan

last: Cao

state: jilin

address: 5268 Renmin Street

department: Institute of Genetics and Cytology

institute: Northeeast Normal University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain  Kit  (Cat#900720,  Affymetrix,  Santa  Clara,  CA,  US) in  Hybridization  Oven  645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw  data  were  normalized  by  MAS  5.0  algorithm,  Gene  Spring  Software  11.0 (Agilent technologies, Santa Clara, CA, US).
probe group file: HuGene-1_0-st-v1.r4.pgf/HG-U133_Plus_2.pgf
meta-probeset_file: HuGene-1_0-st-v1.r4.mps/HG-U133_Plus_2.mps

label: Biotin

source_name: Human brest cancer cell

label_protocol: Total  RNA  were  amplified,  labeled  and  purified  by  using  GeneChip 3’IVT  Express  Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: MDA-MB-231 cells were cultured in Leibovitz’s L-15 medium with 10% FBS at 37 ºC without CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: expression

value: MYOSIN10 shRNA


title: DGC_10X1aF GAP6_sh3_rep1

description: ARHGAP6 shRNA-expressing cells


title: single cell RNA-low 89


title: T2_ATAC-seq


title: Hypoxic Glioblastoma 13 Stem-like cell line, exposed to Normoxia for 48 h

city: Hamburg

first: Katrin

last: Lamszus

address: Martinistrasse 52

institute: UKE

hyb_protocol: Standard Affymetrix protocols

scan_protocol: Standard Affymetrix protocols

data_processing: Background-adjusted, normalized intensities were computed using the gcRMA package. Gene detection was performed using the PANP package (http://bioconductor.org/packages/bioc/vignettes/panp/inst/doc/panp.pdf) for the R program.

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 13, exposed to Normoxia for 48 h

label_protocol: Standard Affymetrix protocols

growth_protocol: Glioblastoma stem-like cell lines (GS lines): neurobasal medium with B27 supplement (20 μl ml−1), Glutamax (10 μl ml−1), fibroblast growth factor-2 (20 ng ml−1), epidermal growth factor (20 ng ml−1) and heparin (32 IE ml−1)

extract_protocol: Total RNA was extracted from cells using the RNeasy Protect Mini Kit (Qiagen). Genomic DNA contamination was removed through an on-column DNase digestion step

treatment_protocol: Cell dissociation and exposure to normoxic or hypoxic conditions for 48 h

value: exposed to Normoxia for 48 h


title: single cell RNA-low 87


title: MDA-MB-231 stably expressing scramble shRNA 3

value: scramble shRNA


title: MDA-MB-231 stably expressing MYOSIN10 shRNA 3


title: MDA-MB-231 stably expressing scramble shRNA 1


title: MDA-MB-231 stably expressing scramble shRNA 2


title: Normoxic Glioblastoma 13 Stem-like cell line

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 13


title: T1_ATAC-seq


title: Hypoxic Glioblastoma 12 Stem-like cell line

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 12


title: Normoxic Glioblastoma 13 Stem-like cell line, exposed to Hypoxia for 48 h

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 13, exposed to Hypoxia for 48 h

value: exposed to Hypoxia for 48 h


title: Normoxic Glioblastoma 12 Stem-like cell line

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 12


title: Hypoxic Glioblastoma 12 Stem-like cell line, exposed to Normoxia for 48 h

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 12, exposed to Normoxia for 48 h


title: single cell RNA-low 85


title: single cell RNA-low 83


title: DGC_10X1aF Cont_sh_rep1

description: Control shRNA-expressing cells


title: Hypoxic Glioblastoma 13 Stem-like cell line

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 13


title: Hypoxic Glioblastoma 11 Stem-like cell line

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 11


title: single cell RNA-low 82


title: single cell RNA-low 86


title: single cell RNA-low 81


title: DGC_10X1aF GAP6_sh5_rep2

description: ARHGAP6 shRNA-expressing cells


title: Hypoxic Glioblastoma 11 Stem-like cell line, exposed to Normoxia for 48 h

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 11, exposed to Normoxia for 48 h


title: single cell RNA-low 80


title: Normoxic Glioblastoma 12 Stem-like cell line, exposed to Hypoxia for 48 h

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 12, exposed to Hypoxia for 48 h


title: single cell RNA-low 79


title: Normoxic Glioblastoma 11 Stem-like cell line, exposed to Hypoxia for 48 h

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 11, exposed to Hypoxia for 48 h