title: 13R1493

city: Los Angeles

first: Roel

middle: A

last: Ophoff

address: 695 Charles E. Young Drive South

department: Center for Neurobehavioral Genetics

institute: UCLA

data_processing:
Reads were mapped to human reference genome hg19 using tophat/2.0.14 allowing for two mismatches.
Known Ensembl gene levels were quantified using HTSeq in the union mode to obtain integral counts of reads that intersect the union of all transcripts of genes.
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene-level counts for all genes (rows) and samples (columns) are included in the tab-delimited count_matrix.txt file.

source_name: BP1_peripheral whole blood

extract_protocol:
Whole blood was collected in PaxGene Blood RNA tubes and total RNA extracted using the PAXgene isolation kit (Qiagen) according to manufacturer’s protocols.
Sample libraries were prepared using the TruSeq Stranded RNA plus Ribo-Zero Gold library prep kit to remove ribosomal and globin RNA to enrich for messenger and noncoding RNAs. Concentration of the sequencing library was determined on a TapeStation and a pool of barcoded libraries were layered on eight lanes of the Illumina flow cell bridge amplified to raw clusters.

tag: bipolar disorder diagnosis

tag: Sex

value: M

tag: lithium use (non-user=0, user = 1)

tag: tobacco use

tag: assessment group

value: A

tag: tissue/cell type

value: peripheral whole blood

tag: rin

tag: sequencing plate

tag: sequencing metric pc1

tag: sequencing metric pc2

tag: sequencing metric pc3

tag: monocytes

tag: eosinophils

tag: neutrophils

tag: included in final analysis

value: TRUE


title: 13R1199

status: Public on Oct 24 2019

type: SRA

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Control_peripheral whole blood

value: Control

tag: age

value: F

value: B

value: FALSE


title: 13R1200


title: AC8938

city: Barcelona

first: Joan

middle: Anton

last: Puig-Butillé

state: Spain

address: Villarroel 170

department: Department of Biochemical and Molecular Genetics

country: Spain

institute: IDIBAPS-Hospital Clinic of Barcelona

data_processing:
RNA-seq reads were processed with STAR-fusion version 0.80 with default parameters
with Gencode 25 annotation
The processed files data files included the analyses of putative fusion transcripts detected in whole gene expression captured by RNA-sequencing in congenital melanocytic nevi. Each file includes the putative fusion transcripts of each biopsy.
Files include common parameters obtained in the analyses:
The "JunctionReads" column indicates the number of RNA-Seq fragments containing a read that aligns as a split read at the site of the putative fusion junction.
The "SpanningFrags" column indicates the number of RNA-Seq fragments that encompass the fusion junction such that one read of the pair aligns to a different gene than the other paired-end read of that fragment.
The "SpliceType" indicates whether the proposed breakpoint occurs at reference exon junctions as provided by the reference transcript structure annotations (ex. gencode).
The following columns: Left Gene, LeftBreakpoint, right Gene and Right Breakpoint; indicate genes and its genomic breakpoint involved in the fusion transcript.
The "LargeAnchorSupport" column indicates whether there are split reads that provide 'long' (set to length of 25 bases) alignments on both sides of the putative breakpoint. Those fusions supported only by split reads (no spanning fragments) and lack LargeAnchorSupport are often highly suspicious and tend to be false positives. Those with LargeAnchorSupport are labeled as 'YES_LDAS' (where LDAS = long double anchor support.... yes, more jargon).
Additional information about the analyses can be found in https://github.com/STAR-Fusion/STAR-Fusion/wiki
Genome_build: GRCh38
Supplementary_files_format_and_content: candidate fusions xls

source_name: human skin biopsies

extract_protocol:
Skin lesions were biopsied, stabilized in RNA-later and frozen at 80ºC . Total RNA was isolated from fresh tissue with Trizol (Invitrogen, USA) followed by purification with the RNeasy mini kit (Qiagen, USA). RNASeq libraries were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: lesion type

value: CMN

tag: nras status


title: 13R1190

tag: bipolar disorder diagnosis


title: 13R1191

tag: Sex

tag: lithium use (non-user=0, user = 1)


title: 13R1051

tag: tobacco use

tag: assessment group


title: 13R1484

tag: tissue/cell type

tag: rin


title: 13R1193

tag: sequencing plate

tag: sequencing metric pc1


title: AC8937

value: Wild-Type


title: 13R1054

tag: sequencing metric pc2

tag: sequencing metric pc3


title: 13R1050

tag: monocytes

tag: eosinophils


title: AC8936


title: 13R1028

tag: neutrophils

tag: included in final analysis


title: AC8935

tag: lesion type


title: 13R1018

tag: age


title: sample1 24h uninfected, cord blood CD34+ cells

city: Florianopolis

first: Edgar

middle: Ernesto

last: Gonzalez Kozlova

state: Santa Catarina

address: Corrego Grande s/n

department: Farmacologia

country: Brazil

institute: Universidade Federal de Santa Catarina

description:
counts_matrix_RNAseq_data.tsv
AB1

data_processing:
Phred, Read Quality filter
Trimmomatic, Trimming and removing adaptors
STAR, aligment to hg38 genome
FeatureCounts
Genome_build: Hg38
Supplementary_files_format_and_content: Raw count matrix from FeatureCounts output

source_name: Purified cord blood CD34+ cells

growth_protocol: StemSpan Expantion Media – SFEM II (STEMCELL Technologies)

extract_protocol:
Trizol LS Invitrogen; 10296010
Nugen Ovation Trio input RNA Library Systems V2
Illumina HiSeq 2500 adaptors for v4 chemistry

treatment_protocol: Optimal cell density for replication was 5 x 10e4 CD34+ cell/mL. Following 4 days of expansion, cells were washed and diluted in SFEM II media without cytokine cocktail to the desired concentration. Culture purity was assessed by FACS and showed more than 90% of CD34+ events after expansion.

tag: infection

value: uninfected

tag: time

tag: individual

tag: cell type

value: purified CD34+ Cells


title: AC8934

tag: nras status


title: AC8933


title: 13R0972

tag: bipolar disorder diagnosis

tag: Sex

tag: lithium use (non-user=0, user = 1)

tag: tobacco use

tag: assessment group

tag: tissue/cell type


title: 13R1012

tag: rin

tag: sequencing plate

tag: sequencing metric pc1

tag: sequencing metric pc2

tag: sequencing metric pc3

tag: monocytes


title: AC8932

tag: lesion type


title: 13R0967

tag: age

tag: eosinophils

tag: neutrophils

tag: included in final analysis


title: AC8931

tag: nras status


title: AC8939


title: AC8929

value: Satellite


title: 13R0952

tag: bipolar disorder diagnosis

tag: Sex


title: AC8930


title: AC8927


title: 13R0903

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 13R0901

tag: assessment group

tag: tissue/cell type


title: AC8926

value: Healthy skin


title: 13R0938

tag: rin

tag: sequencing plate


title: AC8928

value: Background


title: 13R0898

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 13R0855

tag: sequencing metric pc3

tag: monocytes


title: ChEC7

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

data_processing:
The raw sequencing fastq files were trimmed using  Trim Galore! in paired-end mode with default parameters, to remove adaptor sequences and low quality bases.
The trimmed data were mapped to human reference genome hg38 using STAR aligner in paired-end mode with default parameters.
The mapping results were inputted into featureCounts, to count number of reads map to each gene in each sample.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample.

source_name: trophoblasts

growth_protocol: Human embryos generated by in vitro fertilization were cultured with addition of endometrium cells.

extract_protocol:
Embryos were treated with trypsin to detach from dishes. Embryos then be and manually transferred to a new dish containing trypsin for further dissociation for 3 to 5 minutes with repeated aspiration using a mouth-controlled, finely drawn capillary pipette. Single cell was then manually picked using the capillary pipette into a 0.2-ml thin-wall PCR tube contains lysis buﬀer.
Library construction is done using SMART-seq2 protocol with minor modification.
Single cell RNA sequencing

tag: development day

value: Endometrial

tag: Stage


title: ChEC5


title: ChEC4


title: 13R0828

tag: age

tag: eosinophils

tag: neutrophils


title: ChEC6


title: ChEC3


title: ChEC8


title: 13R0825

tag: bipolar disorder diagnosis

tag: included in final analysis


title: ChEC32


title: 13R0821

tag: Sex

tag: lithium use (non-user=0, user = 1)


title: 13R0820

tag: tobacco use

tag: assessment group


title: 13R0959

tag: tissue/cell type

tag: rin


title: ChEC30


title: ChEC31


title: ChEC29


title: 13R0807

tag: sequencing plate

tag: sequencing metric pc1


title: 13R0950

tag: sequencing metric pc2

tag: sequencing metric pc3


title: 13R0805

tag: monocytes


title: ChEC28

tag: development day

tag: Stage


title: 13R0806

tag: age

tag: eosinophils


title: 13R0889

tag: bipolar disorder diagnosis

tag: neutrophils


title: ChEC27


title: 13R0793

tag: Sex

tag: included in final analysis


title: 13R0783

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: ChEC26


title: ChEC25


title: 13R0840

tag: assessment group

tag: tissue/cell type


title: 13R0781

tag: rin

tag: sequencing plate


title: ChEC23


title: 13R0757

tag: sequencing metric pc1

tag: sequencing metric pc2


title: ChEC22


title: 13R0753

tag: sequencing metric pc3

tag: monocytes


title: 13R0711


title: 13R0742


title: ChEC20

tag: development day

tag: Stage


title: ChEC1


title: 13R0710

tag: age

tag: eosinophils


title: 13R0708

tag: bipolar disorder diagnosis

tag: neutrophils


title: 13R0707

tag: Sex

tag: included in final analysis


title: ChEC14


title: ChEC15


title: ChEC16


title: 13R0704

source_name: BP2_peripheral whole blood

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: ChEC13


title: 13R0705

tag: assessment group

tag: tissue/cell type


title: 13R0803

tag: rin

tag: sequencing plate


title: ChEC24


title: 13R0519

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9C9

value: post-implantation


title: ChEC12


title: C9C96


title: 13R0506

value: M

tag: sequencing metric pc3

tag: monocytes


title: C9C93

tag: development day

tag: Stage


title: 13R0509

tag: age

value: A

tag: eosinophils


title: 13R0495

tag: bipolar disorder diagnosis

value: peripheral whole blood

tag: neutrophils


title: C9C90


title: ChEC21


title: C9C89


title: 13R0451

tag: Sex

tag: included in final analysis


title: 13R0438

tag: lithium use (non-user=0, user = 1)

tag: tobacco use

value: TRUE


title: C9C87


title: 13R0433

value: Control

tag: assessment group

tag: tissue/cell type


title: C9C88


title: 13R0432

tag: rin

tag: sequencing plate


title: C9C86


title: C9C85


title: 13R0430

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9C84


title: 13R0428

tag: sequencing metric pc3

tag: monocytes


title: C9C82

tag: development day

tag: Stage


title: 13R0337

tag: age

value: F

tag: eosinophils


title: 13R0338

tag: bipolar disorder diagnosis

tag: neutrophils


title: 13R0391

tag: Sex

tag: included in final analysis


title: 13R0336

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9C62


title: C9C70


title: 13R0329

tag: assessment group

tag: tissue/cell type


title: C9C71


title: 13R0332

tag: rin

tag: sequencing plate


title: C9C5


title: 13R0133

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 13R0382

tag: sequencing metric pc3

tag: monocytes


title: C9C60

tag: development day

tag: Stage


title: C9C4


title: C9C46


title: C9C59


title: 13R0100

tag: age

tag: eosinophils


title: C9C63


title: C9C45


title: 13R0075

tag: bipolar disorder diagnosis

tag: neutrophils


title: 13R0070

tag: Sex

tag: included in final analysis


title: C9C44


title: C9C43


title: 13R0090

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9C42


title: 13R0062

tag: assessment group

tag: tissue/cell type


title: 13R0060

tag: rin

tag: sequencing plate


title: C9C41


title: C9C3


title: C9C39


title: 13R0029

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R2396

tag: sequencing metric pc3

tag: monocytes


title: 12R2392


title: 13R0285


title: C9C36

tag: development day

tag: Stage


title: C9C30


title: C9C2_S99_L007_R1_001.fastq.gz


title: 12R2269

tag: age

tag: eosinophils


title: C9C28


title: C9C22


title: C9C26


title: 12R2214

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R2219

tag: Sex

tag: included in final analysis


title: 12R2215

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R2211

tag: assessment group

tag: tissue/cell type


title: C9C21


title: C9C20


title: C9C1_S98_L007_R1_001.fastq.gz


title: 12R2193

tag: rin

tag: sequencing plate


title: 12R2210

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9C19


title: 12R2175

tag: sequencing metric pc3

tag: monocytes


title: C9C18

tag: development day

tag: Stage


title: 12R2173

tag: age

tag: eosinophils


title: 12R2273

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R2172

tag: Sex

tag: included in final analysis


title: C9C14


title: C9C15


title: C9C12


title: 12R2171

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R2257

tag: assessment group

tag: tissue/cell type


title: C9C11


title: 12R2160

tag: rin

tag: sequencing plate


title: C9C24


title: 12R2158

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R2157

tag: sequencing metric pc3

tag: monocytes


title: 12R2155


title: C9B92_S96_L007_R1_001.fastq.gz

tag: development day

tag: Stage


title: C9B86_S94_L007_R1_001.fastq.gz


title: C9B91_S95_L007_R1_001.fastq.gz


title: 12R2192

tag: age

tag: eosinophils


title: C9B85_S93_L007_R1_001.fastq.gz


title: C9B84_S92_L007_R1_001.fastq.gz


title: 12R2137

tag: bipolar disorder diagnosis

tag: neutrophils


title: C9B7


title: C9B82_S91_L007_R1_001.fastq.gz


title: 12R2135

tag: Sex

tag: included in final analysis


title: 12R2136

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R2134

tag: assessment group

tag: tissue/cell type


title: C9B79_S90_L007_R1_001.fastq.gz


title: 12R2143

tag: rin

tag: sequencing plate


title: 12R2144

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9B78_S89_L007_R1_001.fastq.gz


title: 12R2138

tag: sequencing metric pc3

tag: monocytes


title: C9B95_S97_L007_R1_001.fastq.gz

tag: development day

tag: Stage


title: 12R2071

tag: age

tag: eosinophils


title: 12R2066

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R2052

tag: Sex

tag: included in final analysis


title: 12R2111

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9B72


title: C9B70


title: 12R2015

tag: assessment group

tag: tissue/cell type


title: 12R2013

tag: rin

tag: sequencing plate


title: C9B61


title: 12R2044

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R1998

value: B

tag: sequencing metric pc3

tag: monocytes


title: 12R2018


title: C9B60

tag: development day

tag: Stage


title: 12R1997

tag: age

tag: eosinophils


title: C9B53


title: C9B68


title: 12R1980

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R1930

tag: Sex

tag: included in final analysis


title: C9B52


title: C9B76


title: C9B51


title: 12R1698

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9B74


title: 12R1845

tag: assessment group

tag: tissue/cell type

value: FALSE


title: 12R0941

tag: rin

tag: sequencing plate


title: C9B50


title: C9B4


title: C9B47


title: C9B48


title: C9B6


title: C9B46


title: 12R0937

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R0935

tag: sequencing metric pc3

tag: monocytes


title: C9B65

tag: development day

tag: Stage


title: 12R0926

tag: age

tag: eosinophils


title: C9B45


title: 12R0923

tag: bipolar disorder diagnosis

tag: neutrophils


title: C9B44


title: C9B42


title: 12R0908

tag: Sex

tag: included in final analysis


title: C9B43


title: 12R0907

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9B41


title: 12R0902

tag: assessment group

tag: tissue/cell type


title: 12R1372

tag: rin

tag: sequencing plate


title: C9B40


title: C9B3


title: 12R0897

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9B37


title: C9B38


title: 12R0895

tag: sequencing metric pc3

tag: monocytes


title: 12R0893


title: 12R0891


title: C9B39

tag: development day

tag: Stage


title: C9B36


title: 12R0888

tag: age

tag: eosinophils


title: C9B34


title: C9B33


title: C9B35


title: 12R0885

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0879

tag: Sex

tag: included in final analysis


title: C9B30


title: 12R0903

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9B29


title: 12R0898

tag: assessment group

tag: tissue/cell type


title: C9B25


title: C9B24


title: C9B28


title: C9B26


title: 12R0865

tag: rin

tag: sequencing plate


title: 12R0870

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R0867

tag: sequencing metric pc3

tag: monocytes


title: 12R0862


title: 12R0835


title: 12R0873


title: C9B22

tag: development day

tag: Stage


title: 12R0833

tag: age

tag: eosinophils


title: C9B21


title: C9B19


title: 12R0832

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0830

tag: Sex

tag: included in final analysis


title: C9B20


title: 12R0826

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9B18


title: 12R0868

tag: assessment group

tag: tissue/cell type


title: 12R0828

tag: rin

tag: sequencing plate


title: C9B17


title: 12R0824

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R0820

tag: sequencing metric pc3

tag: monocytes


title: 12R0847


title: C9B2

tag: development day

tag: Stage


title: 12R0846

tag: age

tag: eosinophils


title: C9B23


title: C9B27


title: C9B14


title: 12R0819

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0799

tag: Sex

tag: included in final analysis


title: C9B10


title: C9A92


title: C9B12


title: 12R0803

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0794

tag: assessment group

tag: tissue/cell type


title: C9A95


title: C9A94


title: 12R0742

tag: rin

tag: sequencing plate


title: 12R0738

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9A7


title: C9A8


title: 12R0737

tag: sequencing metric pc3

tag: monocytes


title: C9B16

tag: development day

tag: Stage


title: 12R0741

tag: age

tag: eosinophils


title: 12R0797

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0793

tag: Sex

tag: included in final analysis


title: C9A77


title: C9A87


title: 12R0736

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0734

tag: assessment group

tag: tissue/cell type


title: 12R0818

tag: rin

tag: sequencing plate


title: C9A74


title: C9B15


title: C9A75


title: 12R0730

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9B13


title: C9A6


title: C9A64


title: 12R0729

tag: sequencing metric pc3

tag: monocytes


title: 12R0722


title: C9A61

tag: development day

tag: Stage


title: C9A60


title: 12R0720

tag: age

tag: eosinophils


title: 12R0716

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0715

tag: Sex

tag: included in final analysis


title: 12R0719

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C9A5


title: 12R0712

tag: assessment group

tag: tissue/cell type


title: 12R0714

tag: rin

tag: sequencing plate


title: C9A52


title: C9A56


title: 12R0707

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9A50


title: 12R0710

tag: sequencing metric pc3

tag: monocytes


title: C9A62

tag: development day

tag: Stage


title: C9A46


title: C9A58


title: C9A45


title: C9A43


title: 12R0698

tag: age

tag: eosinophils


title: C9A40


title: C9A42


title: 12R0691

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0699

tag: Sex

tag: included in final analysis


title: 12R0695

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0687

tag: assessment group

tag: tissue/cell type


title: C9A36


title: C9A39


title: C9A34


title: 12R0678

tag: rin

tag: sequencing plate


title: C9A33


title: 12R0684

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9A32


title: 12R0672

tag: sequencing metric pc3

tag: monocytes


title: C9A2

tag: development day

tag: Stage


title: 12R0703

tag: age

tag: eosinophils


title: C9A29


title: 12R0675

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0683

tag: Sex

tag: included in final analysis


title: C9A27


title: 12R0667

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0646

tag: assessment group

tag: tissue/cell type


title: 12R0648

tag: rin

tag: sequencing plate


title: C9A22


title: 12R0624

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C9A3


title: C9A21


title: 12R0620

tag: sequencing metric pc3

tag: monocytes


title: 12R0622


title: C9A1

tag: development day

tag: Stage


title: C9A17


title: 12R0688

tag: age

tag: eosinophils


title: 12R0617

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8C96


title: 12R0616

tag: Sex

tag: included in final analysis


title: C9A31


title: C8C95

value: implantation


title: 12R0668

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0614

tag: assessment group

tag: tissue/cell type


title: C8C92


title: C8C94


title: 12R0609

tag: rin

tag: sequencing plate


title: 12R0615

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8C91


title: 12R0596

tag: sequencing metric pc3

tag: monocytes


title: 12R0563


title: 12R0559


title: C8C87

tag: development day

tag: Stage


title: 12R0567

tag: age

tag: eosinophils


title: C8C88


title: 12R0552

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8C84


title: C8C85


title: 12R0548

tag: Sex

tag: included in final analysis


title: C8C86


title: 12R0547

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0542

tag: assessment group

tag: tissue/cell type


title: 12R0551

tag: rin

tag: sequencing plate


title: C8C83


title: C8C82


title: 12R0531

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8C89


title: 12R0527

tag: sequencing metric pc3

tag: monocytes


title: C8C79

tag: development day

tag: Stage


title: C8C90


title: 12R0519

tag: age

tag: eosinophils


title: 12R0511

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8C78


title: 12R0510

tag: Sex

tag: included in final analysis


title: 12R0483

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0493

tag: assessment group

tag: tissue/cell type


title: C8C7


title: C9A26


title: C8C71


title: 12R0482

tag: rin

tag: sequencing plate


title: C8C77


title: C8C70


title: 12R0475

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8C68


title: C8C67


title: C8C69


title: 12R0472

tag: sequencing metric pc3

tag: monocytes


title: C8C63

tag: development day

tag: Stage


title: C8C80


title: 12R0471

tag: age

tag: eosinophils


title: 12R0473

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0470

tag: Sex

tag: included in final analysis


title: 12R0474

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8C62


title: C8C81


title: C8C65


title: 12R0463

tag: assessment group

tag: tissue/cell type


title: 12R0460

tag: rin

tag: sequencing plate


title: 12R0459

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8C61


title: 12R0454

tag: sequencing metric pc3

tag: monocytes


title: 12R0453


title: C8C58

tag: development day

tag: Stage


title: C8C59


title: 12R0452

tag: age

tag: eosinophils


title: 12R0430

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8C52


title: 12R0433

tag: Sex

tag: included in final analysis


title: C8C56


title: 12R0429

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8C53


title: C8C40


title: C8C48


title: 12R0427

tag: assessment group

tag: tissue/cell type


title: 12R0428

tag: rin

tag: sequencing plate


title: C8C39


title: 12R0424

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8C37


title: 12R0421

tag: sequencing metric pc3

tag: monocytes


title: C8C36

tag: development day

tag: Stage


title: C8C38


title: 12R0419

tag: age

tag: eosinophils


title: 12R0416

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0413

tag: Sex

tag: included in final analysis


title: C8C33


title: C8C34


title: C8C31


title: 12R0412

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0333

tag: assessment group

tag: tissue/cell type


title: C8C29


title: C8C2


title: 12R0332

tag: rin

tag: sequencing plate


title: C8C28


title: 12R0307

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R0300

tag: sequencing metric pc3

tag: monocytes


title: C8C60

tag: development day

tag: Stage


title: 12R0298

tag: age

tag: eosinophils


title: C8C25


title: C8C27


title: C8C21


title: 12R0295

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0294

tag: Sex

tag: included in final analysis


title: C8C14


title: 12R0289

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0267

tag: assessment group

tag: tissue/cell type


title: C8C10


title: C8C13


title: 12R0261

tag: rin

tag: sequencing plate


title: C8B9


title: C8C57


title: 12R0260

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8B96


title: 12R0325

tag: sequencing metric pc3

tag: monocytes


title: C8B95

tag: development day

tag: Stage


title: C8C26


title: C8B94


title: 12R0254

tag: age

tag: eosinophils


title: 12R0249

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8B93


title: 12R0247

tag: Sex

tag: included in final analysis


title: 12R0244

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0245

tag: assessment group

tag: tissue/cell type


title: C8B87


title: C8B92


title: 12R0242

tag: rin

tag: sequencing plate


title: C8B88


title: C8B85


title: C8B86


title: C8C11


title: 12R0281

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8B84


title: 12R0240

tag: sequencing metric pc3

tag: monocytes


title: 12R0237


title: 12R0239


title: 12R0235


title: C8B79

tag: development day

tag: Stage


title: 12R0253

tag: age

tag: eosinophils


title: C8B74


title: C8B71


title: 12R0234

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8B70


title: 12R0229

tag: Sex

tag: included in final analysis


title: 12R0210

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0202

tag: assessment group

tag: tissue/cell type


title: 12R0213

tag: rin

tag: sequencing plate


title: C8B67


title: C8B75


title: C8B65


title: 12R0199

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R0198

tag: sequencing metric pc3

tag: monocytes


title: 12R0197


title: C8B61

tag: development day

tag: Stage


title: 12R0182

tag: age

tag: eosinophils


title: C8B60


title: 12R0175

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8B58


title: 12R0172

tag: Sex

tag: included in final analysis


title: C8B57


title: C8B54


title: 12R0232

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0174

tag: assessment group

tag: tissue/cell type


title: C8B69


title: 12R0165

tag: rin

tag: sequencing plate


title: C8B5


title: C8B68


title: C8B52


title: 12R0164

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8B51


title: 12R0158

tag: sequencing metric pc3

tag: monocytes


title: 12R0163


title: C8B64

tag: development day

tag: Stage


title: 12R0169

tag: age

tag: eosinophils


title: C8B50


title: C8B4


title: C8B48


title: C8B49


title: 12R0157

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8B47


title: 12R0170

tag: Sex

tag: included in final analysis


title: 12R0150

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0149

tag: assessment group

tag: tissue/cell type


title: C8B45


title: C8B53


title: C8B46


title: C8B43


title: 12R0147

tag: rin

tag: sequencing plate


title: C8B42


title: 12R0139

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 12R0137

tag: sequencing metric pc3

tag: monocytes


title: 12R0130


title: C8B41

tag: development day

tag: Stage


title: C8B40


title: 12R0128

tag: age

tag: eosinophils


title: C8B3


title: 12R0117

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8B39


title: 12R0115

tag: Sex

tag: included in final analysis


title: 12R0156

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0114

tag: assessment group

tag: tissue/cell type


title: C8B36


title: 12R0155

tag: rin

tag: sequencing plate


title: C8B38


title: C8B35


title: 12R0109

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8B33


title: 12R0113

tag: sequencing metric pc3

tag: monocytes


title: 12R0110


title: 12R0106


title: C8B34

tag: development day

tag: Stage


title: 12R0104

tag: age

tag: eosinophils


title: 12R0102

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8B30


title: C8B29


title: C8B28


title: 12R0094

tag: Sex

tag: included in final analysis


title: 12R0081

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 12R0080

tag: assessment group

tag: tissue/cell type


title: C8B27


title: C8B26


title: 12R0071

tag: rin

tag: sequencing plate


title: C8B25


title: 12R0060

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8B24


title: C8B23


title: C8B21


title: 12R0052

tag: sequencing metric pc3

tag: monocytes


title: 12R0059


title: 12R0050


title: 12R0048


title: C8B20

tag: development day

tag: Stage


title: C8B1


title: C8B31


title: C8B32


title: C8B17


title: 12R0047

tag: age

tag: eosinophils


title: 12R0038

tag: bipolar disorder diagnosis

tag: neutrophils


title: 12R0096

tag: Sex

tag: included in final analysis


title: 12R0036

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8B16


title: 12R0033

tag: assessment group

tag: tissue/cell type


title: 11R0888

tag: rin

tag: sequencing plate


title: C8B13


title: 12R0031

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8B11


title: C8B10


title: C8A79


title: 11R0882

tag: sequencing metric pc3

tag: monocytes


title: C8A78

tag: development day

tag: Stage


title: 12R0042

tag: age

tag: eosinophils


title: C8A75


title: C8B18


title: C8A77


title: 12R0032

tag: bipolar disorder diagnosis

tag: neutrophils


title: 11R0878

tag: Sex

tag: included in final analysis


title: 11R0866

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 11R0861

tag: assessment group

tag: tissue/cell type


title: 11R0879

tag: rin

tag: sequencing plate


title: C8A74


title: C8A73


title: C8A72


title: 11R0857

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 11R0858

tag: sequencing metric pc3

tag: monocytes


title: C8B15

tag: development day

tag: Stage


title: 11R0860

tag: age

tag: eosinophils


title: C8B14


title: C8A70


title: 11R0853

tag: bipolar disorder diagnosis

tag: neutrophils


title: 11R0856

tag: Sex

tag: included in final analysis


title: C8A69


title: C8A67


title: 11R0852

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8A68


title: 11R0851

tag: assessment group

tag: tissue/cell type


title: 11R0850

tag: rin

tag: sequencing plate


title: C8A66


title: 11R0849

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8A64


title: C8A63


title: 11R0847

tag: sequencing metric pc3

tag: monocytes


title: C8A62

tag: development day

tag: Stage


title: C8A71


title: 11R0848

tag: age

tag: eosinophils


title: C8A61


title: C8A57


title: 11R0846

tag: bipolar disorder diagnosis

tag: neutrophils


title: 11R0845

tag: Sex

tag: included in final analysis


title: 11R0839

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8A59


title: 11R0835

tag: assessment group

tag: tissue/cell type


title: C8A54


title: 11R0837

tag: rin

tag: sequencing plate


title: 11R0821

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8A52


title: 11R0832

tag: sequencing metric pc3

tag: monocytes


title: C8A55

tag: development day

tag: Stage


title: C8A53


title: 11R0809

tag: age

tag: eosinophils


title: 11R0807

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8A4


title: 11R0669

tag: Sex

tag: included in final analysis


title: C8A49


title: C8A60


title: 11R0652

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8A48


title: C8A47


title: 11R0647

tag: assessment group

tag: tissue/cell type


title: C8A45


title: 11R0645

tag: rin

tag: sequencing plate


title: C8A46


title: C8A44


title: C8A43


title: 11R0631

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8A40


title: 11R0634

tag: sequencing metric pc3

tag: monocytes


title: C8A3

tag: development day

tag: Stage


title: 11R0613

tag: age

tag: eosinophils


title: C8A39


title: C8A50


title: 11R0808

tag: bipolar disorder diagnosis

tag: neutrophils


title: 11R0612

tag: Sex

tag: included in final analysis


title: 11R0635

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 11R0603

tag: assessment group

tag: tissue/cell type


title: 11R0616

tag: rin

tag: sequencing plate


title: 11R0663

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8A38


title: 11R0610

tag: sequencing metric pc3

tag: monocytes


title: C8A37

tag: development day

tag: Stage


title: 11R0596

tag: age

tag: eosinophils


title: C8A36


title: 11R0589

tag: bipolar disorder diagnosis

tag: neutrophils


title: C8A35


title: 11R0580

tag: Sex

tag: included in final analysis


title: 11R0577

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8A33


title: 11R0575

tag: assessment group

tag: tissue/cell type


title: C8A32


title: C8A42


title: 11R0571

tag: rin

tag: sequencing plate


title: C8A30


title: C8A29


title: C8A2


title: 11R0564

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C8A28


title: 11R0569

tag: sequencing metric pc3

tag: monocytes


title: 11R0565


title: 11R0561


title: 11R0557


title: 11R0553


title: C8A27

tag: development day

tag: Stage


title: 11R0549

tag: age

tag: eosinophils


title: 11R0548

tag: bipolar disorder diagnosis

tag: neutrophils


title: 11R0547

tag: Sex

tag: included in final analysis


title: C8A24


title: C8A26


title: 11R0546

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C8A23


title: C8A20


title: C8A25


title: 11R0545

tag: assessment group

tag: tissue/cell type


title: C8A34


title: C8A18


title: C8A17


title: C8A14


title: C8A15


title: 11R0540

tag: rin

tag: sequencing plate


title: 11R0541

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 11R0544

tag: sequencing metric pc3

tag: monocytes


title: 11R0539


title: 118271A


title: C8A11

tag: development day

tag: Stage


title: C7C8


title: C7C6


title: 118214B

tag: age

tag: eosinophils


title: C7C7


title: C8A22


title: 118206B

tag: bipolar disorder diagnosis

tag: neutrophils


title: 118195A

tag: Sex

tag: included in final analysis


title: C7C5


title: 118205A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 118179B

tag: assessment group

tag: tissue/cell type


title: 118194A

tag: rin

tag: sequencing plate


title: C7C39


title: 118176B

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C7C40


title: C7C3


title: C7C36


title: 118178B

tag: sequencing metric pc3

tag: monocytes


title: 118175A


title: C7C38

tag: development day

tag: Stage


title: 118156B

tag: age

tag: eosinophils


title: 118164A

tag: bipolar disorder diagnosis

tag: neutrophils


title: C7C35


title: 118155A

tag: Sex

tag: included in final analysis


title: C7C34


title: C7C33


title: C7C32


title: 118207B

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 118149A

tag: assessment group

tag: tissue/cell type


title: C7C31


title: 118146A

tag: rin

tag: sequencing plate


title: C7C30


title: C7C2


title: C7C29


title: 118142B

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 118148A

tag: sequencing metric pc3

tag: monocytes


title: C7C28

tag: development day

tag: Stage


title: 118141A

tag: age

tag: eosinophils


title: C7C27


title: C7C4


title: 118140B

tag: bipolar disorder diagnosis

tag: neutrophils


title: 118082B

tag: Sex

tag: included in final analysis


title: C7C26


title: 118059B

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 118139A

tag: assessment group

tag: tissue/cell type


title: C7C24


title: 118035A

tag: rin

tag: sequencing plate


title: C7C23


title: 118046A

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C7C25


title: C7C22


title: 109694A

tag: sequencing metric pc3

tag: monocytes


title: 109646A


title: C7C1

tag: development day

tag: Stage


title: 109551B

tag: age

tag: eosinophils


title: C7C20


title: 109559B

tag: bipolar disorder diagnosis

tag: neutrophils


title: C7C21


title: 109549A

tag: Sex

tag: included in final analysis


title: C7C18


title: 109548A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 109530A

tag: assessment group

tag: tissue/cell type


title: C7C16


title: C7C14


title: 109503A

tag: rin

tag: sequencing plate


title: C7C10


title: C7C12


title: C7C13


title: 109464A

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 109435B

tag: sequencing metric pc3

tag: monocytes


title: 109434A


title: 109505B


title: 109529A


title: 109424B


title: C7C15

tag: development day

tag: Stage


title: C7B8


title: C7B6


title: C7B7


title: 109381B

tag: age

tag: eosinophils


title: C7C17


title: 109350B

tag: bipolar disorder diagnosis

tag: neutrophils


title: 109368A

tag: Sex

tag: included in final analysis


title: 109326A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C7B38


title: C7B37


title: C7B5


title: 109329A

tag: assessment group

tag: tissue/cell type


title: C7C19


title: C7B3


title: 109327A

tag: rin

tag: sequencing plate


title: 109275B

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C7B36


title: C7B31


title: C7B35


title: C7B30


title: 109274B

tag: sequencing metric pc3

tag: monocytes


title: C7B29

tag: development day

tag: Stage


title: 109254B

tag: age

tag: eosinophils


title: 109191B

tag: bipolar disorder diagnosis

tag: neutrophils


title: 109213B

tag: Sex

tag: included in final analysis


title: C7B34


title: C7B21


title: C7B9


title: 109188B

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 109384A

tag: assessment group

tag: tissue/cell type


title: 109184A

tag: rin

tag: sequencing plate


title: C7B1


title: 109281B

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C7B18


title: C7B17


title: 109138B

tag: sequencing metric pc3

tag: monocytes


title: C7B15

tag: development day

tag: Stage


title: C7B10


title: 109106B

tag: age

tag: eosinophils


title: 109137A

tag: bipolar disorder diagnosis

tag: neutrophils


title: 109189A

tag: Sex

tag: included in final analysis


title: 109105B

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C7A9


title: C7A5


title: C7B28


title: 109088B

tag: assessment group

tag: tissue/cell type


title: 109087A

tag: rin

tag: sequencing plate


title: C7B20


title: C7A7


title: C7A3


title: C7A4


title: 109156B

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 109157A

tag: sequencing metric pc3

tag: monocytes


title: 109014B


title: C7A38

tag: development day

tag: Stage


title: C7A37


title: 109089A

tag: age

tag: eosinophils


title: 109042B

tag: bipolar disorder diagnosis

tag: neutrophils


title: 108990A

tag: Sex

tag: included in final analysis


title: C7A39


title: C7A36


title: C7A35


title: 108932A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C7A33


title: C7A40


title: 108983B

tag: assessment group

tag: tissue/cell type


title: 109078B

tag: rin

tag: sequencing plate


title: 109056A

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 108981B

tag: sequencing metric pc3

tag: monocytes


title: C7A29

tag: development day

tag: Stage


title: C7A32


title: C7A30


title: C7A28


title: C7A27


title: 108816A

tag: age

tag: eosinophils


title: 108931A

tag: bipolar disorder diagnosis

tag: neutrophils


title: 108844A

tag: Sex

tag: included in final analysis


title: 108857A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C7A26


title: 108773A

tag: assessment group

tag: tissue/cell type


title: 108765B

tag: rin

tag: sequencing plate


title: 108747B

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 108499A

tag: sequencing metric pc3

tag: monocytes


title: 108555A


title: 108611B


title: C7A24

tag: development day

tag: Stage


title: C7A21


title: C7A22


title: C7A23


title: C7A20


title: 108741B

tag: age

tag: eosinophils


title: C7A25


title: C7A19


title: 108082A

tag: bipolar disorder diagnosis

tag: neutrophils


title: 108180B

tag: Sex

tag: included in final analysis


title: C7A17


title: C7A18


title: C7A16


title: 108338A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: 108032A

tag: assessment group

tag: tissue/cell type


title: 099407A

tag: rin

tag: sequencing plate


title: 099598A

tag: sequencing metric pc1

tag: sequencing metric pc2


title: C7A14


title: C7A13


title: C7A15


title: 099329A

tag: sequencing metric pc3

tag: monocytes


title: C7A11

tag: development day

tag: Stage


title: C7A10


title: C14C15


title: 099328A

tag: age

tag: eosinophils


title: 108350A

tag: bipolar disorder diagnosis

tag: neutrophils


title: C14B34


title: C14B33


title: 099219A

tag: Sex

tag: included in final analysis


title: 099207A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C14C13


title: C14A12


title: C14C71


title: 099252A

tag: assessment group

tag: tissue/cell type


title: 099147B

tag: rin

tag: sequencing plate


title: C10C96


title: 099192A

tag: sequencing metric pc1

tag: sequencing metric pc2


title: 089687A

tag: sequencing metric pc3

tag: monocytes


title: 099408A


title: C10C9

tag: development day

tag: Stage


title: 089412B

tag: age

tag: eosinophils


title: 099394A

tag: bipolar disorder diagnosis

tag: neutrophils


title: 089425B

tag: Sex

tag: included in final analysis


title: 089366A

tag: lithium use (non-user=0, user = 1)

tag: tobacco use


title: C10C95


title: 089357B

tag: assessment group

tag: tissue/cell type


title: C10C93


title: C10C94


title: C10C91


title: Sample_40_TET2mut_AML_Input_rep2_ChIPseq

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
LSD1 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<1e-10 and fold-change threshold 2) (Giannopoulou and Elemento, 2011). Histone ChIP-seq peaks were called into peaks using MACS2 (q<0.01)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited

molecule: genomic DNA

source_name: AML ex vivo culture

extract_protocol: DNA was extracted using Qiagen Puregene kit protocol

tag: tissue

value: patient-derived TET2 mutant AML


title: C10C90


title: Sample_39_TET2mut_AML_Input_rep1_ChIPseq


title: C10C88


title: C13A20


title: Sample_38_TET2mut_AML_H3K4me27ac_rep2_ChIPseq


title: C10C87


title: 099175B

tag: rin

tag: sequencing plate

tag: sequencing metric pc1


title: C10C85


title: Sample_36_TET2mut_AML_H3K4me1_rep2_ChIPseq


title: Sample_35_TET2mut_AML_H3K4me1_rep1_ChIPseq


title: C10C82


title: 089851B

tag: sequencing metric pc2

tag: sequencing metric pc3

tag: monocytes


title: C10C81

tag: development day

tag: Stage


title: C10C78


title: C10C84


title: C10C92


title: Sample_22_TET2mut_AML_Input_ChIPseq

data_processing:
Illumina Casava1.8 software used for basecalling.
LSD1 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<1e-10 and fold-change threshold 2) (Giannopoulou and Elemento, 2011). Histone ChIP-seq peaks were called into peaks using MACS2 (q<0.01)
Genome_build: hg19


title: Sample_20_TET2mut_AML_LSD1iplus5Aza_RNAseq3

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
CPM were obtained using Rsubread
ERRBS reads were filtered from the adapter sequences using FAR software and aligned to genome using the bismark alignment software, retaining uniquely aligning reads with maximum of 2 directional mismatches
methylCall files were generated using methylKit
Genome_build: hg19

extract_protocol: RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)


title: Sample_21_TET2mut_AML_LSD1_ChIPseq


title: C10C76


title: Sample_18_TET2mut_AML_LSD1iplus5Aza_RNAseq1


title: C10C77


title: C10C74


title: Sample_16_TET2mut_AML_LSD1i_RNAseq2


title: Sample_19_TET2mut_AML_LSD1iplus5Aza_RNAseq2


title: Sample_17_TET2mut_AML_LSD1i_RNAseq3


title: C10C75


title: Sample_15_TET2mut_AML_LSD1i_RNAseq1


title: Sample_37_TET2mut_AML_H3K4me27ac_rep1_ChIPseq


title: Sample_14_TET2mut_AML_5Aza_RNAseq3


title: C10C71


title: C10C69


title: Sample_13_TET2mut_AML_5Aza_RNAseq2


title: C10C70


title: Sample_12_TET2mut_AML_5Aza_RNAseq1


title: Sample_10_TET2mut_AML_DMSO_RNAseq2


title: C10C68


title: C10C67


title: Sample_11_TET2mut_AML_DMSO_RNAseq3


title: Sample_9_TET2mut_AML_DMSO_RNAseq1

extract_protocol: RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer.


title: Sample_8_TET2mut_AML_LSD1iplus5Aza_ERRBS2

extract_protocol: DNA was extracted using Qiagen Puregene kit protocol; Libraries were prepared using RRBS and ERRBS as described in manuscript


title: C10C66


title: C10C50


title: C10C53


title: Sample_6_TET2mut_AML_LSD1i_ERRBS2


title: C10C65


title: Sample_5_TET2mut_AML_LSD1i_ERRBS1


title: Sample_4_TET2mut_AML_5Aza_ERRBS2


title: Sample_7_TET2mut_AML_LSD1iplus5Aza_ERRBS1


title: C10C73


title: C10C46


title: C10C44


title: C10C4


title: C10C72


title: C10C47


title: Sample_1_TET2mut_AML_DMSO_ERRBS1


title: Sample_230_1m-r1_RNA

data_processing:
The RNA-seq part of the data were first trimmed using Trim Galore! with default parameters to remove adapter sequence and low-quality bases. Trimmed reads were then aligned to mouse reference genome SNP-masked mm10 using STAR aligner. Only reads that uniquely mapped to mm10 were retained and read count on each gene in each sample was computed using featureCounts. SNP-masked genome was generated by masking C57BL/6 and CAST/Ei strain-specific SNPs as “N” in mm10 genome to avoid potential mapping bias.
Whole genome bisulfate sequencing reads were first trimmed using Trim Galore! to remove adapter and low-quality bases. The trimmed reads were then aligned to SNP-masked mm10 and CpG and non-CpG methylation signal was extracted using Bismark. Aligning reads to the masked genome can eliminate mapping bias and false-positive methylation result from C/G SNPs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each gene in each sample, generated by featureCounts.
Supplementary_files_format_and_content: coverage file generated by bismark

organism: Mus musculus

source_name: DRG sensory neuron

extract_protocol:
L4 and L5 DRGs were diaassociated by enzymatic treatment, and single sensory neurons were manually isolated.
Libraries were constructed using scMT-seq following our previous published protocol. scMT-seq consists of three steps: isolation of nucleus cytoplasma, single cell RNA-seq using cytoplasma and single cell whole genome bisulfate sequencing using the nucleus. Briefly, cell membrane specific lysis buffer were used to lyse membrane. Cell nucleus were picked out and put into nucleus lysis buffer. The remaining cell plasma were used for transcriptomic profiling by SMART-seq2. For the single cell whole genome bisulfate sequencing, the library was constructed by performing the single cell whole genome bisulfate sequencing protocol on the isolated nucleus. Both RNA-seq and WGBS libraries were sequenced on a Hiseq 4000 machine in pair-end, 150bp mode.
scMT-seq, low-input RNA-seq and low input whole genome bisulfate seqeuncing.

tag: strain

value: C57BL/6 X CAST/Ei

tag: age

tag: condition

value: injury

value: low-input


title: C10C31


title: Sample_229_8m-r1_RNA


title: Sample_228_1y-r1_RNA


title: C10C30


title: C10C28


title: C10C41


title: Sample_227_1m-l3_RNA

value: intact


title: C10C25


title: C10C17


title: Sample_225_1y-l3_RNA


title: Sample_224_1m-l2_RNA


title: Sample_226_8m-l3_RNA


title: C10C14


title: Sample_2_TET2mut_AML_DMSO_ERRBS2


title: C10C15


title: Sample_3_TET2mut_AML_5Aza_ERRBS1


title: Sample_221_L2_RNA


title: C10B94


title: Sample_222_1y-l2_RNA


title: Sample_220_R21m_RNA


title: C10B93


title: C10C12


title: C10B92


title: C10B91


title: Sample_219_R12L_RNA


title: Sample_218_L4L11M_meth

data_processing:
Library strategy: scMT-seq
The RNA-seq part of the data were first trimmed using Trim Galore! with default parameters to remove adapter sequence and low-quality bases. Trimmed reads were then aligned to mouse reference genome SNP-masked mm10 using STAR aligner. Only reads that uniquely mapped to mm10 were retained and read count on each gene in each sample was computed using featureCounts. SNP-masked genome was generated by masking C57BL/6 and CAST/Ei strain-specific SNPs as “N” in mm10 genome to avoid potential mapping bias.
Whole genome bisulfate sequencing reads were first trimmed using Trim Galore! to remove adapter and low-quality bases. The trimmed reads were then aligned to SNP-masked mm10 and CpG and non-CpG methylation signal was extracted using Bismark. Aligning reads to the masked genome can eliminate mapping bias and false-positive methylation result from C/G SNPs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each gene in each sample, generated by featureCounts.
Supplementary_files_format_and_content: coverage file generated by bismark


title: Sample_217_L5L23M_meth


title: C10C32


title: C10B90


title: Sample_216_L4R8M_meth


title: C10B88


title: C10B87


title: Sample_215_R10S_RNA


title: Sample_213_R5L_RNA


title: Sample_214_R8S_RNA


title: C10B86


title: Sample_223_8m-l2_RNA


title: C10B85


title: C10B84


title: C10B83


title: Sample_209_L5L22m_RNA


title: C10B82


title: Sample_211_L5L22M_meth


title: Sample_208_L5L21M_RNA


title: C10B80


title: Sample_212_L4L10M_meth


title: Sample_210_L4R7M_meth


title: Sample_207_L4L17S_RNA


title: C10B79


title: C10B78


title: Sample_206_L4L9M_meth


title: C10B75


title: C10B77


title: C10B81


title: C10B74


title: Sample_202_L4L12S_RNA


title: Sample_204_L4R5S_meth


title: C10B65


title: Sample_203_L16_meth


title: C10B64


title: C10B63


title: Sample_199_L4L8M_meth


title: C10B61


title: Sample_201_L4L8M_RNA


title: C10B59


title: Sample_194_L5R8S_RNA


title: C10B60


title: Sample_197_L4R16_meth


title: C10B58


title: C10B57


title: C10B56


title: Sample_192_L4L6M_meth


title: Sample_205_L4L17S_meth


title: Sample_198_L5R5S_meth


title: C10B55


title: Sample_196_L4R4M_meth


title: Sample_193_L5R5S_RNA


title: C10B54


title: Sample_195_L4L3M_RNA


title: C10B52


title: Sample_190_L4R15M_meth


title: Sample_191_L5R2L_meth


title: C10B53


title: Sample_200_L4L4M_RNA


title: C10B51


title: Sample_189_L4R3_meth


title: C10B49


title: Sample_188_L5R3L_RNA


title: C10B50


title: Sample_187_L5R2L_RNA


title: C10B38


title: C10B39


title: Sample_185_L4L5S_meth


title: Sample_184_L5R1M_meth


title: Sample_180_L4R15M_RNA


title: C10B36


title: Sample_183_L4R14L_meth


title: C10B35


title: Sample_181_L4R16_RNA


title: Sample_182_L4R2_meth


title: Sample_179_L4R14L_RNA


title: C10B37


title: C10B32


title: C10B34


title: Sample_178_R23S_meth


title: Sample_177_L4R11M_meth


title: C10B33


title: C10B31


title: Sample_175_L4R11M_RNA


title: C10B28


title: C10B30


title: Sample_186_L5R1M_RNA


title: Sample_176_L4R1_meth


title: C10B27


title: C10B29


title: Sample_172_L4L3M_meth


title: C10B26


title: Sample_173_L4R1_RNA


title: Sample_174_L4R8M_RNA


title: C10B24


title: Sample_170_R12L_meth


title: Sample_171_R22M_meth


title: C10B25


title: C10B22


title: Sample_167_L14_RNA


title: Sample_169_R8S_meth


title: C10B20


title: C10B19


title: Sample_166_L11_RNA


title: Sample_163_R24S_meth


title: C10A80


title: C10B13


title: Sample_165_L10_RNA


title: C10B14


title: C10B11


title: C10A73


title: Sample_164_L3_meth


title: Sample_162_R16L_meth


title: Sample_160_R24S_RNA


title: C10A74


title: C10B10


title: Sample_159_R23S_RNA


title: C10A70


title: Sample_161_R7M_meth


title: C10A30


title: A-22

value: blastocyst


title: Sample_168_L15_RNA


title: B-3


title: Sample_157_R18ML_RNA


title: Sample_156_L12_meth


title: Sample_154_R21S_meth


title: Sample_153_R15M_meth


title: Sample_152_R2L_meth


title: A-18


title: A-16


title: A-20


title: A-21


title: Sample_150_R15M_RNA


title: A-15


title: Sample_148_R13L_RNA


title: 7G-8


title: Sample_158_R21S_RNA


title: A-13


title: A-14


title: Sample_149_R14L_RNA


title: 7G-7


title: Sample_145_L5_meth


title: 7G-6


title: C10A25


title: Sample_144_R20S_meth


title: Sample_155_L7_meth


title: 7G-5


title: Sample_143_R1M_meth


title: A-19


title: Sample_142_R17ML_RNA


title: Sample_151_R16L_RNA


title: 7G-3


title: 7G-2


title: Sample_147_R14L_meth


title: 7G-1


title: Sample_139_R6M_RNA


title: 7F-8


title: Sample_138_R4M_RNA


title: Sample_146_L9_meth


title: Endo_D3

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for cell surface phenotype-CD3+CD4+CD25hiCD127lo (D3)

data_processing:
Cellranger 2.1.1 default-parameters
Monocle
Genome_build: Mmul8
Supplementary_files_format_and_content: tab-delim file of genes(rows) and cells (columns)

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Cells were cryopreserved, sorted using FACS and captured using 10x genomics single cell platform
10x single cell 3' v2

tag: cell type

value: PBMC


title: CFSEpos_D3

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for CFSE+ (D3)


title: CD127posCD25pos_D20

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for cell surface phenotype-CD3+CD4+CD25posCD127pos (D20)


title: CD127posCD25neg_D20

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for cell surface phenotype-CD3+CD4+CD25negCD127pos (D20)


title: Sample_137_R3S_RNA


title: 7G-4


title: 7F-6


title: Endo_D20

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for cell surface phenotype-CD3+CD4+CD25hiCD127lo (D20)


title: 7F-7


title: Sample_136_L2_meth


title: CFSEpos_D20

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for CFSE+ (D20)


title: 7F-5


title: Sample_140_R7M_RNA


title: CD127posCD25pos_D3

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for cell surface phenotype-CD3+CD4+CD25posCD127pos (D3)


title: Sample_141_R9M_RNA


title: P9-S3 [discovery cohort]

type: RNA

city: Toronto

first: Jouhyun

last: Jeon

state: Ontario

address: 101 College Street

country: Canada

institute: Ontario Institute for Cancer Research

description:
Biological replicate 2 from Patient 9
BB_9c_09

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: miRNAs abundance was normalized using the R package NanoStringNorm.

source_name: Prostate cancer urine

extract_protocol: Small RNA molecules were isolated from urinary cell sediments using the Urine miRNA Purification kit (Norgen Biotek Corp., Thorold, Ontario, Canada, Catalogue # 29000) according to the manufacturer’s protocol.

tag: subject id

value: Patient 9

tag: subject status

value: prostate cancer patient

tag: nccn-risk

tag: cohort type

value: Discovery

tag: batch

tag: cell/sample type

value: urinary cell sediments


title: P9-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 9
BB_9b_08


title: CD127posCD25neg_D3

description: PBMC were cryopreserved on date indicated.  Cells were thawed on December 8, 2017.  Cells were enriched for CD4+ using immunomagnetic kit and sorted for cell surface phenotype-CD3+CD4+CD25negCD127pos (D3)


title: P10-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 1
BB_10b_11

value: Patient 1


title: 7F-4


title: Sample_135_R19L_meth


title: P10-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 10
BB_10a_10

value: Patient 10


title: Control sample 2 [discovery cohort]

description:
Control sample
BB_Cell_Line_12

source_name: Prostate cancer cell lines


title: P9-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 9
BB_9a_07


title: Sample_134_R10S_meth


title: P8-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 8
BB_8b_06

value: Patient 8


title: 7F-3


title: P8-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 8
BB_8a_05


title: Sample_133_R5L_meth


title: 7F-2


title: P7-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 7
BB_7a_03

value: Patient 7


title: P7-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 7
BB_7b_04


title: Control sample 1 [discovery cohort]

description:
Control sample
Bapat_12.Cell_Line_12


title: 7F-1


title: Sample_131_R1M_RNA


title: P6-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 6
BB_6a_01

value: Patient 6


title: P6-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 6
BB_6b_02


title: P5-S3 [discovery cohort]

description:
Biological replicate 2 from Patient 5
Bapat_11.5c_11

value: Patient 5


title: 7F-12

value: implantation


title: P5-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 5
Bapat_10.5b_10


title: Sample_130_L1_RNA

value: C57BL/6 X CAST/Ei


title: 7F-11


title: Sample_129_L16_RNA


title: 7E-9


title: 7E-8


title: Sample_132_R2L_RNA

value: injury


title: P4-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 4
Bapat_7.4a_07

value: Patient 4


title: P4-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 4
Bapat_8.4b_08


title: P2-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 2
Bapat_4.2b_04

value: Patient 2


title: Sample_127_R18ML_meth


title: P3-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 3
Bapat_6.3b_06

value: Patient 3


title: P3-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 3
Bapat_5.3a_05


title: 7E-7


title: Sample_126_R9M_meth


title: 7E-6


title: P2-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 2
Bapat_3.2a_03


title: P1-S2 [discovery cohort]

description:
Biological replicate 2 from Patient 1
Bapat_2.1b_02


title: P1-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 1
Bapat_1.1a_01


title: Sample_125_R6M_meth


title: P122 [validation cohort]

tag: tissue/sample type

value: Prostate cancer urine

value: H

tag: gs-risk

value: Validation


title: Sample_124_L16_RNA

value: intact


title: P123 [validation cohort]

value: L


title: 7E-5


title: 7E-4


title: Sample_123_1y-r1_meth

value: low-input


title: P5-S1 [discovery cohort]

description:
Biological replicate 1 from Patient 5
Bapat_9.5a_09

value: prostate cancer patient

value: Discovery

value: urinary cell sediments


title: P106 [validation cohort]


title: P120 [validation cohort]


title: P112 [validation cohort]


title: Sample_128_L8_meth


title: 7E-3


title: P100 [validation cohort]


title: P98 [validation cohort]


title: P97 [validation cohort]


title: P93 [validation cohort]


title: 7E-10


title: P96 [validation cohort]


title: 7E-1


title: Sample_120_L14_RNA


title: P90 [validation cohort]


title: P80 [validation cohort]


title: 7A-8


title: P76 [validation cohort]


title: 7A-7


title: Sample_118_L1_RNA


title: P70 [validation cohort]


title: Sample_117_R13L_RNA


title: Sample_122_1y-l3_meth


title: P67 [validation cohort]


title: 7A-6


title: P66 [validation cohort]


title: P65 [validation cohort]


title: 7E-2


title: 7A-5


title: P63 [validation cohort]


title: Sample_121_8m-r2_meth


title: P55 [validation cohort]


title: Sample_115_L5L23M_RNA


title: P62 [validation cohort]


title: P61 [validation cohort]


title: P52 [validation cohort]


title: 7A-1


title: Sample_119_R14L_RNA


title: Sample_114_L11_RNA


title: Sample_113_1m-r3_RNA

value: 1 month


title: P49 [validation cohort]


title: P44 [validation cohort]


title: 7A-14


title: P43 [validation cohort]


title: Sample_112_R23S_RNA


title: Sample_116_R24S_RNA


title: P42 [validation cohort]


title: P41 [validation cohort]


title: P40 [validation cohort]


title: 7A-12


title: Sample_111_L5L21M_RNA


title: P39 [validation cohort]


title: 6C-9

value: blastocyst


title: Sample_110_L10_RNA


title: Sample_109_R21S_RNA


title: P36 [validation cohort]


title: P34 [validation cohort]


title: 6C-7


title: 7A-16

value: implantation


title: Sample_108_R9M_RNA

value: C57BL/6 X CAST/Ei


title: P25 [validation cohort]


title: P32 [validation cohort]


title: P31 [validation cohort]


title: 6C-5


title: P24 [validation cohort]


title: P30 [validation cohort]


title: 6C-4


title: Sample_107_L5L20L_RNA


title: 6C-3


title: Sample_106_L5L19L_RNA


title: P17 [validation cohort]


title: Sample_105_R19L_RNA

value: injury


title: 7A-11


title: P20 [validation cohort]


title: Sample_104_R7M_RNA


title: P8 [validation cohort]


title: P15 [validation cohort]


title: 6C-2


title: P33 [validation cohort]


title: P7 [validation cohort]


title: 6C-15


title: Sample_103_R6M_RNA


title: 6C-14


title: Sample_102_L15_RNA


title: 6C-13


title: KO3-WNV-2_S16

city: Galveston

first: Rajsbaum

last: Ricardo

state: TX

address: 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch at Galveston

data_processing:
Cluster formation of the library DNA templates was performed using the TruSeq PE Cluster Kit v3 (Illumina) and the Illumina cBot workstation using conditions recommended by the manufacturer.
Paired end 50 base sequencing by synthesis was performed using TruSeq SBS kit v3 (Illumina) on an Illumina HiSeq 1500 using protocols defined by the manufacturer.
Alignment of NGS sequence reads was performed using the Spliced Transcript Alignment to a Reference (STAR) program, version  2.5.1b, using default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen) followed by DNase I treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Airway epithelial cells

tag: genotype/variation

value: TRIM6 Knockout

tag: infection

value: WNV at MOI = 5

tag: tissue

value: Lung

tag: sample type

value: Test


title: KO3-WNV-1_S15


title: KO3-mock-1_S13

value: Mock with PBS

value: Control


title: A549-WNV-2_S12

value: Wild-type


title: KO3-mock-2_S14


title: A549-WNV-1_S11


title: Sample_101_R17ML_RNA

tag: strain


title: A549-wt-mock-2_S10


title: A549-wt-mock-1_S9


title: 6C-12

tag: development day

tag: Stage


title: 6C-11


title: P2 [validation cohort]

value: Prostate cancer urine

value: H

value: Validation


title: Sample_98_R4M_RNA

tag: age

tag: condition


title: Sample_97_R15M_RNA


title: Sample_99_R16L_RNA


title: 6B-5


title: P1 [validation cohort]

value: L


title: 6B-3


title: Sample_96_R3S_RNA


title: Sample_100_L4_RNA

value: intact


title: Sample_95_8m-r3_RNA

value: 8 month

value: low-input


title: 6B-1

value: blastocyst


title: Sample_94_1y-r3_RNA

value: C57BL/6 X CAST/Ei

value: 12 month

value: injury


title: 6B-20


title: 6B-14


title: Sample_93_L4L1M_RNA


title: 6A-9


title: Sample_92_L4R13S_RNA


title: Sample_91_1m-r2_RNA

value: 1 month


title: Sample_90_8m-r2_RNA


title: 6A-6


title: 6A-5


title: 6A-7


title: 6A-4


title: 6A-3


title: 6C-10


title: Sample_88_L5R7S_meth


title: 6A-2


title: Sample_87_L4L7M_meth


title: 6A-19


title: Sample_84_L4L11M_RNA


title: Sample_86_L5R8S_RNA


title: 6A-17


title: Sample_82_L4R9M_meth


title: 6A-18


title: Sample_85_L4R12m_RNA


title: 6A-15


title: Sample_83_L5R7S_RNA


title: 6A-16


title: Sample_81_L4L10M_RNA


title: 6A-14


title: 6A-11


title: Sample_79_L4R10S_RNA


title: 6A-13


title: Sample_89_1y-r2_RNA


title: Sample_78_L4L9M_RNA


title: Control sample 9 [training cohort]

description:
Control sample
X20170419_H.miRNA.v3.40.BB_I.Cell.Line_12

value: Prostate cancer cell lines

value: Training


title: Sample_75_L5R4M_RNA


title: Sample_76_L4R9M_RNA


title: Sample_74_L4L7M_RNA


title: Sample_73_L5R3L_RNA


title: I6 [training cohort]


title: I7 [training cohort]


title: I9 [training cohort]


title: I8 [training cohort]


title: Sample_80_L5R6S_RNA


title: Sample_72_L5R2L_RNA


title: Sample_71_1m-r1_meth


title: Sample_69_L5L18L_RNA


title: Sample_70_L4R6L_RNA


title: I5 [training cohort]


title: Sample_68_L4L5S_RNA


title: I3 [training cohort]


title: Sample_66_L4R16_RNA


title: I11 [training cohort]


title: I4 [training cohort]


title: Sample_67_L4L17S_RNA


title: Sample_64_L4L2L_RNA


title: Sample_65_L4R4M_RNA


title: H9 [training cohort]


title: I10 [training cohort]


title: Control sample 8 [training cohort]

description:
Control sample
X20170419_H.miRNA.v3.39.BB_H.Cell.Line_12


title: I1 [training cohort]


title: Sample_77_L5R5S_RNA


title: H8 [training cohort]


title: Sample_61_1m-r1_RNA


title: Sample_63_L4R14L_RNA


title: Sample_62_L4R2_RNA


title: Sample_59_1y-r1_RNA


title: H7 [training cohort]


title: H6 [training cohort]


title: Sample_60_8m-r1_RNA


title: H5 [training cohort]


title: H4 [training cohort]


title: H3 [training cohort]


title: Sample_58_L5R4M_meth


title: H2 [training cohort]


title: I2 [training cohort]


title: Sample_52_1y-l3_RNA


title: Sample_56_1m-l3_meth


title: Sample_57_L4L12S_meth


title: Sample_55_L14_meth


title: H11 [training cohort]


title: H1 [training cohort]


title: Sample_50_L5L18L_meth


title: G9 [training cohort]


title: Sample_54_1m-l3_RNA


title: Sample_53_8m-l3_RNA


title: G8 [training cohort]


title: H10 [training cohort]


title: Sample_51_L5R6S_meth


title: Control sample 7 [training cohort]

description:
Control sample
X20170413_H.miRNA.v3.38.BB_G.Cell.Line_12


title: G4 [training cohort]


title: Sample_49_R3S_meth


title: G7 [training cohort]


title: G6 [training cohort]


title: Sample_47_1m-l2_RNA


title: Sample_45_1y-l2_RNA


title: Sample_46_8m-l2_RNA


title: G5 [training cohort]


title: G3 [training cohort]


title: G2 [training cohort]


title: G11 [training cohort]


title: Sample_43_L4_meth


title: Sample_42_L5L19L_meth


title: G1 [training cohort]


title: Sample_44_R17ML_meth


title: Sample_41_L15_meth


title: Sample_40_1m-l1_RNA


title: Sample_48_L11_meth


title: Sample_39_8m-l1_RNA


title: G10 [training cohort]


title: Control sample 6 [training cohort]

description:
Control sample
X20170413_H.miRNA.v3.37.BB_F.Cell.Line_12


title: Sample_36_L4R12M_meth


title: F9 [training cohort]


title: Sample_38_1y-l1_RNA


title: F8 [training cohort]


title: F6 [training cohort]


title: Sample_35_R4M_meth


title: F7 [training cohort]


title: F5 [training cohort]


title: F4 [training cohort]


title: Sample_34_L10_meth


title: F2 [training cohort]


title: Sample_32_L4_RNA


title: F3 [training cohort]


title: F11 [training cohort]


title: Sample_30_R4M_RNA


title: F1 [training cohort]


title: F10 [training cohort]


title: Sample_37_L1_meth


title: Sample_29_R2L_RNA


title: Sample_27_L4L5S_RNA


title: Sample_28_R1M_RNA


title: Control sample 5 [training cohort]

description:
Control sample
X20170412_H.miRNA.v3.36.BB_E.Cell.Line_12


title: Sample_26_L4L2L_RNA


title: E7 [training cohort]


title: Sample_25_L4L1M_RNA


title: Sample_24_L4R6L_RNA


title: Sample_33_L10_RNA


title: E6 [training cohort]


title: Sample_21_R3S_RNA


title: Sample_22_L4R2_RNA


title: Sample_31_L1_RNA


title: Sample_20_1MR3_meth


title: E2 [training cohort]


title: E11 [training cohort]


title: E1 [training cohort]


title: Sample_17_1MR2_meth


title: Sample_18_1YR3_meth


title: Control sample 4 [training cohort]

description:
Control sample
X20170412_H.miRNA.v3.35.BB_D.Cell.Line_12


title: E10 [training cohort]


title: D9 [training cohort]


title: E9 [training cohort]


title: Sample_15_1YR2_meth


title: E8 [training cohort]


title: Sample_16_8MR2_meth


title: E5 [training cohort]


title: D8 [training cohort]


title: Sample_23_L4R4M_RNA


title: E4 [training cohort]


title: Sample_12_1YR1_meth


title: D7 [training cohort]


title: E3 [training cohort]


title: Sample_19_8MR3_meth


title: D6 [training cohort]


title: Sample_11_8MNL2_meth


title: D5 [training cohort]


title: Sample_10_1ML3_meth


title: D4 [training cohort]


title: D3 [training cohort]


title: Sample_13_8MR1_meth


title: Sample_7_1YL3_meth


title: Sample_8_8MNL1_meth


title: D11 [training cohort]


title: D2 [training cohort]


title: Sample_9_8ML3_meth


title: Sample_14_1MR1_meth


title: Sample_6_1ML2_meth


title: D10 [training cohort]


title: Sample_4_1YL2_meth


title: D1 [training cohort]


title: Control sample 3 [training cohort]

description:
Control sample
X20170411_H.miRNA.v3.34.BB_C.Cell.Line_12


title: Sample_5_8ML2_meth


title: Sample_2_8ML1_meth


title: Sample_3_1ML1_meth


title: C9 [training cohort]


title: C8 [training cohort]


title: siNT OSS 3

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.80
Supplementary_files_format_and_content: raw counts

source_name: NT OSS rep3

growth_protocol: bEnd.3 cells were grown were grown in DMEM (41966-029, Gibco) supplemented with 10% fetal bovine serum (FBS) and 5000 U/L penicillin and 5 mg/ml streptomycin (Mediatach) on Ibidi μ-Slide VI0.4 coated with 1.5% gelatin (Sigma Aldrich).

extract_protocol:
Total RNA was isolated using NucleoSpin RNA II (Macherey-Nagel) according to the manufacturers’ instructions. Quality of the 3 samples per condition was verified using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit (Agilent Technologies).
cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA sample Preparation Kit according to the manufacturers’ protocol.
Libraries were sequenced using single-end (50nt-long) on Illumina HiSeq2000. FastQ reads were mapped to the ENSEMBL reference genome (GRCm38.80) using STAR version 2.4.0j [22] with standard settings, except that any reads mapping to more than one location of the genome (ambiguous reads were discarded (m=1)).

treatment_protocol: Silencing of KLF4 or Cx40 in bEnd.3 cells was done using short interfering RNA (siRNA) SMARTpool ON-TARGETplus Mouse KLF4 siRNA or Mouse Gja5 siRNA (Dharmacon). As negative control the ON-TARGETplus Non-targeting (NT) Pool (Dharmacon) was used. The transfections were performed under serum-free conditions with 25 nmol/L siRNA and 5 mg/L DharmaFECT4 (Dharmacon).

tag: cell type

value: endothelial cells

tag: treatment

value: OSS

tag: knockdown

value: control


title: C6 [training cohort]

value: Prostate cancer urine

tag: nccn-risk

tag: cohort type

tag: batch


title: Sample_1_1YL1_meth


title: C4 [training cohort]

tag: tissue/sample type

tag: gs-risk

value: H


title: C5 [training cohort]


title: C2 [training cohort]


title: siNT OSS 2

source_name: NT OSS rep2


title: siNT OSS 1

source_name: NT OSS rep1


title: C7 [training cohort]


title: siNT HLSS 2

source_name: NT HLSS rep2

value: HLSS


title: siNT HLSS 3

source_name: NT HLSS rep3


title: 97121

type: genomic

city: Providence

first: Karl

middle: T

last: Kelsey

state: Rhode Island

address: 40 Ship St

department: Epidemiology

institute: Brown University

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Removed probes with detetction p-value > 0.05, preprocessed using functional and BMIQ normalization

label: Cy3, Cy5

source_name: Sperm

label_protocol: Standard Illumina protocol

extract_protocol: Standard Illumina protocol

value: sperm

tag: dioxin

tag: dioxin group

value: HIGH

tag: smoking

value: Former

tag: bmi


title: C11 [training cohort]

value: L


title: 35034

value: MED

value: Never


title: siNT HLSS 1

source_name: NT HLSS rep1


title: 97107

value: CONTROL


title: siCx40 OSS 3

source_name: Cx40 OSS rep3

value: knock-down of Cx40


title: 35040


title: 97109


title: C1 [training cohort]


title: 35081

value: LOW


title: 97129


title: 97134


title: 35051


title: siCx40 OSS 2

source_name: Cx40 OSS rep2


title: 35013


title: 97119


title: C3 [training cohort]


title: siCx40 HLSS 3

source_name: Cx40 HLSS rep3


title: siCx40 OSS 1

source_name: Cx40 OSS rep1


title: B9 [training cohort]


title: 35070


title: 35029


title: B7 [training cohort]


title: siCx40 HLSS 2

source_name: Cx40 HLSS rep2


title: Control sample 2 [training cohort]

description:
Control sample
X20170411_H.miRNA.v3.33.BB_B.Cell.Line_12

value: Prostate cancer cell lines


title: 35038


title: siCx40 HLSS 1

source_name: Cx40 HLSS rep1


title: 35053


title: Sample_1181

city: Shanghai

first: Haifang

last: Wang

address: NO 320, Yue Yang Road

country: China

institute: Institute of Neuroscience

data_processing:
Sequence images were transformed to per read base call files (fastq files) with Illumina software BaseCaller and CASAVA v1.8.2.
We first check the quality of the data via fastqc (v.0.10.0, Babraham Bioinformatics). Raw sequence reads were aligned to mouse genome (mm9) by Tophat program (V2.0.8 custom parameters: --no-coverage-search) (Trapnell et al. 2009, Bioinformatics). Then bedtools (v2.16.2 default parameters) (Aaron et al. 2010, Bioinformatics) were applied to calculate the number of reads of each transcript based on the gene annotations from UCSC genome browser. The reads counts were then normalized to RPKM (Reads per kilobases per milionreads) by R scripts.
Genome_build: mm9
Supplementary_files_format_and_content: text file of normalized read counts (RPKM) for each gene

source_name: hippocampal CA1, Control

extract_protocol:
RNA was extracted using Phenol Chloroform extraction.
1 μg of total RNA were converted into Illumina sequencing libraries using the TruSeq RNA Sample Preparation Kit (Illumina, RS-122-2002) as per manufacturer’s protocol.

treatment_protocol: Adult male Tip60 cKO mice and their respective control littermates were used for the experiments. Mice were tamoxifen-treated at 2 months of age and sacrificed 10 days after the last tamoxifen injection.

tag: tissue

value: hippocampal CA1

tag: strain

tag: Sex

value: Male

tag: genotype

value: Control


title: 97104

tag: age


title: Sample_1182

source_name: hippocampal CA1, cKO

value: cKO


title: 35043

tag: cell type


title: B4 [training cohort]

source_name: Prostate cancer urine

value: Prostate cancer urine

value: Training


title: Sample_1179


title: B8 [training cohort]

value: H


title: B2 [training cohort]


title: B3 [training cohort]


title: B5 [training cohort]


title: Sample_1171


title: B11 [training cohort]


title: Sample_1164


title: B6 [training cohort]


title: B1 [training cohort]


title: 35041

value: sperm


title: Control sample 1 [training cohort]

description:
Control sample
X20170407_H.miRNA.v3.32.BB_A.Cell.Line_12

source_name: Prostate cancer cell lines


title: Sample_1159


title: A9 [training cohort]


title: Sample_1165


title: 35079

value: HIGH


title: C10 [training cohort]


title: 35052

value: Former


title: B10 [training cohort]


title: Sample_1157


title: Sample_1156


title: Sample_1155


title: 35082


title: A7 [training cohort]


title: A6 [training cohort]

value: L


title: ipL_KO5

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

department: Surgery

institute: Vanderbilt University Medical Center

description:
Tamoxifen-induced VillinCreERT2;MYO5Bflox/flox mice treated with LPA for 4 days
LPA (3 mg/kg) was intraperitoneally injected  for 4 days

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
Alignments were parsed using Tophat program.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene (Mortazavi et al. 2008).
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (v2.4.3), in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecularlevel information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: Excel includes comparisons of differential expression genes by FPKM

source_name: Jejunal epithelial cells

extract_protocol:
Epithelial cells were mechanically isolated from jejunum by micro forceps in ice-cold PBS containing 10 mM EDTA and immersed in TRIzol Reagent (Invitrogen 15596018).
Libraries were prepared by Novogene Corporation Inc. (Sacramento, CA). mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented  randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and  RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified doublestranded  cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA  fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select  cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system  (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR  products by AMPure XP beads.

treatment_protocol: Adult male VillinCreERT2;MYO5Bflox/flox mice were given a single dose of 2 mg of tamoxifen (KO, 7 mice) or corn oil (control, 3 mice) by ip injection.

value: Jejunum

tag: phenotype


title: ipL_KO4


title: A5 [training cohort]


title: EN_6m_4

city: Lexington

first: Shavahn

middle: C

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

description: processed data file: processed_data.xlsx

data_processing:
The sequencing results were initially trimmed for adapters and quality using TrimGalore Version 0.4.4 (Babraham Bioinformatics; www.bioinformatics.babraham.ac.uk).
Mapped to EquCab3.0 using STAR-2.5.2b (github.com/alexdobin/STAR).
Cufflinks-2.2.1 (cole-trapnell-lab.github.io/cufflinks/) was used to quantify data in fragments per kilobase/million (FPKM), with the Equus_caballus_Ensembl_95 gtf file used for annotation (-G).
Genome_build: EquCab3.0
Supplementary_files_format_and_content: processed_data.xlsx: Excel file includes FPKM values.

organism: Equus caballus

source_name: endometrium

extract_protocol:
Isolation of RNA from tissue was performed using RNeasy Mini Kit (Qiagen, Gaithersburg, MD, USA), per manufacturer’s instructions. After extraction, RNA was analyzed by NanoDrop® (Thermo Fisher Scientific) and Bioanalyzer® (Agilent, Santa Clara, CA, USA) to evaluate concentration, purity and integrity. All samples had a 230/260 ratio > 1.8, a 260/280 ratio > 2.0 and an RNA integrity number > 8.0.
Library preparation was performed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), per manufacturer’s instructions. The adapter for Read 1 was AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG, with NNNNNN signifying the index sequence. The read 2 adapter was AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT. All reads were quantified with qPCR. Sequencing was performed on a HiSeq 4000 (Illumina) using a HiSeq 4000 sequencing kit version 1, generating 150 bp paired-end reads (University of Illinois Roy J. Carver Biotechnology Center). FASTQ files were generated and demultiplexed using bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Female

value: Endometrium of placenta

tag: gestational age


title: EN_6m_3


title: 97112

value: Current


title: A8 [training cohort]

tag: nccn-risk


title: Sample_1173


title: A4 [training cohort]

tag: cohort type


title: 97128

value: CONTROL


title: 97152

value: Never


title: Tmx_KO7

description:
Tamoxifen-induced VillinCreERT2;MYO5Bflox/flox mice treated with vehicle for 4 days
Vehicle (0.1% BSA in PBS) was intraperitoneally injected  for 4 days


title: 97125

value: MED


title: 35094


title: 35071


title: A3 [training cohort]

tag: batch


title: 97153

value: LOW


title: 35084


title: EN_6m_2


title: 97154


title: EN_6m_1


title: EN_4m_4


title: 97149


title: Tmx_KO6


title: 35037


title: EN_4m_3


title: Tmx_KO5


title: Tmx_KO3


title: A2 [training cohort]

tag: tissue/sample type


title: ipL_KO1

description:
Tamoxifen-induced VillinCreERT2;MYO5Bflox/flox mice treated with vehicle for 4 days
LPA (3 mg/kg) was intraperitoneally injected  for 4 days


title: Sample_1158

value: hippocampal CA1

value: Male


title: 97148


title: Non_KO5

description: Non-induced VillinCreERT2;MYO5Bflox/flox mice

value: WT


title: A1 [training cohort]

value: Prostate cancer urine

tag: gs-risk

value: Training


title: EN_4m_1


title: 35077

value: sperm

tag: dioxin


title: A10 [training cohort]


title: A11 [training cohort]


title: Sample treated with Sinorhizobium fredii USDA257, replicate 3

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

description:
Sample 9
USDA_257_3
Compatible: Glycine max L76-1988, Sinorhizobium fredii USDA257

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were qulaity checked with fastqc, mapped to Glycine max (a2.v1)  whole genome using STAR v2.5.2a
FeatureCounts (v1.4.6) from subread was used to estimate read counts for genes
Genome_build: a2.v1 (https://soybase.org/dlpages/, https://soybase.org/data/public/Glycine_max/Wm82.gnm2.DTC4/glyma.Wm82.gnm2.DTC4.genome_main.fna.gz)
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each Sample

organism: Glycine max

source_name: Leaf

growth_protocol: Soybean (Glycine max (L.) Merr.) L76-1988 was grown in the green house with day and night temperatures of 25°C and 20°C, respectively.

extract_protocol:
RNA from leaf tissues was extracted at 24 h post rhizobia inoculation using the TRIzol reagent (Invitrogen, Carlsbad, CA), per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA Library Prep Kit), Paired-end

treatment_protocol: Plants were grown in sterile vermiculite and roots of plants (V1 stage) were inoculated with B. japonicum USDA122 or S. fredii USDA257 (0.5 OD600).

tag: growth stage

value: V1 stage

tag: line

tag: treatment

value: Sinorhizobium fredii USDA257

value: Leaf


title: EN_11m_4

tag: tissue


title: 97117

tag: dioxin group

tag: smoking

value: Former

tag: bmi


title: Sample treated with Sinorhizobium fredii USDA257, replicate 2

description:
Sample 8
USDA_257_2
Compatible: Glycine max L76-1988, Sinorhizobium fredii USDA257


title: Non_KO2

tag: strain

value: Jejunum

tag: genotype


title: 35097

tag: cell type

value: HIGH

tag: age


title: EN_11m_3

tag: Sex

value: Female

value: Endometrium of placenta

tag: gestational age


title: EN_11m_2


title: Non_KO4

tag: phenotype


title: Sample treated with Bradyrhizobium japonicum USDA122, replicate 3

description:
Sample 6
USDA_122_3
Incompatible: Glycine max L76-1988, Bradyrhizobium japonicum USDA122

value: Bradyrhizobium japonicum USDA122


title: EN_10m_4


title: Sample treated with Sinorhizobium fredii USDA257, replicate 1

description:
Sample 7
USDA_257_1
Compatible: Glycine max L76-1988, Sinorhizobium fredii USDA257


title: Sample treated with Bradyrhizobium japonicum USDA122, replicate 2

description:
Sample 5
USDA_122_2
Incompatible: Glycine max L76-1988, Bradyrhizobium japonicum USDA122


title: Cpmedia_3

first: Christopher

last: Lopez

state: Tennessee

address: 1161 21st Avenue South, Medical Center North

data_processing:
Libraries diluted to 12.5 nM and pooled equimolar prior to clustering. Paired end sequencing performed on Illumina HiSeq2500 sequencer
QC performed on raw sequence data from each sample using FastQC (Babraham Bioinformatics)
Curated raw reads imported into the data analysis platform Avadis NGS and mapped to reference C. difficile R20291 genome
Aligned reads were filtered on various criteria to ensure high quality
Replicate samples were grouped and quantification of transcripts performed using Trimmed Means of M-Values as the normalization method
Differential expression of genes was calculated using fold change observed between conditions and p-value was estimated by Z-score calculations using Benjamini Hochberg FDR correction of 0.05
Genome_build: GCA_000027105.1
Supplementary_files_format_and_content: Excel file of normalized transcript values

organism: Clostridioides difficile

source_name: bacterial RNA

growth_protocol: Overnight culture of C. difficile grown in brain heart infusion plus yeast extract supplement (BHIS) was diluted 1:100 into media composed of 1:1 BHIS broth:calprotectin buffer (20 mM Tris pH 7.5, 100 mM NaCl, 3 mM CaCl2). Bacteria were grown at 37C anaerobically to an approximate optical density (OD) 600 of 0.3.

extract_protocol:
bacterial cells were stored at -80°C in a 1:1 solution of acetone and ethanol in a volume equal to the culture volume. To extract RNA, samples were thawed on ice, pelleted, and resuspended in LETS buffer (1 M LiCl, 0.5 M EDTA, and 1 M Tris pH 7.4). Cells were transferred to lysing matrix B tubes (MP Biomedicals) and lysed using a FastPrep-24 (MP Biomedicals) bead beater for 45 seconds at 6 m/s. Samples were then incubated at 55°C for 5 minutes and pelleted by centrifugation. The supernatant was transferred to a tube containing 1 mL TRIzol reagent (Thermo Scientific) and 200 mL chloroform. The mixture was vortexed, then centrifuged at max speed for 15 minutes. The aqueous upper layer was then transferred to a fresh tube with 1 mL isopropyl alcohol to precipitate RNA. RNA was pelleted, then washed with 200 ml 70% ethanol. Samples were air dried for 1 minute, then resuspended in 100 mL RNase free water. DNA contamination was removed using RQ1 DNase I (Promega) following manufacturer instructions. After DNase treatment, RNA was further purified using the RNeasy miniprep RNA cleanup kit (Qiagen) following manufacturer instructions
RNA-seq library construction and sequencing was performed by HudsonAlpha. Concentration was determined using the Quant-iT RiboGreen RNA assay (Thermo Scientific) and integrity was visualized using an RNA 6000 nano chip (Agilent) on an Agilent 2100 Bioanalyzer (Applied Biosystems). RNA was normalized to 500 ng of total RNA for each sample and the ribosomal RNA (rRNA) was removed using Ribo-Zero rRNA Removal Kit (Illumina). Directly after rRNA removal, the RNA was fragmented and primed for first strand synthesis using the NEBNext First Strand synthesis module (New England BioLabs Inc.) followed by second strand synthesis using NEBNext Ultra Directional Second Strand synthesis kit. Library preparation was achieved using NEBNext DNA Library Prep Master Mix set for Illumina with minor modifications. PolyA addition and custom adapter ligation was performed following end–repair. Post-ligated samples were individually barcoded with unique in-house Genomic Services Lab (GSL) primers and amplified through 12 cycles of PCR. Library quantity was assessed by Qubit 2.0 Fluorometer (Invitrogen), and quality was determined using a DNA High Sense chip on a Caliper Gx (Perkin Elmer). Final quantification of the complete libraries for sequencing applications was measured using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc.).

treatment_protocol: Bacteria were grown in media alone or media with 0.35 mg/mL recombinant calprotectin


title: Sample treated with Bradyrhizobium japonicum USDA122, replicate 1

description:
Sample 4
USDA_122_1
Incompatible: Glycine max L76-1988, Bradyrhizobium japonicum USDA122


title: EN_10m_3


title: media_3


title: Mock treated with MgCl2, replicate 3

description:
Sample 3
Control 3

value: control


title: Cpmedia_1


title: Mock treated with MgCl2, replicate 2

description:
Sample 2
Control 2


title: Cpmedia_2


title: EN_10m_2


title: media_1


title: EN_10m_1


title: Mock treated with MgCl2, replicate 1

description:
Sample 1
Control 1


title: media_2


title: 97126

value: CONTROL


title: EN_11m_1


title: Non-malignant lung 3039_N

status: Public on Oct 23 2019

city: Vancouver

first: Katey

middle: SS

last: Enfield

state: BC

address: 675 West 10th Ave

institute: BC Cancer Research Centre

description: Fresh frozen non-malignant lung sample

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scan protocol

data_processing: DNA methylation levels are reported as  Î²-values, calculated from mean non-background corrected methylated (M) and unmethylated (U) signal intensities for each locus for each sample using the formula (Î²=M/(M+U)) and the Illumina BeadStudio software v3.2. Probes with detection p-values of >0.05 as described previously (Noushemehr et al., 2010) were deemed not significantly different from background noise and were labeled NA.

source_name: Non-malignant lung

label_protocol: Standard Illumina protocol with Cy3 and Cy5

growth_protocol: Fresh-frozen tissue

extract_protocol: Genomic DNA was extracted after macrodissection and a proteinase K digstion using standard phenol:chloroform methods

treatment_protocol: Bisulfite treatment

value: Non-malignant lung

tag: patient

tag: age (years)

tag: race

value: Caucasian

value: Never

tag: Stage

tag: egfr mutation

tag: kras mutation


title: Lung adenocarcinoma L2_T

description: Fresh frozen lung adenocarcinoma sample

source_name: Lung adenocarcinoma

tag: tissue

value: Lung adenocarcinoma

value: Asian

value: IIIA

value: MUT

value: WT


title: Non-malignant lung L1_N

description: Fresh frozen non-malignant lung sample

value: Male

value: Current


title: Non-malignant lung L12_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma L1_T

description: Fresh frozen lung adenocarcinoma sample

value: IB


title: Non-malignant lung L2_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 3039_T

description: Fresh frozen lung adenocarcinoma sample

value: IIB


title: Lung adenocarcinoma 3033_T

description: Fresh frozen lung adenocarcinoma sample

value: Female


title: Non-malignant lung 3036_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma L9_T

description: Fresh frozen lung adenocarcinoma sample

value: Former

value: IA


title: Lung adenocarcinoma 3035_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung L15_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 3032_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma L12_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3033_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 3024_T

description: Fresh frozen lung adenocarcinoma sample

value: III


title: Non-malignant lung 3024_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 3036_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung L9_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma L15_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 3031_T

description: Fresh frozen lung adenocarcinoma sample

value: IIA


title: Lung adenocarcinoma 3032_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 3030_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3035_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung


title: Non-malignant lung 3031_N

description: Fresh frozen non-malignant lung sample

value: Caucasian


title: Lung adenocarcinoma 3022_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 3023_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3030_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 3022_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 3023_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 3021_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 3021_T

description: Fresh frozen lung adenocarcinoma sample


title: Lung adenocarcinoma 3014_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3014_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L66_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3013_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L51_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 07L66_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 3012_N

description: Fresh frozen non-malignant lung sample


title: Non-malignant lung 07L6_N

description: Fresh frozen non-malignant lung sample

value: Never


title: Lung adenocarcinoma 3012_T

description: Fresh frozen lung adenocarcinoma sample

value: Lung adenocarcinoma


title: Lung adenocarcinoma 07L6_T

description: Fresh frozen lung adenocarcinoma sample

value: Asian


title: Lung adenocarcinoma 3003_T

description: Fresh frozen lung adenocarcinoma sample


title: Non-malignant lung 3003_N

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 07L36_T

description: Fresh frozen lung adenocarcinoma sample

value: American Indian or Alaska Native


title: Non-malignant lung 07L31_N

description: Fresh frozen non-malignant lung sample