title: GC0499

description: miRNA


title: GC0497

status: Public on Nov 12 2022

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing:
The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.
Normalized signal intensity by internal control miRNAs.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: gastric cancer

tag: Sex

value: Male

tag: age

tag: Stage

tag: grade for glioma


title: GC0496

description: miRNA


title: GC0495

description: miRNA


title: GC0494

description: miRNA


title: GC0492

description: miRNA


title: GC0466

description: miRNA


title: GC0464

description: miRNA


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description: miRNA


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description: miRNA

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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0308

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0273

description: miRNA


title: GC0275

description: miRNA


title: GC0277

description: miRNA


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description: miRNA


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description: miRNA


title: GC0294

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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0290

description: miRNA


title: GC0262

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0253

description: miRNA


title: GC0259

description: miRNA


title: GC0258

description: miRNA


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description: miRNA


title: GC0256

description: miRNA


title: GC0254

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0239

description: miRNA


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description: miRNA


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description: miRNA


title: GC0211

description: miRNA


title: GC0210

description: miRNA


title: GC0208

description: miRNA


title: GC0205

description: miRNA


title: GC0209

description: miRNA


title: GC0207

description: miRNA


title: GC0204

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0167

description: miRNA


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description: miRNA


title: GC0163

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0075

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0044

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0036

description: miRNA


title: GC0033

description: miRNA


title: GC0031

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0026

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0022

description: miRNA


title: GC0021

description: miRNA


title: GC0020

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: GC0002

description: miRNA


title: GC0004

description: miRNA


title: GC0003

description: miRNA


title: GC0019

description: miRNA


title: GC0001

description: miRNA


title: EC0620

description: miRNA

value: esophageal squamous cell cancer


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title: GC0010

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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: EC0515

description: miRNA


title: EC0510

description: miRNA


title: EC0511

description: miRNA


title: EC0507

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: EC0494

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: EC0493

description: miRNA


title: EC0489

description: miRNA


title: EC0488

description: miRNA


title: EC0492

description: miRNA


title: EC0508

description: miRNA


title: EC0490

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: EC0484

description: miRNA


title: EC0481

description: miRNA


title: EC0482

description: miRNA


title: EC0483

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: EC0468

description: miRNA


title: EC0473

description: miRNA


title: EC0463

description: miRNA


title: EC0459

description: miRNA


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description: miRNA


title: EC0456

description: miRNA


title: EC0485

description: miRNA


title: EC0458

description: miRNA


title: EC0486

description: miRNA


title: EC0455

description: miRNA


title: EC0457

description: miRNA


title: EC0454

description: miRNA


title: EC0453

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: EC0445

description: miRNA


title: EC0443

description: miRNA


title: EC0446

description: miRNA


title: EC0441

description: miRNA


title: EC0442

description: miRNA


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description: miRNA


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description: miRNA


title: EC0448

description: miRNA


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description: miRNA


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description: miRNA


title: EC0433

description: miRNA


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description: miRNA


title: EC0429

description: miRNA


title: EC0427

description: miRNA


title: EC0428

description: miRNA


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description: miRNA


title: EC0431

description: miRNA


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description: miRNA


title: EC0425

description: miRNA


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description: miRNA


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description: miRNA


title: EC0451

description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


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description: miRNA


title: EC0416

description: miRNA


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description: miRNA


title: EC0439

description: miRNA


title: EC0417

description: miRNA


title: EC0412

description: miRNA


title: EC0411

description: miRNA


title: EC0413

description: miRNA


title: EC0409

description: miRNA


title: EC0410

description: miRNA


title: EC0407

description: miRNA


title: EC0408

description: miRNA


title: EC0424

description: miRNA


title: EC0405

description: miRNA


title: EC0401

description: miRNA


title: EC0403

description: miRNA


title: EC0404

description: miRNA


title: EC0402

description: miRNA


title: EC0400

description: miRNA


title: EC0406

description: miRNA


title: EC0398

description: miRNA


title: EC0397

description: miRNA


title: EC0399

description: miRNA


title: EC0396

description: miRNA


title: EC0394

description: miRNA


title: EC0395

description: miRNA


title: EC0414

description: miRNA


title: EC0389

description: miRNA


title: EC0387

description: miRNA


title: EC0386

description: miRNA


title: EC0393

description: miRNA


title: EC0390

description: miRNA


title: EC0384

description: miRNA


title: EC0388

description: miRNA


title: EC0385

description: miRNA


title: EC0383

description: miRNA


title: EC0382

description: miRNA


title: EC0381

description: miRNA


title: EC0380

description: miRNA


title: EC0378

description: miRNA


title: EC0377

description: miRNA


title: EC0376

description: miRNA


title: EC0374

description: miRNA


title: EC0375

description: miRNA


title: EC0371

description: miRNA


title: EC0373

description: miRNA


title: EC0372

description: miRNA


title: EC0370

description: miRNA


title: EC0369

description: miRNA


title: EC0368

description: miRNA


title: EC0365

description: miRNA


title: EC0366

description: miRNA


title: EC0367

description: miRNA


title: EC0364

description: miRNA


title: EC0392

description: miRNA


title: EC0363

description: miRNA


title: EC0362

description: miRNA


title: EC0360

description: miRNA


title: EC0359

description: miRNA


title: EC0361

description: miRNA


title: EC0358

description: miRNA


title: EC0356

description: miRNA


title: EC0357

description: miRNA


title: EC0354

description: miRNA


title: EC0355

description: miRNA


title: EC0353

description: miRNA


title: EC0352

description: miRNA


title: EC0351

description: miRNA


title: EC0350

description: miRNA


title: EC0348

description: miRNA


title: EC0347

description: miRNA


title: EC0346

description: miRNA


title: EC0342

description: miRNA


title: EC0341

description: miRNA


title: EC0340

description: miRNA


title: EC0345

description: miRNA


title: EC0339

description: miRNA


title: EC0344

description: miRNA


title: EC0343

description: miRNA


title: EC0338

description: miRNA


title: EC0332

description: miRNA


title: EC0333

description: miRNA


title: EC0337

description: miRNA


title: EC0331

description: miRNA


title: EC0336

description: miRNA


title: EC0329

description: miRNA


title: EC0335

description: miRNA


title: EC0324

description: miRNA


title: EC0321

description: miRNA


title: EC0318

description: miRNA


title: EC0317

description: miRNA


title: EC0314

description: miRNA


title: EC0312

description: miRNA


title: EC0309

description: miRNA


title: EC0334

description: miRNA


title: EC0310

description: miRNA


title: EC0330

description: miRNA


title: EC0328

description: miRNA


title: EC0305

description: miRNA


title: EC0304

description: miRNA


title: EC0349

description: miRNA


title: EC0325

description: miRNA


title: EC0327

description: miRNA


title: EC0322

description: miRNA


title: EC0320

description: miRNA


title: EC0316

description: miRNA


title: EC0326

description: miRNA


title: EC0323

description: miRNA


title: EC0313

description: miRNA


title: EC0319

description: miRNA


title: EC0311

description: miRNA


title: EC0308

description: miRNA


title: EC0296

description: miRNA


title: EC0307

description: miRNA


title: EC0306

description: miRNA


title: EC0303

description: miRNA


title: EC0301

description: miRNA


title: EC0299

description: miRNA


title: EC0294

description: miRNA


title: EC0302

description: miRNA


title: EC0290

description: miRNA


title: EC0300

description: miRNA


title: EC0297

description: miRNA


title: EC0298

description: miRNA


title: EC0280

description: miRNA


title: EC0293

description: miRNA


title: EC0292

description: miRNA


title: EC0291

description: miRNA


title: EC0278

description: miRNA


title: EC0289

description: miRNA


title: EC0285

description: miRNA


title: EC0286

description: miRNA


title: EC0288

description: miRNA


title: EC0287

description: miRNA


title: EC0283

description: miRNA


title: EC0284

description: miRNA


title: EC0295

description: miRNA


title: EC0274

description: miRNA


title: EC0282

description: miRNA


title: EC0269

description: miRNA


title: EC0270

description: miRNA


title: EC0268

description: miRNA


title: EC0279

description: miRNA


title: EC0267

description: miRNA


title: EC0276

description: miRNA


title: EC0275

description: miRNA


title: EC0264

description: miRNA


title: EC0272

description: miRNA


title: EC0271

description: miRNA


title: EC0273

description: miRNA


title: EC0261

description: miRNA


title: EC0281

description: miRNA


title: EC0260

description: miRNA


title: EC0259

description: miRNA


title: EC0262

description: miRNA


title: EC0256

description: miRNA


title: EC0257

description: miRNA


title: EC0258

description: miRNA


title: EC0277

description: miRNA


title: EC0253

description: miRNA


title: EC0254

description: miRNA


title: EC0255

description: miRNA


title: EC0251

description: miRNA


title: EC0265

description: miRNA


title: EC0248

description: miRNA


title: EC0252

description: miRNA


title: EC0240

description: miRNA


title: EC0241

description: miRNA


title: EC0250

description: miRNA


title: EC0238

description: miRNA


title: EC0249

description: miRNA


title: EC0237

description: miRNA


title: EC0266

description: miRNA


title: EC0236

description: miRNA


title: EC0246

description: miRNA


title: EC0263

description: miRNA


title: EC0243

description: miRNA


title: EC0239

description: miRNA


title: EC0242

description: miRNA


title: EC0245

description: miRNA


title: EC0235

description: miRNA


title: EC0230

description: miRNA


title: EC0234

description: miRNA


title: EC0224

description: miRNA


title: EC0231

description: miRNA


title: EC0226

description: miRNA


title: EC0233

description: miRNA


title: EC0232

description: miRNA


title: EC0228

description: miRNA


title: EC0227

description: miRNA


title: EC0244

description: miRNA


title: EC0223

description: miRNA


title: EC0222

description: miRNA


title: EC0220

description: miRNA


title: EC0217

description: miRNA


title: EC0219

description: miRNA


title: EC0214

description: miRNA


title: EC0215

description: miRNA


title: EC0213

description: miRNA


title: EC0216

description: miRNA


title: EC0229

description: miRNA


title: EC0208

description: miRNA


title: EC0212

description: miRNA


title: EC0207

description: miRNA


title: EC0204

description: miRNA


title: EC0205

description: miRNA


title: EC0210

description: miRNA


title: EC0209

description: miRNA


title: EC0203

description: miRNA


title: EC0202

description: miRNA


title: EC0201

description: miRNA


title: EC0198

description: miRNA


title: EC0199

description: miRNA


title: EC0225

description: miRNA


title: EC0197

description: miRNA


title: EC0221

description: miRNA


title: EC0196

description: miRNA


title: EC0193

description: miRNA


title: EC0194

description: miRNA


title: EC0195

description: miRNA


title: EC0192

description: miRNA


title: EC0191

description: miRNA


title: EC0188

description: miRNA


title: EC0187

description: miRNA


title: EC0190

description: miRNA


title: EC0211

description: miRNA


title: EC0206

description: miRNA


title: EC0185

description: miRNA


title: EC0186

description: miRNA


title: EC0184

description: miRNA


title: EC0183

description: miRNA


title: EC0179

description: miRNA


title: EC0178

description: miRNA


title: EC0177

description: miRNA


title: EC0176

description: miRNA


title: EC0173

description: miRNA


title: EC0175

description: miRNA


title: EC0172

description: miRNA


title: EC0170

description: miRNA


title: EC0171

description: miRNA


title: EC0169

description: miRNA


title: EC0189

description: miRNA


title: EC0168

description: miRNA


title: EC0167

description: miRNA


title: EC0166

description: miRNA


title: EC0165

description: miRNA


title: EC0162

description: miRNA


title: EC0160

description: miRNA


title: EC0159

description: miRNA


title: EC0182

description: miRNA


title: EC0181

description: miRNA


title: EC0163

description: miRNA


title: EC0180

description: miRNA


title: EC0158

description: miRNA


title: EC0156

description: miRNA


title: EC0161

description: miRNA


title: EC0154

description: miRNA


title: EC0157

description: miRNA


title: EC0152

description: miRNA


title: EC0155

description: miRNA


title: EC0151

description: miRNA


title: EC0174

description: miRNA


title: EC0149

description: miRNA


title: EC0148

description: miRNA


title: EC0146

description: miRNA


title: EC0147

description: miRNA


title: EC0150

description: miRNA


title: EC0145

description: miRNA


title: EC0144

description: miRNA


title: EC0143

description: miRNA


title: EC0141

description: miRNA


title: EC0140

description: miRNA


title: EC0137

description: miRNA


title: EC0138

description: miRNA


title: EC0139

description: miRNA


title: EC0164

description: miRNA


title: EC0136

description: miRNA


title: EC0135

description: miRNA


title: EC0134

description: miRNA


title: EC0132

description: miRNA


title: EC0130

description: miRNA


title: EC0129

description: miRNA


title: EC0126

description: miRNA


title: EC0131

description: miRNA


title: EC0127

description: miRNA


title: EC0124

description: miRNA


title: EC0122

description: miRNA


title: EC0120

description: miRNA


title: EC0121

description: miRNA


title: EC0119

description: miRNA


title: EC0118

description: miRNA


title: EC0117

description: miRNA


title: EC0115

description: miRNA


title: EC0114

description: miRNA


title: EC0113

description: miRNA


title: EC0112

description: miRNA


title: EC0101

description: miRNA


title: EC0106

description: miRNA


title: EC0105

description: miRNA


title: EC0099

description: miRNA


title: EC0110

description: miRNA


title: EC0100

description: miRNA


title: EC0103

description: miRNA


title: EC0125

description: miRNA


title: EC0123

description: miRNA


title: EC0095

description: miRNA


title: EC0093

description: miRNA


title: EC0091

description: miRNA


title: EC0092

description: miRNA


title: EC0096

description: miRNA


title: EC0088

description: miRNA


title: EC0086

description: miRNA


title: EC0097

description: miRNA


title: EC0087

description: miRNA


title: EC0085

description: miRNA


title: EC0090

description: miRNA


title: EC0082

description: miRNA


title: EC0083

description: miRNA


title: EC0081

description: miRNA


title: EC0102

description: miRNA


title: EC0079

description: miRNA


title: EC0098

description: miRNA


title: EC0078

description: miRNA


title: EC0072

description: miRNA


title: EC0066

description: miRNA


title: EC0076

description: miRNA


title: EC0077

description: miRNA


title: EC0073

description: miRNA


title: EC0068

description: miRNA


title: EC0094

description: miRNA


title: EC0064

description: miRNA


title: EC0062

description: miRNA


title: EC0089

description: miRNA


title: EC0058

description: miRNA


title: EC0059

description: miRNA


title: EC0060

description: miRNA


title: EC0063

description: miRNA


title: EC0057

description: miRNA


title: EC0056

description: miRNA


title: EC0052

description: miRNA


title: EC0051

description: miRNA


title: EC0055

description: miRNA


title: EC0053

description: miRNA


title: EC0084

description: miRNA


title: EC0048

description: miRNA


title: EC0049

description: miRNA


title: EC0046

description: miRNA


title: EC0047

description: miRNA


title: EC0041

description: miRNA


title: EC0037

description: miRNA


title: EC0042

description: miRNA


title: EC0045

description: miRNA


title: EC0040

description: miRNA


title: EC0038

description: miRNA


title: EC0080

description: miRNA


title: EC0035

description: miRNA


title: EC0043

description: miRNA


title: EC0034

description: miRNA


title: EC0036

description: miRNA


title: EC0054

description: miRNA


title: EC0039

description: miRNA


title: EC0029

description: miRNA


title: EC0028

description: miRNA


title: EC0031

description: miRNA


title: EC0032

description: miRNA


title: EC0033

description: miRNA


title: EC0030

description: miRNA


title: EC0024

description: miRNA


title: EC0022

description: miRNA


title: EC0021

description: miRNA


title: EC0027

description: miRNA


title: EC0026

description: miRNA


title: EC0017

description: miRNA


title: EC0025

description: miRNA


title: EC0020

description: miRNA


title: EC0018

description: miRNA


title: EC0019

description: miRNA


title: EC0016

description: miRNA


title: EC0010

description: miRNA


title: EC0009

description: miRNA


title: EC0012

description: miRNA


title: EC0007

description: miRNA


title: EC0008

description: miRNA


title: EC0014

description: miRNA


title: EC0013

description: miRNA


title: EC0006

description: miRNA


title: EC0005

description: miRNA


title: EC0002

description: miRNA


title: EC0004

description: miRNA


title: EC0003

description: miRNA


title: EC0001

description: miRNA


title: CHC928

description: miRNA

value: no cancer


title: CHC915

description: miRNA


title: CHC912

description: miRNA


title: CHC926

description: miRNA


title: CHC921

description: miRNA


title: CHC916

description: miRNA


title: CHC902

description: miRNA


title: CHC914

description: miRNA


title: EC0011

description: miRNA


title: CHC909

description: miRNA


title: CHC908

description: miRNA


title: CHC900

description: miRNA


title: CHC898

description: miRNA


title: CHC899

description: miRNA


title: CHC884

description: miRNA


title: CHC878

description: miRNA


title: CHC888

description: miRNA


title: CHC887

description: miRNA


title: CHC891

description: miRNA


title: CHC885

description: miRNA


title: CHC874

description: miRNA


title: CHC877

description: miRNA


title: CHC870

description: miRNA


title: CHC871

description: miRNA


title: CHC868

description: miRNA


title: CHC873

description: miRNA


title: CHC866

description: miRNA


title: CHC864

description: miRNA


title: CHC861

description: miRNA


title: CHC860

description: miRNA


title: CHC863

description: miRNA


title: CHC850

description: miRNA


title: CHC849

description: miRNA


title: CHC846

description: miRNA


title: CHC851

description: miRNA


title: CHC845

description: miRNA


title: CHC857

description: miRNA


title: CHC844

description: miRNA


title: CHC896

description: miRNA


title: CHC838

description: miRNA


title: CHC842

description: miRNA


title: CHC841

description: miRNA


title: CHC892

description: miRNA


title: CHC834

description: miRNA


title: CHC833

description: miRNA


title: CHC826

description: miRNA


title: CHC828

description: miRNA


title: CHC829

description: miRNA


title: CHC821

description: miRNA


title: CHC815

description: miRNA


title: CHC819

description: miRNA


title: CHC814

description: miRNA


title: CHC812

description: miRNA


title: CHC810

description: miRNA


title: CHC807

description: miRNA


title: CHC803

description: miRNA


title: CHC805

description: miRNA


title: CHC798

description: miRNA


title: CHC799

description: miRNA


title: CHC796

description: miRNA


title: CHC795

description: miRNA


title: CHC786

description: miRNA


title: CHC788

description: miRNA


title: CHC785

description: miRNA


title: CHC781

description: miRNA


title: CHC783

description: miRNA


title: CHC777

description: miRNA


title: CHC782

description: miRNA


title: CHC776

description: miRNA


title: CHC825

description: miRNA


title: CHC772

description: miRNA


title: CHC775

description: miRNA


title: CHC771

description: miRNA


title: CHC769

description: miRNA


title: CHC768

description: miRNA


title: CHC760

description: miRNA


title: CHC759

description: miRNA


title: CHC755

description: miRNA


title: CHC757

description: miRNA


title: CHC754

description: miRNA


title: CHC746

description: miRNA


title: CHC745

description: miRNA


title: CHC741

description: miRNA


title: CHC758

description: miRNA


title: CHC740

description: miRNA


title: CHC748

description: miRNA


title: CHC743

description: miRNA


title: CHC791

description: miRNA


title: CHC737

description: miRNA


title: CHC736

description: miRNA


title: CHC731

description: miRNA


title: CHC735

description: miRNA


title: CHC723

description: miRNA


title: CHC761

description: miRNA


title: CHC738

description: miRNA


title: CHC714

description: miRNA


title: CHC713

description: miRNA


title: CHC707

description: miRNA


title: CHC708

description: miRNA


title: CHC700

description: miRNA


title: CHC699

description: miRNA


title: CHC703

description: miRNA


title: CHC691

description: miRNA


title: CHC750

description: miRNA


title: CHC688

description: miRNA


title: CHC681

description: miRNA


title: CHC684

description: miRNA


title: CC1609

description: miRNA

value: colorectal cancer


title: CC1608

description: miRNA


title: CC1607

description: miRNA


title: CHC673

description: miRNA


title: CC1606

description: miRNA


title: CHC726

description: miRNA


title: CC1604

description: miRNA


title: CC1602

description: miRNA


title: CHC672

description: miRNA


title: CC1600

description: miRNA


title: CC1601

description: miRNA


title: CC1597

description: miRNA


title: CC1598

description: miRNA


title: CC1595

description: miRNA


title: CC1603

description: miRNA


title: CC1596

description: miRNA


title: CHC689

description: miRNA


title: CC1594

description: miRNA


title: CC1593

description: miRNA


title: CC1592

description: miRNA


title: CC1599

description: miRNA


title: CHC722

description: miRNA


title: CC1590

description: miRNA


title: CC1589

description: miRNA


title: CC1588

description: miRNA


title: CC1587

description: miRNA


title: CC1586

description: miRNA


title: CC1585

description: miRNA


title: CC1605

description: miRNA


title: CC1584

description: miRNA


title: CC1582

description: miRNA


title: CC1581

description: miRNA


title: CC1580

description: miRNA


title: CC1578

description: miRNA


title: CC1579

description: miRNA


title: CC1575

description: miRNA


title: CC1573

description: miRNA


title: CC1572

description: miRNA


title: CC1576

description: miRNA


title: CC1571

description: miRNA


title: CC1570

description: miRNA


title: CC1591

description: miRNA


title: CC1567

description: miRNA


title: CC1566

description: miRNA


title: CC1565

description: miRNA


title: CC1564

description: miRNA


title: CC1562

description: miRNA


title: CC1568

description: miRNA


title: CC1561

description: miRNA


title: CC1563

description: miRNA


title: CC1560

description: miRNA


title: CC1557

description: miRNA


title: CC1558

description: miRNA


title: CC1556

description: miRNA


title: CC1583

description: miRNA


title: CC1554

description: miRNA


title: CC1552

description: miRNA


title: CC1577

description: miRNA


title: CC1550

description: miRNA


title: CC1551

description: miRNA


title: CC1549

description: miRNA


title: CC1546

description: miRNA


title: CC1547

description: miRNA


title: CC1544

description: miRNA


title: CC1542

description: miRNA


title: CC1543

description: miRNA


title: CC1569

description: miRNA


title: CC1545

description: miRNA


title: CC1539

description: miRNA


title: CC1540

description: miRNA


title: CC1537

description: miRNA


title: CC1541

description: miRNA


title: CC1559

description: miRNA


title: CC1536

description: miRNA


title: CC1535

description: miRNA


title: CC1534

description: miRNA


title: CC1555

description: miRNA


title: CC1531

description: miRNA


title: CC1553

description: miRNA


title: CC1530

description: miRNA


title: CC1528

description: miRNA


title: CC1529

description: miRNA


title: CC1527

description: miRNA


title: CC1526

description: miRNA


title: CC1525

description: miRNA


title: CC1548

description: miRNA


title: CC1524

description: miRNA


title: CC1522

description: miRNA


title: CC1521

description: miRNA


title: CC1523

description: miRNA


title: CC1538

description: miRNA


title: CC1520

description: miRNA


title: CC1517

description: miRNA


title: CC1518

description: miRNA


title: CC1519

description: miRNA


title: CC1574

description: miRNA


title: CC1515

description: miRNA


title: CC1512

description: miRNA


title: CC1516

description: miRNA


title: CC1514

description: miRNA


title: CC1511

description: miRNA


title: CC1510

description: miRNA


title: CC1513

description: miRNA


title: CC1533

description: miRNA


title: CC1508

description: miRNA


title: CC1509

description: miRNA


title: CC1507

description: miRNA


title: CC1506

description: miRNA


title: CC1505

description: miRNA


title: CC1532

description: miRNA


title: CC1504

description: miRNA


title: CC1502

description: miRNA


title: CC1500

description: miRNA


title: CC1501

description: miRNA


title: CC1499

description: miRNA


title: CC1498

description: miRNA


title: CC1497

description: miRNA


title: CC1496

description: miRNA


title: CC1494

description: miRNA


title: CC1495

description: miRNA


title: CC1492

description: miRNA


title: CC1489

description: miRNA


title: CC1490

description: miRNA


title: CC1491

description: miRNA


title: CC1487

description: miRNA


title: CC1486

description: miRNA


title: CC1484

description: miRNA


title: CC1483

description: miRNA


title: CC1482

description: miRNA


title: CC1481

description: miRNA


title: CC1485

description: miRNA


title: CC1503

description: miRNA


title: CC1480

description: miRNA


title: CC1477

description: miRNA


title: CC1478

description: miRNA


title: CC1476

description: miRNA


title: CC1479

description: miRNA


title: CC1473

description: miRNA


title: CC1472

description: miRNA


title: CC1471

description: miRNA


title: CC1470

description: miRNA


title: CC1469

description: miRNA


title: CC1493

description: miRNA


title: CC1468

description: miRNA


title: CC1466

description: miRNA


title: CC1488

description: miRNA


title: CC1465

description: miRNA


title: CC1464

description: miRNA


title: CC1463

description: miRNA


title: CC1461

description: miRNA


title: CC1462

description: miRNA


title: CC1460

description: miRNA


title: CC1457

description: miRNA


title: CC1456

description: miRNA


title: CC1475

description: miRNA


title: CC1454

description: miRNA


title: CC1474

description: miRNA


title: CC1455

description: miRNA


title: CC1453

description: miRNA


title: CC1452

description: miRNA


title: CC1450

description: miRNA


title: CC1451

description: miRNA


title: CC1449

description: miRNA


title: CC1446

description: miRNA


title: CC1447

description: miRNA


title: CC1445

description: miRNA


title: CC1448

description: miRNA


title: CC1443

description: miRNA


title: CC1467

description: miRNA


title: CC1442

description: miRNA


title: CC1441

description: miRNA


title: CC1439

description: miRNA


title: CC1435

description: miRNA


title: CC1436

description: miRNA


title: CC1440

description: miRNA


title: CC1459

description: miRNA


title: CC1437

description: miRNA


title: CC1444

description: miRNA


title: CC1434

description: miRNA


title: CC1458

description: miRNA


title: CC1432

description: miRNA


title: CC1430

description: miRNA


title: CC1433

description: miRNA


title: CC1429

description: miRNA


title: CC1428

description: miRNA


title: CC1431

description: miRNA


title: CC1426

description: miRNA


title: CC1427

description: miRNA


title: CC1425

description: miRNA


title: CC1423

description: miRNA


title: CC1422

description: miRNA


title: CC1424

description: miRNA


title: CC1420

description: miRNA


title: CC1421

description: miRNA


title: CC1419

description: miRNA


title: CC1418

description: miRNA


title: CC1416

description: miRNA


title: CC1438

description: miRNA


title: CC1415

description: miRNA


title: CC1414

description: miRNA


title: CC1412

description: miRNA


title: CC1413

description: miRNA


title: CC1407

description: miRNA


title: CC1411

description: miRNA


title: CC1406

description: miRNA


title: CC1408

description: miRNA


title: CC1410

description: miRNA


title: CC1409

description: miRNA


title: CC1405

description: miRNA


title: CC1398

description: miRNA


title: CC1404

description: miRNA


title: CC1397

description: miRNA


title: CC1401

description: miRNA


title: CC1400

description: miRNA


title: CC1403

description: miRNA


title: CC1396

description: miRNA


title: CC1402

description: miRNA


title: CC1399

description: miRNA


title: CC1395

description: miRNA


title: CC1392

description: miRNA


title: CC1390

description: miRNA


title: CC1391

description: miRNA


title: CC1417

description: miRNA


title: CC1394

description: miRNA


title: CC1393

description: miRNA


title: CC1389

description: miRNA


title: CC1388

description: miRNA


title: CC1387

description: miRNA


title: CC1386

description: miRNA


title: CC1385

description: miRNA


title: CC1384

description: miRNA


title: CC1383

description: miRNA


title: CC1381

description: miRNA


title: CC1382

description: miRNA


title: CC1380

description: miRNA


title: CC1377

description: miRNA


title: CC1379

description: miRNA


title: CC1378

description: miRNA


title: CC1376

description: miRNA


title: CC1375

description: miRNA


title: CC1374

description: miRNA


title: CC1371

description: miRNA


title: CC1370

description: miRNA


title: CC1373

description: miRNA


title: CC1372

description: miRNA


title: CC1369

description: miRNA


title: CC1366

description: miRNA


title: CC1365

description: miRNA


title: CC1364

description: miRNA


title: CC1363

description: miRNA


title: CC1361

description: miRNA


title: CC1360

description: miRNA


title: CC1368

description: miRNA


title: CC1362

description: miRNA


title: CC1359

description: miRNA


title: CC1358

description: miRNA


title: CC1357

description: miRNA


title: CC1356

description: miRNA


title: CC1355

description: miRNA


title: CC1353

description: miRNA


title: CC1354

description: miRNA


title: 66462_25_00

type: genomic

city: Melbourne

first: Elizabeth

middle: Louise

last: Christie

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised using the above protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings.

data_processing:
Methylation data quality control assessment and processing were performed using the R package minfi (v1.32.0). Probes failing detection (P > 0.01), SNP positions, and cross reactive probes (as collected in https://github.com/sirselim/illumina450k_filtering) were excluded. Data was normalized using the minfi function "preprocessFunnorm" and beta values were generated for each EPIC and 450k arrays separately. The beta values for each array were then merged by the probe ID into file "betaVals.all.txt.gz" file.
Beta value

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Autopsy Tumour

label_protocol: Infinium Human Methylation EPIC 850k arrays (Illumina)

extract_protocol: Tumor DNA extractions were performed using the DNeasy Blood and Tissue kit (QIAGEN), and DNA was quantified using the Qubit dsDNA BR assay (Invitrogen)

tag: gender

tag: tissue

value: Autopsy Tumour

tag: batch


title: 66142_24_00


title: 66462_23_00


title: 66142_25


title: 66462_26_00


title: CC1351

description: miRNA


title: CC1367

description: miRNA


title: 66114_32


title: 66114_11_00


title: CC1349

description: miRNA


title: 66043_15_00


title: 65938_22_00


title: CC1350

description: miRNA


title: CC1348

description: miRNA


title: 65938_17_00


title: CC1347

description: miRNA


title: CC1344

description: miRNA


title: CC1346

description: miRNA


title: CC1345

description: miRNA


title: 65914_17_00


title: 65914_11_00


title: CC1343

description: miRNA


title: 65913_26


title: CC1342

description: miRNA


title: 65913_16_00


title: CC1341

description: miRNA


title: CC1352

description: miRNA


title: 65862_22_00


title: CC1338

description: miRNA


title: CC1339

description: miRNA


title: CC1337

description: miRNA


title: 65862_19_00


title: CC1336

description: miRNA


title: CC1335

description: miRNA


title: 15306_16_00


title: 65659_10_00


title: 65659_20_00


title: 15306_15_00


title: 65914_23_00


title: CC1334

description: miRNA


title: CC1333

description: miRNA


title: 15306_13WT


title: 15295_19_00


title: CC1332

description: miRNA


title: 15295_18_00


title: CC1330

description: miRNA


title: 15295_14_00


title: 15292_22_00


title: CC1328

description: miRNA


title: 15292_13_00


title: 15292_14_20


title: CC1340

description: miRNA


title: CC1327

description: miRNA


title: CC1326

description: miRNA


title: 65659_16_00


title: CC1325

description: miRNA


title: CC1324

description: miRNA


title: S33: Uninfected, Replicate C

type: SRA

city: Charlotte

first: Morgan

middle: Brittany

last: Johnson

state: North Carolina

address: 9201 University City BLVD

department: Biological Sciences

country: USA

institute: University of North Carolina at Charlotte

description: Uninfected, Replicate C

library_source: transcriptomic

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26/
Supplementary files format and content: tab-delimited table of counts per gene for each sample

organism: Mus musculus

source_name: osteoblasts

growth_protocol: primary murine OBs were isolated from whole calvaria and differentiated in αMEM supplemented with 10% FBS, 0.1 M ascorbic acid, 1 M β-glycerol phosphate, and 1% penicillin/streptomycin at 37℃ in a 5% CO2 atmosphere for 10 days prior to S. aureus infection.

extract_protocol:
PureLink RNA mini kit
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: S. aureus infection MOI 75:1

tag: cell line

value: osteoblasts

tag: cell type

value: WT

tag: treatment

value: uninfected

tag: timepoint

value: 4 hrs. post infection


title: S30: S. aureus infection MOI 75:1, Replicate B

value: S. aureus infection MOI 75:1


title: S34: S. aureus infection MOI 75:1, Replicate C


title: S29: Uninfected, Replicate B

description: Uninfected, Replicate B


title: CC1323

description: miRNA


title: S26: S. aureus infection MOI 75:1, Replicate A


title: CC1322

description: miRNA


title: CC1321

description: miRNA


title: S25: Uninfected, Replicate A

description: Uninfected, Replicate A


title: CC1320

description: miRNA


title: CC1331

description: miRNA


title: CC1316

description: miRNA


title: CC1315

description: miRNA


title: LPS_R3

city: Qingdao

first: Mengqiang

last: Wang

state: Shandong

address: Nanhai Road

country: China

institute: The Institute of Oceanology, Chinese Academy of Science

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: http://mgb.ouc.edu.cn/cfbase/html/download.php
Supplementary_files_format_and_content: excel,expression profiles

organism: Azumapecten farreri

source_name: Hemocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Hemocytes

tag: molecule subtype

value: Small RNA


title: PBS_R3


title: CC1329

description: miRNA


title: LPS_R2


title: CC1318

description: miRNA


title: PBS_R1


title: CC1314

description: miRNA


title: NOR_R3


title: NOR_R2


title: NOR_R1


title: LPS_R1


title: CC1310

description: miRNA


title: Ishikawa_8hrDMSO_H3K27Ac_rep2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

library_source: genomic

data_processing:
Reads were aligned to hg19 using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
Peaks with a P-value cutoff of 1 x 10-10 and an mfold parameter between 15 and 100 were called by Model Based Analysis of ChIP-seq-2 (MACS2)
Assembly: hg38
Supplementary files format and content: BigWig files
Supplementary files format and content: narrowPeak files from MACS2

source_name: Ishikawa

growth_protocol: HCI-EC-23 and Ishikawa was cultured in RPMI 1640 (Gibco, 11875119) supplemented with 10% fetal bovine serum (Gibco, 26140079) and 1% penicillin-streptomycin (Gibco, 15140163). Hormone deprived media consisted of phenol red-free RPMI1640 (Gibco, 11835055) supplemented with 10% charcoal-stripped fetal bovine serum (Sigma Aldrich, F6765) and 1% penicillin-streptomycin (Gibco, 15140163). HCI-EC-23 or Ishikawa cell lines were cultured in hormone-deprived media for at least five days prior to experiments using hormones. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
Cells were fixed using 1% formaldehyde (Sigma Aldrich, 252549) for 10 minutes at room temperature to cross-link DNA and proteins. Cross-linking was stopped by addition of glycine (Fisher Scientific, BP381) to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via scraping in Farnham lysis buffer supplemented with protease and phosphatase inhibitors (Thermo Scientific, A32959).
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with an Anti-Estrogen receptor alpha (ESR1) antibody (Millipore Sigma, 06-935) or H3K27ac antibody (Active Motif, 39133).

treatment_protocol: Media was changed and cells were treated with either 0.1% DMSO (vehicle) for 8 hr (H3K27ac ChIPs) or 10 nM E2  for 1 hour (ER ChIPs) in hormone-deprived media.

value: Ishikawa

value: endometrioid adenocarcinoma

tag: chip antibody

value: H3K27ac (Active Motif, 39133)

value: 0.1% DMSO


title: CC1308

description: miRNA


title: HCI-EC-23_8hrDMSO_H3K27Ac_rep2


title: 66462_1900015_26

description: CASCADE.HTSeq.all.raw.txt.gz

data_processing:
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8)
Reads were trimmed for low quality, adapters, N content and poly-A tails using fastq-mcf (v1.05)
Contamination was checked using FastQ Screen (v0.11.4)
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b)
Mapped reads were sorted using Picard Tools (v2.17.3)
Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4)
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the “intersection-nonempty” mode
Assembly: hg19
Supplementary files format and content: Raw counts, gene by sample matrix. The GeneID column is in the format "EnsemblID|Chromosome|Start|End|Strand|Whole_Gene_Length|Exon_Only_Length|Gene_Symbol|Gene_Biotype", eg.. "ENSG00000000003|X|99883667|99894988|-|11322|2968|TSPAN6|protein_coding"

extract_protocol:
Total RNA was used for library preparation using the NEB Ultra II Directional RNA library Prep kit (Illumina) with poly(A) enrichment, as per the manufacturer’s low-throughput protocol.
Libraries were sequenced as paired-end 50 or 100 bp on a NextSeq or NovaSeq (Illumina), generating approximately 30 million paired reads per sample.

tag: case id

value: High Grade Serous Ovarian Cancer

tag: library strand_orientation

value: reverse stranded


title: PBS_R2


title: CC1307

description: miRNA

value: Female


title: CC1312

description: miRNA


title: HCI-EC-23_8hrDMSO_H3K27Ac_rep1


title: CC1317

description: miRNA

value: Male


title: CC1311

description: miRNA

value: colorectal cancer


title: CC1309

description: miRNA


title: CC1319

description: miRNA


title: 66462_1900015_25

description: CASCADE.HTSeq.all.raw.txt.gz

value: Autopsy Tumour


title: 66462_1900015_23

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1305

description: miRNA


title: 65862_1700108_22

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1306

description: miRNA


title: Ishikawa_8hrDMSO_H3K27Ac_rep1


title: CC1313

description: miRNA


title: CC1304

description: miRNA


title: CC1301

description: miRNA


title: 15306_1400539_16

description: CASCADE.HTSeq.all.raw.txt.gz

value: unstranded


title: 65862_1700108_19

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1300

description: miRNA


title: 15306_1400539_15

description: CASCADE.HTSeq.all.raw.txt.gz


title: 15306_1400539_10

description: CASCADE.HTSeq.all.raw.txt.gz

source_name: Primary Tumour

value: Primary Tumour


title: 15295_1500175_19

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1298

description: miRNA


title: 15295_1500175_18

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1299

description: miRNA


title: 15292_1400654_22

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1296

description: miRNA


title: CC1297

description: miRNA


title: CC1295

description: miRNA


title: 15292_1400654_14

description: CASCADE.HTSeq.all.raw.txt.gz


title: 66142_1700044_24

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1293

description: miRNA


title: CC1290

description: miRNA


title: 15292_1400097_99

description: CASCADE.HTSeq.all.raw.txt.gz

source_name: Ascites

value: Ascites


title: CC1303

description: miRNA


title: CC1302

description: miRNA


title: CC1294

description: miRNA


title: 15292_1400654_13

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1292

description: miRNA


title: CC1289

description: miRNA


title: 66142_1700044_25

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1291

description: miRNA


title: 66142_1700044_20

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1287

description: miRNA


title: 15306_1400539_13

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1285

description: miRNA


title: 66114_1700033_16

description: CASCADE.HTSeq.all.raw.txt.gz


title: 66114_1700033_28

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1286

description: miRNA


title: 66043_1600281_13

description: CASCADE.HTSeq.all.raw.txt.gz


title: 66043_1600281_15

description: CASCADE.HTSeq.all.raw.txt.gz


title: 66114_1700033_11

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1284

description: miRNA


title: 15292_1400654_10

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1282

description: miRNA


title: 65913_1600143_22

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1281

description: miRNA


title: CC1280

description: miRNA


title: 65913_1600143_16

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1279

description: miRNA


title: 66114_1700033_32

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1278

description: miRNA


title: CC1277

description: miRNA


title: 65914_1500182_17

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1276

description: miRNA


title: CC1288

description: miRNA


title: Streptavidin_pull-down_H1KO_asynchrony

city: Beijing

first: Yu

last: Juan

address: 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
Assembly: mm9, dm6
Supplementary files format and content: bedgraph files

source_name: mouse embryonic stem cells

growth_protocol:
ChIP-seq: mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.
ChOR-seq: mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol:
ChIP-seq: Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
ChIP-seq: H3K27me3 were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using Nova seq.
ChOR-seq: Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
ChOR-seq: H3K27me3 were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using Nova seq.

value: mouse embryonic stem cells

tag: strain

tag: genotype

value: no


title: Streptavidin_pull-down_WT_asynchrony

value: Wild type


title: 65914_1500182_11

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1275

description: miRNA

tag: disease state

tag: Sex


title: CC1274

description: miRNA

tag: age

tag: Stage


title: CC1283

description: miRNA

tag: grade for glioma


title: 65938_1700045_27

description: CASCADE.HTSeq.all.raw.txt.gz

tag: tissue


title: Streptavidin_pull-down_H1KO_synchronization


title: CC1272

description: miRNA


title: 65913_1600143_26

description: CASCADE.HTSeq.all.raw.txt.gz


title: ChOR-seq_AID_decrease_WT_T4_asynchrony

data_processing:
library strategy: ChOR-seq (Chromatin Occupancy after Replication)
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
Assembly: mm9, dm6
Supplementary files format and content: bedgraph files


title: 65914_1500182_23

description: CASCADE.HTSeq.all.raw.txt.gz


title: Streptavidin_pull-down_WT_synchronization


title: CC1273

description: miRNA


title: CC1268

description: miRNA


title: 65938_1700045_22

description: CASCADE.HTSeq.all.raw.txt.gz


title: 65938_1700045_17

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1269

description: miRNA


title: CC1267

description: miRNA


title: CC1266

description: miRNA


title: ChOR-seq_AID_decrease_WT_T2_asynchrony


title: 65938_1700045_13

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1265

description: miRNA


title: ChOR-seq_AID_decrease_WT_T1_asynchrony


title: CC1270

description: miRNA


title: 65938_1700045_10

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1263

description: miRNA


title: CC1261

description: miRNA


title: 65682_1400096_14

description: CASCADE.HTSeq.all.raw.txt.gz


title: 65682_1400096_11

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1271

description: miRNA


title: ChOR-seq_AID_increase_WT_T4_asynchrony


title: ChOR-seq_AID_increase_WT_T1_asynchrony


title: 65682_1400096_20

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1262

description: miRNA


title: CC1260

description: miRNA


title: ChOR-seq_AID_increase_WT_T2_asynchrony


title: CC1259

description: miRNA


title: ChOR-seq_AID_WT_T0_asynchrony


title: 65659_1400598_20

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1256

description: miRNA


title: CC1257

description: miRNA


title: CC1255

description: miRNA


title: CC1254

description: miRNA


title: ChOR-seq_H1KO_T3_asynchrony


title: 65659_1400598_16

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1252

description: miRNA


title: CC1253

description: miRNA


title: 65659_1400598_10

description: CASCADE.HTSeq.all.raw.txt.gz


title: 65629_1300786_27

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1264

description: miRNA


title: CC1251

description: miRNA


title: ChOR-seq_H1KO_T0_asynchrony


title: ChOR-seq_H1KO_T1_asynchrony


title: CC1250

description: miRNA


title: CC1249

description: miRNA


title: 65629_1300786_18

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1248

description: miRNA


title: CC1258

description: miRNA


title: ChOR-seq_WT_T3_asynchrony


title: CC1247

description: miRNA


title: CC1245

description: miRNA


title: ChOR-seq_WT_T2_asynchrony


title: CC1244

description: miRNA


title: CC1243

description: miRNA


title: ChOR-seq_H1KO_T2_asynchrony


title: ChOR-seq_WT_T0_asynchrony


title: ChOR-seq_WT_T1_asynchrony


title: CC1242

description: miRNA


title: CC1241

description: miRNA


title: CC1239

description: miRNA


title: CC1240

description: miRNA


title: ChIP-seq_H1KO_HA_tetR_EED_targeting_H3K27me3


title: ChIP-seq_H1KO_HA_tetR_EZH2_targeting_H3K27me3


title: CC1235

description: miRNA


title: CC1237

description: miRNA


title: CC1238

description: miRNA


title: CC1236

description: miRNA


title: ChIP-seq_WT_HA_tetR_EZH2_targeting_H3K27me3


title: ChIP-seq_WT_HA_tetR_EED_targeting_H3K27me3


title: CC1232

description: miRNA


title: CC1231

description: miRNA


title: CC1230

description: miRNA


title: CC1246

description: miRNA


title: 65629_1300786_17

description: CASCADE.HTSeq.all.raw.txt.gz


title: CC1228

description: miRNA


title: CC1227

description: miRNA


title: CC1226

description: miRNA


title: CC1225

description: miRNA


title: Distal_Colon_WT_R20291-1

city: Nashville

first: Christopher

last: Peritore-Galve

state: Tennessee

address: 1161 21st Avenue South, MCN A4208

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

description:
CountsPerMillion_DistalColon.csv
R20291_v_Mock

data_processing:
Data were aligned to GRCm39 mouse genome with STAR alignment tool with default settings
Differential expression was performed with limma-voom.
Assembly: GRCm39 Mus musculus genome (GenBank accession number GCA_000001635.9)
Supplementary files format and content: Normalized read counts as counts per million (csv file)
Supplementary files format and content: Differential expression files (csv files)

source_name: Distal colon

growth_protocol: Mice maintained on normal chow diet and access to normal drinking water ad libitum

extract_protocol:
Excised tissue was immediately placed in RNAlater on ice. Next day, tissues were sashed with sterile PBS then RNA was extracted by disrupting tissue in TRIzol, then precipitating RNA with addition of chloroform. Contaminating DNA was depleted with TURBO DNA-free kit, then RNA was cleand with Monarch RNA Cleanup Kit.
Eukaryotic ribosomal RNA was depleted with NEBNext rRNA Depletion kit, then library was synthesized with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Multiplex oligos wer added using the Unique Dual Index Primer Pairs Set 3 from NEB.

value: Distal colon

value: 11 weeks old

tag: time

value: 2 days post-inoculation

tag: molecule type

value: Eukaryotic mRNA


title: Distal_Colon_WT_R20291-3


title: Distal_Colon_AgtxB+-3

description:
CountsPerMillion_DistalColon.csv
Mock_v_AgtxB

value: 1000 Agtx B+ spores


title: Distal_Colon_WT_R20291-2


title: Distal_Colon_AgtxB+-2


title: CC1224

description: miRNA


title: CC1223

description: miRNA


title: CC1222

description: miRNA


title: CC1221

description: miRNA


title: Distal_Colon_AgtxB+-1


title: Distal_Colon_A+Bgtx-3

description:
CountsPerMillion_DistalColon.csv
Mock_v_ABgtx

value: 1000 A+ Bgtx spores


title: CC1220

description: miRNA


title: CC1233

description: miRNA


title: CC1234

description: miRNA


title: Distal_Colon_A+Bgtx-2


title: Distal_Colon_A+Bgtx-1


title: CC1229

description: miRNA


title: Distal_Colon_ΔtcdAΔtcdB-3

description:
CountsPerMillion_DistalColon.csv
Mock_v_DKO

value: 1000 ΔtcdAΔtcdB spores


title: RNA-seq.KO.PCIF1.rep3

city: San Diego

first: Lingling

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

data_processing:
Single-end and paired-end sequencing data were trimmed by single-end and paired-end model of cutadapt software respectively. Reads longer than 15bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 software using the default parameter for single or pair-end model
For RNA-seq, reads were counted by htseq, then gene expression was quantified by DESeq2.
For m6A-exo-seq, reads were counted by featureCount, then differential methylation sites at cap-region was detected by hypergeometric test through in-house scripts. The m6A marked genes are listed in m6Am.marked.genes.csv, with the gene names at first column, differential methylation FDR and p-value at second and third columns, change of enrichment fold in KO PCIF1 compared to KO control samples at the fourth column.
Input and IP samples bam files in m6A-exo-seq were converted to bigwig files by bamCoverage script in deepTools for visualization and analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files for m6A-exo-seq coverage. m6Am.marked.genes.csv for m6Am marked genes in m6A-exo-seq. RNAseq.counts.csv for raw gene counts in RNA-seq,

source_name: HCT116 cells

growth_protocol: HCT 116 (CCL-247) cell line was purchased from ATCC. The cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37°C in 5% CO2 incubators according to ATCC’s culture methods.

extract_protocol:
After the extraction of total RNA, for RNA-seq, ribosomal RNA was depleted by RiboMinus Transcriptom Isolation Kit (life technology, K1500-02). For m6A-exo-seq, mRNA was purified using Magnetic mRNA Isolation Kit (New England Biolabs, S1550S)
For m6A-exo-seq, mRNA was fragmented with Fragmentation Reagents Kit (Invitrogen, AM8740) following the manufacturer’s protocol, then phosphorylated with T4 PNK (NEB, M0201S), and then treated with Terminator 5’-Phosphate-Dependent Exonuclease (Lucigen) to remove phosphorylation of transcripts. Lastly, Cap-Clip (CellScript) were added to remove capped transcripts. 10% uncapped 5’RNA fragments were reserved as input, the rest of fragmented RNA were proceeded to do the immunoprecipitation with anti-N6-methyladenosine (m6A) antibody (abcam, ab151230). Immunoprecipated and input RNA for m6A-exo-seq as well as ribosomal depleted and fragmented RNA for RNA-seq were both subjected to library preparation using a TruSeq mRNA library preparation kit (Illumina)
RNA-seq and m6A-exo-seq. RNA-seq was sequenced at Illumina HiSeq 4000 platform with single-end model. m6A-exo-seq was sequenced at  Illumina NovaSeq 6000 platform with paired-end model

treatment_protocol: For lentiviral producing, 293FT cells were co-transfected with packaging plasmids, including psPAX2 and pMD2.G and CRISPRV2 with the indicated sgRNA in 10 cm dishes using Lipofectamine (Life Technologies, 11668027) in Opti-MEM medium (Gibco). The media was replaced with fresh completed DMEM after 4–6 h. After 48h, supernatants were harvested and then infect the indicated cells by spin transduction.

tag: cell line

tag: cell type

tag: genotype/variation

value: FCIF1 KO


title: RNA-seq.KO.PCIF1.rep2


title: Artery 3

city: Suita

first: Isao

last: Ono

address: 6-1 Kishibe-Shinmachi

institute: National Cerebral, and Cardiovascular Center

data_processing:
Paired-end sequencing (2 × 75 base pair) was performed on a NextSeq500 (Illumina). Each read was aligned to the UCSC hg38 genome using CLC genomics workbench (version 11, QIAGEN). Differential expression analyses, including principal component analysis and clustering analysis, were performed using the iDEP.93.
Assembly: hg38
Supplementary files format and content: text files

source_name: endothelial cell

growth_protocol: human umbilical artery endothelial cells were passaged 5 times in Endothelial Cell Growth Medium  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using SMART-Seq® Single Cell PLUS Kit (TAKARA BIO INC.) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using SMART-Seq® Single Cell PLUS Kit (TAKARA BIO INC.) following manufacturer's protocols.

treatment_protocol: Primary cultured endothelial cells were seeded on the 3D-casted mold surface. After 12 h, the 3D-casted mold was perfused with a complete culture medium in a pulsatile manner (55 ml/min, 60 Hz, 3 h).

value: endothelial cell

value: primary, #C-12202

value: human umbilical artery endothelial cell

value: WT

tag: treatment

value: perfusion with a complete culture medium in a pulsatile manner (55 ml/min, 60 Hz, 3 h)


title: Artery 2


title: Artery 1


title: RNA-seq.KO.PCIF1.rep1

value: colorectal cancer


title: Distal_Colon_ΔtcdAΔtcdB-2

value: Female


title: Distal_Colon_Mock-2

value: Sterile PBS


title: Airway organoid, DNAH5 mutation, rep1

city: chengdu

first: Wenhao

last: Yang

address: Renmin Rode 17

institute: West China Second University Hospital, Sichuan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (http://software.10xgenomics.com/single-cell/overview/welcome)
Assembly: Homo_sapiens.GRCh38.93.sorted.gtf
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Airway epithelium

extract_protocol:
The airway organoid with DNAH5 mutation and normal airway organoid pellets, derived from the biopsy, were resuspended with 1 mL of TrypLE 1× (Gibco, A1217701), separately, incubated for 15-30 min at 37 °C, and mechanically sheared with 1-ml pipettes. After washing twice with AdDF+++, the cell pellets were filtered with a 40-μm strainer. Cellular suspensions (∼6000 cells) were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single-cell GEMs. Sample processing and single-cell RNA-seq library preparation were performed using Chromium Single Cell 3′ v2 reagents. Sequencing was performed on an Illumina NextSeq500 following the manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Airway epithelium

value: Airway orgnaoid

value: DNAH5 mutation

value: 12 years old


title: RNA-seq.KO.control.rep3

value: control


title: Distal_Colon_Mock-3

value: Distal colon

value: 11 weeks old

value: 2 days post-inoculation

value: Eukaryotic mRNA


title: RNA-seq.KO.control.rep4


title: Airway organoid, Normal, rep1

description: 10x Genomics

value: wild type


title: Aneurysm 4

value: endothelial cell

value: primary, #C-12202


title: Aneurysm 5

value: human umbilical artery endothelial cell

value: WT


title: Aneurysm 3

value: perfusion with a complete culture medium in a pulsatile manner (55 ml/min, 60 Hz, 3 h)


title: Distal_Colon_ΔtcdAΔtcdB-1

value: Female

value: 1000 ΔtcdAΔtcdB spores


title: RNA-seq.KO.control.rep2

value: colorectal cancer


title: Distal_Colon_Mock-1

value: Sterile PBS


title: RNA-seq.KO.control.rep1


title: Aneurysm 2


title: Aneurysm 1


title: RNA-seq.KO.PCIF1.rep4

value: FCIF1 KO


title: CT26 cells, Knockout PCIF1, bio rep4

data_processing:
Paired-end sequencing data were trimmed by paired-end model of cutadapt software. Reads longer than 15bp were retained for mapping.
Trimmed reads were aligned to mm10 genome assembly by hisat2 software using the default parameter for pair-end model
For RNA-seq, reads were counted by htseq, then gene expression was quantified by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include reads counts of individual genes for each Sample

growth_protocol: CT26 (CRL-2638; murine colon carcinoma) was cultured in DMEM, RPMI (Gibco) or McCoy's 5A medium (ATCC) supplemented with 10% fetal bovine serum (Gibco) at 37℃ in 5% CO2 incubators.

extract_protocol:
After the extraction of total RNA, for RNA-seq, ribosomal RNA was depleted by RiboMinus Transcriptom Isolation Kit (life technology, K1500-02).
Ribosomal depleted RNA was subjected to RNA-seq library prepration using Illumina Truseq standard library preparation protocol

treatment_protocol: After retroviral transdution and knockout by PCIF1 and control sgRNA, 2 × 10 6 CT26 cells were suspended in 200 μl of PBS/Matrigel (Corning) (1:1) and then subcutaneously inoculated into flank of each mouse. BALB/c mice bearing CT26 tumors were injected intraperitoneally (i.p.) with 200 μg (10 mg/kg) of anti–CTLA-4 (Bio X Cell, mCD152) and/or anti–PD1 (Bio X Cell, clone 29F.1A12) and IgG (Bio X Cell, clone 2A3, BE0089) antibodies on days 11, 14, 17, 20 and 23 as recommend.

value: colon cancer cells

value: knockout PCIF1


title: CT26 cells, Knockout PCIF1, bio rep5


title: CT26 cells, Knockout PCIF1, bio rep3


title: H3K27me3-RingKO-+indRing1a-WT-DOX-Rep2

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

country: United Kingdom

institute: Queen's University Belfast

data_processing:
FASTQ files were mapped against human genome (hg19) and Drosophila genome (Dm6) using Bowtie 2 (bowtie-bio.sourceforge.net) and default parameters. SAM files were further filtered for uniquely mapped reads and high-quality mapping (-q 10) using SAMtools, and PCR duplicates were removed using MarkDuplicates in PICARD tools. For ChIP-Rx, total reads in Drosophila BAM files were used to calculate the spike-in normalization factors and were used for downscaling the corresponding human BAM files as described (49). Normalized human BAM files were further downscaled on the basis of the BAM file with the lowest total read counts to normalize for sequencing depth. Next, BAM files were converted to BED files using BEDTools, and reads were extended by 160 nt and converted to BedGraph using bamCoverage tool from the deepTools suite. BedGraphs were converted to BigWig files using bedGraphToBigWig from UCSC tool suite for further visualization using Integrative Genomics Viewer browser.
Assembly: hg19
Supplementary files format and content: xls, normalized ChIP-seq counts
Supplementary files format and content: bigwig

source_name: colorectal

growth_protocol: Culture medium for DLD1 RING1A/B-DKO cells with stable integration of pTRE3GBI-eGFP-Ring1A WT/I50S/C72A or pLEX_305-N-dTAG-Ring1B was supplemented with G-418 DiSulphate (200 μg/ml; G418; Formedium) or puromycin (3.3 μg/ml; Invitrogen), respectively.

extract_protocol:
Biological duplicates of DLD1 WT, DLD1-DKO-Dox-RING1A, DLD1-KO-Dox-USP7, HAP1 WT, and HAP1 RING1A/B-KO cells were grown in two 15-cm dishes per condition, which were processed independently. GFP-USP7 or GFP-RING1A expression was induced by addition of Dox (1 μg/ml) for 3 days (+Dox). Two other plates were mock-treated (−Dox). Cells were harvested by trypsinization, followed by cell counting. For cross-linking, 17 million cells were suspended in 10 ml of PBS. Cells were fixed by the addition of 1% formaldehyde and incubation on a roller mixer for 10 min. Fixation was stopped by the addition of glycine (125 mM). Next, cells were washed twice with PBS and lysed in 1 ml of lysis buffer: 50 mM tris-HCl (pH 8.0), 10 mM EDTA, and 1% SDS, supplemented with protease inhibitors pepstatin A (1 μl/ml), leupeptin (1 μg/ml), aprotinin (1 μg/ml), and 0.2 mM AEBSF. These protease inhibitors were present in all subsequent buffers until elution. Cross-linked chromatin was sheared to approximately 200–base pair (bp) DNA length in a Bioruptor Pico sonication system. The normalization reference exogenous genome was isolated from ~80 million Drosophila S2 cells (one 15-cm2 dish). Fixation was performed as above with 1% formaldehyde in PBS for 10 min. S2 cells were lysed in 1.2 ml of 0.75% SDS, 10 mM EDTA, and 50 mM tris-HCl (pH 8.0), supplemented with protease inhibitors. Drosophila chromatin was sheared to 200- to 300-bp DNA length. DLD1-KO-Dox-USP7 chromatin (180 μl) was combined with 20 μl of S2 chromatin and diluted 10-fold with dilution buffer [20 mM tris (pH 8.0), 1% Triton X-100, 2 mM EDTA, and 150 mM NaCl], cleared by centrifugation at 15,000g for 20 min. The supernatant was transferred to a fresh tube and incubated overnight at 4°C in the presence of either 10 μl of anti-H3K27me3 (Cell Signaling Technology, #9733) or 5 μl of anti-H2AK119ub1 (Cell Signaling Technology, #8240) on a rotating wheel. The next morning, 50 μl of Dynabeads protein A slurry (Invitrogen), which was blocked overnight with 1% BSA in dilution buffer, was added, followed by a 3-hour incubation. Next, beads were washed four times with wash buffer [20 mM tris-HCl (pH 8.0), 2 mM EDTA, 0.1% SDS, and 1% Triton X-100] containing 150 mM NaCl, followed once with wash buffer containing 500 mM NaCl. DNA was eluted with 0.1 M NaHCO3, 1% SDS, and proteinase K (0.5 mg/ml) for 2 hours at 37°C, followed by an overnight incubation at 65°C. DNA was subsequently purified by double phenol/chloroform extraction, followed by ethanol precipitation.
ChIP-Rx-seq libraries were prepared using the ThruPLEX DNA-Seq Kit (Takara Bio, R400675), according to the manufacturer’s instructions. ChIP-Rx DNA was repaired to obtain blunt-ended double-stranded DNA followed by ligation of stem-loop adapters. The stem loop was cleaved off, and a library amplification was performed that extended the template with dual indices and sequence needed for posterior sequencing on an Illumina HiSeq 2500 sequencer (dual-indexed 50-bp paired-end reads).

treatment_protocol: Transgene expression was induced with Dox (1 μg/ml).

value: colorectal

value: Colorectal-cancer

value: +DOX

tag: antibody


title: CT26 cells, Knockout PCIF1, bio rep2


title: m6A-exo-seq.KO.PCIF1.input.rep2

data_processing:
Library strategy: m6A-exo-seq
Single-end and paired-end sequencing data were trimmed by single-end and paired-end model of cutadapt software respectively. Reads longer than 15bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 software using the default parameter for single or pair-end model
For RNA-seq, reads were counted by htseq, then gene expression was quantified by DESeq2.
For m6A-exo-seq, reads were counted by featureCount, then differential methylation sites at cap-region was detected by hypergeometric test through in-house scripts. The m6A marked genes are listed in m6Am.marked.genes.csv, with the gene names at first column, differential methylation FDR and p-value at second and third columns, change of enrichment fold in KO PCIF1 compared to KO control samples at the fourth column.
Input and IP samples bam files in m6A-exo-seq were converted to bigwig files by bamCoverage script in deepTools for visualization and analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files for m6A-exo-seq coverage. m6Am.marked.genes.csv for m6Am marked genes in m6A-exo-seq. RNAseq.counts.csv for raw gene counts in RNA-seq,

molecule: polyA RNA

value: m6A antibody (abcam, ab151230)


title: H3K27me3-RingKO-+indRing1a-WT-NO-DOX-Rep2

value: No-DOX


title: H3K27me3-RingKO-+indRing1a-WT-DOX-Rep1


title: CT26 cells, Knockout PCIF1, bio rep1


title: H3K27me3-RingKO-+indRing1a-WT-NO-DOX-Rep1


title: m6A-exo-seq.KO.PCIF1.input.rep1


title: CT26 cells, Knockout control, bio rep5

value: knockout control


title: H3K27me3-WT-Rep1


title: CT26 cells, Knockout control, bio rep3


title: m6A-exo-seq.KO.PCIF1.ip.rep1


title: m6A-exo-seq.KO.control.input.rep2

value: control


title: H3K27me3-WT-Rep2


title: CT26 cells, Knockout control, bio rep1


title: m6A-exo-seq.KO.control.ip.rep2


title: CT26 cells, Knockout control, bio rep4


title: m6A-exo-seq.KO.control.ip.rep1


title: m6A-exo-seq.KO.control.input.rep1


title: CT26 cells, Knockout control, bio rep2


title: 1-PH-1

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

description: maize stalk (without epidermis) 24 hours post water treatment

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads containing adapters, more than 10% of unknown nucleotides and more than 50% of low quality (Q-value≤20) bases were further filtered by fastp (v0.18.0).
Reads were mapped to ribosome RNA (rRNA) database using Bowtie2 (v2.2.8). The rRNA mapped reads were then removed.
Clean reads were mapped to the reference genome using HISAT (v2.2.4)
The mapped reads of each sample were assembled by using StringTie (v1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Zea mays (Ensembl_release45)
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: maize stalk internodes (without epidermis) infected by F. graminearum

growth_protocol: After being mixed with cooked soil, perlite, vermiculite and black soil, it is autoclaved and sub packed into a flower pot of appropriate size. Compound fertilizer, potassium dihydrogen phosphate, calcium superphosphate and urea are added to it. After mixing, it is soaked with tap water. Corn seeds were placed in the shallow soil layer in the artificial climate chamber. After a week, the corn seeds will germinate. During the growth period, it is necessary to properly water and apply green fertilizer to ensure the vigorous growth of corn. The growth conditions of corn in the artificial climate chamber are 14 hours of light / 10 hours of darkness, the relative humidity is about 65%, the temperature is controlled at 26 ℃ in the daytime and 22 ℃ at night. The stem infection experiment of maize can be carried out after planting for about 2 months

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
The RNA sequencing was performed at GENE DENOVO. The libraries for sequencing were prepared using Clontech SMARTer PCR cDNA Synthesis Kit

treatment_protocol: The maize B73 plants were inoculated after about two months growth. Use alcohol wiped tweezers to make a hole wound on the stalk, and then infiltrate 20 μL PH-1 conidia suspension (concentration of 106/mL) into the wound of each maize stalk. Then wrap the wound of maize stalk with moist sterile gauze and put it in the light incubator for infection experiment

value: stalks

tag: cultivar

value: two-month-old maize stalks

value: 24 hours post PH-1 infection


title: f356: Axial Nerve Cord - FLAMseq

status: Public on Nov 11 2022

city: Berlin

first: Grygoriy

last: Zolotarov

address: Hannoversche Strasse 28

department: Berlin Institute of Medical Systems Biology

country: Germany

institute: Max Delbruck Center for Molecular Medicine

data_processing:
bcl2fastq software has been used for basecalling for PolyA, total RNA and Small RNA libraries. For FLAMseq and Isoseq FLAMAnalysis and isoseq3 pipelines have been used to obtain full-length non-chimeric ( FLNC) reads.
PolyA and totalRNA sequencing data have been mapped to the genome using STAR aligner (Dobin et al. 2013) using default parameters
Iso-seq and FLAMseq FLNCs have been mapped to the genome with minimap2 (v 2.17-r941) using the parameters "--cs -ax splice:hq -uf --secondary=no -C5"
MicroRNA counts file has been generated using quantifier.pl script from miRDeep2 package and the sequences of microRNAs predicted in this study
*_clean_genomic_tail_length.txt.gz files for FLAMseq have been generated by FLAMAnalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis).
Genome_build: GCF_006345805.1_ASM634580v1
Supplementary_files_format_and_content: miRNAs_expressed_all_samples_mirgenedb.csv.gz contains raw and normalized counts for each microRNA in every tissue in the dataset
Supplementary_files_format_and_content: totalRNA_fc_221221.txt.gz, polyARNA_fc_221221.txt.gz - tab-separated file with read counts for individual genes in the genome produced with featureCounts
Supplementary_files_format_and_content: *bed files for Isoseq have been obtained by collapsing reads into individual libraries into the sets of putative isoforms using TAMA collapse (https://github.com/GenomeRIK/tama)
Supplementary_files_format_and_content: *_clean_genomic_tail_length.txt.gz files contain the poly(A) tail length, sequence and a read_ID for every read in the dataset

organism: Octopus vulgaris

source_name: Axial Nerve Cord

extract_protocol:
Adult specimens of O. vulgaris (body weight 800 g ± 50 g, mean ± SD) were collected from the Bay of Naples (Italy) and transferred to the Department of Biology, University of Naples Federico II (Italy). Samples (N=8) were anesthetized by isoflurane insufflation (Polese et al. 2014), and tissues were dissected under sterile conditions following institutional guidelines. The collected samples were snap frozen in liquid nitrogen and immediately put in Trizol, then stored at −80 °C. The RNA has been extracted from the tissues using Direct-zolTM RNA Miniprep (Zymo Research), following the manufacturer’s protocol. RNA has been stored at -80 C prior to sequencing, and it was transported using dry ice. The quality of RNA has been accessed with Bioanalyzer and only samples with intact RNA have been kept for library preparation.
Library construction protocols are listed in the columns of SAMPLES section above

value: Axial Nerve Cord

value: FLAMseq

tag: strategy

value: FL cDNA

tag: basecalling

value: SMRT Link

tag: downstream analysis

value: lima, FLAMAnalysis, TAMA collapse