title: Serum_ESCC patient_rep52

city: Beijing

first: Fen

address: Youanmenwai Street

department: Department of Epidemiology and Health Statistics

institute: Capital Medical University

description: micro RNAs expression in serum from ESCC patients

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: Serum, ESCC patient, pre-operative

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using miRNeasy Serum/Plasma Kit (Cat # 217184, Qiagen, German), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 5 mL venous blood (usually in the morning) were collected from each participant in  tubes. Blood samples were allowed to stand for 1 hour at room temperature or kept at 4℃ and processed within 24 hours after collection and serum separation was accomplished by centrifugation at 820g for 10 min at 4℃. Then the serum samples were transferred into new tubes and stored at -80℃ for next procedure.

value: serum

value: Female


title: c706-input_1

status: Public on Feb 07 2019

type: SRA

city: Emeryville

first: Tobias

last: Flecken

state: CA

address: 5300 Chiron Way

department: Infectious Diseases

country: USA

institute: Novartis Institutes for Biomedical Research

description:
run 1
Aligned to EU787447.1.

library_source: genomic

data_processing:
base calling: RTA 1.18.54 (from Illumina MCS 2.6.2)
alignment: bowtie2 2.3.0 was used for alignment to 1.1mer viral genomes (with -t -no-unal -no-discordant -no-mixed -I 120 -X 200 option) and all sequences (combined hg38/HBV/phiX; only -t option)
paired read merging: custom script was used to merge paired reads in the output SAM file based on viral genome coordinates. Unsequenced insert was represented as N with low quality score.
BAM conversion: SAM file was converted to BAM, sorted, and indexed using samtools 0.1.19
BEDGRAPH conversion: BAM file was converted to BEDGRAPH using bedtools 2.18.1 (-bg -trackline options)
1mer conversion: custom script was used to wrap around reads that aligned in the overhang of the 1.1mer to the start of the sequence
scaling and wig conversion: custom script was used to convert BEDGRAPH to WIG files while simultaneously scaling it per 106 total reads in the library (hg38+HBV+phiX)
Genome_build: HBV reference genomes are indicated in the sample overview (protocl column). GRCh38.p10 was used for the human genome, NC_001422.1 for phiX
Supplementary_files_format_and_content: WIG files contain the number of HBV reads per million total reads for each position of the respective HBV reference genome. Sequences are shifted by -500 nt compared to EcoRI site.

molecule: genomic DNA

organism:
Homo sapiens
Hepatitis B virus

source_name: liver

extract_protocol:
Cells were fixed in freshly prepared 1% formaldehyde in PBS (both ThermoFisher Scientific) for 5 min prior to quenching with 125 mM glycine in PBS. Pelleted cells were either used directly for analysis or snap-frozen and stored at -80°C until use. Next, cells were washed with cold lysis buffer [PBS with 0.1% Triton X-100, 0.1% NP-40, 1 mM dithiothreitol (DTT), 50 ng/ml trichostatin A (TSA) and 1x EDTA-free protease inhibitor (Roche, Basel, Switzerland)] and lysed in the same buffer for 10 min on ice. Nuclei were pelleted, resuspended in digestion buffer [H2O with 50 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 10% glycerol, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)] and digested with 600 IU/ml micrococcal nuclease (MNase; ThermoFisher Scientific) for 12 min at 37°C. Digestion was stopped by addition of 10 mM EDTA. Nuclei were pelleted at 6500 x g and supernatants collected. The pellet was resuspended in digestion buffer with 10 mM EDTA and 300 mM NaCl and mildly sonicated using a W 375 sonicator (Qsonica, Newtown, CT) at 50% duty cycle and power setting 3. Nuclei were again pelleted, supernatants combined and mixed with an equal amount of sucrose buffer [H2O with 50 mM Tris-HCl pH 7.5, 50 mM NaCl, 5 mM EDTA, 0.01% NP-40, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)]. Samples were concentrated using Amicon Ultra-4 100 kDa centrifugal filter units (Millipore-Sigma; Merck KGaA, Darmstadt, Germany) and spun on a 5-30% continuous sucrose gradient in sucrose buffer for 4 h at 40,000 x g and 4°C using a SW41Ti rotor (Beckman Coulter Inc., Brea, CA). Chemicals were obtained from Millipore-Sigma unless noted otherwise. Mononucleosome containing fractions were pooled and concentrated to ~500 µl prior to addition of 100 ng/µl bovine serum albumin (ThermoFisher Scientific). Mononucleosomes were either stored at -20°C or used immediately for ChIP. Antibodies were bound to 20 µl/ChIP Dynabeads Protein G (ThermoFisher) in ChIP buffer [H2O with 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 200 µg/ml BSA] at 4°C and added to 2 µg of chromatin in ChIP buffer and allowed to bind overnight. Samples were washed six times in LiCl wash buffer [H2O with 150 mM LiCl, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, and 0.7% sodium deoxycholate] and eluted in 100 µl elution buffer [H2O with 1% SDS and 100 mM NaHCO3]. Crosslinks were reversed by digestion with Proteinase K (ThermoFisher) for 5 h at 65°C and then digested for another 30 min with DNase-free RNase A (ThermoFisher) at 37°C. DNA was purified using the QIAquick PCR purification kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
1 ng of DNA was used for sequencing library construction with the KAPA Hyper Prep Kit (Roche) according to the manufacturer’s instructions. For barcoding, 2 µl of TruSeq RNA adapters stocks were used (Illumina, Inc., San Diego, CA). Up to 6 libraries were pooled per sequencing run and 500 ng pooled library subject to HBV-specific target enrichment using the xGen Lockdown Reagents Hybridization and Wash Kit (Integrated DNA technologies, Skokie, IL) according to the manufacturer’s instructions. A custom set of xGen lockdown probes of 60 bp length tiling the entire HBV genome of genotypes A-D was used for target enrichment (Integrated DNA technologies) together with Dynabeads MyOne T-270 Streptavidin (ThermoFisher). The pull-down was amplified for 12 or 8 PCR cycles (biopsies vs. de novo infected cells/cell lines; KAPA HiFi HotStart ReadyMix, Roche) and the product cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Inc.). The product was used to dilute the original library to 20 nM. Sequencing was performed using an Illumina MiSeq sequencer with a MiSeq v3 reagent kit for 2x76 bp paired-end reads (Illumina, Inc.).

treatment_protocol: Biopsy specimens were thawed in pre-warmed 0.05% Trypsin-EDTA (ThermoFisher Scientific, Waltham, MA) and mixed with 8x106 uninfected HepG2-hNTCP cells.

tag: cell line

tag: cell type

value: liver biopsy

tag: tissue

value: liver

tag: hbv genotype

value: D

tag: disease stage

value: Under therapy (Lamivudin), HBeAg-

tag: ChIP

value: input

tag: chip antibody


title: DSC-A22-11

type: RNA

city: Hong Kong

first: Tongtong

last: Kan

address: 83 Tat Chee Avenue

country: China

institute: City University of Hong Kong

data_processing:
Raw Crt, “relative threshold”, values were generated by OpenArray system, the undetected Crt values were replaced by 40 (Matrix non-normalized); the Crt values were normalized to 18S using the -△Crt method (Matrix normalized); fold change was calculated by 2^-△Crt.
Fold Change worksheet reports relative single cell gene expression level.

label: TaqMan

molecule: total RNA

organism: Homo sapiens

label_protocol: The single-cell reverse transcription and pre-amplification procedures were provided by the same kit. Single-cell RT-PCR was performed in OpenArray chips, using QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems).

extract_protocol: The single cells were lysed directly using Single cell-to-CT qRT-PCR Kit (Ambion).

treatment_protocol: The single cells were picked up manually under a microscope using Kuiqpick through a glass capillary from purified ascites.

tag: subgroup

value: DSC-M

value: Epithelial ovarian cancer ascites


title: DSC-A22-10

value: DSC-E


title: DSC-A22-9


title: Serum_ESCC patient_rep50

last: Liu

tag: gender

tag: age


title: DSC-A22-14


title: Serum_ESCC patient_rep51

value: Male


title: c687-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: HBeAg- hepatitis

value: rabbit polyclonal, abcam ab8580


title: Serum_ESCC patient_rep49


title: DSC-A22-8


title: S2_HTMC_H2O2

city: Tianjin

first: Bingqing

last: Huang

address: Nanjing Road 288, Heping District

department: Department of Pathology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression for human trabecular meshwork cells with hydrogen peroxide treatment

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HTMC,hydrogen peroxide,replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)/TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were treated with 300 μM H2O2 in serum-free medium for 2 hrs, and then the medium was replaced with serum-free media without H2O2 cultured for another 2 hrs

value: human trabecular meshwork cells

tag: treatment

value: hydrogen peroxide


title: c687-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.

value: rabbit monoclonal B0422, abcam ab41969


title: S1_HTMC_no

description: Gene expression for human trabecular meshwork cells without any treatment

source_name: HTMC,no treatment,replicate 1

value: no treatment


title: S3_HTMC_no

source_name: HTMC,no treatment,replicate 3


title: DSC-A22-7


title: S2_HTMC_no

source_name: HTMC,no treatment,replicate 2


title: S1_HTMC_H2O2

source_name: HTMC,hydrogen peroxide,replicate 1


title: c687-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c666-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: rabbit monoclonal C36B11, Cell Signaling Technology 9733S


title: Serum_Healthy control_rep52

source_name: Serum, Healthy control, Matched by age and sex

value: serum

value: Female


title: S3_HTMC_H2O2

source_name: HTMC,hydrogen peroxide,replicate 3


title: c687-input_1

description:
run 1
Aligned to EU787447.1.

value: liver biopsy

value: liver


title: DSC-A22-6


title: DSC-A22-5


title: Serum_ESCC patient_rep48


title: c666-H3K9me3-ChIP_2

description:
run 2
Aligned to EU787447.1.

value: D

value: rabbit polyclonal, abcam ab8898


title: c666-H3K9me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: Serum_Healthy control_rep51


title: Serum_Healthy control_rep48


title: Serum_Healthy control_rep50


title: DSC-A22-4


title: DSC-A22-2


title: Serum_Healthy control_rep47


title: c666-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: DSC-A22-1


title: Serum_Healthy control_rep49


title: DSC-A22-3


title: DSC-A20-30

value: DSC-L


title: c666-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c666-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Serum_Healthy control_rep46


title: c666-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: DSC-A20-28

value: Epithelial ovarian cancer ascites


title: Serum_ESCC patient_rep46


title: Serum_ESCC patient_rep47


title: Serum_Healthy control_rep45


title: c666-input_1

description:
run 1
Aligned to EU787447.1.

value: input


title: DSC-A20-27


title: Serum_ESCC patient_rep44


title: c537-H3K9me3-ChIP_2

description:
run 2
Aligned to EU410079.1.

value: C

value: HBeAg+ infection


title: Serum_ESCC patient_rep45

value: Male


title: c537-H3K27me3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: DSC-A20-25


title: DSC-A20-26


title: c537-H3K9me3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: DSC-A20-23


title: DSC-A20-24


title: Serum_ESCC patient_rep43


title: c537-H3K4me3-ChIP_1

description:
run 1
Aligned to EU410079.1.

value: rabbit polyclonal, abcam ab8580


title: DSC-A20-22


title: Serum_ESCC patient_rep41


title: Serum_ESCC patient_rep40


title: Serum_ESCC patient_rep42


title: DSC-A20-21


title: DSC-A20-29


title: c537-input_1

description:
run 1
Aligned to EU410079.1.


title: c357-H3K27me3-ChIP_1

description:
run 1
Aligned to AM494708.1.

value: E

value: HBeAg+ hepatitis


title: DSC-A20-20

value: DSC-M


title: Serum_ESCC patient_rep39


title: c357-H3K4me3-ChIP_1

description:
run 1
Aligned to AM494708.1.


title: c357-H3K4me3-ChIP_2

description:
run 2
Aligned to AM494708.1.


title: DSC-A20-19


title: Serum_ESCC patient_rep38


title: c537-H3K4me3-ChIP_2

description:
run 2
Aligned to EU410079.1.


title: DSC-A20-18


title: c317-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: HBeAg- hepatitis

value: rabbit monoclonal C36B11, Cell Signaling Technology 9733S


title: Serum_ESCC patient_rep36

value: serum

value: Female


title: DSC-A20-17


title: Serum_ESCC patient_rep37


title: Serum_ESCC patient_rep35


title: c317-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.

value: liver biopsy

value: liver


title: c317-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: D


title: Serum_ESCC patient_rep34


title: c317-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.

value: rabbit monoclonal B0422, abcam ab41969


title: DSC-A20-13

value: Epithelial ovarian cancer ascites


title: DSC-A20-14


title: Serum_ESCC patient_rep33


title: DSC-A20-12


title: Serum_ESCC patient_rep31


title: Serum_ESCC patient_rep30


title: c317-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c357-input_1

description:
run 1
Aligned to AM494708.1.

value: input


title: c313-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: DSC-A20-11


title: DSC-A20-16


title: Serum_ESCC patient_rep29


title: DSC-A20-15


title: DSC-A20-9

value: DSC-E


title: Serum_ESCC patient_rep28


title: c317-input_1

description:
run 1
Aligned to EU787447.1.


title: DSC-A20-10


title: c313-H3K9me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: rabbit polyclonal, abcam ab8898


title: DSC-A20-8


title: Serum_ESCC patient_rep32


title: c313-H3K9me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Serum_ESCC patient_rep27


title: DSC-A20-7


title: DSC-A20-6


title: c313-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: DSC-A20-5


title: c313-input_1

description:
run 1
Aligned to EU787447.1.


title: Serum_ESCC patient_rep23


title: Serum_ESCC patient_rep22

value: Male


title: DSC-A20-4


title: Serum_ESCC patient_rep24


title: Serum_ESCC patient_rep21


title: c162-H3K27me3-ChIP_1

description:
run 1
Aligned to EU594392.1.

value: A


title: c162-H3K4me3-ChIP_1

description:
run 1
Aligned to EU594392.1.

value: rabbit polyclonal, abcam ab8580


title: c162-H3K4me3-ChIP_2

description:
run 2
Aligned to EU594392.1.


title: Serum_ESCC patient_rep20


title: c313-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Immuno DTCC-68

treatment_protocol: The cell clusters were picked up then dissociated into single cells. Both the cell clusters and single cells were picked up manually under a microscope using Kuiqpick through a glass capillary.

value: DTCC-M


title: DSC-A20-1


title: DSC-A20-2


title: Serum_ESCC patient_rep19


title: Immuno DTCC-67


title: c162-H3-ChIP_2

description:
run 2
Aligned to EU594392.1.


title: c162-H3-ChIP_1

description:
run 1
Aligned to EU594392.1.


title: Immuno DTCC-66


title: Serum_ESCC patient_rep18


title: Serum_ESCC patient_rep17


title: Immuno DTCC-65


title: DSC-A22-30

value: DSC-L


title: c162-input_1

description:
run 1
Aligned to EU594392.1.

value: HBeAg- hepatitis


title: Serum_ESCC patient_rep16


title: Serum_ESCC patient_rep15


title: Immuno DTCC-64


title: Serum_ESCC patient_rep14


title: c161-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.

value: Under therapy (Tenofovir), HBeAg-


title: Serum_ESCC patient_rep13

value: serum


title: Serum_ESCC patient_rep11


title: Serum_ESCC patient_rep12


title: c161-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c161-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Immuno DTCC-63


title: Immuno DTCC-61


title: Immuno DTCC-60


title: Serum_ESCC patient_rep10

value: Female


title: Immuno DTCC-59


title: c313-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.

value: liver biopsy


title: Immuno DTCC-62


title: c161-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: liver

value: rabbit monoclonal C36B11, Cell Signaling Technology 9733S


title: c143-H3K27me3-ChIP_1

description:
run 1
Aligned to EU594392.1.

value: A/D

value: HBeAg+ hepatitis


title: Immuno DTCC-58

value: Epithelial ovarian cancer ascites


title: Serum_ESCC patient_rep9


title: c143-H3K9me3-ChIP_2

description:
run 2
Aligned to EU594392.1.


title: c161-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: D


title: Immuno DTCC-57


title: Serum_ESCC patient_rep25


title: Serum_ESCC patient_rep26


title: Immuno DTCC-56


title: c143-H3K9me3-ChIP_1

description:
run 1
Aligned to EU594392.1.

value: rabbit polyclonal, abcam ab8898


title: Serum_ESCC patient_rep8

value: Male


title: c161-input_1

description:
run 1
Aligned to EU787447.1.

value: input


title: c143-H3K4me3-ChIP_2

description:
run 2
Aligned to EU594392.1.

value: rabbit polyclonal, abcam ab8580


title: Immuno DTCC-55

value: DTCC-M


title: Immuno DTCC-54


title: Immuno DTCC-53


title: c143-input_1

description:
run 1
Aligned to EU594392.1.


title: Serum_ESCC patient_rep4


title: Serum_ESCC patient_rep5


title: Serum_ESCC patient_rep6


title: Immuno DTCC-51


title: Serum_ESCC patient_rep7


title: Immuno DTCC-52


title: c23-H3K27me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c23-H3K27me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Serum_ESCC patient_rep3


title: Immuno DTCC-50


title: Serum_ESCC patient_rep2


title: Immuno DTCC-49

value: DTCC-L


title: Serum_Healthy control_rep44


title: Serum_ESCC patient_rep1


title: c23-H3K9me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Serum_Healthy control_rep43


title: Immuno DTCC-47


title: c143-H3K4me3-ChIP_1

description:
run 1
Aligned to EU594392.1.


title: c23-H3K9me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: c23-H3K4me3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Immuno DTCC-48


title: c23-H3K4me3-ChIP_1

description:
run 1
Aligned to EU787447.1.


title: Immuno DTCC-46


title: Immuno DTCC-44


title: Immuno DTCC-45


title: Serum_Healthy control_rep41


title: c23-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: rabbit monoclonal B0422, abcam ab41969


title: Serum_Healthy control_rep40


title: c23-input_2

description:
run 2
Aligned to EU787447.1.


title: DSC-A20-3

value: DSC-E


title: Immuno DTCC-43


title: b880-H3K27me3-ChIP_2

description:
run 2
Aligned to EU410079.1.

value: C


title: c23-input_1

description:
run 1
Aligned to EU787447.1.


title: b880-H3K27me3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: Serum_Healthy control_rep42

value: serum

value: Female


title: Immuno DTCC-42


title: Serum_Healthy control_rep35


title: Serum_Healthy control_rep39


title: Serum_Healthy control_rep38


title: Serum_Healthy control_rep36


title: Serum_Healthy control_rep37


title: b880-H3K9me3-ChIP_2

description:
run 2
Aligned to EU410079.1.

value: liver biopsy

value: liver


title: Immuno DTCC-40


title: Immuno DTCC-41


title: b880-H3K9me3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: c23-H3-ChIP_2

description:
run 2
Aligned to EU787447.1.


title: Immuno DTCC-39


title: Serum_Healthy control_rep34


title: b880-H3K4me3-ChIP_2

description:
run 2
Aligned to EU410079.1.


title: Immuno DTCC-38


title: Serum_Healthy control_rep33


title: PC-3_siCSNK1G3_1

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street

country: Canada

institute: University of Toronto

library_source: transcriptomic

data_processing:
RNA-Seq reads were mapped to GRCh37 with Gencode  v24lift37 annotation using STAR (v2.5.3)
RNA abundance quantified using raw counts from STAR by setting the GeneCounts parameter to quantMode
MACS2 (version 2.0.10.20131216) was used to call peak on the bam files
Trimmed Means of M-Values (TMM) normalization was performed on the library size adjusted read counts before being converted to FPKM with the Bioconductor package edgeR (v3.12.1)
Genome_build: GRCh37
Supplementary_files_format_and_content: txt file with gene level read counts

growth_protocol: PCa cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA from the cell-lines was purified with RNeasy Mini Kit (QIAGEN, Cat. #74106), and the DNA was digested by RNase-Free DNase Set (QIAGEN, Cat. #79254) during the RNA purification.
RNA-Seq libraries for circCSNK1G3, circGOLPH3, circSTAU2 and CSNK1G3 were constructed with the kit from Illumina (TruSeq Stranded mRNA Library Prep Kit) according to the manufacturer’s protocol. RNA-Seq libraries were sequenced as paired-end reads in duplicates at ~30 million reads per library using HiSeq 2000 platforms.

treatment_protocol: For knockdown, The shRNA expressing lentiviral transfer vector was transfected together with the packaging (psPAX2) and envelope plasmid (pMD2.G) by lipo3000. The medium was harvested at 24 and 48 hours after transfection before storing at -80 °C. For infection, 5 x 104 cells were seeded per well in six-well plates and infected with lentivirus on the next day. Infected cells were selected with 3 μg/mL puromycin. For overexpression, PCa cells were transfected with 1.2 μg circRNA overexpressing plasmids or empty vector by lipo3000 transfection reagent (Invitrogen, USA) as per the manufacturer’s protocol. The transfected cells were harvested 24 hours after transfection for RNA extraction or other assays.

value: prostate cancer cell line


title: PC-3_siCSNK1G3_2


title: Immuno DTCC-37


title: Serum_Healthy control_rep32


title: b880-H3-ChIP_2

description:
run 2
Aligned to EU410079.1.

value: HBeAg+ hepatitis


title: Immuno DTCC-36

value: Epithelial ovarian cancer ascites


title: PC-3_siCtrl_1


title: b880-H3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: Serum_Healthy control_rep30


title: b880-input_2

description:
run 2
Aligned to EU410079.1.


title: b880-input_1

description:
run 1
Aligned to EU410079.1.


title: PC-3_shcircGOLPH3_2


title: PC-3_shcircSTAU2_1


title: Immuno DTCC-33


title: Immuno DTCC-35


title: Serum_Healthy control_rep27


title: Serum_Healthy control_rep28


title: Immuno DTCC-32


title: PC-3_shcircSTAU2_2


title: PC-3_siCtrl_2


title: b880-H3K4me3-ChIP_1

description:
run 1
Aligned to EU410079.1.


title: d6723

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz

data_processing:
HiSeq2000 using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
map to combined genome genome_pair.fa and genome_pair.gtf with STAR 2.5.3a
quantify transcripts with rsem 1.3.0 and samtools 1.3
Reads were aligned to a combined S. cerevisiae (Saccer3) and C. albicans (SC5314_A22, www.candidagenome.org) genomic target using STAR version 2.5.3.a (Dobin et al., 2013) and a merged annotation file consisting of the ensemble S. cerevisiae annotation and SC5314_A22 annotation. Gene expression was quantified using rsem version 1.3.0 (Li and Dewey, 2011). S. cerevisiae read counts were manually normalized to gene length and number of total C. albicans reads in the sample to give fragments per kilo base mRNA per million C. albicans reads (fpkmCa).
Genome_build: sacCer3 with Ensembl annotation combined with C. albicans SC5314 genome and annotation.
Supplementary_files_format_and_content: genome_pair.gtf.gz is a combined geneome annotation for S. cerevisiae and C. albicans
Supplementary_files_format_and_content: genome_pair.fa.gz is a combined genome file consisting of the  S. cerevisiae (Saccer3) and C. albicans (SC5314_A22) assemblies.
Supplementary_files_format_and_content: Albicans_Total_counts.txt.gz is parsed integer counts for samples from rsem genes.results files
Supplementary_files_format_and_content: Cerevisiae_counts.txt.gz is parsed integer counts for samples from rsem genes.results files
Supplementary_files_format_and_content: Cerevisiae_length.txt.gz is a listing of the transcript lengths used in the manual FPKM calculations
Supplementary_files_format_and_content: CerevisiaeNormalizedToAlbicans_fpkm.txt.gz is manualy calculated fpkm values. S. cerevisiae read counts were manually normalized to gene length and number of total C. albicans reads in the sample to give fragments per kilo base mRNA per million C. albicans reads (fpkmCa)

organism:
Saccharomyces cerevisiae
Candida albicans

growth_protocol: Yeast strains were grown in yeast extract/peptone (YEP) supplemented with adenine (0.055mg/mL) and tryptophan (0.8 mg/mL) and either 2% glucose (YEPD) at 37 degrees.

extract_protocol:
RNeasy mini-kit (Qiagen)
Truseq followed by Nextera XT

treatment_protocol: For total RNA sequencing, an equal number (~1x10E7) of S. cerevisiae cells of different sizes were mixed with a constant number (~1.5x10E6) of exponentially growing C. albicans cells.

tag: cell density (od600) at beginning

tag: drug treatment

value: 5nm Rapamycin

tag: hours in g1 arrest


title: Immuno DTCC-34


title: Serum_Healthy control_rep31


title: Serum_Healthy control_rep29


title: d6722


title: Immuno DTCC-31


title: c313-H3-ChIP_1

description:
run 1
Aligned to EU787447.1.

value: D

value: HBeAg- hepatitis


title: PC-3_shGFP_2


title: Serum_Healthy control_rep26


title: Serum_Healthy control_rep25


title: Immuno DTCC-30


title: PC-3_OE_circSTAU2_2


title: d6721


title: Immuno DTCC-29


title: d6720

value: untreated


title: PC-3_shcircGOLPH3_1


title: Serum_Healthy control_rep24


title: Immuno DTCC-28


title: d6719


title: PC-3_OE_circSTAU2_1


title: PC-3_OE_circGOLPH3_2


title: d6718


title: Serum_Healthy control_rep23


title: d6717


title: Serum_Healthy control_rep22


title: Immuno DTCC-27


title: Immuno DTCC-26


title: d6703


title: PC-3_OE_circGOLPH3_1


title: Serum_Healthy control_rep20

value: Male


title: Immuno DTCC-25

value: DTCC-E


title: d6702


title: PC-3_OE_VEH_2


title: Serum_Healthy control_rep21


title: PC-3_OE_VEH_1


title: Immuno DTCC-24


title: Immuno DTCC-23


title: Serum_Healthy control_rep19


title: d6701


title: R24

city: WuHan

first: Li

last: Ssenyang

state: HuBei

address: shizishan road

institute: State Key Laboratory of Agricultural Microbiology

data_processing:
miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Raw data (raw reads) of fastq format were firstly processed through custom perl  and python scripts. The small RNA tags were mapped to reference sequence by Bowtiewithout mismatch to analyze their expression and distribution on the  reference.
Genome_build: Sus scrofa:Sscrofa11.1
Supplementary_files_format_and_content: miRNA expression levels were estimated by Transcript per million (TPM).

organism: Sus scrofa

source_name: macrophages

extract_protocol:
Porcine alveolar macrophages infected with RH strain and Me49 strain were harvested at 12h and 24h,and RNA was extracted using Trizol reagent,library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA  High Sensitivity Chips.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.)

value: porcine alveolar macrophages

value: lung

tag: infection

value: Rh (Type I) strain

tag: time


title: d4690

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4690

data_processing:
HiSeq2000 using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
map to combined genome genome_pair.fa and genome_pair.gtf with STAR 2.5.3a
quantify transcripts with rsem 1.3.0 and samtools 1.3
Reads were aligned to a combined S. cerevisiae (Saccer3) and C. albicans (SC5314_A22, www.candidagenome.org) genomic target using STAR version 2.5.3.a (Dobin et al., 2013) and a merged annotation file consisting of the ensemble S. cerevisiae annotation and SC5314_A22 annotation. Gene expression was quantified using rsem version 1.3.0 (Li and Dewey, 2011). S. cerevisiae read counts were manually normalized to gene length and number of total C. albicans reads in the sample to give fragments per kilo base mRNA per million C. albicans reads (fpkmCa).
Genome_build: sacCer3 with Ensembl annotation combined with C. albicans SC5314 genome and annotation. Files used for read alignment are available on series record.
Supplementary_files_format_and_content: genome_pair.gtf.gz is a combined geneome annotation for S. cerevisiae and C. albicans
Supplementary_files_format_and_content: genome_pair.fa.gz is a combined genome file consisting of the  S. cerevisiae (Saccer3) and C. albicans (SC5314_A22) assemblies.
Supplementary_files_format_and_content: Albicans_Total_counts.txt.gz is parsed integer counts for samples from rsem genes.results files
Supplementary_files_format_and_content: Cerevisiae_counts.txt.gz is parsed integer counts for samples from rsem genes.results files
Supplementary_files_format_and_content: Cerevisiae_length.txt.gz is a listing of the transcript lengths used in the manual FPKM calculations
Supplementary_files_format_and_content: CerevisiaeNormalizedToAlbicans_fpkm.txt.gz is manually calculated fpkm values. S. cerevisiae read counts were manually normalized to gene length and number of total C. albicans reads in the sample to give fragments per kilo base mRNA per million C. albicans reads (fpkmCa)

tag: cell volume (mode, fl)

tag: yeast strain background

tag: yeast genotype

tag: candida strain background


title: D24

tag: cell line

tag: cell type

tag: tissue

value: control


title: d4689

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4689


title: M24

value: Me49 strain (Type II)


title: R12


title: Serum_Healthy control_rep17

value: serum


title: d4688

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4688


title: Immuno DTCC-20


title: Serum_Healthy control_rep16


title: D12


title: Serum_Healthy control_rep15


title: Serum_Healthy control_rep14


title: d4686

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4686


title: Serum_Healthy control_rep18


title: Serum_Healthy control_rep13


title: nsg-1f12-2-PT2 H3K27ac ChIP Seq

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

description: One of 2 peritoneal tumors formed by intrasplenic injection of 1f12-2 cells into female nude mouse.

data_processing:
Adapter and quality trimming of ChIP-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.2.6, using default parameters.
Potential PCR duplicates were removed from aligned ChIP Seq reads files
ChIP-Seq peaks were called using MACS v2.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated using Deeptools 3.1.2 and normalized using the RPGC option

source_name: CRC cell line

growth_protocol: LoVo cells were grown in media supplemented as previously described; COLO205-derived subclones were grown in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin for approximately 2.5 months, then subcloned and expanded.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of ~250 bp were band isolated from an agarose gel.

tag: sample type

value: peritoneal tumors

tag: chip antibody

value: rabbit anti-H3K27ac (Abcam #4729).


title: Immuno DTCC-18

tag: subgroup


title: d4685

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4685


title: Immuno DTCC-17


title: Serum_Healthy control_rep11

tag: gender

tag: age


title: Serum_Healthy control_rep12


title: d4684

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4684


title: d4683

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4683


title: nsg-1f12-2-PT1 H3K27ac ChIP Seq


title: nude-6e6-3-LM4 H3K27ac ChIP Seq

description: One of 4 liver metastaes formed by intrasplenic injection of 6e6-3 cells into female nude mouse.

value: liver metastasis


title: Immuno DTCC-21


title: Immuno DTCC-22


title: d4682

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4682


title: Immuno DTCC-19


title: Serum_Healthy control_rep10


title: d4687

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4687


title: M12


title: nude-6e6-3-LM3 H3K27ac ChIP Seq


title: d4681

description:
Albicans_Total_counts.txt.gz
Cerevisiae_counts.txt.gz
CerevisiaeNormalizedToAlbicans_fpkm.txt.gz
sample name: d4681


title: Immuno DTCC-15


title: nude-6e6-3-LM2 H3K27ac ChIP Seq


title: nude-6e6-3-LM1 H3K27ac ChIP Seq


title: Immuno DTCC-16


title: Serum_Healthy control_rep7


title: Serum_Healthy control_rep8


title: Serum_Healthy control_rep9


title: nsg-6e6-3-LM1 H3K27ac ChIP Seq

description: Liver metastasis formed by intrasplenic injection of 6e6-3 cells into female nsg mouse.


title: Tumor treated with Bev rep3

city: Okayama

first: Kazuhiko

last: Kurozumi

state: Okayama

address: 2-5-1, Shikata-cho, Kita-ku

department: Neurological Surgery

country: Japan

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

description:
Test
SAMPLE 7

data_processing:
A gene was defined as being upregulated when the bevacizumab treatment/control average intensity ratio was >2.0, and downregulated when the bevacizumab treatment/control ratio was <0.5. Data were extracted using the following criteria: P-value < 0.05. The array included controls to assess cDNA quality and DNA contamination.
Fold Change worksheet reports test/control ratios.

label: SYBR Green

source_name: Tumor treated with Bev

label_protocol: RNA analysis was conducted with an Extracellular Matrix & Adhesion Molecules RT Profiler PCR Array (PAHS-013Z) (QIAGEN; Hilden, Germany), according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from the brain tumor tissue of mice that had been treated with PBS or cilengitide using the TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Eighteen days after tumor implantation, U87ΔEGFR mouse models treated with bevacizumab or PBS were sacrificed (n=4 per group). RNA was extracted as previously described (10).

tag: cells

value: U87ΔEGFR human glioma cells Xenograft in nude mouse

tag: agent

value: Bevacizumab

value: 18 days after tumor implantation


title: Serum_Healthy control_rep6

description: micro RNAs expression in serum from ESCC patients


title: Tumor treated with Bev rep2

description:
Test
SAMPLE 6


title: Serum_Healthy control_rep5


title: Tumor treated with Bev rep1

description:
Test
SAMPLE 5


title: human mono.3

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

institute: Jichi Medical University Saitama Medical Center

hyb_protocol: The product of cDNA was then hybridized into a human Clariom™ S Assay (Thermo Fisher Scientific) with a GeneChip™ Hybridization, Wash, and Stain Kit, and a GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific) via incubation at 45°C with rotation at 60 rpm for 16 hours.

scan_protocol: The arrays were automatically stained and read using a GeneChip™ Fluidics Station 450 and a GeneChip™ Scanner 3000 7G (Thermo Fisher Scientific), according to the protocol provided by the manufacturer.

data_processing:
The raw data were analysed according to the algorithm of a Transcriptome Analysis Console (Thermo Fisher Scientific).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Human
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: human mono

label_protocol: Using 6ng of the extracted RNA in each sample with a GeneChip™ 3' IVT Pico Kit (Thermo Fisher Scientific), cDNA was made by reverse transcription, and cRNA was then synthesized and amplified by in vitro transcription. After the quality assessments, the cRNA was converted to biotinylated double-stranded cDNA hybridization targets.

extract_protocol: From cryopreserved PBSC grafts of three donors, approximately 1x10^4 CD34+mono cells, 3x10^5 CD34-positive cells (CD34+cells, Lin-CD34highCD33-CD14-CD11b- cells), and 3x10^5 conventional monocytes (con-mono, Lin-CD34-CD33+CD14+CD11b+ cells) were directly sorted into tubes using FACSAriaTM II (BD Biosciences). After the collection of individual cell types, total RNA extraction was immediately performed with an RNeasyPlus Micro kit (QIAGEN) according to the manufacturer’s instructions. Thereafter, electrophoresis analyses were performed to examine the quality of the extracted RNAs using an Agilent 2100 Bioanalyzer (Agilent Technologies) with RNA Pico Chips (Agilent Technologies).

tag: subject status

value: healthy donor 3

value: Peripheral blood stem cells (PBSCs)

tag: cell subtype

tag: treatment

value: mobilized by G-CSF


title: 6d10-1 H3K27ac ChIP Seq

description: One of 2 MLH1-/- clones derived from COLO-205 cells.

value: MLH1-/- COLO-205 subclones


title: 1e2-3 H3K27ac ChIP Seq

description: One of 2 parental WT clones derived from COLO-205 cells.

value: parental WT


title: 6e6-3 H3K27ac ChIP Seq


title: Serum_Healthy control_rep2

value: Male


title: Tumor untreated with Bev rep4

description:
Control
SAMPLE 4

source_name: Tumor untreated with Bev

value: PBS

tag: time


title: Tumor untreated with Bev rep3

description:
Control
SAMPLE 3


title: Tumor untreated with Bev rep2

description:
Control
SAMPLE 2


title: human CD34mono.1

source_name: human CD34mono

value: healthy donor 1

value: CD34+mono cells


title: Serum_Healthy control_rep4


title: 1f12-2 H3K27ac ChIP Seq


title: human CD34.2

source_name: human CD34

value: healthy donor 2

value: CD34-positive cells (CD34+cells, Lin-CD34highCD33-CD14-CD11b- cells)


title: Serum_Healthy control_rep3

value: serum


title: human mono.2

value: conventional monocytes (con-mono, Lin-CD34-CD33+CD14+CD11b+ cells)


title: human mono.1


title: human CD34mono.3


title: human CD34.3


title: circRNA_Patient8 cancer tissue

status: Public on Feb 06 2019

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

institute: Soochow university

description:
circular RNA expression
S8_2

hyb_protocol: not provided

scan_protocol: The slides were scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 10 out of 30 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: Tissue specimen

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer’s guideline for CircRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including CircRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: patient id

value: colorectal cancer tissue

value: male


title: circRNA_Patient7 cancer tissue

description:
circular RNA expression
S7_2

value: female


title: circRNA_Patient10 cancer tissue

description:
circular RNA expression
S10_2


title: circRNA_Patient9 cancer tissue

description:
circular RNA expression
S9_2


title: human CD34mono.2


title: circRNA_Patient3 cancer tissue

description:
circular RNA expression
S3_2


title: circRNA_Patient4 cancer tissue

description:
circular RNA expression
S4_2


title: circRNA_Patient1 cancer tissue

description:
circular RNA expression
S1_2


title: circRNA_Patient7 corresponding normal-appearing tissue

description:
circular RNA expression
S7_1

value: normal-appearing colorectal tissue


title: circRNA_Patient5 cancer tissue

description:
circular RNA expression
S5_2


title: circRNA_Patient8 corresponding normal-appearing tissue

description:
circular RNA expression
S8_1


title: Tumor untreated with Bev rep1

description:
Control
SAMPLE 1

value: U87ΔEGFR human glioma cells Xenograft in nude mouse

value: 18 days after tumor implantation


title: circRNA_Patient2 corresponding normal-appearing tissue

description:
circular RNA expression
S2_1


title: circRNA_Patient1 corresponding normal-appearing tissue

description:
circular RNA expression
S1_1


title: circRNA_Patient3 corresponding normal-appearing tissue

description:
circular RNA expression
S3_1


title: circRNA_Patient6 corresponding normal-appearing tissue

description:
circular RNA expression
S6_1


title: circRNA_Patient5 corresponding normal-appearing tissue

description:
circular RNA expression
S5_1


title: Patient6 cancer tissue

description:
lncRNA/mRNA
S6_2

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: The data processing were performed with the GeneSpring GX version 12.1 software package (Agilent Technologies). Selecting differentially expressed genes according to the P-value and fold change. P-value <0.05 and fold change >2 for mRNA or lncRNA, were considered as significant difference.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer's instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including lncRNA and mRNA. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: Patient 6

value: colorectal cancer


title: Patient2 cancer tissue

description:
lncRNA/mRNA
S2_2

value: Patient 2


title: Patient3 cancer tissue

description:
lncRNA/mRNA
S3_2

value: Patient 3


title: Patient4 cancer tissue

description:
lncRNA/mRNA
S4_2

value: Patient 4


title: Patient7 cancer tissue

description:
lncRNA/mRNA
S7_2

value: Patient 7


title: Patient8 cancer tissue

description:
lncRNA/mRNA
S8_2

value: Patient 8


title: Patient9 cancer tissue

description:
lncRNA/mRNA
S9_2

value: Patient 9


title: circRNA_Patient10 corresponding normal-appearing tissue

description:
circular RNA expression
S10_1


title: Patient10 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S10_1

value: Patient 10


title: Patient5 cancer tissue

description:
lncRNA/mRNA
S5_2

value: Patient 5


title: Patient1 cancer tissue

description:
lncRNA/mRNA
S1_2

value: Patient 1


title: Patient10 cancer tissue

description:
lncRNA/mRNA
S10_2


title: Patient8 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S8_1


title: Patient9 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S9_1


title: circRNA_Patient6 cancer tissue

description:
circular RNA expression
S6_2

value: colorectal cancer tissue


title: circRNA_Patient9 corresponding normal-appearing tissue

description:
circular RNA expression
S9_1

value: male


title: Patient7 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S7_1

value: female


title: miR-146 WT BMDMs (resting) B

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotech Bldg

department: Molecular Biology and Genetics

institute: Cornell University

description:
BMDMs from miR-146 WT animals were rested for 16 hours
smallRNAdata.txt: WTB

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8.3 (-m 10 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAG --match-read-wildcards) was used to trim and filter reads.
Reads were collapsed using mirdeep2 ‘mapper.pl’ parameters: -e -h -m –d.
Collapsed reads were mapped to mature miRNAs (miRBase v21) using mirdeep2 ‘quantifier.pl’ parameters: -t <spp> -W -d -e 0
Genome_build: miRBase v21
Supplementary_files_format_and_content: Tab delimited text file including raw and normalized read counts (from mirdeep2 output)

organism: Mus musculus

source_name: bone marrow derived macrophages (BMDMs)

growth_protocol: Bone marrow from 6-7 month old mice (three of each genotype, all 129/B6 mix) was flushed from femurs and tibias and plated in replicates at 85,000 cells/cm2 on non tissue culture-treated petri dishes. The cells were cultured for 8-9 days in DMEM complete medium supplemented with M-CSF (10 ng/mL), with a medium change at day 3 prior to medium change (+/- LPS) for experiment.

extract_protocol:
Total RNA from BMDMs was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
TruSeq-barcoded RNAseq libraries were be generated with the NEBNext Small RNA Library Prep Kit (New England  Biolabs) and size selected for insert sizes ~18-35bp. Each library were quantified with a Qubit 2.0 (dsDNA HS kit;  Thermo Fisher).

treatment_protocol: Separate cultures of BMDMs derived from each of the three genotypes were subjected to LPS-free medium and harvested after 16 hours.

tag: genotype

value: miR-146 Wild-type

value: Fresh LPS-free medium change at same time as stimulated cells.  Harvested at 16 hours.

value: Bone marrow cells were cultured for 8-9 days in DMEM complete medium supplemented with M-CSF (10 ng/mL)


title: miR-146 3'F BMDMs (resting)

description:
BMDMs from miR-146 3'F animals were rested for 16 hours
smallRNAdata.txt: 3FA

value: miR-146 non-seed swap (swapped the 3' half of miR-146 pre-miRNA duplex)


title: miR-146 3'F BMDMs (resting) rep2

description:
BMDMs from miR-146 3'F animals were rested for 16 hours
counts_protein_coding.txt: 3FBm

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8.3 (-a GATCGGAAGAGCACACGTCTGAACTCCAGT -m 20) was used to trim and filter reads.
Reads originating from rRNA were removed by aligning the reads to rDNA using HISAT2 v2.1.0 (−−no-spliced-alignment −−un)
hisat v2.1.0 (--min-intronlen 70, --rna-strandness R, --known-splicesite-infile) was used to map reads to the mouse mm10 reference genome (UCSC).
featureCounts v1.5.3 (-s 2 -Q 50) was used to count mapped reads to all genes based on annotations from Gencode(M15).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited text file including raw read counts

source_name: miR-146 3'F BMDMs (resting)

extract_protocol:
Total RNA from BMDMs was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Directional RNA-seq libraries were prepared from rRNA-depleted total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Separate cultures of BMDMs derived from each of the three genotypes were subjected to medium change with or without 1 ng/ml LPS and harvested after 16 hours.

tag: strain

value: bone marrow derived macrophages (BMDMs)

tag: cell culture protocol

value: bone marrow cells were cultured for 8-9 days in DMEM complete medium supplemented with M-CSF (10 ng/mL)

value: fresh LPS-free medium change at same time as stimulated cells.  Harvested at 16 hours alongside stimulated cells.


title: miR-146 KO BMDMs (resting)

description:
BMDMs from miR-146 KO animals were rested for 16 hours
smallRNAdata.txt: KOA

value: miR-146 Knock-out


title: Patient5 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S5_1

value: normal-appearing colorectal tissue


title: miR-146 3'F BMDMs (resting) rep1

description:
BMDMs from miR-146 3'F animals were rested for 16 hours
counts_protein_coding.txt: 3FAm

tag: cell type


title: miR-146 3'F BMDMs (resting) rep3

description:
BMDMs from miR-146 3'F animals were rested for 16 hours
counts_protein_coding.txt: 3FCm


title: Patient3 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S3_1

value: Patient 3

tag: tissue


title: miR-146 WT BMDMs (resting) A

description:
BMDMs from miR-146 WT animals were rested for 16 hours
smallRNAdata.txt: WTA


title: miR-146 3'F BMDMs (stimulated) rep2

description:
BMDMs from miR-146 3'F animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: 3FBp

source_name: miR-146 3'F BMDMs (stimulated)

value: stimulated with 1 ng/ml LPS in fresh culture medium for 16 hours


title: Patient2 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S2_1

value: Patient 2


title: Patient1 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S1_1


title: miR-146 3'F BMDMs (stimulated) rep1

description:
BMDMs from miR-146 3'F animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: 3FAp


title: circRNA_Patient4 corresponding normal-appearing tissue

description:
circular RNA expression
S4_1


title: miR-146 3'F BMDMs (stimulated) rep3

description:
BMDMs from miR-146 3'F animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: 3FCp


title: miR-146 KO BMDMs (resting) rep1

description:
BMDMs from miR-146 KO animals were rested for 16 hours
counts_protein_coding.txt: KOAm

source_name: miR-146 KO BMDMs (resting)


title: miR-146 KO BMDMs (resting) rep2

description:
BMDMs from miR-146 KO animals were rested for 16 hours
counts_protein_coding.txt: KOBm


title: miR-146 KO BMDMs (resting) rep3

description:
BMDMs from miR-146 KO animals were rested for 16 hours
counts_protein_coding.txt: KOCm


title: miR-146 KO BMDMs (stimulated) rep2

description:
BMDMs from miR-146 KO animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: KOBp

source_name: miR-146 KO BMDMs (stimulated)


title: miR-146 KO BMDMs (stimulated) rep3

description:
BMDMs from miR-146 KO animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: KOCp


title: miR-146 KO BMDMs (stimulated) rep1

description:
BMDMs from miR-146 KO animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: KOAp


title: miR-146 WT BMDMs (resting) rep3

description:
BMDMs from miR-146 WT animals were rested for 16 hours
counts_protein_coding.txt: WTCm

source_name: miR-146 WT BMDMs (resting)


title: miR-146 WT BMDMs (resting) rep1

description:
BMDMs from miR-146 WT animals were rested for 16 hours
counts_protein_coding.txt: WTAm


title: miR-146 WT BMDMs (stimulated) rep3

description:
BMDMs from miR-146 WT animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: WTCp

source_name: miR-146 WT BMDMs (stimulated)


title: miR-146 WT BMDMs (resting) rep2

description:
BMDMs from miR-146 WT animals were rested for 16 hours
counts_protein_coding.txt: WTBm


title: miR-146 WT BMDMs (stimulated) rep2

description:
BMDMs from miR-146 WT animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: WTBp


title: miR-146 WT BMDMs (stimulated) rep1

description:
BMDMs from miR-146 WT animals were stimulated using LPS for 16 hours
counts_protein_coding.txt: WTAp


title: PC-3_shGFP_1

value: prostate cancer cell line

tag: cell line


title: HT29-MTX + MRx0518 heat-killed, Biological Replicate 3

city: Aberdeen

first: Imke

last: Mulder

address: Cornhill Road

country: United Kingdom

institute: 4D Pharma Research Ltd

description: Gene expression data from HT29-MTX cells co-incubated with heat-killed MRx0518 at MOI 100:1 for 3 hours

hyb_protocol: 5.2 µg of fragmented and labelled single stranded cDNA was hybridized for 16 h at 45 °C on Affymetrix Human Transcriptome Array 2.0 GeneChips (GEO Accession Number GPL17585; Thermo Fisher Scientific). GeneChips were washed and stained in an Affymetrix Fluidics Station 450 using the Affymetrix GeneChip™ Expression Wash, Stain and Scan kit (Thermo Fisher Scientific) according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using a GeneChip™ Scanner 3000 instrument.

data_processing: Data analysis was carried out using Transcriptome Analysis Console 4.0 software (Thermo Fisher Scientific). Data were normalized using the Robust Multiarray Average (RMA) algorithm, and fold changes were calculated using the normalized log2-transformed values of treated cells relative to respective controls. Data were filtered using cut-offs of p < 0.05, fold change of < -1.5 and ≥ 1.5, and the presence of a gene symbol and coding variants. The supplementary file HTA-2_0.na36.hg19.probeset.csv includes the annotation for all probe sets included in the chp files.

label: Biotin

source_name: HT29-MTX cells treated with heat-killed MRx0518

label_protocol: Biotinylated single stranded cDNA (5.5 µg) was prepared from 100 ng of initial total RNA input, using the Affymetrix GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific, Waltham, MA, USA), according to manufacturer's recommendations.

growth_protocol: HT29-MTX-E12 cells (Public Health England, Salisbury, England, UK) were routinely cultured in Dulbecco’s Minimal Eagle’s Medium (DMEM) supplemented with 10 % (v/v) FBS, 4 mM L-glutamine, 4.5 mg/ml glucose, 8.9 μg/ml L-alanine, 15 μg/ml L-asparagine, 13.3 μg/ml L-aspartic acid, 14.7 μg/ml L-glutamic acid, 7.5 μg/ml glycine, 11.5 μg/ml L-proline, 10.5 μg/ml L-serine, 100 U/ml penicillin, 100 μg/ml streptomycin and 0.25 μg/ml amphotericin B (cDMEM). Cells were seeded into the upper chamber of 24-well Transwells® (Corning, Corning, NY, USA) and cultured for nine days, following which they were washed twice with Hank's Balanced Saline Solution and placed into co-culture medium (cDMEM without antibiotic and supplemented with 5 μg/ml apo-transferrin and 0.2 μg/ml sodium selenite) for 24 hours prior to treatment with bacteria. All cell culture reagents were supplied by Sigma-Aldrich, Gillingham, England, UK. E. gallinarum MRx0518 was routinely cultured in Yeast extract, Casitone, Fatty Acid media (YCFA, E&O Laboratories, Bonnybridge, Scotland, UK) at 37°C in an anaerobic cabinet (Don Whitley Scientific, Shipley, England, UK).

extract_protocol: RNA was isolated using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer's recommendations.

treatment_protocol: Late log phase cultures of Enterococcus gallinarum MRx0518 were centrifuged at 5000 x g for 5 min at room temperature to generate bacterial fractions. Pelleted cells were washed once in phosphate-buffered saline (PBS) (Sigma-Aldrich) and resuspended in antibiotic-free cell culture media to the appropriate dilution to obtain a live treatment. Culture supernatants were harvested and filtered through a 0.22 μm pore size filter and diluted in water to provide equivalents for the live fraction described above (supernatant treatment). Bacterial cultures were heat-inactivated for 40 min at 80 °C and prepared as described above for the live fraction (heat-killed treatment). Viable cells counts were determined by plating. HT29-MTX cells in 24-well Transwells® were washed, and incubated with treatments of live MRx0518 and heat-killed MRx0518 at a multiplicity of infection (MOI) of 100 bacterial cells to 1 human cell, and an equivalent dilution of MRx0518 supernatant for 3 h at 37 °C in anaerobic conditions. Cells were washed with PBS to remove bacteria prior to RNA isolation.

value: Heat-killed MRx0518, MOI 100:1

tag: incubation time

value: 3 h


title: HT29-MTX + MRx0518 heat-killed, Biological Replicate 1


title: HT29-MTX + MRx0518 supernatant, Biological Replicate 2

description: Gene expression data from HT29-MTX cells co-incubated with MRx0518 supernatant at MOI 100:1 equivalent for 3 hours

source_name: HT29-MTX cells treated with MRx0518 supernatant

value: MRx0518 Supernatant, MOI 100:1 equivalent


title: HT29-MTX + MRx0518 supernatant, Biological Replicate 3


title: HT29-MTX + MRx0518 live, Biological Replicate 3

description: Gene expression data from HT29-MTX cells co-incubated with live MRx0518 at MOI 100:1 for 3 hours

source_name: HT29-MTX cells treated with live MRx0518

value: Live MRx0518, MOI 100:1


title: HT29-MTX + MRx0518 supernatant, Biological Replicate 1


title: Untreated HT29-MTX, Biological Replicate 3

description: Gene expression data from untreated HT29-MTX cells

source_name: Untreated HT29-MTX cells

value: Untreated


title: Untreated HT29-MTX, Biological Replicate 2


title: Patient 3 granulomatous inflammation 1

city: Southampton

first: Sara

last: Waise

state: Hampshire

address: Somers Building MP284, Southampton General Hospital, Tremona Road

department: Cancer Sciences

institute: University of Southampton

data_processing:
Base calls performed with bcl2fastq 2.18
All read pairs with a quality score of <10 were filtered
Reads were aligned to the human genome using STAR v2.5
Aligned exonic reads were tagged with a gene name
Digital expression matrices were created by counting the number of unique UMIs per gene per cell. Samples from three individual patients were merged together into a single matrix
Genome_build: hg19
Supplementary_files_format_and_content: Digital expression matrices in tab-delinated text file

source_name: Lung

extract_protocol:
Fresh tissue was disaggregated with Collagenase P and DNAse for 1 hour
Libraries were prepared for sequencing as per the Drop-seq and standard Illumina protocols

value: Lung


title: HT29-MTX + YCFA, Biological Replicate 1

description: Gene expression data from HT29-MTX cells treated with bacterial growth medium (YCFA) for 3 hours

source_name: HT29-MTX cells treated with YCFA

value: Bacterial growth medium (YCFA)


title: Patient 3 granulomatous inflammation 2


title: HT29-MTX + MRx0518 live, Biological Replicate 2


title: HT29-MTX + YCFA, Biological Replicate 3


title: Patient 2 non-involved lung


title: HT29-MTX + MRx0518 live, Biological Replicate 1


title: Patient 2 tumour


title: Patient4 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S4_1

value: Patient 4

value: female


title: HT29-MTX + YCFA, Biological Replicate 2


title: Patient 1 non-involved lung


title: Patient 1 tumour


title: HT29-MTX + MRx0518 heat-killed, Biological Replicate 2


title: PBMC IVM replicate 3 [IVM_6_1]

city: Athens

first: Adrian

middle: J.

last: Wolstenholme

state: GA

address: 501 DW Brooks Dr.

institute: University of Georgia

data_processing:
Read mapping: was performed using TopHat v2.0.14
Raw count extraction: was performed using HTSEQ v0.6.1p1
Genome_build: Genome Reference Consortium Human Build 38 patch release 5 (GRCh38.p5)
Supplementary_files_format_and_content: Tab-delimited txt file, raw count matrix

source_name: PBMC IVM

growth_protocol: PMNs were isolated using the EasySep Direct Human Neutrophil Isolation Kit (Stemcell  Technologies, Vancouver, BC, Canada) according to manufacturer's instructions. PBMCs  were isolated using SepMate-50 Tubes (Stemcell Technologies, Vancouver, BC, Canada)  according to manufacturer's instructions.

extract_protocol: RNA-Seq for the Illumina' TruSeq strand-specific kit

treatment_protocol: Control samples were treated with 1% DMSO. DEC treatment was at 50µM, ivermectin treatment at 100nM in 1% DMSO

value: Peripheral Blood Mononuclear Cells

tag: drug treatment

value: Ivermectin

tag: isolation time, post treatment

value: 16 hours

tag: replicate


title: PBMC IVM replicate 5 [IVM_8_1]


title: PBMC IVM replicate 4 [IVM_7_1]


title: PBMC IVM replicate 1 technical replicate 2 [IVM_4_2]


title: PBMC IVM replicate 2 [IVM_5_1]


title: Untreated HT29-MTX, Biological Replicate 1


title: PBMC DEC replicate 5 [DEC_8_1]

source_name: PBMC DEC

value: DEC


title: human CD34.1

source_name: human CD34

value: healthy donor 1

value: Peripheral blood stem cells (PBSCs)

value: CD34-positive cells (CD34+cells, Lin-CD34highCD33-CD14-CD11b- cells)

value: mobilized by G-CSF


title: PBMC DEC replicate 3 [DEC_6_1]


title: PBMC DEC replicate 2 [DEC_5_1]


title: PBMC DEC replicate 1 [DEC_4_1]


title: PBMC DEC replicate 1 - technical replicate 2 [DEC_4_2]


title: PBMC control replicate 2 [DMSO_5_2]

source_name: PBMC control

value: Control (DMSO)


title: PBMC control replicate 1 -technical replicate 2 [DMSO_4_2]


title: PBMC control replicate 1 [DMSO_4_1]


title: Neutrophil IVM replicate 4 [IVM14]

source_name: Neutrophil IVM

value: Neutrophil

value: 1 hour


title: PBMC control replicate 4 [DMSO_7_1]


title: PBMC control replicate 5 [DMSO_8_1]


title: Neutrophil IVM replicate 5 [IVM15]


title: Neutrophil IVM replicate 2 [IVM12]


title: Neutrophil IVM replicate 1 [IVM11]


title: Neutrophil DEC replicate 5 [DEC5]

source_name: Neutrophil DEC


title: PBMC IVM replicate 1 [IVM_4_1]


title: Neutrophil DEC replicate 4 [DEC4]


title: Neutrophil DEC replicate 3 [DEC3]


title: Neutrophil DEC replicate 1 [DEC1]


title: PBMC DEC replicate 4 [DEC_7_1]


title: Neutrophil control replicate 5 [DMSO10]

source_name: Neutrophil control


title: Neutrophil control replicate 3 [DMSO8]


title: Neutrophil control replicate 2 [DMSO7]


title: Patient6 corresponding normal-appearing tissue

description:
lncRNA/mRNA
S6_1

source_name: Tissue specimen

value: Patient 6

value: normal-appearing colorectal tissue

tag: gender

value: male

tag: age


title: PBMC control replicate 3 [DMSO_6_1]


title: Neutrophil control replicate 1 [DMSO6]


title: Serum_Healthy control_rep1

description: micro RNAs expression in serum from ESCC patients

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: Serum, Healthy control, Matched by age and sex

extract_protocol: Total RNA was extracted and purified using miRNeasy Serum/Plasma Kit (Cat # 217184, Qiagen, German), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: serum

value: Male


title: Neutrophil IVM replicate 3 [IVM13]


title: pLuciferase-1: Post-Senescence pLuciferase Control Rep 1

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Quality control: sequencing reads were trimmed using Trimmomatic to remove leading and trailing low quality base calls (Phred < 3).
Alignment: trimmed reads were aligned to GRCh37.75(hg19) using STAR with default parameters, and alignments with a mapping score lower than 10 were discarded using SAMtools.
Quantification: FeatureCounts was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Differential expression: analysis for differential gene expression was performed using edgeR R package with the cutoff of FDR < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: The read counts calculated by FeatureCounts were tabulated in a text file.

source_name: IMR90 Fibroblasts

growth_protocol: IMR90 cells (ATCC CCL-186) which are female primary lung fibroblasts were obtained from Coriell Institute for Medical Research, Camden, NJ, and grown in standard tissue culture medium (DMEM with 10% FBS and 1% penicillin/streptomycin; Invitrogen) at 3% oxygen. Senescence was induced by replicatively passaging cells until growth ceased. Markers such as p16 expression and β-gal were tested to confirm senescence. Senescent cells were maintained in dishes for 2 weeks to ensure growth termination. Briefly, for each passage, cells were washed with PBS, trypsinized at 37 °C for 5 minutes, and plated on fresh 10 cm plates at 0.5-1e6/plate or fresh 15cm plates at 1-2e6/plate.

extract_protocol:
Total RNA was isolated from frozen pellets of IMR90 cells using the RNeasy kit (Qiagen) following instructions.
1ug of Total RNA was used as input in the Scriptseq Complete kit (Epicentre). Briefly, total RNA was ribodepleted using a Ribozero magnetic protocol for human, mouse and rat (Epicentre, Illumina). The ribodepleted RNA was then ethanol precipitated, fragmented, and tagged at both ends for stranded library preparation using the Scriptseq v2 library preparation protocol. The PCR amplification step was used to index the libraries and multiplexed libraries were quantified by Bioanalyzer (Agilent) and qPCR (Kapa Biosystems). The RNA-seq run was performed on the NextSeq 500 platform (Illumina).

treatment_protocol: Midlife or senescent IMR90 cells were infected with lentiviral hairpin constructs (TRC collection) designed against selected targets in medium containing 8ug/ml polybrene. After 24 hours, the cells were replaced with polybrene-free media and after another 24 hours, selection was initiated with addition of 0.5ug/ml puromycin. After selection was complete, the media was changed back to standard medium.

value: Lung Fibroblasts

tag: shRNA

value: Control


title: CBP-KD-1: Post-Senescence CBP Knockdown Rep 1

value: histone acetyltransferase CBP


title: CBP-KD-2: Post-Senescence CBP Knockdown Rep 2


title: RNA-seq from Senescent Fibroblasts (IR Senescence), Replicate #1

data_processing:
Trimming: sequencing reads were trimmed using Trimmomatic to remove leading and trailing low quality base calls (Phred < 3).
Alignment: trimmed reads were aligned to GRCh37.75(hg19) using STAR with default parameters.
Quality Control: alignments with a mapping score lower than 10 were discarded using SAMtools.
Quantitation: FeatureCounts was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Genome_build: hg19
Supplementary_files_format_and_content: gene_counts.txt is a text table detailing the tag counts per RefSeq annotated gene calculated by FeatureCounts.

growth_protocol: IMR90 cells (ATCC CCL-186) were obtained from Coriell Institute for Medical Research, Camden, NJ, and grown in standard tissue culture medium (DMEM with 10% FBS and 1% penicillin/streptomycin; Invitrogen) at 3% oxygen.

extract_protocol:
Total RNA was isolated from frozen pellets of IMR90 cells using the RNeasy kit (Qiagen) following instructions. 1ug was used as input in the Scriptseq Complete kit (Epicentre).
Briefly, total RNA was ribodepleted using a Ribozero magnetic protocol for human, mouse and rat (Epicentre, Illumina). The ribodepleted RNA was then ethanol precipitated, fragmented, and tagged at both ends for stranded library preparation using the Scriptseq v2 library preparation protocol. The PCR amplification step was used to index the libraries and multiplexed libraries were quantified by Bioanalyzer (Agilent) and qPCR (Kapa Biosystems). The RNA-seq run was performed on the NextSeq 500 platform (Illumina). RNA-seq libraries were sequenced using an Illumina NextSeq 500 platform (only forward reads in the paired-end sequencing were used, 48bp).

treatment_protocol: Cells were replicatively passaged until growth ceased. For each passage, cells were washed with PBS, trypsinized at 37 °C for 5 minutes, and plated on fresh 10 cm plates at 0.5-1e6/plate or fresh 15cm plates at 1-2e6/plate. p16 expression and β-gal were tested to confirm senescence. Additionally, senescent cells were maintained in dishes for 2 weeks to ensure growth termination.

tag: population doubling

tag: library type

value: paired

tag: senescence induction

value: Irradiation


title: RNA-seq from Senescent Fibroblasts (p300 knockdown shRNA #1), Replicate #1

value: CAGACAAGTCTTGGCATGGTA

value: single

value: Replicative Senescence


title: RNA-seq from Senescent Fibroblasts (p300 knockdown shRNA #2), Replicate #1

value: TACACTAGAGACACCTTGTAT


title: RNA-seq from Senescent Fibroblasts (IR Senescence), Replicate #3


title: RNA-seq from Senescent Fibroblasts (p300 knockdown control vector), Replicate #1

value: control vector


title: RNA-seq from Senescent Fibroblasts (p300 knockdown shRNA #1), Replicate #2


title: RNA-seq from Proliferating Fibroblasts, Replicate #2

source_name: RNA-seq from Proliferating Fibroblasts


title: RNA-seq from Senescent Fibroblasts (IR Senescence), Replicate #2


title: RNA-seq from Senescent Fibroblasts (p300 knockdown control vector), Replicate #2


title: Yamato-SS RNA-seq [YAMA_XO5]

city: Birmingham

first: Yanfeng

last: Zhang

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using tophat2 with default parameters
Gene abundance measurements were generationed and normalized using Cufflinks. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human synovial sarcoma

growth_protocol: SYO-1 and Yamato-SS cells were cultured in RMPI-1640 and DMEM, respectively, supplemented with 10% FBS (37℃, 95% humidity, 5%CO2).

extract_protocol:
RNA extraction was performed using qiagen RNeasy kit along with Dnase treatment for 30 minutes at RT.
500 ng of total RNA was subjected to library synthesis using theNEB Ultra II RNA Library kit.NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to enriched for the Poly-A mRNA . Illumina indexes prior to 12 cycles of PCR.
Sequencing was performed using 12.5 pM hybridization to a HiSeq V4 2x50 paired end flow cell.

value: Yamato-SS

value: human synovial sarcoma cell line


title: RNA-seq from Senescent Fibroblasts (p300 knockdown shRNA #2), Replicate #2


title: Neutrophil control replicate 4 [DMSO9]

value: Neutrophil

value: Control (DMSO)

value: 1 hour


title: RNA-seq from Senescent Fibroblasts, Replicate #2

source_name: RNA-seq from Senescent Fibroblasts


title: RNA-seq from Proliferating Fibroblasts, Replicate #1


title: Nuetrophil DEC replicate 2 [DEC2]

source_name: Nuetrophil DEC

value: DEC


title: RNA-seq from Senescent Fibroblasts, Replicate #1


title: SYO-1 RNA-seq [SYO1_XO1]


title: WT_14 rep4

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description:
read_count_table.txt
WT_14_4_S4

data_processing:
Reads from multiple sequencer lanes were pooled into a single file. The raw data files submitted to GEO contain pooled reads from all lanes for any given sample.
To remove adapter and low-quality sequences, raw RNA-seq reads were trimmed using Trimmomatic v0.36 (Bolger et al., 2014). Reads < 70 bp after trimming were discarded.
reads were aligned to the BDGP D. melanogaster genome release 6 (dm6) using hisat2 v2.1.0 with the following non-default parameters: -k 2 (Kim et al., 2015).
Reads aligning to multiple locations were discarded.
Reads were assigned to annotated genes using featureCounts v1.5.3 (Liao et al., 2014) using default parameters and the UCSC annotation (r6.20).
differential expression was determined using DESeq2 v1.14.1. (Love et al., 2014).
Genome_build: dm6
Supplementary_files_format_and_content: TXT file produced by the FeatureCounts program. Tab-delimited text file containing a table of read counts mapping to all genes in the Drosophila melanogaster genome. This read count table can be used to reproduce analysis of differential expression in DESeq2.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: All stocks were grown on molasses food at 25°C

extract_protocol:
Thirty minutes into nuclear cycle 14, embryos were picked into Trizol (Invitrogen #15596026) with 200 ug/ml glycogen (Invitrogen #10814010) and pierced with a 27G needle to release the RNA.
libraries were prepared using the TruSeq RNA sample prep kit v2 (Ilumina) according to manufacturer instructions

treatment_protocol: Single His2AvRFP or CRY2-ZLD; His2AvRFP embryos were dechorionated in 50% bleach and then exposed to 488 nm light on a Nikon ECLIPSE Ti-E eplifluorescence microscope for the indicated period with brief switches to 587 nm light to image His2AvRFP for precise developmental staging.

tag: developmental stage

value: nuclear cycle 14 + 30 minutes

tag: treatment

value: Blue light during cycle 14


title: WT_14 rep3

description:
read_count_table.txt
WT_14_3_S3

tag: genotype


title: WT_14 rep2

description:
read_count_table.txt
WT_14_2_S2


title: WT_14 rep1

description:
read_count_table.txt
WT_14_1_S1


title: WT_13 rep4

description:
read_count_table.txt
WT_13_4_S14

value: Blue light from nuclear cycle 13-14


title: WT_12 rep4

description:
read_count_table.txt
WT_12_4_S4

value: Blue light from nuclear cycle 10-12


title: WT_13 rep1

description:
read_count_table.txt
WT_13_1_S5


title: control cells rep2

city: Beijing

first: Runsheng

last: Chen

address: 15 Datun Road, Chaoyang District

department: CAS Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinsese Academy of Sciences

hyb_protocol: 45C hybridization for overnight in Gex Hyb Buffer

scan_protocol: 42C wash for total 5 times, scan with Agilent scanner G2565CA

data_processing: The microarray data were quantile normalized using the R limma package.

source_name: control cells rep2

label_protocol: Klenow Fragment along with Cy5-dCTP or Cy3-dCTP were used to label cDNA

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 μg/ml penicillin G, and 100 U/ml streptomycin (Invitrogen, NY, USA)

extract_protocol: Use standard Trizol approach to extract total RNA

treatment_protocol: Cells were collected as regular by Trypsin digestion and PBS wash


title: control cells rep3

source_name: control cells rep3


title: hand2-as KO rep2

source_name: hand2-as KO rep2


title: shINO80 rep1

source_name: shINO80 rep1


title: control cells rep4

source_name: control cells rep4


title: shINO80 rep2

source_name: shINO80 rep2


title: WT_13 rep2

description:
read_count_table.txt
WT_13_2_S6


title: WT_13 rep3

description:
read_count_table.txt
WT_13_3_S13


title: control cells rep1

source_name: control cells rep1


title: WT_12 rep2

description:
read_count_table.txt
WT_12_2_S2


title: CRY_NL rep1

description:
read_count_table.txt
CRY_NL_1_S9

value: CRY2-ZLD; His2AvRFP

value: No light


title: WT_10 rep1

description:
read_count_table.txt
WT_10_1_S1

value: Blue light from nuclear cycle 10-14


title: CRY_14 rep3

description:
read_count_table.txt
CRY_14_3_S7


title: CRY_NL rep3

description:
read_count_table.txt
CRY_NL_3_S17


title: CRY_NL rep2

description:
read_count_table.txt
CRY_NL_2_S10


title: WT_12 rep3

description:
read_count_table.txt
WT_12_3_S3


title: WT_12 rep1

description:
read_count_table.txt
WT_12_1_S1


title: CRY_NL rep4

description:
read_count_table.txt
CRY_NL_4_S18


title: WT_10 rep4

description:
read_count_table.txt
WT_10_4_S11


title: CRY_13 rep4

description:
read_count_table.txt
CRY_13_4_S16


title: CRY_14 rep1

description:
read_count_table.txt
CRY_14_1_S5


title: CRY_14 rep2

description:
read_count_table.txt
CRY_14_2_S6


title: CRY_14 rep4

description:
read_count_table.txt
CRY_14_4_S8


title: CRY_13 rep1

description:
read_count_table.txt
CRY_13_1_S7


title: CRY_13 rep2

description:
read_count_table.txt
CRY_13_2_S8


title: WT_10 rep2

description:
read_count_table.txt
WT_10_2_S2


title: hand2-as KO rep1

source_name: hand2-as KO rep1


title: CRY_12 rep4

description:
read_count_table.txt
CRY_12_4_S8


title: CRY_12 rep2

description:
read_count_table.txt
CRY_12_2_S6


title: CRY_12 rep1

description:
read_count_table.txt
CRY_12_1_S5


title: CRY_10 rep2

description:
read_count_table.txt
CRY_10_2_S4


title: CRY_10 rep4

description:
read_count_table.txt
CRY_10_4_S12


title: CRY_12 rep3

description:
read_count_table.txt
CRY_12_3_S7


title: CRY_10 rep1

description:
read_count_table.txt
CRY_10_1_S3


title: RNA_lin-65_met-2_eemb_20oC_rep1

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: tab file of genes significantly upregulated in the corresponding mutants as determined by differential analysis using edgeR. First column is the WormbaseID followed by fold change/wt for each genotype and replica

organism: Caenorhabditis elegans

source_name: early embryo

growth_protocol: RNA was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in three independent biological replicates.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.
Libraries were prepared using the TruSeq Illumina Total RNA-seq Library Prep Kit (Illumina, San Diego, CA, USA).

tag: strain

value: lin-65(delta) I, met-2(n4256) III


title: RNA_N2_eemb_20oC_rep1

value: N2 (Bristol)


title: RNA_lin-65_eemb_20oC_rep3

value: lin-65(delta) I


title: RNA_lin-65_eemb_20oC_rep2


title: RNA_met-2_eemb_20oC_rep3


title: RNA_met-2_eemb_20oC_rep1


title: RNA_lin-65_met-2_eemb_20oC_rep3


title: RNA_lin-65_eemb_20oC_rep1


title: RNA_N2_eemb_20oC_rep2


title: RNA_N2_eemb_20oC_rep3


title: CRY_13 rep3

description:
read_count_table.txt
CRY_13_3_S15


title: circRNA_Patient2 cancer tissue

description:
circular RNA expression
S2_2

source_name: Tissue specimen

tag: patient id

value: colorectal cancer tissue

value: male


title: input_met2_eemb_20oC_rep3

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2).
Gene expression was quantified using WS220 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains seqnames, followed by start and end position and columns contain raw counts of reads overlapping each fragment for each genotype and replica.

growth_protocol: Chromatin was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in three independent biological replicates.

extract_protocol:
Embryos were fixed with 2% Formalin for 30min at room temperature. Fixed chromatin was extracted using the FastPrep-24™ (MPI) homogenizer and sonicated using the Bioruptor (Diagenode)
Libraries were prepared from chromatin IP and input samples using the TruSeq ChIP Library Preparation Kit (Illumina IP-202-1012)

tag: antibody


title: input_met2_eemb_20oC_rep1


title: input_set25_eemb_20oC_rep1


title: input_N2_eemb_20oC_rep3


title: input_set25_eemb_20oC_rep3


title: input_set25_eemb_20oC_rep2


title: input_N2_eemb_20oC_rep1


title: input_N2_eemb_20oC_rep2


title: RNA_lin-65_met-2_eemb_20oC_rep2


title: ChIP_lem-2_set-25_eemb_20oC_rep3

value: Lem-2 antibody (Novus Biologicals 48540002)


title: ChIP_lem-2_set-25_eemb_20oC_rep1


title: ChIP_lem-2_set-25_eemb_20oC_rep2


title: ChIP_lem-2_met-2_eemb_20oC_rep2


title: RNA_met-2_eemb_20oC_rep2


title: ChIP_lem-2_met-2_eemb_20oC_rep1


title: HNAD2-AS1 ChIRP rep2

data_processing:
The paired-end sequencing reads were mapped to the human genome (hg19) sequence using bowtie2
The duplicate reads were subsequently removed by Picard with default parameters.
The enriched peaks were called by MACS2. For each peak, we filtered for peaks that share the same shape from the three independent experiments. Only peaks with high correlation of the raw data profile, and high coverage across the peak were accepted. For HAND2-AS1 ChIRP-seq sample, thresholds of average coverage >1.5, Pearson correlation >0.3, and fold enrichment against input >2 were applied to filter MACS predicted peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are generated by bedtools

source_name: ChIRP-seq with probes of lncRNA HAND2-AS1 from liver CSCs repliate 2

growth_protocol: We isolated HCC cells from tumor tissues of primary liver cancer patients.And sorted liver CSCs (CD13+ and CD133+） using FACS analysis.

extract_protocol:
Chromatin isolation by RNA purification (ChIRP) was performed as described previously.In brief, human liver cells were cross-linked using glutaraldehyde. After glycine quenching, the nuclear lysate was sonicated for 25–30 cycles, 30 s on 30 s off at 4 °C, with BioRuptor twin sonicator (Diagenode). HAND2-AS1 and LacZ pulldown probes with BiotinTEG were designed by Biosearch Tecnologies and allowed to hybridize overnight with sonicated chromatin at 37°C (100 pmol probe per 1 ml chromatin). After hybridization, C1 Dynabeads (Life Technologies) were added and incubated for 30 min.
Strictly follow protocols from NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
ChIRP-seq

treatment_protocol: FACS sorting CD13+CD133+ liver CSCs.

tag: cell type

value: HCC liver CSCs cells


title: ChIP_lem-2_N2_eemb_20oC_rep1


title: input rep1

source_name: ChIRP-seq control sample from HCC liver CSCs cells repliate 1


title: Spleen_223_ILC3_C

first: Christian

middle: Thomas

last: Covington

state: Massachusetts

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

description: counts.txt

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to hg19 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by gene ID) in each sample. Four samples are missing due to low read counts.

source_name: Spleen

extract_protocol:
Tissue digestion as described in STAR methods
SmartSeq2

tag: tissue

value: Spleen


title: Spleen_223_NK_B

description: counts.txt

value: natural killer cells


title: input rep2

source_name: ChIRP-seq control sample  from HCC liver CSCs cells repliate 2


title: Spleen_223_ILC1_D

description: counts.txt


title: Spleen_223_ILC3_B

description: counts.txt


title: Spleen_223_ILC3_A

description: counts.txt


title: ChIP_lem-2_N2_eemb_20oC_rep2


title: HNAD2-AS1 ChIRP rep1

source_name: ChIRP-seq with probes of lncRNA HAND2-AS1 from liver CSCs repliate 1


title: Spleen_223_ILC1_C

description: counts.txt


title: Spleen_223_ILC2_B

description: counts.txt


title: input rep3

source_name: ChIRP-seq control sample  from HCC liver CSCs cells repliate 3


title: Spleen_223_NK_A

description: counts.txt


title: Spleen_223_ILC2_A

description: counts.txt


title: Spleen_223_NK_C

description: counts.txt


title: HNAD2-AS1 ChIRP rep3

source_name: ChIRP-seq with odd probes of lncRNA HAND2-AS1 from liver CSCs repliate 3


title: ChIP_lem-2_met-2_eemb_20oC_rep3


title: Spleen_223_ILC1_A

description: counts.txt


title: ChIP_lem-2_N2_eemb_20oC_rep3


title: Spleen_217_NK_B

description: counts.txt


title: Spleen_217_NK_A

description: counts.txt


title: Primary adipocytes treated with LPS+IFNb 1

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Primary adipocytes derived from Inguinal white adipose tissue from a male C57BL/6 mouse treated with LPS+IFNb

data_processing:
Following removal of barcodes and primers, raw reads were aligned to the mm10 mouse genome using annotations provided by UCSC.
Data were log2 transformed, normalized using a 75th percentile shift, and baselined to the median of all samples. Transcripts with low expression across all conditions were removed from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: text file with gene symbol and FPKM

source_name: Inguinal white adipose tissue

growth_protocol: Inguinal white adipose tissue was isolated and digested; stromal vascular fraction containing preadipocytes was cultured until confluence.  Preadipocytes were differentiated into adipocytes using the following steps: 1) initiation media for 2 days, continuation media for 2 days, and differentiation media for 2 days.

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit, with standard Illumina protocols
Standard Illumina protocols.

treatment_protocol: Cultured primary adipocytes were treated with IFNb (200U/ml) or saline for 3 hours and thereafter with LPS (100ng/ml) or saline for 4 hours.  Cells were isolated for RNA extraction.

value: Primary adipocytes

value: LPS+IFNb

tag: Sex

tag: background strain


title: Primary adipocytes treated with LPS 2

description: Primary adipocytes derived from Inguinal white adipose tissue from a male C57BL/6 mouse treated with LPS

value: LPS


title: Primary adipocytes treated with LPS+IFNb 2


title: Primary adipocytes treated with LPS 1


title: Primary adipocytes treated with IFNb 2

description: Primary adipocytes derived from Inguinal white adipose tissue from a male C57BL/6 mouse treated with IFNb

value: IFNb


title: Spleen_217_NK_C

description: counts.txt


title: input_met2_eemb_20oC_rep2


title: Spleen_217_ILC3_B

description: counts.txt


title: Primary adipocytes treated with Saline 2

description: Primary adipocytes derived from Inguinal white adipose tissue from a male C57BL/6 mouse treated with Saline

value: Saline


title: Primary adipocytes treated with IFNb 1


title: Primary adipocytes treated with Saline 1


title: Spleen_217_ILC3_A

description: counts.txt


title: Spleen_216_NK_B

description: counts.txt


title: Spleen_216_NK_C

description: counts.txt


title: Spleen_217_ILC1_A

description: counts.txt


title: Spleen_216_ILC3_C

description: counts.txt


title: Spleen_217_ILC3_C

description: counts.txt


title: Spleen_217_ILC1_B

description: counts.txt


title: Spleen_217_ILC1_C

description: counts.txt


title: DMSO_HBV_8h2

city: Wako-shi

first: Yutaka

last: Furutani

state: Saitama

address: 2-1 Hirosawa

department: Center for Integrative Medical Sciences

institute: RIKEN

description: replicate 2

hyb_protocol: The converted cRNA was then labeled and hybridized using the Human HT-12 v4 Expression BeadChip Kit according to the manufacturer’s instruction.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed with a package from Bioconductor (lumi) using a free software environment, R (http://www.r-project.org/).

source_name: Primary cultured human hepatocytes (PXB cells)

label_protocol: Five hundred nanograms of total RNA was used for first-stranded cDNA and second-stranded cRNA preparation with the Illumina TotalPrep RNA Amplification Kit (Ambion, USA).

growth_protocol: PXB cells cultured in 24-well plates were not infected or were infected with 3 genome equivalents per cell of HBV C_AT.

extract_protocol: Following treatments, total RNA was purified from the cells using an RNeasy mini kit (Qiagen).

treatment_protocol: After 30 days of infection, the cells were treated with DMSO, 30 microM CDM-3008 or 10 ng/ml pegylated IFNalpha2a (Pegasys, Chugai pharmaceutical) for 4 and 8 h (n=3).

value: PXB cells

tag: hbv infection

value: HBV-infected

value: DMSO for 8h


title: DMSO_8h3

description: replicate 3

value: HBV-noninfected


title: Spleen_216_ILC3_B

city: Cambridge

description: counts.txt


title: CDM-3008_HBV_8h3

description: replicate 3

value: 30 microM CDM-3008 for 8h


title: CDM-3008_HBV_8h2

description: replicate 2


title: CDM-3008_HBV_4h1

description: replicate 1

value: 30 microM CDM-3008 for 4h


title: IFN_HBV_4h3

description: replicate 3

value: 10 ng/ml pegylated IFNalpha2a for 4h


title: Spleen_216_NK_A

description: counts.txt


title: IFN_HBV_8h2

description: replicate 2

value: 10 ng/ml pegylated IFNalpha2a for 8h


title: DMSO_8h1

description: replicate 1


title: IFN_HBV_8h3

description: replicate 3


title: DMSO_HBV_8h3

description: replicate 3


title: IFN_HBV_8h1

description: replicate 1


title: Spleen_216_ILC2_C

description: counts.txt


title: CDM-3008_HBV_8h1

description: replicate 1


title: CDM-3008_HBV_4h2

description: replicate 2


title: IFN_HBV_4h2

description: replicate 2


title: DMSO_8h2

description: replicate 2


title: Spleen_216_ILC2_B

description: counts.txt


title: DMSO_HBV_8h1

description: replicate 1


title: DMSO_HBV_4h2

description: replicate 2

value: DMSO for 4h


title: IFN_HBV_4h1

description: replicate 1


title: DMSO_HBV_4h3

description: replicate 3


title: CDM-3008_HBV_4h3

description: replicate 3


title: Spleen_216_ILC3_A

description: counts.txt


title: Spleen_216_ILC1_C

description: counts.txt


title: Spleen_216_ILC1_B

description: counts.txt


title: Spleen_216_ILC2_A

description: counts.txt


title: Spleen_201_NK_C

description: counts.txt


title: Spleen_216_ILC1_A

description: counts.txt


title: Spleen_201_NK_A

description: counts.txt


title: Spleen_201_NK_B

description: counts.txt


title: 453W_PBMC_rep5

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

institute: Freiburg Medical Center

description:
replicate 5
453W_PBMC

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation

source_name: PBMCs

label_protocol: Aminoallyl-aRNA were prepared with the TargetAmp™ 2-Round aRNA Amplification Kit 2.0 (Epicentre)

extract_protocol: RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease status

value: healthy

tag: gender

value: M

tag: chip batch


title: CR3L_PBMC_rep13

description:
replicate 13
CR3L_PBMC

value: F


title: Spleen_201_ILC3_C

description: counts.txt

value: Spleen


title: 4DUY_PBMC_rep11

description:
replicate 11
4DUY_PBMC


title: CZJE_PBMC_rep7

description:
replicate 7
CZJE_PBMC


title: CYFZ_PBMC_rep9

description:
replicate 9
CYFZ_PBMC


title: FLWA_PBMC_rep10

description:
replicate 10
FLWA_PBMC


title: DMSO_4h3

description: replicate 3


title: 36TS_PBMC_rep12

description:
replicate 12
36TS_PBMC


title: FY2H_PBMC_rep8

description:
replicate 8
FY2H_PBMC


title: Spleen_201_ILC3_B

description: counts.txt


title: DMSO_4h1

description: replicate 1


title: DZQV_PBMC_rep4

description:
replicate 4
DZQV_PBMC


title: Spleen_201_ILC3_A

description: counts.txt


title: NFATc2_shRNA 2 [9031313088_L]

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: Human Melanoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: melanoma

tag: genotype/variation

value: NFATc2 knockdown


title: G4YW_PBMC_rep3

description:
replicate 3
G4YW_PBMC


title: 9JD4_PBMC_rep1

description:
replicate 1
9JD4_PBMC


title: DMSO_HBV_4h1

description: replicate 1


title: Spleen_201_ILC1_B

description: counts.txt


title: NFATc2_shRNA 1 [9031313088_I]


title: 684C_PBMC_rep6

description:
replicate 6
684C_PBMC


title: NFATc2_shRNA 2 [9031313088_J]


title: 925L_PBMC_rep2

description:
replicate 2
925L_PBMC


title: DMSO_4h2

description: replicate 2


title: NFATc2_shRNA 1 [9031313088_H]


title: NFATc2_shRNA 2 [9031313088_K]


title: NFATc2_shRNA 1 [9031313088_G]


title: Ctrl _shRNA 1 [9031313088_C]

value: control


title: Spleen_201_ILC1_C

description: counts.txt


title: naïve_2

city: Heidelberg

first: Juan

last: Rodriguez-Vita

address: Im Neuenheimer Feld 280

institute: DKFZ

hyb_protocol: Samples were prepared and were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays according to Affymetrix specifications

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only.
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.

source_name: Cell sorting by flow cytometry

label_protocol: end-labelling

extract_protocol: Tumor associated macrophages were isolated from tumor bearing mice. Cells were sorted with the following sorting strategy: CD45.2+, CD19-, CD11b+, CD115+, F4/80+

value: peritoneal macrophages

tag: time point

value: Day 0