title: FF, rat 3

description: Gene expression data from rat striatums (fresh frozen)

hyb_protocol: Fragmented and labelled samples were hybridized to GeneChip Rat Gene 2.0 ST Arrays.

data_processing: The data were analyzed with Affymetrix Expression Console software (v1.4.1) using RMA-Sketch algorithm for data normalization. FF and FFPE datasets were normalized together. Normalization was done to gene level as well as to exon level.

organism: Rattus norvegicus

source_name: Fresh frozen rat striatum; rat 3

value: brain; striatum


title: FFPE, rat 4

status: Public on Apr 13 2018

type: RNA

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Gene expression data from rat striatums (formalin-fixed paraffin-embedded)

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G (with AGCC v3.1.1 software)

label: Biotin

molecule: total RNA

source_name: Formalin-fixed paraffin-embedded rat striatum; rat 4

label_protocol: Biotinylated cRNA samples were prepared using the Affymetrix GeneChip WT Pico Reagent Kit from 2 ng total RNA.

extract_protocol: Total RNA was isolated using the High Pure FFPE RNA Micro Kit (Roche) according to the manufacturer's instructions.

tag: tissue


title: FFPE, rat 5

source_name: Formalin-fixed paraffin-embedded rat striatum; rat 5


title: CPA_M_160ppm_4d_1

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: Agilent Mouse miRNA arrays (G4472A) were hybridized, washed and scanned on an Agilent Microarray Scanner following manufacturer instructions.

scan_protocol: Arrays ware scanned on an Agilent Microarray Scanner. Images from the scanner were processed using Agilent Feature Extraction Software v10.5.1.

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

organism: Mus musculus

source_name: Cyproterone Acetate, male, 3 days

label_protocol: 100 ng Total RNA (diluted to 50ng/µl) were labelled using miRNA complete labelling (PCp-Cy3) and hybridization kit (Agilent# 5190-0456).

growth_protocol: CD-1 male and female mice were orally treated with a set of genotoxic carcinogens (CIDB, DMN and MDA), nongenotoxic carcinogens (DCB, PB and PBO), non-hepatocarcinogens (CFX, Praz and Prop) and a group of undefined compounds (CPA, Wy-14643 and TAA) over a period of 3 and 14 days.

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany). RNA integrity was checked using the Agilent Bioanalyzer.

treatment_protocol: After 3 and 14 days of compound treatment mice were anaesthetized in isoflurane and exsanguinated from the heart and subjected to necropsy. The left lateral liver lobe was extracted and snap frozen under -80°C conditions.

tag: strain

tag: gender

value: male

value: liver

tag: treatment short name

value: CPA

tag: treatment

value: Cyproterone Acetate

tag: treatment duration

value: 3 days

tag: treatment dose

value: 16 mg/kg/d

tag: treatment group

tag: corresponding control


title: CO_M_G77_15d_2

source_name: Corn Oil, male, 14 days

value: CO

value: Corn Oil

value: 14 days


title: CO_M_G77_15d_3


title: CO_M_G77_15d_4


title: CO_M_G76_4d_4

source_name: Corn Oil, male, 3 days


title: CO_M_G77_15d_1


title: CPA_M_160ppm_15d_5

source_name: Cyproterone Acetate, male, 14 days


title: CO_M_G76_4d_2


title: CO_M_G76_4d_3


title: FFPE, rat 6

source_name: Formalin-fixed paraffin-embedded rat striatum; rat 6


title: DMN_F_2ppm_15d_3

source_name: Dimethylnitrosamine, female, 14 days

value: female

value: DMN

value: Dimethylnitrosamine

value: 2 mg/kg/d


title: DMN_F_2ppm_15d_2


title: DMN_F_2ppm_15d_4


title: DMN_F_2ppm_15d_1


title: DMN_F_2ppm_4d_3

source_name: Dimethylnitrosamine, female, 3 days


title: DMN_F_2ppm_4d_2


title: CPA_M_160ppm_4d_4


title: CPA_M_160ppm_15d_3


title: DMN_F_2ppm_4d_1


title: CIDB_F_2500ppm_15d_6

source_name: C.I. Direct Black, female, 14 days

value: CIDB

value: C.I. Direct Black

value: 25 mg/kg/d


title: High Fat Mouse 2

type: SRA

city: St. Louis

first: Christopher

middle: W

last: Farnsworth

state: Missouri

address: 425 So Euclid Ave

department: Pathology

country: USA

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
Illumina Hiseq  reads were trimmed and clipped using Trimmomatic-0.32 read cleaning
Reads were Mapped to Mouse genome mm10 via SHRiMP2.2.3
Diff. expression determined  via. cufflinks 2.0.2 w/ FDR of 0.05
Perl Script was used to further clean files
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: text file with FPKM

source_name: Sterile HF mouse popliteal lymph node

extract_protocol:
Flash frozen PLN's were pulverized at 4C using lysing matrix B tubes in ice cold acid phenol.  Total RNA was enriched for poly-A mRNA and reverse transcribed to cDNA.
Epicentre ScriptSeq v2 library preparation from RiboZero depleted total RNA; 100nt single-end reads

value: popliteal lymph node

tag: age at beginning of treatment

value: 5 wks old

tag: diet

value: Fed HF-diet 12 weeks (60% Kcal fat)


title: High Fat Mouse 3


title: CIDB_F_2500ppm_15d_5

value: liver


title: Lean Mouse 2

source_name: Sterile Lean mouse popliteal lymph node

value: Fed lean chow 12 weeks (10%kcal fat)


title: High Fat Mouse 1


title: Lean Mouse 1


title: FF, rat 2

source_name: Fresh frozen rat striatum; rat 2

extract_protocol: Total RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: brain; striatum


title: FF, rat 1

source_name: Fresh frozen rat striatum; rat 1


title: CO_M_G76_4d_1

value: male

value: 3 days


title: DMN_F_2ppm_4d_4


title: WS8_VEH_H3K27Ac_KC139_Rep1

city: Durham

first: Jeff

last: Jasper

state: NC

department: Pharmacology and Cancer Biology

institute: Duke University

description: MCF7-derived 4-OHT sensitive.

library_source: genomic

data_processing:
FASTQ files were clipped using Skewer and aligned with BWA mem.
Peak calling was performed using Homer.
Differential peak calling was performed using PePr.
BigWig files (bw) are normalized using deeptools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bed: Bed files include peak calls from Homer.
Supplementary_files_format_and_content: *.bw: bigWig files include peak calls from PePr.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Phenol red free DMEM/F12 with 8% charcoal stripped FBS, supplemented with NaPyr and NEAA.

extract_protocol:
Cell pellets were thawed on ice, and then resuspended in Lysis Buffer containing 1% SDS, 0.25mM EDTA, 2.5mM Tris-HCl, pH 8.0, protease inhibitor cocktail. Cell lysates were sonicated using the Covaris.
KAPA HTP

treatment_protocol: 3 days in media, 45min hormone treatment. ETOH, 10-8 E2, 10^-7 4OHT.

tag: cell line

value: VEH

tag: treatment time

tag: factor

tag: chip antibody

value: Diagenode, C15410196

tag: replicate


title: WS8_VEH_GRHL2_KC1216-03_Rep3

description: MCF7-derived 4-OHT sensitive.

value: Sigma, HPA004820


title: WS8_VEH_INPUT_KC1216-08_Rep2

description:
MCF7-derived 4-OHT sensitive.
Input

value: INPUT


title: WS8_VEH_INPUT_KC177_Rep3

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_VEH_FOXA1_KC123_Rep1

description: MCF7-derived 4-OHT sensitive.

value: Abcam, ab23738


title: WS8_VEH_FOXA1_KC125_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_VEH_FOXA1_KC124_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_VEH_H3K4Me2_KC156_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_VEH_INPUT_KC1216-07_Rep1

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_VEH_INPUT_KC1216-09_Rep3

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_VEH_INPUT_KC175_Rep1

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_VEH_GRHL2_KC1216-01_Rep1

description: MCF7-derived 4-OHT sensitive.


title: WS8_VEH_GRHL2_KC1216-02_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_VEH_H3K27Ac_KC141_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_INPUT_KC178_Rep1

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_VEH_H3K4Me2_KC157_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_H3K4Me2_KC158_Rep1

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_H3K4Me2_KC159_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_INPUT_KC179_Rep2

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_E2_H3K4Me2_KC160_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_INPUT_KC180_Rep3

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_VEH_H3K4Me2_KC155_Rep1

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_H3K27Ac_KC143_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_VEH_H3K27Ac_KC140_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_FOXA1_KC128_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_H3K27Ac_KC144_Rep3

description: MCF7-derived 4-OHT sensitive.


title: Microglia-depleted (day 10) mouse, somatosensory cortex 4

description: Gene expression data from mouse somatosensory cortex (FFPE tissue)

hyb_protocol: Fragmented and labelled samples were hybridized to a GeneChip Mouse Gene 2.1 ST 16-Array Plate

scan_protocol: GeneChips were scanned using Affymetrix GeneTitan MC Instrument.

data_processing: The data were analyzed with Affymetrix Expression Console software (v1.4.1) using RMA-Sketch algorithm for data normalization. Normalization was done to gene level.

source_name: Microdissected somatosensory cortex from mouse 10 days after microglia depletion

value: brain; somatosensory cortex

value: tamoxifen and diphtheria toxin to induce the depletion of microglia cells


title: WS8_4OHT_INPUT_KC181_Rep1

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_4OHT_INPUT_KC182_Rep2

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_E2_FOXA1_KC126_Rep1

description: MCF7-derived 4-OHT sensitive.


title: WS8_4OHT_H3K4Me2_KC163_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_4OHT_H3K4Me2_KC162_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_4OHT_H3K27Ac_KC147_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_4OHT_H3K4Me2_KC161_Rep1

description: MCF7-derived 4-OHT sensitive.


title: WS8_4OHT_INPUT_KC183_Rep3

description:
MCF7-derived 4-OHT sensitive.
Input


title: WS8_4OHT_H3K27Ac_KC145_Rep1

description: MCF7-derived 4-OHT sensitive.


title: WS8_4OHT_FOXA1_KC131_Rep3

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_H3K27Ac_KC142_Rep1

description: MCF7-derived 4-OHT sensitive.


title: WS8_4OHT_H3K27Ac_KC146_Rep2

description: MCF7-derived 4-OHT sensitive.


title: WS8_E2_FOXA1_KC127_Rep2

description: MCF7-derived 4-OHT sensitive.


title: Microglia-depleted (day 10) mouse, motor cortex 4

description: Gene expression data from mouse motor cortex (FFPE tissue)

source_name: Microdissected motor cortex from mouse 10 days after microglia depletion

value: brain; motor cortex


title: Microglia-depleted (day 10) mouse, motor cortex 2


title: Control mouse, somatosensory cortex 1

source_name: Microdissected somatosensory cortex from control

value: tamoxifen


title: Control mouse, somatosensory cortex 2


title: Control mouse, somatosensory cortex 3


title: Control mouse, motor cortex 3

source_name: Microdissected motor cortex from control


title: Microglia-depleted (day 10) mouse, somatosensory cortex 3


title: Microglia-depleted (day 10) mouse, somatosensory cortex 1


title: WS8_4OHT_FOXA1_KC130_Rep2

description: MCF7-derived 4-OHT sensitive.


title: Microglia-depleted (day 10) mouse, motor cortex 1


title: WS8_4OHT_FOXA1_KC129_Rep1

description: MCF7-derived 4-OHT sensitive.


title: TAMR_VEH_INPUT_KC185_Rep2

description:
MCF7-derived 4-OHT resistant.
Input

source_name: TAMR

value: TAMR


title: Microglia-depleted (day 10) mouse, somatosensory cortex 2


title: Control mouse, motor cortex 4


title: TAMR_VEH_INPUT_KC186_Rep3

description:
MCF7-derived 4-OHT resistant.
Input


title: Control mouse, somatosensory cortex 4


title: TAMR_VEH_INPUT_KC184_Rep1

description:
MCF7-derived 4-OHT resistant.
Input


title: TAMR_VEH_INPUT_KC1216-10_Rep1

description:
MCF7-derived 4-OHT resistant.
Input


title: TAMR_VEH_INPUT_KC1216-11_Rep2

description:
MCF7-derived 4-OHT resistant.
Input


title: Microglia-depleted (day 10) mouse, motor cortex 3


title: Control mouse, motor cortex 2


title: Control mouse, motor cortex 1


title: TAMR_VEH_H3K4Me2_KC165_Rep2

description: MCF7-derived 4-OHT resistant.


title: TAMR_VEH_H3K4Me2_KC166_Rep3

description: MCF7-derived 4-OHT resistant.


title: MPP_rep3

city: Fukuoka

first: Kohta

last: Miyawaki

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

description: Gene expression of MPP in steady state

hyb_protocol: Labeled cDNAs (1.65 µg) were hybridized to the microarray chip (SurePrint G3 Unrestricted GE 8x60K; Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing with Agilent SureScan Microarray Scanner (G4900DA) using the 1-color scan setting for 8360k array slides (scan resolution of 3mm; dye channel was set to green, and green photo-multiplier tube sensitivity was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent) using default parameters (protocol GE1_1105_Oct12 and grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended processed signal intensities.

source_name: Bone Marrow, MPP, replicate 3

label_protocol: Amplified complementary DNAs (cDNAs) from each sample were obtained using Ovation PicoSL WTA System V2 (NuGEN) and Cyanine3-labeled using SureTag DNA Labeling Kit (Agilent Technologies).

extract_protocol: Target HSPC populations were double sorted directly into Trizol reagent (Life Technologies). Total RNAs were extracted according to the manufacturer’s instructions.

value: Bone Marrow

tag: cell type

value: MPP


title: CMP_rep3

description: Gene expression of CMP in steady state

source_name: Bone Marrow, CMP, replicate 3

tag: tissue

value: CMP


title: CD35-HSC_rep3

description: Gene expression of CD35-HSC in steady state

source_name: Bone Marrow, CD35-HSC, replicate 3


title: TAMR_VEH_H3K4Me2_KC164_Rep1

description: MCF7-derived 4-OHT resistant.


title: MEP_rep3

description: Gene expression of MEP in steady state

source_name: Bone Marrow, MEP, replicate 3

value: MEP


title: TAMR_VEH_H3K27Ac_KC150_Rep3

description: MCF7-derived 4-OHT resistant.


title: TAMR_VEH_INPUT_KC1216-12_Rep3

description:
MCF7-derived 4-OHT resistant.
Input


title: TAMR_VEH_H3K27Ac_KC148_Rep1

description: MCF7-derived 4-OHT resistant.


title: TAMR_VEH_H3K27Ac_KC149_Rep2

description: MCF7-derived 4-OHT resistant.


title: Lean Mouse 3

tag: strain

value: popliteal lymph node

value: 5 wks old

value: Fed lean chow 12 weeks (10%kcal fat)


title: TAMR_VEH_GRHL2_KC1216-06_Rep3

description: MCF7-derived 4-OHT resistant.

value: VEH


title: CD35+HSC_rep3

description: Gene expression of CD35+HSC in steady state

source_name: Bone Marrow, CD35+HSC, replicate 3


title: MEP_rep2

description: Gene expression of MEP in steady state

source_name: Bone Marrow, MEP, replicate 2


title: GMP_rep3

description: Gene expression of GMP in steady state

source_name: Bone Marrow, GMP, replicate 3

value: GMP


title: TAMR_VEH_GRHL2_KC1216-05_Rep2

description: MCF7-derived 4-OHT resistant.

value: Sigma, HPA004820


title: CMP_rep2

description: Gene expression of CMP in steady state

source_name: Bone Marrow, CMP, replicate 2


title: TAMR_VEH_GRHL2_KC1216-04_Rep1

description: MCF7-derived 4-OHT resistant.


title: TAMR_VEH_FOXA1_KC134_Rep3

description: MCF7-derived 4-OHT resistant.


title: TAMR_VEH_FOXA1_KC133_Rep2

description: MCF7-derived 4-OHT resistant.


title: GMP_rep2

description: Gene expression of GMP in steady state

source_name: Bone Marrow, GMP, replicate 2


title: CD35-HSC_rep2

source_name: Bone Marrow, CD35-HSC, replicate 2


title: MPP_rep2

description: Gene expression of MPP in steady state

source_name: Bone Marrow, MPP, replicate 2


title: CD35+HSC_rep2

source_name: Bone Marrow, CD35+HSC, replicate 2


title: MEP_rep1

description: Gene expression of MEP in steady state

source_name: Bone Marrow, MEP, replicate 1


title: A1-50

city: Guangzhou

first: Tan

last: yi

address: No.7 West Street, Yuancun, Guangzhou, P. R. China

country: China

institute: South China Institute of Environmental Science (SCIES), Ministry of Environmental Protection (MEP)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 –r 70 --library-type fr-unstranded
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Treatment group (50μg/mLPM2.5)

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal human  bronchial epithelial cel

tag: treated with

value: 50μg/mL PM2.5


title: A1-100

source_name: Treatment group (100μg/mLPM2.5)


title: TAMR_E2_INPUT_KC189_Rep3

description:
MCF7-derived 4-OHT resistant.
Input

value: INPUT


title: A1-0

source_name: control group (NO PM2.5)

value: none (control)


title: TAMR_E2_INPUT_KC188_Rep2

description:
MCF7-derived 4-OHT resistant.
Input

source_name: TAMR


title: GMP_rep1

description: Gene expression of GMP in steady state

source_name: Bone Marrow, GMP, replicate 1


title: TAMR_VEH_FOXA1_KC132_Rep1

description: MCF7-derived 4-OHT resistant.

value: Abcam, ab23738


title: TAMR_E2_INPUT_KC187_Rep1

description:
MCF7-derived 4-OHT resistant.
Input


title: WS8_VEH_INPUT_KC176_Rep2

description:
MCF7-derived 4-OHT sensitive.
Input


title: CMP_rep1

description: Gene expression of CMP in steady state

source_name: Bone Marrow, CMP, replicate 1


title: TAMR_E2_H3K4Me2_KC169_Rep3

description: MCF7-derived 4-OHT resistant.


title: MPP_rep1

description: Gene expression of MPP in steady state

source_name: Bone Marrow, MPP, replicate 1


title: CD35-HSC_rep1

source_name: Bone Marrow, CD35-HSC, replicate 1


title: TAMR_E2_H3K4Me2_KC168_Rep2

description: MCF7-derived 4-OHT resistant.


title: TAMR_E2_H3K4Me2_KC167_Rep1

description: MCF7-derived 4-OHT resistant.


title: CD35+HSC_rep1

source_name: Bone Marrow, CD35+HSC, replicate 1


title: TAMR_E2_H3K27Ac_KC153_Rep3

description: MCF7-derived 4-OHT resistant.

value: Diagenode, C15410196


title: TAMR_E2_H3K27Ac_KC151_Rep1

description: MCF7-derived 4-OHT resistant.

value: TAMR


title: TAMR_E2_H3K27Ac_KC152_Rep2

description: MCF7-derived 4-OHT resistant.


title: Identification of si-SERPINH1 target genes in 786-O

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: renal cancer

tag: transfection

value: no transfection

source_name: si-SERPINH1 transfected cell line


title: genomic DNA of PASMCs  from CTEPH4

type: genomic

city: Beijing

first: Ying

last: Wang

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

institute: Beijing Chao-Yang Hospital

description:
SAMPLE 7
PASMCs 7

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: Genome Studio software (version v1.8/2010.3)

label: Cy5 and Cy3

source_name: CTEPH PASMCs

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PASMCs using QIAamp DNA Mini Kit according to standard instructions

value: cultured PASMCs from patient endarterectomy tissues

tag: disease state

value: chronic thromboembolic pulmonary hypertension (CTEPH)


title: TAMR_E2_FOXA1_KC135_Rep1

description: MCF7-derived 4-OHT resistant.

tag: treatment


title: Identification of miR-148a-5p target genes in MKN

value: MKN

value: gastric cancer

source_name: miR-148a-5p transfected cell line


title: Identification of miR-99a-3p target genes in MDA-MB-231

value: breast cancer

source_name: miR-99a-3p transfected cell line


title: Identification of si-SDC3_2 target genes in 786-O

source_name: si-SDC3-2 transfected cell line


title: wildtype_3

city: Madison

first: Shannon

middle: C

last: Kenney

state: WI

address: 1111 Highland Avenue

department: Oncology

institute: University of Wisconsin-Madison

description: processed data file: PCT101801029_expression_table_human.xlsx

data_processing:
The fastQC program is used to verify raw data quality of the Illumina reads.
The sequence data was mapped to human, mouse and virus genomes separately. The hg19 human genome and Ensembl gene annotations (v75), GRCm38 (mm10) mouse genome and Ensembl gene annotations (v82), and user-supplied virus genome and annotation, were used for mapping.
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread.
Then, we took the human and mouse alignment files (bam files), and assigned a read to one of the following categories (in the order listed below): 1. Mapped to Both - Mapping sores for both human and mouse >20, the difference between human and mouse mapping scores <=10; 2. Mapped mostly to human - Human mapping sore>20, mapping to human genome better than to mouse genome (higher mapping sore and fewer mismatches); 3. Mapped mostly to mouse - Mouse mapping sore>20, mapping to mouse genome better than to human genome (higher sore and fewer mismatches); 4. Map to human - Human mapping score minus mouse mapping score >10; 5. Map to mouse - Mouse mapping score minus human mapping score >10; 6. No mapping: both mapping scores are 0; 7. Others.
Reads from categories 2 and 4 were combined as human-only reads (17-42% of all reads).
These human-only alignment bam files were compared against corresponding gene annotation GFF files, and raw counts for each gene were generated using the featureCounts tool from Subread.
The raw counts data were normalized using TMM normalization method in the program edgeR, and the normalized gene counts were transformed to log2 scale using voom method from the R Limma package, then used for differential expression analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: PCT101801029_expression_table_human.xlsx: Excel file includes RPKM values for each Sample and comparison statistics.

source_name: tumor

growth_protocol: Human tumor cells (infected with virus) grown in mouse.

extract_protocol:
Tumors isolated from humanized mice were flash frozen on dry ice, homogenized and then RNA extracted using the Trizol reagent.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Prep kit (Illumina).

treatment_protocol: 6 samples: 3 infected with wildtype Epstein-Barr virus, and 3 infected with ebna3c-deleted virus.

value: human tumor cells (infected with wildtype Epstein-Barr virus) grown in mouse


title: dEBNA3C_2

value: human tumor cells (infected with ebna3c-deleted virus) grown in mouse


title: wildtype_1


title: TAMR_4OHT_INPUT_KC122_Rep3

description:
MCF7-derived 4-OHT resistant.
Input


title: Identification of miR-451a target genes in SK-MES

value: SK-MES

value: lung cancer

source_name: miR-451a transfected cell line


title: TAMR_4OHT_INPUT_KC121_Rep2

description:
MCF7-derived 4-OHT resistant.
Input


title: dEBNA3C_1


title: Identification of si-SDC3_1 target genes in 786-O

source_name: si-SDC3-1 transfected cell line


title: TAMR_4OHT_INPUT_KC190_Rep1

description:
MCF7-derived 4-OHT resistant.
Input


title: OCI-LY3 3H_2

city: Portland

first: Alexey

last: Danilov

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: Oregon Health and Science Univeristy

description:
RNA180105AD_2_LY3_3h
RNA180105AD_RAW_2_LY3_3h_300AZ_S15_L005

data_processing:
Illumina
Alignment: STAR2.5.3a, Default parameters
Filtering: Genes expressed in at least one sample
Differential Expression/Normalization: DESeq2 rld (regularlized log transform)
Genome_build: grch38
Supplementary_files_format_and_content: Tab delimited files

source_name: OCI-LY3 3H

growth_protocol: Both cell lines were grown in RPMI 1640 supplemented with 10% FBS and 1% pencillin streptomycin in a T75 flasks. Both cell lines were kept in 5% CO2 and 37 celsius

extract_protocol:
Both cell lines at time 0, 3 hours, or 6 hours were collected and spun in a table top centrifuge for 5 min at 800xg. They were washed with PBS and respun for 5 min at 800xg. Countertops were then sprayed with Rnase spray (Fisher cat no. 7002). Samples were homogenized with Omega Homogenizer columns and total RNA was collected with the Omega E.Z.N.A. Total RNA kit
Total RNA was run on the Bioanalyzer (Agilent) to verify intactness. Following this test, RNA-seq libraries were constructed using Illumina's TruSeq RNA Library Prep Kit v2: Poly(A)+ RNA was isolated from 200ng of total RNA using oligo-dT bound to magnetic beads. The resulting Poly(A)+ RNA was then chemically fragmented. RNA fragments were converted to double stranded cDNA using random hexamer priming. Fragment ends were treated to remove overhanging nucleotides and then a single “A” was added to the 3’ end of each strand to facilitate ligation. Unique Illumina adaptors with barcode sequences were ligated to the fragments. The resulting libraries were then amplified using 13-rounds of PCR. Unincorporated nucleotides and adaptor dimers were removed using AMPure XP beads (Agencourt). Libraries were quantitated using qPCR (Kapa Biosystems), pooled for multiplexing, 6 samples per lane, and sequenced on a HiSeq 2500 sequencer (Illumina) on a Single Read flow cell, 100 cycles.

treatment_protocol: Both cell lines were plated at one million cells in a 6 well plate in 2mL of the media listed above. Time 0 cells were collected at the same time as treatment (300nM of AZ5576) of the 3 and 6 hour samples.

value: diffuse large B-cell lymphoma (DLBCL)  cell line

value: AZ5576 at 300 nM for 3hrs


title: genomic DNA of PASMCs  from Normal 2

description:
SAMPLE 2
PASMCs 2

source_name: normal PASMC cell line

value: normal  pulmonary arterial smooth muscle (PASMC) cell line

value: control


title: genomic DNA of PASMCs  from CTEPH1

description:
SAMPLE 4
PASMCs 4


title: OCI-LY3 6H_2

description:
RNA180105AD_2_LY3_6h
RNA180105AD_RAW_2_LY3_6h_300AZ_S16_L005

source_name: OCI-LY3 6H

value: AZ5576 at 300 nM for 6hrs


title: TAMR_4OHT_H3K4Me2_KC174_Rep3

description: MCF7-derived 4-OHT resistant.

source_name: TAMR

value: TAMR


title: genomic DNA of PASMCs  from CTEPH3

description:
SAMPLE 6
PASMCs 6


title: genomic DNA of PASMCs  from CTEPH5

description:
SAMPLE 8
PASMCs 8


title: Identification of miR-99a-5p target genes in MDA-MB-231

source_name: miR-99a-5p transfected cell line


title: TAMR_4OHT_H3K4Me2_KC173_Rep2

description: MCF7-derived 4-OHT resistant.


title: TAMR_E2_FOXA1_KC137_Rep3

description: MCF7-derived 4-OHT resistant.

value: Abcam, ab23738


title: Identification of miR-148a-3p target genes in MKN

value: no transfection

source_name: miR-148a-3p transfected cell line


title: genomic DNA of PASMCs  from CTEPH2

description:
SAMPLE 5
PASMCs 5

value: cultured PASMCs from patient endarterectomy tissues


title: OCI-LY3 0H_2

description:
RNA180105AD_2_LY3_0h
RNA180105AD_RAW_2_LY3_0h_300AZ_S14_L005

source_name: OCI-LY3 0H

value: none (untreated)


title: genomic DNA of PASMCs  from Normal 1

description:
SAMPLE 1
PASMCs 1


title: TAMR_4OHT_H3K4Me2_KC170_Rep1

description: MCF7-derived 4-OHT resistant.


title: TAMR_4OHT_H3K27Ac_KC172_Rep3

description: MCF7-derived 4-OHT resistant.

value: Diagenode, C15410196


title: genomic DNA of PASMCs  from Normal 3

description:
SAMPLE 3
PASMCs 3


title: TAMR_4OHT_H3K27Ac_KC154_Rep1

description: MCF7-derived 4-OHT resistant.


title: Pt-Delta pRNAi embryo

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

institute: JT Biohistory Research Hall

description: There were no biological replicates.

hyb_protocol: cRNA probes were hybridized to a microarray in Hybridization buffer (5x SSC, 0.1% SDS, 10% formamide) at 42˚C for 16-20 h.

scan_protocol: Microarray slides were scanned using a GenePix 4000B Scanner (Molecular Devices).

data_processing: Obtained images were analyzed using an Array-Pro Analyzer Ver. 4.5 (Media Cybernetics, Inc.). The quantitative data were subjected to Loess normalization.

organism: Parasteatoda tepidariorum

source_name: d-RNAi

label_protocol: cRNA labeled with Cy3 or Cy5 was prepared from 2 µg of total RNA using RNA Transcript SureLABEL Core Kit (Takara)

growth_protocol: Embryos were incubated at 25˚C.

extract_protocol: Total RNA was extracted from approximately 250 embryos of the same stage using MagExtractor (Toyobo). RNA integrity was examined with an Agilent Bioanalyzer 2100.

treatment_protocol: A mated female was injected with approximately 1.5µl of Pt-Delta dsRNA solution (2µg/µl) four times at 2-3 days intervals. Embryos derived from an egg sac produced by this female 25 days after the first injection of Pt-Delta dsRNA were used for RNA extraction.

value: whole embryo

tag: developmental stage

value: late stage 6

value: Pt-Delta pRNAi

source_name: normal

treatment_protocol: Embryos derived from a different egg sac produced by the same female one day before the first injection of Pt-Delta dsRNA were used for RNA extraction.


title: OCI-LY3 0H_1

description:
RNA180105AD_1_LY3_0h
RNA180105AD_raw_1_LY3_0h_300AZ_S11_L005


title: TAMR_4OHT_H3K27Ac_KC171_Rep2

description: MCF7-derived 4-OHT resistant.


title: OCI-LY3 3H_1

description:
RNA180105AD_1_LY3_3h
RNA180105AD_RAW_1_LY3_3h_300AZ_S12_L005


title: VAL 6H_2

description:
RNA180105AD_2_Val_6h
RNA180105AD_RAW_2_Val_6h_300AZ_S10_L004

source_name: VAL 6H

value: VAL


title: VAL 3H_2

description:
RNA180105AD_2_Val_3h
RNA180105AD_RAW_2_Val_3h_300AZ_S9_L004

source_name: VAL 3H


title: VAL 0H_2

description:
RNA180105AD_2_Val_0h
RNA180105AD_RAW_2_Val_0h_300AZ_S8_L004

source_name: VAL 0H


title: TAMR_4OHT_FOXA1_KC120_Rep3

description: MCF7-derived 4-OHT resistant.


title: TAMR_4OHT_FOXA1_KC138_Rep1

description: MCF7-derived 4-OHT resistant.


title: VAL 3H_1

description:
RNA180105AD_1_Val_3h
RNA180105AD_RAW_1_Val_3h_300AZ_resubmitted_S6_L004


title: TAMR_4OHT_FOXA1_KC119_Rep2

description: MCF7-derived 4-OHT resistant.


title: VAL 6H_1

description:
RNA180105AD_1_Val_6h
RNA180105AD_RAW_1_Val_6h_300AZ_resubmitted_S7_L004


title: VAL 0H_1

description:
RNA180105AD_1_Val_0h
RNA180105AD_RAW_1_Val_0h_300AZ_resubmitted_S5_L004


title: Weight_stable [ID149_020F]

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: A total of 5.5 µg of fragmented and biotinylated sense-strand DNA target were hybridized to the arrays in a GeneChip Hybridization Oven 645 for 16-18h at 45°C.

scan_protocol: The arrays were washed and stained in the Gene Chip Fluidics Station 450 followed by scanning in an Affymetrix Gene Chip Scanner 7.

data_processing: CEL files were analyzed in Affymetrix Expression Console (v. 1.4.1) using the SST-RMA method. Microarray gene expression (log2-values) was analyzed in Qlucore (www.qlucore.com).

label: biotin

source_name: Subcutaneous adipose tissue

label_protocol: The WT Plus Kit was used to generate amplified and biotinylated sense-strand DNA targets from total RNA (Thermo Fisher).

extract_protocol: Total RNA was isolated using the RNeasy kit (cat no. 217004, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Biopsies from the abdominal subcutaneous adipose tissue depot were obtained by aspiration needle biopsly. Samples were immediately washed in NacCl (9 mg/ml) and thereafter frozen in liquid nitrogen and kept at -70C for subsequent RNA preparation.

tag: weight status

value: White adipose tissue

tag: genotype

value: female

tag: age


title: Weight_gain [ID142_070F]


title: Weight_stable [ID126_072F]


title: Weight_gain [ID134_024F]


title: Weight_stable [ID128_017F]


title: Weight_gain [ID140_067F]


title: human week 17 kidney cortex single cell RNA-Seq, Kidney 1 [H17w_K1]

city: Los Angeles

first: Guilherme

last: de Sena Brandine

state: CA

address: 1050 Child's Way

department: Quantitative and Computational Biology

institute: University of Southern California

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Reads were mapped using STAR 2.5.1b and the NCBI GTF annotation accession NCBI:GCA_000001405.14
Count tables were generated from the FASTQ files using the Cell Ranger software version 1.3.1 with default parameters.
Read 1 is the Cell Barcode + UMI and read 2 is the actual RNA sequence
bam file contains cell barcode for each read at CR:Z tag
Genome_build: GRCh37.p13

source_name: human kidney cortex

extract_protocol:
10X Genomics: Chromium Single Cell 3’ v2
single cell RNA-Seq of poly A selected mRNA;

tag: developing stage

value: Week 17

value: kidney

value: human embryonic kidney cortex cells


title: Weight_gain [ID127_052F]


title: human week 17 kidney cortex single cell RNA-Seq, Kidney 2 [H17w_K2]


title: Sporadic NFPA5

city: London

first: Sayka

last: Barry

address: Charterhouse SQ

department: Endocrinology

country: United Kingdom

institute: QMUL

description: This sample failed quality control assessment: no processed data

hyb_protocol: Fifteen micrograms of labelled biotinylated cRNA was fragmented, mixed with the hybridization solution and hybridised to Affymetrix high density Oligo arrays for 16 h at 45oC.

scan_protocol: Each array was washed and stained in a GeneChip Fluidics station 450 (Affymetrix) and scanned by a GeneChip 3000 scanner (Affymetrix) according to the manufacturer’s instructions.

data_processing: Raw data files were analysed using Bioconductor packages (http://www.bioconductor.org/) within the open source R (v2.15.3) statistical environment.Quality control (QC) evaluations were conducted using the arrayMvout package.Data files were normalised using GC-RMA.The resulting normalised expression matrix was filtered using standard deviation calls to select the top 10,000 most variable probes across all experiments. To identify genes differentially expressed between the biological groups limma was used. Benjamini and Hochberg (BH) false discovery rate was used for multiple testing corrections. A double cut-off of false discovery rate (FDR) < 0.05 and unlogged fold change of ≥ 2 was used.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng of total RNA

extract_protocol: Total RNA was isolated from tissues using the RNeasy micro kit (Qiagen), according to the manufacturer’s protocol.

tag: aip mutation status

value: Negative

tag: tumour status

value: Macroadenoma

tag: tissue preparation

value: Freshly frozen


title: Weight_gain [ID119_050F]


title: Weight_stable [ID120_064F]


title: Weight_stable [ID116_019F]


title: Weight_gain [ID125_045F]


title: Weight_gain [ID108_076F]


title: Weight_stable [ID113_002F]


title: NP2

source_name: Normal Pituitary

value: Normal Pituitary

value: Autopsy


title: Weight_stable [ID106_065F]


title: NP3


title: Weight_stable [ID097_001F]


title: Sporadic NFPA4


title: NP5


title: OCI-LY3 6H_1

description:
RNA180105AD_1_LY3_6h
RNA180105AD_RAW_1_LY3_6h_300AZ_S13_L005

tag: cell line

value: diffuse large B-cell lymphoma (DLBCL)  cell line

value: AZ5576 at 300 nM for 6hrs


title: Plasma 500uL BiooScientific NextFlex

city: Boston

first: SAUMYA

last: Das

state: MA

address: 185 Cambridge Street

institute: MGH

description: Total extracellular RNA

data_processing:
The raw sequence image files from the Illumina HiSeq 2500 or Illumina MiSeq in the form of .bcl are converted to the fastq format using bcltofastq v1.8.4 and checked for quality to ensure the quality scores do not deteriorate drastically at the read ends. The adapters from the 3’ end are clipped using cutadapt v.1.10 [28] (http://cutadapt.readthedocs.io/en/stable/guide.html). Reads shorter than 15 nts are discarded and after adapter trimming, the 3’ bases below a quality score of 30 are trimmed as well.
Reads that arise from human rRNA and contamination from library preparation protocols are removed before they are mapped to the human genome. The reads are first mapped to a library of UniVec contaminants, a collection of common vector, adapter, linker and PCR primer sequences collated by the NCBI. They are then mapped to human rRNA sequences obtained from NCBI The reads are mapped to the rRNA and UniVec sequences using Bowtie2 [29] and those that map are removed from the analysis. The alignment to the human genome and transcriptome takes place in two stages. First, the rRNA and UniVec free reads are mapped to the human genome (hg19) using STAR [30]. The reads that map to the genome are then mapped to the human transcriptome. Also, the reads that are not mapped to the human genome are mapped to the human transcriptome, The library for the human transcriptome is built by concatenating miRNAs and hairpins from miRBase 21 [31], tRNAs from gtRNAdb [32], piRNAs from piRBase v1.0 [33], protein-coding, non-coding and and other RNA sequences from ENSEMBL 75. The STAR alignment is performed end to end with a single mismatch allowed while mapping and each read is allowed to multimap to at most 40 RNA annotations. Here, there is no mismatch allowed and each read is allowed to multimap to at most 40 RNA annotations.
Genome_build: hg19
Supplementary_files_format_and_content: text files with normalized counts

source_name: Plasma

growth_protocol: A large pool of plasma (30 mL) was used for comparison of kits and input volumes. Whole blood was collected from normal healthy volunteers in EDTA tubes, spun at 2500 rpm to separate plasma. Plasma was pooled, and 1 mL aliquots placed in tubes and stored at –80° C. The appropriate number of tubes were combined and isolated for each comparison. For example, for the 5 mL input volume, 5 aliquots were selected and the RNA isolated (using miRVana Paris, ThermoFisher AM1556, with modifications [25] and sample preparation for sequencing performed.

extract_protocol:
RNA was isolated (using miRVana Paris, ThermoFisher AM1556.
Illumina TruSeq Small RNA Library Preparation: Small RNA libraries were generated using Illumina TruSeq Small RNA Sample kit (RS-200-0048; Illumina). The reagents were utilized with the following modifications. The 3’ adapter, 5’ adapter, Stop Solution, RNase Inhibitor and RT primer were diluted by 50% with water [25]. During PCR amplification, the Index primer and RNA PCR primer volumes were reduced by 50% and the volume replaced with water. PCR amplification was performed based on the upper and lower recommendation of the kits. A total of 16 cycles for the 10 ng starting material and 11 cycles for the 1 μg starting material. The libraries were then run in a 6% TBE Gel for 55 minutes at 140 volts and the between 140 to 160bp were excised from the gels. These gel pieces were fractured into smaller pieces and allowed to incubation on a rotator overnight in water. Then an ethanol precipitation was performed to precipitate the RNA and the resulting pellet of RNA was resuspended in 11ul of ultra pure water. BiooScientific NEXTFlex Small RNA Library Preparation: Small RNA libraries were generated using NEXTFlex Small RNA Library Prep Kit v2 (Cat #5132-03). The manufacturer’s instructions where followed through PCR amplification. The optional stop point was used post the RT reaction prior to clean up and PCR amplification. In regards to PCR amplification the 1 μg samples received 12 cycles and the 10 ng sample received 18 cycles. Following PCR amplification, the libraries where then run in a 6% TBE Gel for 30 minutes at 200 volts and the between 150 to 170bp were excised from the gels. At this point there was a divergence from the manufactures instruction, an ethanol precipitation was used in place of the recommenced bead purification.  The resulting pellet of RNA was resuspended in 11 μl of ultra pure water.

value: Plasma


title: Weight_gain [ID089_055F]


title: Weight_stable [ID101_054F]


title: Sporadic NFPA2


title: Plasma 5 mL BiooScientific NextFlex

description: Total extracellular RNA


title: Sporadic NFPA3


title: Plasma 3 mL Illumina TruSeq

description: Total extracellular RNA


title: Weight_gain [ID094_014F]


title: NP4


title: NP1


title: Weight_stable [ID107_029F]


title: Sporadic GH4


title: Plasma 200uL Illumina TruSeq

description: Total extracellular RNA


title: Plasma 3 mL BiooScientific NextFlex

description: Total extracellular RNA


title: Plasma 2 mL BiooScientific NextFlex

description: Total extracellular RNA


title: Plasma 2 mL Illumina TruSeq

description: Total extracellular RNA


title: AIPneg  familial NFPA2


title: Plasma 200uL BiooScientific NextFlex

description: Total extracellular RNA


title: Weight_stable [ID085_074F]


title: Weight_stable [ID084_077F]


title: Plasma 500uL Illumina TruSeq

description: Total extracellular RNA


title: Infected A549 by Mycobacterium tuberculosis(CAS1-DELHI)[TLR]

city: Tehran

first: Shima

last: Hadifar

address: 12th Farvardin Ave, Jomhhoori St

department: Mycobacteriology and Pulmonary Research

country: Iran

institute: Pasteur Institute of Iran

description:
Test
SAMPLE 2

data_processing:
RT2 Profiler PCR Array Data Analysis Webportal was applied (https://www.qiagen.com/ir/resources/geneglobe/).
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target ? Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control

label: SYBR Green

source_name: adenocarcinomic human alveolar basal epithelial cell

label_protocol: The qRT-PCR was performed by RT² Profiler? PCR Array kits (QIAGEN) which including RT² Profiler? PCR Array Human Toll-Like Receptor Signalling Pathway (QIAGEN, Cat.No. PAHS-018ZF-2)according to the manufacturer?s instructions. Quantitative real-time PCR were performed (Light Cycler 96, Roche) with 40cycles at 95 oC for 15 sec and 55oC for 40sec ,72oC for 30sec

extract_protocol: Total RNA from infected and mock cells were extracted using a commercial RNA extraction kit (QIAGEN, USA, Cat.No.74104,) according to the manufacturer?s instructionsThe CDNA was synthesized using RT2 First Strand CDNA synthesis kit (QIAGEN, Cat.No.330401) according to the manufacturer?s instructions.

tag: activation agent

value: CAS1-DELHI genotype

tag: time

value: 3 days


title: Plasma 1 mL Illumina TruSeq

description: Total extracellular RNA

tag: cell type


title: A549 [TLR]

description:
Control
SAMPLE 1

value: adenocarcinomic human alveolar basal epithelial cell

value: control


title: Infected A549 by Mycobacterium tuberculosis(NEW-1)[TLR]

description:
Test
SAMPLE 3

value: NEW-1 genotype


title: AIPneg  GH3


title: Sporadic GH1


title: Sporadic GH2


title: Plasma 1 mL BiooScientific NextFlex

description: Total extracellular RNA


title: AIPneg  GH1


title: Sporadic NFPA1


title: Weight_gain [ID082_038F]

tag: tissue

value: White adipose tissue

value: female


title: AIPneg  GH2


title: Weight_stable [ID081_022F]


title: Weight_stable [ID043_006F]


title: Weight_stable [ID054_047F]


title: AIPneg  familial NFPA1


title: Weight_stable [ID028_058F]


title: Weight_stable [ID075_069F]


title: Weight_stable [ID037_049F]


title: Weight_stable [ID023_005F]


title: Weight_stable [ID038_003F]


title: AIPpos GH2

value: Positive


title: KO-12h-8

city: Hang Zhou

first: Juan

last: Liu

address: 866 Yuhangtang Road

institute: Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University

description: Gene expression in infected Hfe KO BMDMs for 12 h

hyb_protocol: pre-hybridization: 1)Assembled  CustomArray™ microarray with Hybridization Cap and Clips； 2)Fill the hybridization chambers with nuclease-free water.Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation. 3)Incubate at 65°C for 10min. 4)Remove the microarray from the incubator and bring to room temperature.Remove the adhesive tape and aspirate the water out of the hybridization chambers. 5)Fill the hybridization chambers with Pre-hybridization Solution.Mix gently by pipetting.A small air bubble can be introduced to improve the mixing process if the arrays are rotated.Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape. 6)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation. Hybridization: 1)Prepare the hybridization solution with labeled mRNA target . 2)Denature the hybridization solution at 95°C for 3 minutes, and then cool for 20 seconds on ice.Remove the hybridization solution from ice and keep it at room temperature. 3)Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed. 4)Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers. 5)Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting.A small air bubble wil form, and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven. 6)Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue, and cover the solution portals with adhesive tape. 7)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation. Hybridization washing: 1)Remove the microarray from the hybridization oven.Remove the adhesive tape and pipet the hybridization solution out of the chambers. 2)Using the Wash solution 1, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 1 from the hybridization chambers. 3)Using the Wash solution 2, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 2 from the hybridization chambers. 4)Using the Wash solution 3, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 3 from the hybridization chambers. 5)Repeat step one more time for a total of two washings with the Wash solution 3.

scan_protocol: Imaging is done by laser scanner GenePix4000B(Molecular Device). At first, remove the microarray from the clamp and place it horizontally. Then cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip cover it, taking care not to introduce air bubbles. At last, load the microarray into the scanner to scan.

data_processing: Raw signals were normalized with subtract background correction and quantile normalization method, Normalized intensities were transformed to gene expression log2 value. Ratio and log2 ratio of normalized spot intensites between test sample and control sample were calculated. The p-values are calculated with ANOVA Method(O'Mahony, Michael (1986). Sensory Evaluation of Food: Statistical Methods and Procedures. CRC Press. pp. 487. ISBN 0-8247-7337-3). It means the probability of control sample and test sample are no differential expression. So, if p-value (Differentially expressed) is greater than thethreshold it means no differential expression was observed.

source_name: BMDMs of mouse

label_protocol:
1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.
2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA.
3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.
4. In Vitro Transcription to Synthesize Amino Allyl-Modified aRNA with aaUTP generates multiple copies of amino allyl-modified aRNA from the double-stranded cDNA templates; this is the amplification step.
5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the aRNA and to facilitate NHS ester coupling or subsequent enzymatic reactions.
6.aRNA:Dye Coupling Reaction takes place between the amino allyl-modified UTP residues on the aRNA and amine reactive Cy5 dyes.
7. Dye Labeled aRNA Purification removes free dye and exchanges the buffer with Nuclease-free Water.

growth_protocol: BMDMs were obtained from femurs and tibias of WT and Hfe KO mice and were cultured for 4 days in DMEM supplemented with 30% (vol/vol) L929 cell-conditioned (ATCC) medium, 20% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 1% essential and nonessential amino acids, and 100 U/mL penicillin/streptomycin.

extract_protocol:
1. For proper amount of cells or homogenized tissue, add 1mL of TRIzol reagent and mix by briefly vortex. Stand for 5 mins at room temperature. If a lot of insoluble material exists after homogenization and room-temperature incubation, remove by centrifugation at 12, 000Xg for 10 mins at 4ºC. Transfer the supernatant to a fresh tube.
2. Add 200ul chloroform for 1ml mixture and vortex for 15 sec. Then stand for 5 mins at room temperature.
3. Centrifuge the mixture for 15 min at ≥12000xg at 4ºC.
4. Transfer the aqueous phase (the upper layer containing RNA) to a fresh tube.
5. Add equal volume of 100% Isopropanol to the aqueous phase, mix by inverting the tube several times.
6. Incubate at ‐20ºC for ≥30 min.
7. Centrifuge at 13000 rpm for 15 min at 4ºC.
8. Wash the pellet with 80% EtOH, invert the tube several times. Centrifuge at 7500 rpm for 5 min at -4ºC.
9. Carefully discard the supernatant without touching the pellet, dry the pellet at room temperature.
10. Dissolve the pellet with 20‐30ul DEPC-treated H2O, based on the size of the pellet. RNA solution should be stored at -80ºC.

treatment_protocol: BMDMs were inoculated with H7N9 virus for 6h and 12h

tag: strain

value: BALB/C

value: Hfe KO

tag: infection

value: avian influenza influenza A (H7N9) virus

value: BMDM


title: KO-6h-7

description: Gene expression in infected Hfe KO BMDMs for 6 h


title: G193_A405_A7_donor7_PBMC_Silicon_T4_9 (silicon_t4; donor7)

city: Thunder Bay

first: Bradley

last: Vis

address: 955 Oliver Rd

country: Canada

institute: Lakehead University

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Scanning of a Affymetrix GeneChip Human Gene 1.1 ST array plates was carried out according to standard Affymetrix protocols on a GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the robust microarray analysis (RMA) algorithm.

source_name: Peripheral blood mononuclear cells from fresh single leukocyte cones

label_protocol: Total RNA (100ng per sample) was labeled by Whole-Transcript  Sense  Target  Assay  (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated from fresh single leukocyte cones (National Blood Service, Cambridge, UK) using density gradient centrifugation. Isolated cells were rested for 2 h prior to treatment. Human PBMC assays were approved by the University of Cambridge Human Biology Research Ethics Committee (ref. HBREC.2015.10)

extract_protocol: Immediately after incubation period, RNA was collected using an RNeasy Mini kit (Qiagen, #74104) according to the manufacturer's suggested protocol with no exceptions

treatment_protocol: Cells were suspended in RPMI + 10% FCS to 1 x 106 cells/mL containing saline or ultrasmall silica nanoparticles (DV0.5 = 3.6 +/- 0.5 nm, at 150 uM Si). Cells were incubated for 4 h and RNA was immediately collected. RNA was also collected from cells prior to separation and treatment (i.e. at time 0).

tag: subject id

value: donor 7

value: ultrasmall silica nanoparticle (3.6 +/-0.5 nm, 150 uM Si), RNA collected after 4 h incubation


title: KO-6h-6


title: KO-0h-5

description: Gene expression in non-infected Hfe KO BMDMs

value: non-infected


title: Weight_stable [ID021_044F]


title: G193_A405_H5_donor7_PBMC_None_T4_8 (none_t4; donor7)

tag: treatment

value: saline, RNA collected after 4 h incubation


title: G193_A405_D5_donor6_PBMC_None_T0_4 (none_t0; donor6)

value: donor 6

value: none, RNA collected at time 0


title: G193_A405_E5_donor6_PBMC_None_T4_5 (none_t4; donor6)


title: AIPpos  GH5

value: Macroadenoma

value: Freshly frozen


title: AIPpos GH3


title: G193_A405_G5_donor7_PBMC_None_T0_7 (none_t0; donor7)


title: Weight_gain [ID018_059F]


title: AIPpos  GH6


title: Weight_stable [ID012_066F]


title: G193_A405_F5_donor6_PBMC_Silicon_T4_6 (silicon_t4; donor6)


title: AIPpos  GH4


title: Infected A549 by Mycobacterium tuberculosis(NEW-1)  [NFkB]

description:
Test
SAMPLE 3

data_processing:
RT2 Profiler PCR Array Data Analysis Webportal was applied (https://www.qiagen.com/ir/resources/geneglobe/).
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control

label_protocol: The qRT-PCR was performed by RT² Profiler™ PCR Array kit (QIAGEN) which including RT² Profiler™ PCR Array Human NFkB Signalling Pathway Plus  (QIAGEN, Cat.No. PAHS-025YF-2)according to the manufacturer’s instructions. Quantitative real-time PCR were performed (Light Cycler 96, Roche) with 40cycles at 95 oC for 15 sec and 55oC for 40sec ,72oC for 30sec

extract_protocol: Total RNA from infected and mock cells were extracted using a commercial RNA extraction kit (QIAGEN, USA, Cat.No.74104,) according to the manufacturer’s instructionsThe CDNA was synthesized using RT2 First Strand CDNA synthesis kit (QIAGEN, Cat.No.330401) according to the manufacturer’s instructions.

value: adenocarcinomic human alveolar basal epithelial cell

value: 3 days


title: AIPpos GH1


title: WT-6h-3

description: Gene expression in infected WT BMDMs for 6 h

value: WT


title: G193_A405_B5_donor5_PBMC_None_T4_2 (none_t4; donor5)

value: donor 5


title: Weight_stable [ID006_039F]

value: White adipose tissue

value: female


title: WT-6h-4

value: BALB/C


title: Weight_stable [ID005_007F]


title: Weight_gain [ID011_046F]


title: Weight_gain [ID002_032F]


title: Plasma 5 mL Illumina TruSeq

description: Total extracellular RNA

value: Plasma


title: Infected A549 by Mycobacterium tuberculosis(CAS1-DELHI)  [NFkB]

description:
Test
SAMPLE 2

value: CAS1-DELHI genotype


title: WT-12h-2

description: Gene expression in infected WT BMDMs for 12 h

value: avian influenza influenza A (H7N9) virus

value: BMDM


title: A549 [NFkB]

description:
Control
SAMPLE 1

value: control


title: G193_A405_C5_donor5_PBMC_Silicon_T4_3 (silicon_t4; donor5)

value: ultrasmall silica nanoparticle (3.6 +/-0.5 nm, 150 uM Si), RNA collected after 4 h incubation


title: WT-0h-1

description: Gene expression in non-infected WT BMDMs

value: non-infected


title: G193_A405_A5_donor5_PBMC_None_T0_1 (none_t0; donor5)

value: none, RNA collected at time 0


title: Sporadic GH3

value: Negative

value: Macroadenoma


title: miRNA [5077.1]

status: Public on Apr 12 2018

city: Sydney

first: Fatemeh

last: Vafaee

state: UNSW

address: Gate 11 Botany Street, UNSW Sydney, School of BABS

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description:
test
5077.1

data_processing: MiRNAs that are missing in > 50% of samples were excluded to acquire acceptable distribution of non-detects for down-stream analysis. Quantile normalization was used to adjust for technical variability across multiple samples.  Missing data was imputed using the nearest-neighbour method (KNNimpute). The pre-processing of miRNA cycle quantification (Cq) values from quantitative RT-qPCR assays were performed using MATLAB 2014b, Bioinformatics Toolbox and Statistics Toolbox.

source_name: plasma, pre-treatment

label_protocol: Global profiling of miRNAs in the plasma samples was carried out using the BioTrove OpenArray platform (Applied Biosystems), according to the manufacturer’s instructions. For each sample, two RT reactions were performed using MegaPlex RT primer pools A and B (Applied Biosystems) on a LabNet Multigene Gradient with 40 cycles of 2 minutes at 16°C, 1 minute at 42°C, and 1 second at 50°C, followed by 5 minutes at 85°C. The entire RT reaction was used for preamplification. Preamplification was carried out on a ViiA 7 instrument (Applied Biosystems) using MegaPlex RT preamplification primer Pools A and B and MegaPlex preamp Master Mix (Applied Biosystems) under the following conditions: 10 minutes at 95°C, 2 minutes at 55°C, 2 minutes at 72°C, followed by 16 cycles of 15 seconds at 95°C, and 4 minutes at 60°C. Preamplification reactions were then incubated at 99.9°C for 10 minutes and cooled to 4°C. The resultant cDNA was diluted, and this frozen at -20°C until further use. The diluted cDNA was thawed, combined with the OpenArray real-time PCR Master Mix and loaded onto the OpenArray miRNA panel plates (Applied Biosystems) using the AccuFill autoloader. The loaded plates were run on the BioTrove OpenArray realtime PCR instrument (Flinders Medical Centre, SA) and run according to the default protocol for reaction conditions.

extract_protocol: Total RNA was isolated from plasma using the MirVana PARIS microRNA isolation kit (Ambion/Applied Biosystems), according to the manufacturer's instructions.

tag: tumour stage (ajcc 7th edition)

tag: primary site

value: rectum

tag: gender

value: male

value: FOLFOX

tag: ethnicity

value: caucasian


title: miRNA [2.1]

description:
test
2.1

tag: overall survival (months)

tag: age


title: miRNA [3.1]

description:
test
3.1

value: colon


title: miRNA [1.1]

description:
test
1.1


title: miRNA [14.1]

description:
test
14.1


title: miRNA [7.1]

description:
test
7.1


title: miRNA [10.1]

description:
test
10.1


title: miRNA [12.1]

description:
test
12.1

value: female

value: FOLFOX/cetuximab


title: miRNA [5.1]

description:
test
5.1


title: miRNA [11.1]

description:
test
11.1

value: FOLFOX/bevacizumab


title: miRNA [16.1]

description:
test
16.1


title: miRNA [8.1]

description:
test
8.1

value: asian


title: miRNA [4.1]

description:
test
4.1


title: miRNA [5064.1]

description:
test
5064.1


title: miRNA [5071.1]

description:
test
5071.1


title: miRNA [5067.1]

description:
test
5067.1

value: 5FU de Gramont


title: miRNA [5070.1]

description:
test
5070.1


title: miRNA [5073.1]

description:
test
5073.1


title: miRNA [6.1]

description:
test
6.1

value: rectosigmoid


title: miRNA [9.1]

description:
test
9.1


title: Weight_stable [ID001_078F]

tag: weight status

value: White adipose tissue

tag: genotype


title: miRNA [5063.1]

description:
test
5063.1


title: miRNA [5062.1]

description:
test
5062.1


title: miRNA [5060.1]

description:
test
5060.1


title: miRNA [5059.1]

description:
test
5059.1


title: miRNA [5056.1]

description:
test
5056.1


title: miRNA [5055.1]

description:
test
5055.1


title: miRNA [5053.1]

description:
test
5053.1


title: miRNA [5050.1]

description:
test
5050.1


title: miRNA [5049.1]

description:
test
5049.1


title: miRNA [5054.1]

description:
test
5054.1


title: miRNA [5052.1]

description:
test
5052.1


title: miRNA [5061.1]

description:
test
5061.1


title: miRNA [5048.1]

description:
test
5048.1


title: miRNA [5046.1]

description:
test
5046.1


title: miRNA [5044.1]

description:
test
5044.1


title: miRNA [5042.1]

description:
test
5042.1


title: miRNA [5043.1]

description:
test
5043.1

value: 5FU Roswell Park


title: miRNA [5041.1]

description:
test
5041.1


title: miRNA [5039.1]

description:
test
5039.1


title: miRNA [5040.1]

description:
test
5040.1

value: capecitabine


title: miRNA [5057.1]

description:
test
5057.1


title: miRNA [5036.1]

description:
test
5036.1


title: miRNA [5033.1]

description:
test
5033.1


title: miRNA [5038.1]

description:
test
5038.1


title: miRNA [5035.1]

description:
test
5035.1


title: miRNA [5031.1]

description:
test
5031.1


title: miRNA [5030.1]

description:
test
5030.1


title: miRNA [5034.1]

description:
test
5034.1


title: miRNA [5028.1]

description:
test
5028.1


title: miRNA [5045.1]

description:
test
5045.1


title: miRNA [5027.1]

description:
test
5027.1


title: miRNA [5032.1]

description:
test
5032.1


title: miRNA [5023.1]

description:
test
5023.1


title: miRNA [5021.1]

description:
test
5021.1

value: FOLFIRI


title: miRNA [5017.1]

description:
test
5017.1


title: miRNA [5015.1]

description:
test
5015.1


title: miRNA [5025.1]

description:
test
5025.1


title: miRNA [5037.1]

description:
test
5037.1


title: miRNA [5024.1]

description:
test
5024.1

value: XELOX


title: miRNA [5014.1]

description:
test
5014.1


title: miRNA [5013.1]

description:
test
5013.1


title: miRNA [5012.1]

description:
test
5012.1


title: miRNA [5008.1]

description:
test
5008.1


title: miRNA [5007.1]

description:
test
5007.1


title: miRNA [5029.1]

description:
test
5029.1


title: miRNA [5006.1]

description:
test
5006.1


title: miRNA [5005.1]

description:
test
5005.1


title: miRNA [5001.1]

description:
test
5001.1

value: FOLFOX/panitumumab


title: miRNA [5004.1]

description:
test
5004.1


title: miRNA [5003.1]

description:
test
5003.1


title: miRNA [5002.1]

description:
test
5002.1

value: rectum

value: 5-FU de Gramont


title: miRNA [5026.1]

description:
test
5026.1

value: male


title: miRNA [5020.1]

description:
test
5020.1

value: FOLFOX

value: caucasian


title: Lung_36N_72hr

city: Utrecht

first: Devanjali

last: Dutta

state: Netherlands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired-end reads from Illumina sequencing were aligned to the human transcriptome genome and C. parvum transcriptome genome (Iowa strain) by BWA. ).
DeSeq (v1.18.0) was used for read normalization and differential expression analysis (p-value adjustment 0.05 by method Benjamini-Hochberg
Gene set enrichment analysis (GSEA) was performed using gene lists for type I interferon response and regulation against normalized RNA-seq reads of injected SI and lung organoids using GSEA software v3.0 beta2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized RNA sequencing data using DEseq2

source_name: Human airway epithelial organoids

extract_protocol:
Same number of oocysts were injected in the organoids in one drop of Matrigel. Total RNA was extracted from organoids in 1-2 drops of Matrigel using RNeasy Micro Kit (Qiagen) according to manufacturer’s protocol including DNaseI treatment. To normalize, 1ng GFP messenger RNAwas added to each sample during RNA extraction.
RNA libraries were prepared for sequencing using Cel-Seq2 protocol

value: lung

value: normal epithelia

tag: hours post-infection

value: 72 hours


title: Lung_116N_24hr

value: 24 hours


title: Lung_36N_24hr


title: Lung_42N_72hr


title: Lung_42N_24hr


title: miRNA [5011.1]

description:
test
5011.1

value: 5FU de Gramont


title: SI_DM_D76_72hr

source_name: Human small intestinal organoids

value: duodenum


title: SI_DM_D72_72hr


title: SI_DM_D74_72hr


title: HumanCellLineSplit_Barcoded_CG_NS500556

first: Ryan

middle: M

last: Mulqueen

address: 3181 SW Sam Jackson Park Rd

department: Molecular and Medical Genetics

institute: Oregon Health and Science

description:
HumanCellLineSplit_Barcoded_CG.bed.gz
The index read is 30 bp long and contains the cell barcode sequence.

data_processing:
Reads were processed using bcl2fastq (Illumina Inc., v2.19.0) with the “--create-fastq-for-index-reads” and “--with-failed-reads” options to produce fastq files.
Fastq reads were then identified by indexes, requiring each index (the two 10-nt indexes introduced by PCR, and the 11-nt index introduced by tagmentation) to independently be within a Hamming distance of two from the expected reference sequences.  Reads with all three indexes assigned  had the respective reference index sequences concatenated to a barcode and appended to the  read name, which served as the cell identifier.
Reads were then trimmed using TrimGalore! (v0.4.0) with option “-a AGATCGGAAGAGC” to identify adapters.
Alignment to the human (GRCh37), or mouse (GRCm38) genome was performed with Bismark (v0.14.3) using “--bowtie2” and “--unmapped” options
Aligned reads were then de-duplicated based on barcode, chromosome, and starting position.
Methylation information was extracted using bismark_methylation_extractor command with "--merge_non_CpG" option from Bismark (v0.14.3)
Genome_build: For Homo sapiens organism experiment: GRCh37. For Mus musculus organism experiment: GRCm38
Supplementary_files_format_and_content: Tab-delimited bed files. For "HumanCellLineSplit_Barcoded_CG" fields are:<Chromosome><Start><End><Barcode><Percent Methylation><Count Methylated><Count Non-methylated> <Cell-Specific Barcode> <Library Preparation Condition> <Tn5 Tracked Condition>. For "MouseCortex_Barcoded" files: <Chromosome> <Start> <End> <Count Methylated> <Count Non-Methylated> <Cell-Specific Barcode> <Mouse Sampled>.
Supplementary_files_format_and_content: The tar archive contains supplemental files including code to split read by index, cell barcode information provided in the barcodes*txt files and a README file with further explanation.

source_name: HEK293, GM12878 and Primary Fibroblast Tissue Culture

growth_protocol: Tissue culture cell lines (GM12878, Coriell; HEK293, ATCC CRL-1554; Primary Fibro., inguinal fibroblast, GM05756, Coriell, passage 7) were cultured in 5% CO2 at 37 C. GM12878 cells were grown in Roswell Park Memorial Institute media (RPMI, Gibco, Cat. 11875093) supplemented with 15% (by volume) fetalbovine serum (FBS, Gibco, Cat. 10082147), 1X L-glutamine (Gibco, Cat. 25030081), 1X Penicillin-Streptomycin (Gibco, Cat. 15140122), and gentamicin (Gibco, Cat. 15750060). HEK293 cells were grown in Dulbecco's Modified Eagle's media (DMEM, Gibco, Cat. 11995065), supplemented with 10% FBS, and 1X L-glutamine. Primary Fibroblasts were cultured in a growth medium comprised of DMEM/F12 (with GlutaMax; Thermo Fisher), 10% fetal bovine serum (FBS; Thermo Fisher), 1% MEM Non-Essential Amino Acids (Thermo Fisher), and 1% Penicillin/Streptomycin (Thermo Fisher). Adherent cell lines were grown to ~90% confluency at the time of harvest.

extract_protocol:
Sample preparation and nuclei isolation. For library preparation, cells were pelleted if cultured in suspension, or trypsinzed (Gibco, Cat. 25200056), if adherent. Cell were washed once with ice cold PBS and carried through cross-linking (for the xSDS method) or directly into nuclei preparation using nuclei isolation buffer (NIB, 10mM TrisHCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% Igepal, 1X protease inhibitors (Roche, Cat. 1187358001)).  Cortical samples were cut with a sterile razor blade and resuspended in a chilled 5mL modified nuclei isolation buffer (NIB-HEPES, 20mM HEPES, 10mM NaCl, 3mM MgCl2, 0.1% Igepal, 1X protease inhibitors). Cells were given 5 minutes to equilibrate to the salt solution before 5 loose strokes in a dounce homogenize, another 5 minutes to equilibrate, another 5 loose strokes and 10 tight strokes. Nuclei were then spun in a pre-chilled 4C centrifuge for 5 minutes at 600xg.
Cross-linking and SDS nucleosome depletion (xSDS): Cells were cross-linked by incubation in 10 mL of media with 1.5% formaldehyde (final conc. by vol.) and incubated at room temperature for 10 minutes with gentle agitation. Cross-linking was quenched with 800 uL 2.5 M glycine and incubated on ice for 5 minutes. Cells were then spun down, washed with ice-cold PBS, and resuspended in ice cold NIB for a 20 minute incubation on ice with gentle agitation. Cells were then pelleted, washed with 900 uL of 1X NEBuffer 2.1m and resuspended in 800 uL 1X NEBuffer 2.1 with 0.3% SDS (Sigma, Cat. L3771) and incubated at 42 ˚C with vigorous shaking for 30 minutes in a thermomixer (Eppendorf). 200 uL of 10% Triton-X was added to quench, and the solution was incubated at for another 30 minutes at 42 ˚C with vigorous shaking. Nuclei were then taken into the combinatorial indexing protocol.
Combinatorial indexing via tagmentation: Nuclei were stained with 8uL of 5mg/mL DAPI (Thermo Fisher, Cat. D1306) and passed through a 35-um cell strainer. A 96-well plate was prepared with 10 uL of 1X TD buffer diluted with NIB in each well. Fluorescence-assisted nuclei sorting (FANS) was performed with a Sony SH800 flow sorter to sort 2,500 single nuclei into each well in fast sort mode (Supplementary Fig. 24). 4uL of 500 nM transposome, pre-loaded with cytosine-depleted, uniquely indexed, custom oligonucleotides were placed in each well (described in supplement, transposomes assembled as described in Amini et. al. 2014. Reactions were incubated at 55˚C for 20 minutes. All wells were then pooled and stained with DAPI as done for the first FANS sort. A second 96-well plate was prepared with each well containing digestion reagents as described by the manufacturer’s protocol for the EZ-96 DNA Methylation MagPrep Kit (Zymo, Cat. D5040) at one-fifth the volumes (for 5 uL per well). 22 post-tagmentation nuclei from the pool of all reactions were sorted into each well using the single-cell sorting setting. Some wells were selected to receive only 10 nuclei, to allow for unmethylated controls. The plate was then spun down at 600 x g for 5 minutes at 4˚C. Library preparation. Prior to bisulfite conversion, several wells, which only received 10 nuclei in the final sort, were spiked with ~35 pg of the prepared unmethylated control DNA, to keep DNA mass constant per well. Nuclei were then processed following manufacturer’s protocol for the EZ-96 DNA Methylation MagPrep Kit, with volumes reduced to one-fifth those described by the manufacturer to allow for single-well reaction processing, and other slight modifications. Following the final post-bisulfite library cleanup, each well was eluted in 25 uL of Zymo M-Elution Buffer and transferred to a well in a 96-well plate prepared with the following reaction mixture for linear amplification: 16 uL PCR-clean ddH2O, 5 uL 10X NEBuffer 2.1 (NEB, Cat. B7202), 2 uL 10 mM dNTP mix (NEB, Cat. N0447), and 2 uL of 10 uM random nonamer primer with a partial sequence of the Illumina Standard Read 2 sequencing primer (9NP, 3’-NNNNNNNNNAGATCGGAAGAGCACACGTCTG-5’). To render libraries single stranded prior to linear amplification, reactions were heat shocked at 95˚C for 45 seconds and then flash cooled on ice. Following cooling, 10 U Klenow (3’->5’ exo-) polymerase (Enzymatics, Cat. P7010-LC-L), was added to each reaction and followed by incubation at 4 ˚C for 5 minutes, then a slow ramp of +1 ˚C/15 seconds, and 37 ˚C for 90 minutes. This was repeated for 2-4 times dependent on library and in accordance with previously describe scWGBS protocols (Supplementary Fig. 1). For each repetition, 1 uL 10 uM 9NP, 1 uL 10 mM dNTP mix, 1.25 4X NEBuffer 2.1, and 10 U Klenow (3’ -> 5’ exo-) polymerase was added after the heat shock and cooling. Following completion of linear amplifications, wells were cleaned with 1.1X (by volume) of 18% PEG SPRI Bead mixture (Sera-Mag SpeedBeads (GE, Cat. 65152105050250) washed and resuspended in 18% PEG 8000 (by mass), 1M NaCl, 10mMTris-HCl, pH 8.0, 1mM EDTA, 0.05% Tween-20), with a 5 minute room temperature incubation, then placed on a magnetic rack until the supernatant was cleared. The supernatant was discarded, and beads were washed with 80% ethanol while held in place by the magnets. Beads were then dried and libraries were eluted in 21 uL 10 mM Tris-Cl (pH 8.5). The full 21 uL eluate was then placed into a 96-well plate prepared with a PCR reaction mixture containing 25 uL 2X KAPA HiFi HotStart ReadyMix (Kapa, Cat. KK2602), 2 uL of 10 uM forward and reverse uniquely indexed primers (each introducing a 10-nt indexing sequence), and 0.5 uL of 100X SYBR Green I (FMC BioProducts, Cat. FC-121-1031). Real time PCR was performed on a Bio-Rad CFX thermocycler with the following conditions: 95°C for 2 minutes, (94°C for 80 seconds, 65°C for 30 seconds, 72°C for 30 seconds [Image]) for 18-22 cycles. PCR was stopped once libraries reached the inflection point of measured SYBR green fluorescence. Following PCR, libraries were then pooled by column (10 uL/well) and with 0.8X (by volume) 18% PEG SPRI Bead Mixture as described previously. Libraries were eluted off the magnetic beads in 25 uL of 10 mM Tris-Cl (pH 8.5). A detailed step-by-step protocol can be found as a Supplementary Protocol document associated with this manuscript.

tag: experiment

value: Human Cell Line Split

value: mixed human cell lines

tag: barcoded cell count

tag: dinucleotide

value: CG


title: Lung_116N_72hr

tag: tissue

tag: cell type


title: SI_DM_D76_24hr


title: SI_DM_D74_24hr


title: SI_DM_D72_24hr


title: AuditoryNerve_Noise_7Day_rep2

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Targets (12.5 ug) were hybridized to Affymetrix Mouse 430 2.0 GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files were imported into Affymetrix Expression Console software and data were normalized by: 1) RMA to obtain probe set expression values, and 2) MAS5 to obtain probe set detection calls. Exression data underwent a preliminary analysis to identify genes that were different between males and females. These genes were excluded from downstream analysis that identified genes affected as a function of noise exposure.

source_name: Auditory nerve, adult, 7 days after noise exposure

label_protocol: Total RNA (50 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME).  All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle.  Mice of both genders were used in the study.  All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.

extract_protocol: Total RNA was prepared from microdissected cochlear tissue containing auditory nerve using the RNeasy Minikit (Qiagen). Total RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

treatment_protocol: Young adult male and female mice (aged 5 weeks to 12 weeks) were exposed to noise (8-16 kHz octave-band noise at 106 dB SPL for 2 hours). At 0, 1, 7 or 14 days after noise exposure, animals were anesthetized, euthanized, and cochleas were collected. Microdissection was performed to remove the outer bony cochlear shell, cochlear lateral wall, and the majority of sensory epithelium, thereby preserving the modiolus portion of the cochlea where the auditory nerve is located.

tag: strain

value: CBA/CaJ

value: auditory nerve

value: Female

tag: noise exposure

value: 8-16 kHz octave-band, 106 dB SPL, 2 hours

tag: time

value: 7 Days after noise


title: AuditoryNerve_Noise_14Day_rep1

source_name: Auditory nerve, adult, 14 days after noise exposure

value: Male

value: 14 Days after noise


title: AuditoryNerve_Noise_14Day_rep3


title: AuditoryNerve_Noise_Immediate_rep3

source_name: Auditory nerve, adult, immediately following noise exposure

value: 0 Days after noise


title: AuditoryNerve_Noise_7Day_rep3


title: AuditoryNerve_Noise_Immediate_rep1


title: AuditoryNerve_Noise_1Day_rep1

source_name: Auditory nerve, adult, 1 day after noise exposure

value: 1 Days after noise


title: AuditoryNerve_Noise_14Day_rep2


title: AuditoryNerve_Noise_1Day_rep2


title: AuditoryNerve_control_rep2

source_name: Auditory nerve, adult, without noise exposure


title: AuditoryNerve_control_rep1


title: AuditoryNerve_Noise_1Day_rep3


title: AuditoryNerve_Noise_Immediate_rep2


title: AuditoryNerve_Noise_7Day_rep1


title: 2i mESCs replicate 1

city: Ghent

first: Sabitri

last: Ghimire

address: De Pintelaan 185

department: Reproductive Medicine

country: Belgium

institute: Ghent University Hospital

description:
2i1
cell culture

hyb_protocol: Labeled RNA was hybridized to a commericial expression microarray (Agilent ID G4858A-028005)

scan_protocol: Arrays were scanned using the Agilent G2565CA Microarray Scanner and Scan Control Software 8.5 according to the manufacturer's instructions.

data_processing:
Probe intensities were extracted using Feature Extraction software (Agilent).
Probe intensities were background corrected and normalized (quantile normalization) using the LIMMA package in R.

source_name: 2i mESCs

label_protocol: Total RNA (100ng) was labeled using the low input Quick Amp WT labeling kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini Kit following the Manufacturer's instruction. RNA was quantified using Qubit® RNA assay Kit on Qubit® 1.0 Fluorometer (Invitrogen).

tag: protocol

tag: pluripotency state

value: Ground

tag: passage number

value: ESC


title: AuditoryNerve_control_rep3

tag: gender


title: 2i mESCs replicate 4

description:
2i4
cell culture


title: 2i mESCs replicate 3

description:
2i3
cell culture


title: mEpiSCs replicate 3

description:
EpiSCI
cell culture

source_name: mEpiSCs

value: Activin A + bFGF

value: Primed


title: LIF serum replicate 4

description:
LSFF2
cell culture

source_name: LIF serum

value: LIF +serum

value: Naive


title: LIF serum replicate 3

description:
LSFF1
cell culture


title: 2iSB mESCs replicate 1

description:
2iSB1
cell culture

source_name: 2iSB mESCs


title: 2iSB mESCs replicate 2

description:
2iSB2
cell culture


title: 2iSB mESCs replicate 3

description:
2iSB4
cell culture


title: 2iSB mESCs replicate 4

description:
2iSB5
cell culture


title: mEpiSCs replicate 1

description:
EpiSCB
cell culture


title: 2i mESCs replicate 2

description:
2i2
cell culture


title: mEpiSCs replicate 4

description:
EpiSC4
cell culture


title: HumanCellLineSplit_Barcoded_CG_ST-E00107

description:
HumanCellLineSplit_Barcoded_CG.bed.gz
The index read is 31 bp long and contains the cell barcode sequence.

value: Human Cell Line Split

value: mixed human cell lines


title: mEpiSCs replicate 2

description:
EpiSCF
cell culture


title: HumanCellLineSplit_Barcoded_CG_G00144

value: CG


title: LIF serum replicate 2

description:
LS2
cell culture


title: LIF serum replicate 1

description:
LS1
cell culture


title: Sca1neg

city: San Francisco

first: Ysbrand

last: Nusse

address: 513 Parnassus Ave

institute: UCSF

description:
Sca-1- crypt cells  (Non-Granuloma)
Single Cell RNAseq
26 bp Read, 8 bp I7 Index, and 98 bp Read2.

data_processing:
Downstream analysis of the results was performed using the Seurat package (v2.0)44,45. Samples were merged after read depth correction, with cells expressing less than 200 genes and genes detected in less than 10 cells filtered out. Variable gene expression was then assessed in the filtered dataset after correction for mitochondrial gene expression, and unsupervised tSNE clustering was performed. Cluster identity was then determined using the DoHeatmap function of the Seurat package and published lists28,31 of markers for various intestinal crypt cell types
Genome_build: mm10
Supplementary_files_format_and_content: Matrix file of reads per cell, and individual clusters

molecule: polyA RNA

source_name: Intestinal crypt epithelium

growth_protocol: Primary cell isolates from  in vivo intestial epithelium

extract_protocol:
Cell suspensions of live Sca1+ and Sca1- sorted cells were submitted for molecular barcoding onto the Chromium Controller apparatus (10X Genomics)
Single cell cDNA libraries were prepared using the Single Cell 3' v2 Library Kit (10X Genomics, PN-120236/37/62) following the manufacturer's recommendations. The resulting single-indexed RNA-seq libraries were loaded at 300 pM on an Illumina HiSeq 4000, and paired-end sequenced using 10X Genomics specific run parameters: 26 bp Read, 8 bp I7 Index, and 98 bp Read2

treatment_protocol: Sca-1+ or Sca-1– crypt cells were sorted from one mouse infected with H. polygyrus for 6 days.

value: Intestinal crypt epithelium

value: non-granuloma

tag: infection status

value: 6d H Polygyrus infection

tag: cell markers


title: Sca1pos

description:
Sca-1+ crypt cells (Granuloma)
Single Cell RNAseq
26 bp Read, 8 bp I7 Index, and 98 bp Read2.

value: granuloma


title: CG rhizomes treated by 2 hours of dehydration, biological rep3

city: Praha 6 - Ruzyně

first: Pavel

last: Svoboda

state: Česká republika

address: Drnovská 507/73

department: Molecular Genetics

country: Czech Republic

institute: Crop Research Institute in Prague

description: Gene expressiond data from couch grass rhizomes under mild dehydration stress

hyb_protocol: The RNA samples were hybridized to an Affymetrix 22K Barley1 GeneChip Genome Array

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The microarray raw data were subjected to pre-processing analysis using functions provided with the Affy package library. Subsequently, the RMA method was implemented to achieve normalization and to eliminate background noise and processing artefacts. An iterative median polishing procedure was used to summarize the data and to generate a single expression value for each probe set. Differentially transcribed genes (DTGs) were defined as those for which the difference in transcript abundance was at least two fold; these were identified using a linear model for microarray analysis provided within the LIMMA library package. Pairwise analyses of treated vs. parallel non-treated samples were accomplished, applying a P value threshold of 0.05.

organism: Elymus repens

source_name: CG rhizomes under D2

label_protocol: Standard controls provided by the supplier were included and B2 oligonucleotides were added to each hybridization cocktail. PolyA controls (lys, phe, thr, dap) and hybridization controls (BioB, BioC, BioD and Cre) were used to monitor labeling and hybridization.

growth_protocol: CG rhizomes were collected from the field (trials were carried out in Prague-Ruzyně - local soil type Orthic Luvisol; average conditions of the field from the day of collection: 14.1°C; wind 8.3m/s; rainfall 1.2mm), washed and cut into 2 cm segments, centered on a single node (the meristematic section of the segment).

extract_protocol: The frozen material was used as a source of RNA, extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and purified using an RNeasy column in the presence of DNase (Qiagen, Hilden, Germany). The RNA's quality was assessed through both agarose gel electrophoresis and the use of an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA was extracted from three rhizome segments per treatment and each sample was represented by three independent replicates.

treatment_protocol: Non-treated segments were snap-frozen in liquid nitrogen and stored at -80°C, and the remaining were subjected to a range of dehydration treatments, comprising exposure to either 2 h, 4.5 h, 8 h and 22 h at 28°C, chosen to simulate an episode of, respectively, mild, medium, severe and lethal dehydration.

value: meristematic region of couch grass rhizomes


title: CG rhizomes treated by 8 hours of dehydration, biological rep3

description: Gene expressiond data from couch grass rhizomes under severe dehydration stress

source_name: CG rhizomes under D8


title: miRNA [5065.1]

description:
test
5065.1

tag: tumour stage (ajcc 7th edition)

tag: primary site

value: rectum

value: male

tag: age

tag: treatment

value: FOLFOX/bevacizumab

tag: ethnicity

value: caucasian


title: CG rhizomes treated by 4.5 hours of dehydration, biological rep2

description: Gene expressiond data from couch grass rhizomes under medium dehydration stress

source_name: CG rhizomes under D4.5


title: CG rhizomes treated by 2 hours of dehydration, biological rep2


title: CG rhizomes treated by 2 hours of dehydration, biological rep1


title: CG rhizomes treated by 8 hours of dehydration, biological rep1


title: CG rhizomes treated by 4.5 hours of dehydration, biological rep1


title: CG rhizomes treated by 4.5 hours of dehydration, biological rep3


title: non-treated CG rhizomes, biological rep2

description: Gene expression data from non-treated couch grass rhizomes

source_name: CG rhizomes under D0


title: CG rhizomes treated by 8 hours of dehydration, biological rep2


title: Nicotiana benthamiana Stage 12 replicate 2

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn
Contigs mapped to Nicotiana tabacum mRNA, and secondarily to Arabidopsis thaliana.  Read counts for mapped contigs were tested for differential expression between stages using DESeq in R.
Supplementary_files_format_and_content: Nicotiana_Means_SDs_DEb.xls: Mean contig read counts, differential expression test results, and associations by similarity to Arabidopsis thaliana genes

organism: Nicotiana benthamiana

source_name: Nectary tissue

extract_protocol:
Six species of tobacco (Nicotiana rustica  [PI-34752; Accession TR-16]; Nicotiana glauca [PI-282690; Accession TW-54]; Nicotiana benthamiana [PI-555684; Accession TW-17]; Nicotiana clevelandii [PI-555490; Accession TW-31]; Nicotiana plumbaginifolia [PI-302476; Accession TW-107]; Nicotiana bonariensis [PI-555489; Accession TW-28]) seeds were obtained from Tobacco Germplasm Collection North Carolina State University Oxford NC 27565 (https://npgsweb.ars-grin.gov/).  These seeds were initially sewn in a single 24-cm pot of Sungro professional growing mix at high density.  After approximately 20 days, the seedlings reached ~15 cm tall. Subsequently individual plants were transplanted to separate 30-cm pots of Sungro mix.  The plants were grown to maturity under 16 h day/ 8 h night conditions until flowering.  Flowers were staged as described in Koltunow, et al., [Plant Cell 2(12): 1201-1224(1990)].  RNA samples were isolated from floral nectaries at floral stages:  Stage 6 [immature; beginning of metabolic switch]; Stage 9 [immature; pre-secretory], Stage 12 [mature flowers at anthesis] and Stage PF [post-fertilization].  All nectary tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina HiSeq 2500 sequencing. Seventy-five TruSeq RNA v2 libraries were created (triplicate samples for nectaries at four timepoints each from six independent species, plus 3 control libraries from Nicotiana plumbaginifolia (leaves, ovaries, and stems) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two full lanes. This generated 200 M reads for each lane and the average quality scores were above Q30.
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

value: nectary

tag: developmental stage

value: stage 12


title: Nicotiana benthamiana Stage 9 replicate 2

tag: tissue

value: stage 9


title: Nicotiana benthamiana Post secretory replicate 3

value: Post secretory


title: Nicotiana benthamiana Stage 12 replicate 1


title: Nicotiana benthamiana Post secretory replicate 1


title: Nicotiana benthamiana Stage 9 replicate 3


title: Nicotiana benthamiana Stage 9 replicate 1


title: Nicotiana benthamiana Stage 12 replicate 3


title: Nicotiana benthamiana Post secretory replicate 2


title: Nicotiana benthamiana Stage 6 replicate 1

value: stage 6


title: non-treated CG rhizomes, biological rep1


title: non-treated CG rhizomes, biological rep3


title: G1- alpha Factor rep3

city: Oxford

first: Hannah

middle: E

last: Mischo

address: South Parks Road

department: Dunn School of Pathology

institute: University of Oxford

description:
Sample 12
BMS-HM-B3_S5.R1

data_processing:
library strategy: NET-seq
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
Bedgraphs are generated by mapping the 3' end of the read corresponding to the position of RNA pol II
NET-seq data have been normalized by uniquely mapping million mapped reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph, Chromosome, Start, End, Score

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: samples 1-3 were grown in minimal complete media and arrested with 0.15 µg/ml alpha factor (sample 2) or 15 µg/ml nocodazole (sample 3) for 2-2.5hrs, prior to harvest and processing according to the NET-seq protocol. Samples 4 and 5 were induced for 3.5 hrs with 2% galactose prior to harvest and processing according to the NET-seq protocol.

extract_protocol:
For NET-seq frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
For NET-seq a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScript III, Invitrogen) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.

tag: cell type

value: G1- alpha Factor

tag: molecule subtype

value: nascent RNA


title: G2/M- nocodazole rep3

description:
Sample 13
BMS-HM-C2_S7.R1

value: G2/M- nocodazole


title: asynchronous rep3

description:
Sample 11
BMS-HM-A5_S10.R1

value: asynchronous


title: Sen1 rep2

description:
Sample 10
BMS-HM-S2_S3.R1


title: Empty vector rep2

description:
Sample 9
BMS-HM-E2_S2.R1

value: Empty vector


title: Nicotiana benthamiana Stage 6 replicate 2


title: G2/M- nocodazole rep2

description:
Sample 8
BMS-HM-C1_S6.R1


title: Nicotiana benthamiana Stage 6 replicate 3


title: G1- alpha Factor rep2

description:
Sample 7
BMS-HM-B1_S4.R1


title: donor liver sample 3 post-reperfusion in ischemia-free liver transplantation

city: Guangzhou

first: Xiaoshun

last: He

address: NO.58 Zhongshan Er Road

department: Organ Transplant Center

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Liver

extract_protocol:
Liver samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type


title: donor liver sample 2 post-reperfusion in ischemia-free liver transplantation


title: MouseCortex_Barcoded_CG & CH_NS500556

city: Portland

description:
MouseCortex_Barcoded_CG.bed.gz
MouseCortex_Barcoded_CH.bed.gz
The index read is 30 bp long and contains the cell barcode sequence.

source_name: Sixty-day old mouse cortices

growth_protocol: All animal studies were approved by the Oregon Health and Science University Institutional Animal Care and Use Committee. C57BL/6J mice were obtained from Jackson Laboratory (stock number 000664). Sixty-day-old C57BL/6J mice were deeply anesthetized using isoflurane. After decapitation the brain was removed and the entire cortex isolated and placed in ice cold PBS.

tag: experiment

value: Mouse Cortex

value: cortex

tag: strain

tag: barcoded cell count

tag: dinucleotide

value: CG & CH


title: donor liver sample 1 at end of preservation in ischemia-free liver transplantation


title: donor liver sample 3 post-reperfusion in conventional liver transplantation


title: donor liver sample 3 at end of preservation in ischemia-free liver transplantation


title: donor liver sample 2 at end of preservation in ischemia-free liver transplantation


title: donor liver sample 3 at end of preservation in conventional liver transplantation


title: donor liver sample 1 at end of preservation in conventional liver transplantation


title: donor liver sample 1 post-reperfusion in conventional liver transplantation


title: asynchronous rep2

description:
Sample 6
BMS-HM-A4_S9.R1


title: Nicotiana clevelandii Post secretory replicate 3

organism: Nicotiana clevelandii


title: Nicotiana clevelandii Post secretory replicate 2


title: donor liver sample 1 post-reperfusion in ischemia-free liver transplantation


title: donor liver sample 2 at end of preservation in conventional liver transplantation