title: T400L_2

city: beijing

first: Huanyong

last: Li

address: xiangshan road

institute: Chinese  academy of forestry

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: The 'common' table includes only those genes expressed in all samples

organism: Nitraria sibirica

source_name: leaf

growth_protocol: The seedlings were grown in the greenhouse at 25±3°C under 14-h days/20±2°C under 10-h nights

extract_protocol:
RNA extracted were used TRNzol accoding to the instruction of TIANGEN（Beijing,China）
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NaCl at a concentration of 50 mM/day was added to avoid osmotic shock and to allow the plants to express their acclimation potential; treatments were initiated such that all treatments reached their target concentration of 0， 100 or 400 mM at the same time. Treated for 3 days.

value: leaf

value: 400 mM NaCl treated 3 days


title: T400L_3

status: Public on Apr 18 2018

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment


title: T400L_1


title: 9312.Gtype

type: genomic

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

description: 9312: L15

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Genomic DNA extracted from ham muscle was genotyped using Illumina Porcine SNP60v2 BeadChip.

molecule: genomic DNA

organism: Sus scrofa

source_name: Ham muscle

label_protocol: Not provided

growth_protocol: Danish Landrace male pigs were slaughtered at 100 kg. Ham muscle samples were collected by punch biopsies, genomic DNA was extracted by Qiagen DNA Minikit and subjected to Illumina Porcine 60K v2 chip

extract_protocol: Punch biopsy at slaughterhouse and Qiagen DNA Minikit

treatment_protocol: Danish Landrace males pigs were categorised into low, medium and high summarised EBVs of skatole and human nose scores, derived from the sires of each pig.

tag: gender

value: male

tag: group

value: low boar taint

value: Ham muscle


title: 3309.Gtype

description: 3309: L10


title: 3102.Gtype

description: 3102: L8


title: 8311.Gtype

description: 8311: L13


title: T100L_2

value: 100 mM NaCl treated 3 days


title: 1127.Gtype

description: 1127: L4


title: T100L_3


title: T0L_3

value: 0 mM NaCl treated 3 days


title: 3109.Gtype

description: 3109: L16


title: 1105.Gtype

description: 1105: L2


title: T0L_1


title: AsPC-1_ANG/hRNase5_1hr

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

country: USA

institute: M.D. Anderson Cancer Center

data_processing:
Use Life Technologies software Life Scope 1.3.1 to process raw SOLiD xsq files, map to human transcriptome (hg19), and generate whole transcriptome read counts and normalized RPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each sample

organism: Homo sapiens

growth_protocol: cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM)/F12 or RPMI 1640 medium (for pancreatic cancer cell lines) supplemented with 10% fetal bovine serum and antibiotics

extract_protocol: Total RNA were extracted using TRIzol Reagent, following the user guide from the manufacturer (Life Technologies #15596018).

treatment_protocol: cells were treated with EGF or ANG/hRNase5 at a concentration of 50 ng/ml and 1 ug/ml respectively in serum-starved conditions for 1hr, 5hr and 24hr

tag: cell line

tag: cell type

value: pancreatic cancer cell line

tag: treated with

value: ANG/hRNase5 1hr


title: voz1 voz2_14d_LD_rep2

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression in 14 day-old voz1 voz2 seedlings grown under long day (LD, 16h light / 8h dark).

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent Arabidopsis thaliana Gene Expression Microarray 8x60K (AMADID No: 37661) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

organism: Arabidopsis thaliana

source_name: voz1 voz2_14 day-old_LD

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Plants were grown on Murashige and Skoog agar medium (Himedia), stratified for 3 days in dark at 4 °C, and then transferred to LDs (16 h light/8 h dark) at 22 °C. Light intensity was ~130 μmol m-2 s-1.

extract_protocol: Total RNA was isolated from 14 day-old Col-0 and voz1 voz2 LD-grown seedlings using the Spectrum Plant Total RNA Isolation Kit  (Sigma, USA) according to manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent Bioanalyzer (Agilent, USA).

tag: ecotype background

tag: genotype/variation

value: voz1 voz2

tag: age

value: 14 day-old

value: Whole seedlings


title: Col-0_14d_LD_rep1

description: Gene expression in 14 day-old Col-0 seedlings grown under long day (LD, 16h light / 8h dark).

source_name: Col-0_14 day-old_LD

value: wild type


title: voz1 voz2_14d_LD_rep1


title: T100L_1


title: 1137.Gtype

description: 1137: L5


title: L5_I3_BAS_G7

status: Public on Apr 17 2018

city: Irvine

first: Kai

last: Kessenbrock

state: CA

address: 839 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

data_processing:
After demultiplexing sequencing libraries to individual cell FASTQ files (observed average read depth per cell was found to be ~1.6 Million reads), each library was aligned to an indexed GRCh38 RefSeq genome using RSEM version 1.2.1242, and bowtie2 version 2.2.3 with the following options enabled: rsem-calculate- expression -p $CORES -- bowtie2 -- paired-end -output- genome-bam. Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were quantified and concatenated into a resulting gene expression matrix for each library
Genome_build: GrCH38
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts expression matrices corresponding to each of the libraries generated from the 3 individuals in this study

molecule: polyA RNA

source_name: Mammoplasty Reduction

extract_protocol:
Viable organoids were thawed and washed using DMEM, and digested with 0.05% trypsin (Corning 25-052-CI) containing DNase (Sigma Aldrich D4263-5VL) to generate single cell suspension. Cells were stained for FACS using fluorescently labeled antibodies for CD31 (eBiosciences 48-0319-42), CD45 (eBiosciences 48-9459-42), EpCAM (eBiosciences 50-9326-42), CD49f (eBiosciences 12-0495-82), SytoxBlue (Life Technologies S34857). We only proceeded with samples showing at least 80% viability as measured using SytoxBlue in FACS
Sorted cells were washed and resuspended at a concentration of approximately 500 cells/µl. For microfluidics-enabled scRNAseq, cell suspensions were mixed with Fluidigm C1 Suspension Reagents (Fluidigm 100-5315) at a ratio of 8:2 before loading mix onto C1 chip (Fluidigm 100-5760). Bright field images of captured cells were collected using a Keyence BZ-X710 microscope (Keyence Corporation, Itasca, Illinois, USA). Single-cell RNA isolation and amplification were performed using the Fluidigm C1 Single Cell Auto Prep IFC following the Fluidigm Protocol: 100-7168 I1. RNA spike-in controls were omitted. cDNA library preparation were performed following the Fluidigm C1 Protocol: 100-7168 I1. Reagents Kits v2 User Guide: CG00052 Rev B.     Quantification of cDNA libraries was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA chips (Agilent. 5067-4626). Quantification of library construction was performed using KAPA qPCR (Kapa Biosystems KK4824). For microfluidics-enabled scRNAseq libraries, we generally multiplexed 96 cells per lane on an Illumina HiSeq2500 resulting in a calculated depth of ~1.6 million reads per cell (Illumina Rapid PE kit v2 402-4002 and Rapid SBS kit v2 FC 401-4022).

treatment_protocol: Samples were washed in PBS (Corning 21-031-CV) and mechanically dissociated using a razor blade. Dissociated samples were digested overnight in DMEM (Corning 10-013-CV) with Collagenase Type I, 2 mg/mL (Life Technologies 17100-017). Viable organoids were separated using differential centrifugation and viably frozen in 50% FBS (Omega Scientific FB-12), 40% DMEM, and 10% DMSO (Sigma-Aldrich D8418) by volume.

tag: Sex

value: female

value: Adult Human Breast Epithelium

tag: location

value: Basal


title: L5_I3_BAS_H2


title: L5_I3_BAS_G10


title: L5_I3_BAS_H8


title: L5_I3_BAS_G9


title: L5_I3_BAS_G6


title: L5_I3_BAS_F5


title: L5_I3_BAS_H12


title: L5_I3_BAS_F6


title: L5_I3_BAS_F2


title: L5_I3_BAS_H5


title: L5_I3_BAS_F12


title: L5_I3_BAS_F3


title: L5_I3_BAS_G1


title: L5_I3_BAS_F11


title: L5_I3_BAS_G8


title: L5_I3_BAS_G11


title: L5_I3_BAS_G5


title: L5_I3_BAS_G12


title: L5_I3_BAS_G3


title: L5_I3_BAS_H1


title: L5_I3_BAS_G2


title: L5_I3_BAS_F1


title: Col-0_14d_LD_rep2


title: L5_I3_BAS_F8


title: L5_I3_BAS_F10


title: L5_I3_BAS_F7


title: L5_I3_BAS_F9


title: L5_I3_BAS_F4


title: L5_I3_BAS_E11


title: L5_I3_BAS_E12


title: L5_I3_BAS_E3


title: L5_I3_BAS_E7


title: T0L_2


title: L5_I3_BAS_E10


title: L5_I3_BAS_D2


title: L5_I3_BAS_D9


title: L5_I3_BAS_D10


title: L5_I3_BAS_E2


title: L5_I3_BAS_D1


title: L5_I3_BAS_D3


title: L5_I3_BAS_D11


title: L5_I3_BAS_D4


title: L5_I3_BAS_C12


title: L5_I3_BAS_E4


title: L5_I3_BAS_E8


title: L5_I3_BAS_D12


title: L5_I3_BAS_E6


title: L5_I3_BAS_C10


title: L5_I3_BAS_D8


title: L5_I3_BAS_D7


title: L5_I3_BAS_D6


title: L5_I3_BAS_C11


title: L5_I3_BAS_C9


title: L5_I3_BAS_C7


title: L5_I3_BAS_D5


title: L5_I3_BAS_C8


title: L5_I3_BAS_C6


title: L5_I3_BAS_C3


title: L5_I3_BAS_C2


title: L5_I3_BAS_B12


title: L5_I3_BAS_B10


title: L5_I3_BAS_C1


title: L5_I3_BAS_B8


title: L5_I3_BAS_B9


title: L5_I3_BAS_B6


title: L5_I3_BAS_B7


title: L5_I3_BAS_B11


title: L5_I3_BAS_B5


title: L5_I3_BAS_B4


title: L5_I3_BAS_B1


title: L5_I3_BAS_A9


title: L5_I3_BAS_A11


title: L5_I3_BAS_B3


title: L5_I3_BAS_B2


title: L5_I3_BAS_A4


title: L5_I3_BAS_A7


title: L5_I3_BAS_A2


title: L5_I3_BAS_A3


title: L5_I3_BAS_A10


title: L5_I3_BAS_A12


title: L5_I3_BAS_A8


title: L5_I3_BAS_A5


title: L5_I3_BAS_A1


title: L3_I3_BAS_H11


title: L3_I3_BAS_H12


title: L3_I3_BAS_H6


title: L3_I3_BAS_H8


title: L5_I3_BAS_A6


title: L3_I3_BAS_H5


title: L3_I3_BAS_H3


title: L3_I3_BAS_H2


title: L3_I3_BAS_H1


title: L3_I3_BAS_G11


title: L3_I3_BAS_G7


title: L3_I3_BAS_G5


title: L3_I3_BAS_G10


title: L3_I3_BAS_G8


title: L3_I3_BAS_G9


title: L3_I3_BAS_G3


title: L3_I3_BAS_G2


title: L3_I3_BAS_G1


title: L3_I3_BAS_F9


title: L3_I3_BAS_F7


title: L3_I3_BAS_F4


title: L3_I3_BAS_F6


title: L3_I3_BAS_F3


title: L3_I3_BAS_F10


title: L3_I3_BAS_G4


title: L3_I3_BAS_E12


title: L3_I3_BAS_E8


title: L3_I3_BAS_E11


title: L3_I3_BAS_F1


title: L3_I3_BAS_E7


title: L3_I3_BAS_E5


title: L3_I3_BAS_F5


title: L3_I3_BAS_H4


title: L3_I3_BAS_E10


title: L3_I3_BAS_E3


title: L3_I3_BAS_E4


title: L3_I3_BAS_E2


title: L3_I3_BAS_F2


title: L3_I3_BAS_D10


title: L3_I3_BAS_D9


title: L3_I3_BAS_D6


title: L3_I3_BAS_D4


title: L3_I3_BAS_E9


title: L3_I3_BAS_D7


title: L3_I3_BAS_D11


title: L3_I3_BAS_D3


title: L3_I3_BAS_D5


title: L3_I3_BAS_C12


title: L3_I3_BAS_C9


title: L3_I3_BAS_C10


title: L3_I3_BAS_D1


title: L3_I3_BAS_D2


title: L3_I3_BAS_C4


title: L3_I3_BAS_C6


title: L3_I3_BAS_C5


title: L3_I3_BAS_C11


title: L3_I3_BAS_C1


title: L3_I3_BAS_C7


title: L3_I3_BAS_B12


title: L3_I3_BAS_C3


title: L3_I3_BAS_E1


title: L3_I3_BAS_B7


title: L3_I3_BAS_B10


title: L3_I3_BAS_B9


title: L3_I3_BAS_B4


title: L3_I3_BAS_B3


title: L3_I3_BAS_B1


title: L3_I3_BAS_A10


title: L3_I3_BAS_B2


title: L3_I3_BAS_A11


title: L3_I3_BAS_A9


title: L3_I3_BAS_C8


title: L3_I3_BAS_A7


title: L3_I3_BAS_A5


title: L3_I3_BAS_A4


title: L3_I3_BAS_A6


title: L3_I3_BAS_C2


title: L3_I3_BAS_A3


title: L3_I3_BAS_A2


title: L2_I3_LUM_H3

value: Luminal


title: L2_I3_LUM_H4


title: L2_I3_LUM_G11


title: L2_I3_LUM_G12


title: L2_I3_LUM_H7


title: L2_I3_LUM_H5


title: L2_I3_LUM_H1


title: L2_I3_LUM_G10


title: L3_I3_BAS_B6


title: L2_I3_LUM_G7


title: L2_I3_LUM_G6


title: L2_I3_LUM_G5


title: L2_I3_LUM_G4


title: L2_I3_LUM_F11


title: L2_I3_LUM_H6


title: L2_I3_LUM_H10


title: L2_I3_LUM_G3


title: L2_I3_LUM_G1


title: L2_I3_LUM_F2


title: L2_I3_LUM_F6


title: L2_I3_LUM_F1


title: L2_I3_LUM_G2


title: L2_I3_LUM_F9


title: L2_I3_LUM_F10


title: L2_I3_LUM_F7


title: L3_I3_BAS_A1


title: L2_I3_LUM_F5


title: L2_I3_LUM_F4


title: L2_I3_LUM_F8


title: L2_I3_LUM_E5


title: L2_I3_LUM_E1


title: L2_I3_LUM_D12


title: L2_I3_LUM_F12


title: L2_I3_LUM_E10


title: L2_I3_LUM_E11


title: L2_I3_LUM_E9


title: L2_I3_LUM_E7


title: L2_I3_LUM_D11


title: L2_I3_LUM_D10


title: L2_I3_LUM_D8


title: L2_I3_LUM_E3


title: L2_I3_LUM_E4


title: L2_I3_LUM_D7


title: L2_I3_LUM_D6


title: L2_I3_LUM_D4


title: L2_I3_LUM_D2


title: L2_I3_LUM_D5


title: L2_I3_LUM_C12


title: L2_I3_LUM_C11


title: L2_I3_LUM_D1


title: L2_I3_LUM_C10


title: L2_I3_LUM_C4


title: L2_I3_LUM_C3


title: L2_I3_LUM_C7


title: L2_I3_LUM_C8


title: L2_I3_LUM_C5


title: L2_I3_LUM_D3


title: L2_I3_LUM_C2


title: L2_I3_LUM_B11


title: L2_I3_LUM_B8


title: L2_I3_LUM_C9


title: L2_I3_LUM_C6


title: L2_I3_LUM_C1


title: L2_I3_LUM_B12


title: L2_I3_LUM_B10


title: L2_I3_LUM_B9


title: L2_I3_LUM_B7


title: L2_I3_LUM_B5


title: L2_I3_LUM_B4


title: L2_I3_LUM_B2


title: L2_I3_LUM_B1


title: L2_I3_LUM_A12


title: L2_I3_LUM_A10


title: L2_I3_LUM_A9


title: L2_I3_LUM_A4


title: L2_I3_LUM_A5


title: L2_I3_LUM_B6


title: L2_I3_LUM_A8


title: L2_I3_LUM_A6


title: L2_I3_LUM_A2


title: L1_I3_BAS_H8


title: L1_I3_BAS_G11


title: L1_I3_BAS_G12


title: L2_I3_LUM_A1


title: L1_I3_BAS_H7


title: L1_I3_BAS_H1


title: L1_I3_BAS_H9


title: L1_I3_BAS_H2


title: L1_I3_BAS_H3


title: L1_I3_BAS_G8


title: L1_I3_BAS_G3


title: L1_I3_BAS_G9


title: L1_I3_BAS_G7


title: L1_I3_BAS_G2


title: L1_I3_BAS_F8


title: L1_I3_BAS_F12


title: L1_I3_BAS_G1


title: L2_I3_LUM_A11


title: L1_I3_BAS_F10


title: L1_I3_BAS_F7


title: L1_I3_BAS_F9


title: L1_I3_BAS_F6


title: L1_I3_BAS_H4


title: L1_I3_BAS_F5


title: L1_I3_BAS_E12


title: L1_I3_BAS_F3


title: L1_I3_BAS_E8


title: L1_I3_BAS_E5


title: L1_I3_BAS_D12


title: L1_I3_BAS_F11


title: L1_I3_BAS_D10


title: L1_I3_BAS_E7


title: L1_I3_BAS_E9


title: L1_I3_BAS_E6


title: L1_I3_BAS_E1


title: L1_I3_BAS_F1


title: L1_I3_BAS_E3


title: L1_I3_BAS_F2


title: L1_I3_BAS_E10


title: L1_I3_BAS_D7


title: L1_I3_BAS_D11


title: L1_I3_BAS_D8


title: L1_I3_BAS_E4


title: L1_I3_BAS_D6


title: L1_I3_BAS_E2


title: L1_I3_BAS_D5


title: L1_I3_BAS_D4


title: L1_I3_BAS_D9


title: L1_I3_BAS_D1


title: L1_I3_BAS_D2


title: L1_I3_BAS_D3


title: L1_I3_BAS_C12


title: L1_I3_BAS_C5


title: L1_I3_BAS_C10


title: L1_I3_BAS_C3


title: L1_I3_BAS_B12


title: L1_I3_BAS_B11


title: L1_I3_BAS_C4


title: L1_I3_BAS_C2


title: L1_I3_BAS_B10


title: L1_I3_BAS_C1


title: L1_I3_BAS_B6


title: L1_I3_BAS_B5


title: L1_I3_BAS_B8


title: L1_I3_BAS_B4


title: L1_I3_BAS_A10


title: L1_I3_BAS_A7


title: L1_I3_BAS_A8


title: L1_I3_BAS_C8


title: L1_I3_BAS_C9


title: L1_I3_BAS_A6


title: L1_I3_BAS_A12


title: L1_I3_BAS_A9


title: L1_I3_BAS_B1


title: L1_I3_BAS_A5


title: L1_I3_BAS_A4


title: L1_I3_BAS_C7


title: L1_I3_BAS_B9


title: L1_I3_BAS_B7


title: L1_I3_BAS_A3


title: L1_I3_BAS_A2


title: L1_I3_BAS_B2


title: L1_I3_BAS_A1


title: L1_I3_BAS_B3


title: L3_I2_BAS_H2


title: L3_I2_BAS_H7


title: L3_I2_BAS_H4


title: L3_I2_BAS_G12


title: L3_I2_BAS_H10


title: L3_I2_BAS_H1


title: L3_I2_BAS_G10


title: L3_I2_BAS_H6


title: L3_I2_BAS_H5


title: L3_I2_BAS_H11


title: L3_I2_BAS_G9


title: L3_I2_BAS_G8


title: L3_I2_BAS_G6


title: L3_I2_BAS_G7


title: L3_I2_BAS_G11


title: L3_I2_BAS_G5


title: L3_I2_BAS_G1


title: L3_I2_BAS_G4


title: L3_I2_BAS_H9


title: L3_I2_BAS_H8


title: L3_I2_BAS_G3


title: L3_I2_BAS_F10


title: L3_I2_BAS_F7


title: L3_I2_BAS_F6


title: L3_I2_BAS_F9


title: L3_I2_BAS_H3


title: L3_I2_BAS_F11


title: L3_I2_BAS_F5


title: L3_I2_BAS_G2


title: L3_I2_BAS_F8


title: L3_I2_BAS_E12


title: L3_I2_BAS_E9


title: L3_I2_BAS_F2


title: L3_I2_BAS_F1


title: L3_I2_BAS_E5


title: L3_I2_BAS_F3


title: L3_I2_BAS_E10


title: L3_I2_BAS_E7


title: L3_I2_BAS_E8


title: L3_I2_BAS_E4


title: L3_I2_BAS_D12


title: L3_I2_BAS_E1


title: L3_I2_BAS_D11


title: L3_I2_BAS_D9


title: L3_I2_BAS_D8


title: L3_I2_BAS_E3


title: L3_I2_BAS_D10


title: L3_I2_BAS_D6


title: L3_I2_BAS_D7


title: L3_I2_BAS_D5


title: L3_I2_BAS_C11


title: L3_I2_BAS_C12


title: L3_I2_BAS_D4


title: L3_I2_BAS_D3


title: L3_I2_BAS_D2


title: L3_I2_BAS_D1


title: L3_I2_BAS_C10


title: L3_I2_BAS_C9


title: L3_I2_BAS_E6


title: L3_I2_BAS_C7


title: L3_I2_BAS_C4


title: L3_I2_BAS_C6


title: L3_I2_BAS_C5


title: L3_I2_BAS_C1


title: L3_I2_BAS_C3


title: L3_I2_BAS_E2


title: L3_I2_BAS_B3


title: L3_I2_BAS_B2


title: L3_I2_BAS_B4


title: L3_I2_BAS_B12


title: L3_I2_BAS_B8


title: L3_I2_BAS_B9


title: L3_I2_BAS_B5


title: L3_I2_BAS_B11


title: L3_I2_BAS_B10


title: L3_I2_BAS_B6


title: L3_I2_BAS_A10


title: L3_I2_BAS_A9


title: L3_I2_BAS_A7


title: L3_I2_BAS_B7


title: L3_I2_BAS_A12


title: L3_I2_BAS_A11


title: L3_I2_BAS_A1


title: L3_I2_BAS_A6


title: L3_I2_BAS_A5


title: L3_I2_BAS_C2


title: L3_I2_BAS_A3


title: L3_I2_BAS_C8


title: L3_I2_BAS_A4


title: L2_I2_LUM_H11


title: L2_I2_LUM_H9


title: L2_I2_LUM_H10


title: L2_I2_LUM_H7


title: L2_I2_LUM_H8


title: L2_I2_LUM_H6


title: L2_I2_LUM_H5


title: L2_I2_LUM_H4


title: L2_I2_LUM_G7


title: L2_I2_LUM_G10


title: L2_I2_LUM_H3


title: L2_I2_LUM_G6


title: L2_I2_LUM_G9


title: L2_I2_LUM_H2


title: L2_I2_LUM_G4


title: L2_I2_LUM_F12


title: L2_I2_LUM_F10


title: L2_I2_LUM_G2


title: L2_I2_LUM_G5


title: L2_I2_LUM_F8


title: L2_I2_LUM_F11


title: L2_I2_LUM_G1


title: L2_I2_LUM_H12


title: L2_I2_LUM_F4


title: L2_I2_LUM_F2


title: L2_I2_LUM_E12


title: L2_I2_LUM_F5


title: L2_I2_LUM_E11


title: L2_I2_LUM_E9


title: L2_I2_LUM_E8


title: L2_I2_LUM_E7


title: L2_I2_LUM_E5


title: L2_I2_LUM_E6


title: L2_I2_LUM_H1


title: L2_I2_LUM_E3


title: L2_I2_LUM_E4


title: L2_I2_LUM_E2


title: L2_I2_LUM_D11


title: L2_I2_LUM_F6


title: L2_I2_LUM_D12


title: L2_I2_LUM_D8


title: L2_I2_LUM_D6


title: L2_I2_LUM_E1


title: L2_I2_LUM_D10


title: L2_I2_LUM_E10


title: L2_I2_LUM_D7


title: L2_I2_LUM_D2


title: L2_I2_LUM_C12


title: L2_I2_LUM_D5


title: L2_I2_LUM_D9


title: L2_I2_LUM_D4


title: L2_I2_LUM_C11


title: L2_I2_LUM_D1


title: L2_I2_LUM_C7


title: L2_I2_LUM_C8


title: L2_I2_LUM_D3


title: L2_I2_LUM_C5


title: L2_I2_LUM_C6


title: L2_I2_LUM_C4


title: L2_I2_LUM_C3


title: L2_I2_LUM_C2


title: L2_I2_LUM_B12


title: L2_I2_LUM_B9


title: L2_I2_LUM_B11


title: L2_I2_LUM_B7


title: L2_I2_LUM_B5


title: L2_I2_LUM_C9


title: L2_I2_LUM_B6


title: L2_I2_LUM_B2


title: L2_I2_LUM_B4


title: L2_I2_LUM_B1


title: L2_I2_LUM_B3


title: L2_I2_LUM_A5


title: L2_I2_LUM_A6


title: L2_I2_LUM_A12


title: L2_I2_LUM_A11


title: L2_I2_LUM_A8


title: L2_I2_LUM_A7


title: L2_I2_LUM_A10


title: L2_I2_LUM_C1


title: L2_I2_LUM_A9


title: L2_I2_LUM_A4


title: L2_I2_LUM_A3


title: L1_I2_BAS_H12


title: L1_I2_BAS_H7


title: L1_I2_BAS_H8


title: L1_I2_BAS_H4


title: L2_I2_LUM_A2


title: L2_I2_LUM_B10


title: L1_I2_BAS_H3


title: L2_I2_LUM_B8


title: L1_I2_BAS_H2


title: L1_I2_BAS_H1


title: L1_I2_BAS_G9


title: L1_I2_BAS_G8


title: L1_I2_BAS_G7


title: L1_I2_BAS_G4


title: L1_I2_BAS_G3


title: L1_I2_BAS_G2


title: L1_I2_BAS_G1


title: L1_I2_BAS_F9


title: L1_I2_BAS_H5


title: L1_I2_BAS_F3


title: L1_I2_BAS_F6


title: L1_I2_BAS_F2


title: L1_I2_BAS_E7


title: L1_I2_BAS_E6


title: L1_I2_BAS_E8


title: L1_I2_BAS_E9


title: L1_I2_BAS_E2


title: L1_I2_BAS_E5


title: L1_I2_BAS_F8


title: L1_I2_BAS_E1


title: L1_I2_BAS_F1


title: L1_I2_BAS_E12


title: L1_I2_BAS_D10


title: L1_I2_BAS_D12


title: L1_I2_BAS_D9


title: L1_I2_BAS_D11


title: L1_I2_BAS_F11


title: L1_I2_BAS_D6


title: L1_I2_BAS_D8


title: L1_I2_BAS_F7


title: L1_I2_BAS_D2


title: L1_I2_BAS_D3


title: L1_I2_BAS_D7


title: L1_I2_BAS_D4


title: L1_I2_BAS_D1


title: L1_I2_BAS_E3


title: L1_I2_BAS_C10


title: L1_I2_BAS_C12


title: L1_I2_BAS_C8


title: L1_I2_BAS_C9


title: L1_I2_BAS_C7


title: L1_I2_BAS_C4


title: L1_I2_BAS_C1


title: L1_I2_BAS_B11


title: L1_I2_BAS_C3


title: L1_I2_BAS_B10


title: L1_I2_BAS_B9


title: L1_I2_BAS_B6


title: L1_I2_BAS_B7


title: L1_I2_BAS_B8


title: L1_I2_BAS_B3


title: L1_I2_BAS_B4


title: L1_I2_BAS_B5


title: L1_I2_BAS_B2


title: L1_I2_BAS_A11


title: L1_I2_BAS_A10


title: L1_I2_BAS_A7


title: L1_I2_BAS_A8


title: L1_I2_BAS_A9


title: L1_I2_BAS_A1


title: L1_I2_BAS_A2


title: L1_I2_BAS_A4


title: L1_I2_BAS_A5


title: L1_I2_BAS_C2


title: L4_I1_LUM_H12


title: L4_I1_LUM_H7


title: L4_I1_LUM_H11


title: L4_I1_LUM_H4


title: L4_I1_LUM_H1


title: L4_I1_LUM_G11


title: L4_I1_LUM_G10


title: L4_I1_LUM_G5


title: L4_I1_LUM_G6


title: L4_I1_LUM_G4


title: L4_I1_LUM_G1


title: L4_I1_LUM_G2


title: L4_I1_LUM_F10


title: L4_I1_LUM_F12


title: L4_I1_LUM_F9


title: L4_I1_LUM_F8


title: L4_I1_LUM_F4


title: L4_I1_LUM_F6


title: L4_I1_LUM_F2


title: L4_I1_LUM_H10


title: L4_I1_LUM_F1


title: L4_I1_LUM_E11


title: L4_I1_LUM_E10


title: L4_I1_LUM_E8


title: L4_I1_LUM_E7


title: L4_I1_LUM_E12


title: L4_I1_LUM_H5


title: L4_I1_LUM_E3


title: L4_I1_LUM_E6


title: L4_I1_LUM_D10


title: L4_I1_LUM_D11


title: L4_I1_LUM_D8


title: L4_I1_LUM_E2


title: L4_I1_LUM_D7


title: L4_I1_LUM_D6


title: L4_I1_LUM_G3


title: L4_I1_LUM_D4


title: L4_I1_LUM_D5


title: L4_I1_LUM_E1


title: L4_I1_LUM_D3


title: L4_I1_LUM_D1


title: L4_I1_LUM_E5


title: L4_I1_LUM_C8


title: L4_I1_LUM_C11


title: L4_I1_LUM_C12


title: L4_I1_LUM_C7


title: L4_I1_LUM_C4


title: L4_I1_LUM_B12


title: L4_I1_LUM_B5


title: L4_I1_LUM_B10


title: L4_I1_LUM_B4


title: L4_I1_LUM_A12


title: L4_I1_LUM_A11


title: L4_I1_LUM_A10


title: L4_I1_LUM_A6


title: L4_I1_LUM_A5


title: L4_I1_LUM_A8


title: L4_I1_LUM_A7


title: L4_I1_LUM_A3


title: L4_I1_LUM_C6


title: L4_I1_LUM_C5


title: L3_I1_BAS_H9


title: L4_I1_LUM_A2


title: L4_I1_LUM_A1


title: L3_I1_BAS_H2


title: L3_I1_BAS_H3


title: L3_I1_BAS_H7


title: L3_I1_BAS_H1


title: L3_I1_BAS_G8


title: L4_I1_LUM_C1


title: L4_I1_LUM_B11


title: L4_I1_LUM_B6


title: L4_I1_LUM_B3


title: L4_I1_LUM_B1


title: L4_I1_LUM_B2


title: L3_I1_BAS_F9


title: L3_I1_BAS_F7


title: L4_I1_LUM_A4


title: L3_I1_BAS_F5


title: L3_I1_BAS_F1


title: L3_I1_BAS_E7


title: L3_I1_BAS_D9


title: L3_I1_BAS_E3


title: L3_I1_BAS_D7


title: L3_I1_BAS_D6


title: L3_I1_BAS_C7


title: L3_I1_BAS_D1


title: L3_I1_BAS_D5


title: L3_I1_BAS_C6


title: L3_I1_BAS_C3


title: L3_I1_BAS_C12


title: L3_I1_BAS_B7


title: L3_I1_BAS_C10


title: L3_I1_BAS_G6


title: L3_I1_BAS_B3


title: L3_I1_BAS_B2


title: L3_I1_BAS_B1


title: L3_I1_BAS_F2


title: L3_I1_BAS_A12


title: L3_I1_BAS_E2


title: L3_I1_BAS_A9


title: L3_I1_BAS_A6


title: L3_I1_BAS_A2


title: L2_I1_LUM_H11


title: L2_I1_LUM_H12


title: L2_I1_LUM_H9


title: L4_I1_LUM_B7


title: L2_I1_LUM_H8


title: L2_I1_LUM_H7


title: L2_I1_LUM_H6


title: L2_I1_LUM_H5


title: L3_I1_BAS_A4


title: L2_I1_LUM_H10


title: L2_I1_LUM_H4


title: L2_I1_LUM_H3


title: L2_I1_LUM_H2


title: L2_I1_LUM_H1


title: L2_I1_LUM_G12


title: L2_I1_LUM_G11


title: L2_I1_LUM_G10


title: brain-DH-14d-rep3

city: Hangzhou

first: shujing

last: zhang

address: Xihu district

department: College of Pharmaceutical Sciences

institute: Zhejiang University

description: total RNA

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028279 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies) with the scan settings for one-color scans.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: Rat brain,DH,14d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The Sprague Dawley (SD) rats were fed with  normal chow diet

extract_protocol: Total RNA was isolated from rat brain tissue using mirVanaTM RNA Isolation Kit and purified using the RNeasy Mini kit (Qiagen, Chatsworth, CA, USA) and RNase-free DNase Set (Qiagen, Chatsworth, CA, USA) following the manufacturer’s instructions.

treatment_protocol: 1.Sham group: sham-operated group  2.Model group:the ischemia-reperfusion group  3.Danhong group:administered with Danhong injection+ ischemia-reperfusion group

tag: strain

value: Sprague Dawley (SD)

value: brain

value: ischemia/reperfusion + Danhong injection


title: L2_I1_LUM_G8


title: brain-DH-14d-rep1

description: total RNA


title: L3_I1_BAS_G7


title: brain-DH-14d-rep2

description: total RNA


title: L2_I1_LUM_G9


title: brain-model-14d-rep3

description: total RNA

source_name: Rat brain,model,14d

value: ischemia/reperfusion


title: L2_I1_LUM_G6


title: L2_I1_LUM_G5


title: brain-model-14d-rep1

description: total RNA


title: brain-model-14d-rep2

description: total RNA


title: brain-sham-14d-rep2

description: total RNA

source_name: Rat brain,sham,14d

value: control


title: cfDNA_CRC_pool_F

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

description:
Sample name: F
Colorectal cancer (CRC) stages I and II pool F

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: serum

label_protocol: Standard Illumina labelling protocol

extract_protocol: Circulating cell-free DNA was isolated from serum samples by a phenol-chloroform protocol

value: serum from patients with colorectal cancer (CRC) stages I and II pool F

tag: molecule subtype

value: circulating cell-free DNA


title: cfDNA_CRC_pool_E

description:
Sample name: E
Colorectal cancer (CRC) stages I and II pool E

value: serum from patients with colorectal cancer (CRC) stages I and II pool E


title: cfDNA_NCF_pool_B

description:
Sample name: B
No colorectal findings (NCF) pool B

value: serum from individuals with no colorectal findings (NCF) pool B


title: cfDNA_NCF_pool_A

description:
Sample name: A
No colorectal findings (NCF) pool A

value: serum from individuals with no colorectal findings (NCF) pool A


title: L2_I1_LUM_G3


title: brain-sham-14d-rep1

description: total RNA


title: cfDNA_AA_pool_D

description:
Sample name: D
Advanced adenomas (AA) pool D

value: serum from patients with advanced adenomas (AA) pool D


title: L2_I1_LUM_G2


title: L2_I1_LUM_G1


title: brain-sham-14d-rep3

description: total RNA


title: L2_I1_LUM_F12


title: L2_I1_LUM_F11


title: L2_I1_LUM_G4


title: L2_I1_LUM_F10


title: HPCVE 106 Trypos 24 hrs, 1

city: Santiago

first: Ulrike

last: Kemmerling

address: Independencia 1027

department: Faculty of Medicine

country: Chile

institute: Universidad de Chile

description: Gene expression after 24 hrs of infection with 106 Trypomastigotes in RPMI media

hyb_protocol: Labeled samples were  hybridized with SurePrint G3 Human GE 8x60K chips  for 17 h at 60° C in an Agilent G2545A hybridization oven at 10 rpm with the instrucvions of Gene ExpressionHybridization Kit (Agilent).

scan_protocol: lides were washed with Gene Expression Wash Buffer 1 and 2 according to mannufacturer's instuctions  and scanned immediately with an Agilent microarray scanner G2565BA. The parameters used were: Scan region Agilent HD (61 × 21.6 mm),Scan resolution 5 µm, Tiff file dynamic range 20 bit, Green PMT gain 100%.

data_processing: Agilent Feature Extraction (version 9.5.1), was used for quality control, data filtering, and data normalization. Standar parameters  and Grid Template  039494_D_F_20140813 were used.  Extracted data from the SurePrintG3 8x60K chips were analyzed using GeneSpring GX 13.0 software

source_name: HPCVE Infected with 106 trypos for 24 hrs in RPMI media Placenta 1

label_protocol: 100ng of total RNA were reverse-transcribed into cDNA, the transcribed to cRNA and Cy3-labeled with Low Input Quick Amp- One color Labeling Kit (Agilent Technologies). The labeled  cRNA  was purified with Illustra RNAspin Mini Isolation kit (GE Healthcare) and the total yield was measured with Qubit RNA HS kit (ThermoFisher Scientific)

growth_protocol: HPCVE were incubated in RPMI media suplemented with 5% FBS and antibiotics (penicillin-streptomycin) at 37°C in a humid atmosphere at 5% CO2. Parasites (Trypomastigotes) from T. cruzi (Y Strain) were obtained from previously infected Vero cells (ATCC® CCL-81). The infective trypomastigotes were separated from cellular debris by low speed centrifugation (500 x g). From the supernatant, the parasites were isolated by centrifugation at 3500 x g, suspended in RPMI media  and quantified in a Neubauer Chamber.

extract_protocol: Total RNA was isolated with the PureLink RNA Mini Kit (Thermo Fisher Scientific). RNA integrity was analyzed with a Bioanalyzer 2100 (Agilent Technologie) obtaining RNA Integrity numbers (RIN) above 8 for all samples. Quantification of total RNA was performed with Qubit RNA quantification kit(Themo Fisher Scientific).

treatment_protocol: 0,5 cm3 explants were incubated in RPMI Media with 105 o 106 T. cruzi trypomastigotes (Y strain) for 2 or 24 hrs. Explants were collected in RNALater (Thermo Fisher Scientific) and stored at -80°C until RNA isolation.

value: Placenta

tag: gestational age

value: Term


title: L2_I1_LUM_F9

value: female


title: HPCVE 106 Trypos 24 hrs, 3

source_name: HPCVE Infected with 106 trypos for 24 hrs in RPMI media Placenta 3


title: LECs on soft matrix, GATA2 siRNA treated, biological rep1

city: Uppsala

first: Maike

last: Frye

address: Dag Hammarskjöldsv. 20

department: IGP

country: Sweden

institute: University Uppsala

hyb_protocol: GeneChip® ST Arrays (GeneChip® Human Transcriptome Array 2.0) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm, according to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA).

scan_protocol: The arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The raw data was normalized to exon level in Expression Console, provided by Affymetrix (http://www.affymetrix.com), using the robust multi-array average (RMA) method69,70. Subsequent analysis of the gene expression data was carried out in the statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org).

label: Biotin

source_name: HDLECs, junvenile foreskin, PromoCell C-12216

label_protocol: 10 ng of total RNA starting amount was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT Pico Reagent Kit User Manual (P/N 703262 Rev 1 Affymetrix Inc., Santa Clara, CA).

extract_protocol: Cells were trypsinized at  37°C and collected with complete medium. Cells were lysed in RLT buffer (Qiagen) and total RNA was extracted using the Qiagen RNeasy Mini Kit.

value: junvenile foreskin

value: lymphatic endothelial cells

tag: genotype

value: Gata2 sIRNA

tag: matrix condition

value: soft


title: HPCVE 105 Trypos 24 hrs, 2

description: Gene expression after 24 hrs of infection with 105 Trypomastigotes in RPMI media

source_name: HPCVE Infected with 105 trypos for 24 hrs in RPMI media Placenta 2

tag: tissue


title: HPCVE 105 Trypos 24 hrs, 1

source_name: HPCVE Infected with 105 trypos for 24 hrs in RPMI media Placenta 1


title: L2_I1_LUM_F8

value: Adult Human Breast Epithelium

value: Luminal


title: ctrl 24 hrs, 3

description: Gene expression after 24 hrs in RPMI media (uninfected control)

source_name: HPCVE Uninfected 24 hrs in RPMI media Placenta 3


title: HPCVE 106 Trypos 24 hrs, 2

source_name: HPCVE Infected with 106 trypos for 24 hrs in RPMI media Placenta 2


title: LECs on soft matrix, GATA2 siRNA treated, biological rep2


title: LECs on stiff matrix, GATA2 siRNA treated, biological rep1

value: stiff


title: ctrl 24 hrs, 1

source_name: HPCVE Uninfected 24 hrs in RPMI media Placenta 1


title: L2_I1_LUM_G7


title: L2_I1_LUM_F5


title: LECs on stiff matrix, ctrl siRNA treated, biological rep1

value: wildtype


title: L2_I1_LUM_F4


title: LECs on stiff matrix, ctrl siRNA treated, biological rep6


title: HPCVE 106 Trypos 2 hrs, 3

description: Gene expression after 2 hrs of infection with 106 Trypomastigotes in RPMI media

source_name: HPCVE Infected with 106 trypos for 2 hrs in RPMI media Placenta 3


title: HPCVE 106 Trypos 2 hrs, 1

source_name: HPCVE Infected with 106 trypos for 2 hrs in RPMI media Placenta 1


title: L2_I1_LUM_F2


title: LECs on stiff matrix, GATA2 siRNA treated, biological rep2


title: L2_I1_LUM_F1


title: L2_I1_LUM_E12


title: LECs on soft matrix, ctrl siRNA treated, biological rep5


title: LECs on stiff matrix, ctrl siRNA treated, biological rep5


title: HPCVE 105 Trypos 2 hrs, 3

description: Gene expression after 2 hrs of infection with 105 Trypomastigotes in RPMI media

source_name: HPCVE Infected with 105 trypos for 2 hrs in RPMI media Placenta 3


title: L2_I1_LUM_E10


title: HPCVE Control 2 hrs, 3

description: Gene expression after 2 hrs in RPMI media (uninfected control)

source_name: HPCVE Uninfected 2hrs in RPMI media Placenta 3


title: cfDNA_AA_pool_C

description:
Sample name: C
Advanced adenomas (AA) pool C

value: serum from patients with advanced adenomas (AA) pool C


title: L2_I1_LUM_E9

source_name: Mammoplasty Reduction


title: HPCVE 105 Trypos 2 hrs, 1

source_name: HPCVE Infected with 105 trypos for 2 hrs in RPMI media Placenta 1


title: L2_I1_LUM_E11


title: LECs on soft matrix, ctrl siRNA treated, biological rep3


title: HPCVE 105 Trypos 2 hrs, 2

source_name: HPCVE Infected with 105 trypos for 2 hrs in RPMI media Placenta 2


title: HPCVE 106 Trypos 2 hrs, 2

source_name: HPCVE Infected with 106 trypos for 2 hrs in RPMI media Placenta 2


title: HPCVE Control 2 hrs, 1

source_name: HPCVE Uninfected 2hrs in RPMI media Placenta 1


title: LECs on soft matrix, ctrl siRNA treated, biological rep6


title: L2_I1_LUM_E7


title: L2_I1_LUM_E6


title: 2o_plasmid_sequencing

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description:
Amplicon DNA sequencing of final plasmid
Synthetic construct/Homo sapiens
plasmid DNA
Processed data file reports barcode abundance in plasmid pool.

library_source: genomic

data_processing:
Reads were binned using variant specific barcodes and reads with incorrect sequence that are barcode adjacent were filtered out (custom python script)
PCR duplicates were collapsed within each bin based on the Unique Molecular Identifier after RT step (custom python script)
Reads were aligned to bin-specific references using STAR version 2.5.2b
STAR outputs were parsed to count reads supporting each isoform (custom python script)
PSI was calculated (custom python script)
Plasmid DNA was aligned using Novoalign V3.02.13
Genome_build: references are subsetted from hg19 and aligned in a variant specific way
Supplementary_files_format_and_content: Processed data files are tab separated value files containing counts for inclusion, exclusion, or other unannotated isoforms as well as Percent Spliced In (PSI) values. There is one file on a barcode specific basis and another on another on a variant specific basis.  .tsv "variant" column header format: chromosome_ hg19 variant coordinate_reference base(s)_alternate base(s).

molecule: other

source_name: pc-AT7-Glo1 with Vex-seq library in configuration 2o

growth_protocol: HepG2 cells were grown to a density of 0.5 x 10^6 per well. K562 cells were grown to a density of 1.0 x 10^6 cells per well.

extract_protocol:
RNA was extracted using the Maxwell 16 LEV simplyRNA purification kit.
Libraries were constructed using amplicon sequencing to attach Illumina compatible adaptors to regions of interest of cDNA resulting from splice reporter transcripts.

treatment_protocol:
Amplicon sequincing of isolated plasmid DNA
HepG2 cells were transfected with 1μg/mL of plasmid DNA and selected with zeocin for 8 days. K562 cells were electroporated with 5 μg of plasmid DNA and selected with 200μg/mL zeocin for 8 days.

tag: sample type

value: 2o_plasmid (final plasmid)


title: 1o_plasmid_sequencing

description:
Amplicon DNA sequencing of plasmid partway through construction
Synthetic construct/Homo sapiens
plasmid DNA
Processed data file reports correct variant barcode pairing read support.

source_name: pc-AT7-Glo1 with Vex-seq library in configuration 1o

value: 1o_plasmid (plasmid partway through construction)


title: 16572_B2B

city: Taichung

first: Jiunn-Liang

last: Ko

address: 110, Sec. 1, Chien-Kuo N. Road

country: Taiwan

institute: Institute of Medicine, Chung Shan Medical University

description: miRNA expression after the treatment with 0 mM NiCl2 for 48 h

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

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

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

source_name: bronchial epithelial cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: BEAS-2B (an SV40-immortalized human bronchial epithelial cell line) cells were cultured in serum-free LHC-9 medium (Invitrogen, Carlsbad, CA).

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BEAS-2B cells  were treated with NiCl2 (0.5 mM) for 48 h.

value: bronchial epithelial


title: HPCVE Control 2 hrs, 2

source_name: HPCVE Uninfected 2hrs in RPMI media Placenta 2


title: ctrl 24 hrs, 2

source_name: HPCVE Uninfected 24 hrs in RPMI media Placenta 2


title: L2_I1_LUM_E8


title: 16574_B2B Ni

description: miRNA expression after the treatment with 0.5 mM NiCl2 for 48 h


title: L2_I1_LUM_E5


title: LECs on stiff matrix, ctrl siRNA treated, biological rep2

source_name: HDLECs, junvenile foreskin, PromoCell C-12216


title: LECs on stiff matrix, ctrl siRNA treated, biological rep4


title: L2_I1_LUM_E3


title: L2_I1_LUM_F7


title: K562_UPF1_KD_rep2

description:
cDNA derived from RNA and report specific RT primer after UPF1 shRNA knockdown
Processed data files report 'barcode isoform count and PSI' and 'variant-specific isoform count and PSI'.

source_name: K562 erythroleukemia cell line

treatment_protocol:
Trnasduced with UPF1 shRNA and selected with puromycin for 5 days. Cells were transfected with plasmid DNA library and RNA harvested after 24 hours
HepG2 cells were transfected with 1μg/mL of plasmid DNA and selected with zeocin for 8 days. K562 cells were electroporated with 5 μg of plasmid DNA and selected with 200μg/mL zeocin for 8 days.

tag: knockdown

value: UPF1 shRNA knockdown


title: K562_UPF1_KD_rep1


title: K562_scrambled_KD_rep3

description:
cDNA derived from RNA and report specific RT primer after scrambled shRNA knockdown
Processed data files report 'barcode isoform count and PSI' and 'variant-specific isoform count and PSI'.

treatment_protocol:
Trnasduced with scrambled control shRNA and selected with puromycin for 5 days. Cells were transfected with plasmid DNA library and RNA harvested after 24 hours
HepG2 cells were transfected with 1μg/mL of plasmid DNA and selected with zeocin for 8 days. K562 cells were electroporated with 5 μg of plasmid DNA and selected with 200μg/mL zeocin for 8 days.

value: scrambled shRNA knockdown


title: L2_I1_LUM_E2


title: K562_scrambled_KD_rep1


title: L2_I1_LUM_D12


title: L2_I1_LUM_E1


title: HepG2_rep3

description:
cDNA derived from RNA and report specific RT primer
Processed data files report 'barcode isoform count and PSI' and 'variant-specific isoform count and PSI'.

source_name: HepG2 liver cancer cell line

treatment_protocol: HepG2 cells were transfected with 1μg/mL of plasmid DNA and selected with zeocin for 8 days. K562 cells were electroporated with 5 μg of plasmid DNA and selected with 200μg/mL zeocin for 8 days.


title: L2_I1_LUM_F6


title: L2_I1_LUM_D11


title: LECs on soft matrix, ctrl siRNA treated, biological rep1


title: L2_I1_LUM_E4


title: HepG2_rep1


title: L2_I1_LUM_D9


title: HepG2_rep2


title: L2_I1_LUM_D10


title: K562_rep2


title: K562_scrambled_KD_rep2


title: L2_I1_LUM_D8


title: K562_rep3


title: K562_rep1


title: L2_I1_LUM_D7


title: L2_I1_LUM_D5


title: L2_I1_LUM_D6


title: L2_I1_LUM_D4


title: L2_I1_LUM_D3


title: L2_I1_LUM_C12


title: LECs on soft matrix, ctrl siRNA treated, biological rep2


title: L2_I1_LUM_D1


title: L2_I1_LUM_D2


title: L2_I1_LUM_C11


title: L2_I1_LUM_C9


title: LECs on stiff matrix, ctrl siRNA treated, biological rep3


title: L2_I1_LUM_C10


title: LECs on soft matrix, ctrl siRNA treated, biological rep4


title: L2_I1_LUM_C8


title: L2_I1_LUM_F3


title: L2_I1_LUM_C7


title: D16Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.

label: biotin

organism: Mus musculus

source_name: Ba/F3-gp130 cells were retrovirally transduced with pMOWS expression plasmid coding for SyCyRGFP:IL-23R

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

growth_protocol: Ba/F3 cell lines were cultured in DMEM with 1% PenStrep and 10%FCS with recombinant Hyper-IL-6 (0,2% cell culture supernatant) in 10 cm cell culture plattes  and were splitted in a ratio from 1:10000 to 1:5

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: Ba/F3-gp130 cell lines were washed four times with sterile PBS and incubated in serum-free DMEM for 3 h. Equal numbers of cells (2 x 106) were stimulated with 100 ng/ml GFP-mCherry, HmIL-23 or 3xGFP and incubated for 1 h at 37°C.

value: Ba/F3 (DSMZ no.:ACC 300)

value: interleukin-3 dependent pro-B cellline


title: D14Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R


title: D19Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R


title: D17Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R


title: D15Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R


title: D20Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R


title: D13Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R


title: L2_I1_LUM_C5

value: female


title: C19Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R

source_name: Ba/F3-gp130 cells were retrovirally transduced with pMOWS expression plasmid coding for SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: L2_I1_LUM_C2


title: L2_I1_LUM_C4


title: D18Ba/F3-gp130 cells transduced with SyCyRGFP:IL-23R


title: L2_I1_LUM_C1


title: L2_I1_LUM_B11


title: C18Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: L2_I1_LUM_C6


title: C20Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: L2_I1_LUM_B12


title: L2_I1_LUM_B10


title: C16Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: B20Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant

source_name: Ba/F3-gp130 cells were retrovirally transduced with pMOWS expression plasmid coding for the IL23R and IL12Rβ1 variant


title: L2_I1_LUM_C3


title: C15Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: C17Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: C13Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: C14Ba/F3-gp130 cells transduced with SyCyRGFP:IL-12Rβ1/2A/SyCyRmCherry:IL-23R


title: B19Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant


title: L2_I1_LUM_B8


title: L2_I1_LUM_B9


title: L2_I1_LUM_B7


title: B18Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant


title: L2_I1_LUM_B6


title: L2_I1_LUM_B5


title: L2_I1_LUM_B4


title: B14Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant


title: B16Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant


title: B15Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant


title: B17Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant


title: A19Ba/F3-gp130 cells transduced with human gp130


title: L2_I1_LUM_B2


title: A20Ba/F3-gp130 cells transduced with human gp130


title: L2_I1_LUM_B3


title: L2_I1_LUM_A10


title: L2_I1_LUM_B1


title: L2_I1_LUM_A9


title: B1_2 Sidt2f/fCre mice of 2-month old

city: Shanghai

first: Huiwen

last: Zhang

address: Kongjiang Road 1665#

institute: Xinhua Hospital

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on Affymetrix Mouse Gene 2.0 ST Array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA(Robust Multi-chip Average ) method.

source_name: skeletal muscle_Sidt2 KO

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: To generate the muscle-specific Sidt2 knockout mice (Sidt2f/fCre), Sidt2 floxed mice were crossed with B6.FVB(129S4)-Tg(Ckmm-cre)5Khn/JNju transgenic mice (Model Animal Research Center of Nanjing University, China) expressing Cre recombinase under the control of muscle creatine kinase

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

value: skeletal muscle

value: Sidt2 KO

value: 2 months


title: B13Ba/F3-gp130 cells transduced with  IL23R and IL12Rβ1 variant


title: B1_1 Sidt2f/fCre mice of 2-month old


title: A16Ba/F3-gp130 cells transduced with human gp130


title: L2_I1_LUM_A8

source_name: Mammoplasty Reduction


title: A17Ba/F3-gp130 cells transduced with human gp130


title: A14Ba/F3-gp130 cells transduced with human gp130


title: A15Ba/F3-gp130 cells transduced with human gp130


title: B1_3 Sidt2f/fCre mice of 2-month old


title: A1_3 Sidt2f/f mice of 2-month old

source_name: skeletal muscle_wildtype


title: A1_1 Sidt2f/f mice of 2-month old


title: A1_2 Sidt2f/f mice of 2-month old


title: A18Ba/F3-gp130 cells transduced with human gp130


title: L2_I1_LUM_A6


title: K562_UPF1_KD_rep3


title: L2_I1_LUM_A7


title: L2_I1_LUM_A5


title: A13Ba/F3-gp130 cells transduced with human gp130


title: Adipocytes donor 2

city: Verona

first: Carmine

last: Carbone

state: Select a State or Province

address: p.zza L.A. Scuro 10

country: Italy

institute: Policlinico Universitario GB Rossi

description: replicate 4

hyb_protocol: Hybridization of cRNAs (750 ng) was carried out using Illumina Human 48k gene chips (Human HT-12 V4 BeadChip). Array washing was performed using Illumina High Temp Wash Buffer for 10’ at 55°C, followed by staining using streptavidin-Cy3 dyes (Amersham Biosciences).

scan_protocol: Standard Illumina scanning protocol. Probe intensity data were obtained using the Illumina Genome Studio software (Genome Studio V2011.1).

data_processing: Raw data were Loess normalized with the Lumi R package

source_name: Adipocytes donor 2

label_protocol: Synthesis of biotinylated cRNA was performed using the IlluminaTotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol using 500ng of total RNA.

growth_protocol: Human Bone Marrow Stromal cells were isolated from bone marrow aspirates of healthy donors (informed consent, approved by Ethical Committee of Azienda Ospedaliera Universitaria Integrata Verona; N. 1828, May 12, 2010- “Institution of cell and tissue collection for biomedical research in Onco-Hematology”). Bone marrow aspirates were cultured in 225-cm2 flasks at 5×105 nucleated cells/cm2 concentration in alpha-minimal essential medium (MEM), 10% heat-inactivated fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin (all from Gibco). After 72 h, nonadherent cells were removed and the medium was replaced twice a week. Published protocol was followed to induce adipogenic differentiation of hBMSCs 18. hBMSCs were cultured at a density of 5000~6000 cells/cm2. After reaching confluence, hBMSCs were cultured for one more week and induced in adipogenic medium containing 0.5 mM isobutyl-methylxanthine (Sigma-Aldrich), 1 μM dexamethasone (Sigma-Aldrich), 10 μM insulin (Roche), 100 μM indomethacin (Sigma-Aldrich) for three days and maintained in medium with 10 μM insulin for one day. The treatment was repeated four times, after which the cells were washed three times with PBS and maintained in DMEM without FBS for four days.

extract_protocol: Total RNA was obtained from subconfluent cells using Trizol reagent (Ambion, Warrington, UK) and following the procedures outlined by the supplier. The quality of RNA was determined by electrophoresis on agarose gel and staining with ethidium bromide, the 18S and 28S bands were visualized by ultraviolet light. Total RNA was quantified by absorbance at 260 nm.

value: adipocytes


title: hBMSC donor 1

description: replicate 1

source_name: hBMSC donor 1

value: Bone Marrow


title: hBMSC donor 2

description: replicate 3

source_name: hBMSC donor 2


title: Adipocytes donor 1

description: replicate 2

source_name: Adipocytes donor 1


title: L2_I1_LUM_A4

value: Adult Human Breast Epithelium

value: Luminal


title: L2_I1_LUM_A3


title: L1_I1_LUM_H12


title: L2_I1_LUM_A2


title: L2_I1_LUM_A1


title: L1_I1_LUM_H11


title: HG-UC MBA_6623

city: Alameda

first: Karen

middle: B.

last: Chapman

address: 1301 Harbor Bay Parkway

institute: OncoCyte Inc.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using percentile shift normalization in Genespring GX (v10.0)

source_name: Urine specimen

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Pico Labeling Kit for Illumina Expression Beadchips

extract_protocol: RNA was extracted with the MasterPure RNA Purification Kit

tag: disease state

value: HG-UC

tag: gender

value: Male

value: urine


title: HG-UC MBA_6627


title: HG-UC MBA_6631

value: Female


title: HG-UC MBA_7368

value: unavailable


title: B2B 0.5 mM NiCl2_2

hyb_protocol: Fluorescent targets were  hybridized to the Human miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber. After 16 hrs hybridization at 37 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 37 ℃ 5 mins；Wash Ⅱ37 ℃, 5 mins 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by AXON4000B scanner (635nm PMT500/power 100 ) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was process by R program. We ﬁltered out spots that the ﬂag <0. Spots that passed the criteria were normalized by 75% media scaling normalization method. Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups. The spots with log2 ratio ≥ 1 or log2 ratio ≤ -1 and P-value < 0.05 are tested for further analysis.

source_name: bronchial epithelial cell line

label_protocol: Fluorescent targets were prepared from 2.5 μg total RNA samples using miRNA ULSTM Labeling Kit (Kreatech Diagnostics, The Netherlands). Labeled miRNA targets enriched by NanoSep 100K (Pall Corporation, USA)

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

tag: cell line

tag: cell type

value: bronchial epithelial


title: HG-UC MBA_6437


title: HG-UC MBA_6633


title: HG-UC MBA_6649


title: L1_I1_LUM_H10


title: HG-UC MBA_7377


title: HG-UC MBA_6676


title: HG-UC MBA_6673


title: HG-UC MBA_6632


title: B2B 0.5 mM NiCl2_1


title: HG-UC MBA_7353


title: HG-UC MBA_6695


title: HG-UC MBA_6648


title: L1_I1_LUM_H9


title: HG-UC MBA_6439


title: L1_I1_LUM_H8


title: B2B control_1


title: B2B control_2


title: HG-UC MBA_6642


title: HG-UC MBA_7355


title: HG-UC MBA_7360


title: L1_I1_LUM_H7


title: L1_I1_LUM_H6


title: HG-UC MBA_6682


title: HG-UC MBA_6693


title: HG-UC MBA_6644


title: HG-UC MBA_7364


title: HG-UC MBA_6684


title: HG-UC MBA_6626


title: HG-UC MBA_6683


title: L1_I1_LUM_H5


title: HG-UC MBA_6643


title: L1_I1_LUM_H4


title: L1_I1_LUM_H3


title: HG-UC MBA_6692


title: Benign MBA_6625

value: Benign


title: Benign MBA_7366


title: HG-UC MBA_6638


title: HG-UC MBA_7361


title: L1_I1_LUM_H1


title: Benign MBA_6634


title: L1_I1_LUM_H2


title: Benign MBA_7357


title: L1_I1_LUM_G11


title: HG-UC MBA_6694


title: L1_I1_LUM_G10


title: L1_I1_LUM_G9


title: L1_I1_LUM_G12


title: L1_I1_LUM_G4


title: L1_I1_LUM_G7


title: L1_I1_LUM_G6


title: L1_I1_LUM_G3


title: L1_I1_LUM_G8


title: L1_I1_LUM_G5


title: L1_I1_LUM_F12


title: L1_I1_LUM_G2


title: L1_I1_LUM_G1


title: Benign MBA_6645


title: Benign MBA_6630


title: Benign MBA_6628


title: Benign MBA_6646


title: Benign MBA_7359


title: Benign MBA_6635


title: Benign MBA_6689


title: Benign MBA_6690


title: Benign MBA_6640


title: Benign MBA_6686


title: Benign MBA_6641


title: Benign MBA_7358


title: Benign MBA_7367


title: L1_I1_LUM_F11


title: Benign MBA_6647


title: L1_I1_LUM_F10


title: col680

city: Zurich

first: Tomas

last: Valenta

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

data_processing:
De-multiplexing, collapsing of unique molecular identifiers (UMIs) and alignment of reads to the Mus musculus transcriptome (GRCm38.p5 Ensembl release 89) were performed using the Cellranger toolkit (version 2.0.2) provided by 10X Genomics
Cells for which fewer than 500 genes were detected were filtered out, leaving 4,464 cells. Genes that were not detected in at least 5 cells were also discarded, leaving 15,190 genes.
Reads were normalized for each cell barcode by scaling by the total number of transcripts and multiplying by 10,000. The data was then natural-log transformed. This normalization was done with Seurat 2.1.0
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: The processed data files are read abundance measurements in TSV format with genes and barcode sequences corresponding to row and column indices

source_name: colon-Gli1-tdTomato cells

extract_protocol:
epithelial cells from Gli1-CreERT2, villin-CreERT2, lox-STOP-lox-tdTomato (24 hrs after tamoxifen) were removed by EDTA, remaining non-epithelial cells were digested with Collagenase/Dispase. Single cells mixture underwent FACS (sorting) for tdTomato-positive cells to get Gli1-tdTomato cells. These cells were further processed.
Single cell RNA libraries were prepared according to the 10x Genomics protocol and sequenced on Illumina HiSeq 2500 v4 system

value: mesenchymal cells

value: colon


title: L1_I1_LUM_F9

value: female


title: L1_I1_LUM_F8


title: L1_I1_LUM_F7


title: L1_I1_LUM_F6


title: Het_DBS_dentate gyrus [HZ11282]

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
Raw reads were aligned to the Mus musculus genome (Gencode Version M10, Ensembl 85) using STAR v2.4.2a
Gene read counts were computed using HTSeq 0.9.1
Differentially expressed genes were computed using DESeq2
Genome_build: mm10 (Gencode Version M10, Ensembl 85)
Supplementary_files_format_and_content: text file with raw gene read counts

source_name: Het_DBS_dentate gyrus

growth_protocol: They were group-housed with up to five mice per cage prior to surgery and individually housed with nesting material in the cage after surgery. They were maintained on a 14h light:10h dark cycle (light on at 06:00) with standard mouse chow and water ad libitum in our AAALAS-accredited facility. All experimental procedures and tests were conducted during the light cycle.

extract_protocol:
RNA extraction and purification was performed using the Aurum™ Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad 7326830) per the kit instructions, and genomic DNA was eliminated using an on-column DNase digestion step.
The TruSeq RNA Library Prep Kit v2 (Illumina RS-122-2001) and 250ng of total RNA was used to make each library, and ERCC RNA Spike-In Mix 1 or 2 (Thermo Fisher 4456740) was added to the samples prior to library preparation.

treatment_protocol: Mice were unilaterally implanted at 6 weeks of age with a bipolar stimulating electrode directed to the fimbria-fornix (FF) and a recording electrode placed in the CA1 and dentate gyrus regions of the hippocampus, respectively. After a two-week recovery period, the mice were assigned to either the DBS group or the sham group, and chronic DBS or sham treatment was performed for 2 weeks. Both groups were exposed to identical conditions except the sham group did not receive electrical stimulation. DBS parameters used were 1 hour of DBS (130 Hz, 60μs, 50μA). Dentate gyrus tissue was collected 17 days after end of the 2 weeks of stimulation or sham treatment.

tag: strain background

value: MeCP2-heterozygous (Het)

tag: treatment

value: deep brain stimulation (DBS)

value: dentate gyrus


title: Benign MBA_6687

tag: age


title: WT_Sham_dentate gyrus [HZ11283]

source_name: WT_Sham_dentate gyrus

tag: genotype/variation

value: wild type (WT)

value: Sham


title: WT_DBS_dentate gyrus [HZ11281]

source_name: WT_DBS_dentate gyrus


title: Het_Sham_dentate gyrus [HZ11280]

source_name: Het_Sham_dentate gyrus


title: WT_DBS_dentate gyrus [HZ11285]


title: Benign MBA_6688


title: F3_BPA_sample4

city: Los Angeles

first: Zeyneb

last: Kurt

address: 2000 Terasaki Life Sciences Bldg 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California Los Angeles

description: The dissected germlines were processed through the NucleoSpin RNA XS, Macherey Nagel kit. cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing, amplified 10X, and purified using agentcourt AMPure beads. Nextera XT Library Prep Kit was used to prepare the sequencing libraries from 1 ng of cDNA. Single-end sequencing at 50 bp length was performed on an Illumina Hiseq 4000 system.

data_processing:
HISAT was used to align the RNA-Seq reads against the C.elegans genome to discover the locations from which the reads originated and to determine the transcript splice sites.
StringTie was used to assemble the RNA-seq alignments into potential transcripts.
Reads Per Kilobase of transcript per Million (RPKM) for each transcript were obtained by Ballgown tool and used as the expression measure.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: Transcription abundances in terms of the RPKM measure of the expressed transcripts in each sample were obtained by using Ballgown R tool.

organism: Caenorhabditis elegans

source_name: Needle-dissected gonads of adult worms

growth_protocol: Worms were maintained on NGM plates streaked with OP50 E. coli and all experiments were performed at 20°C.

extract_protocol:
Total RNA was extracted from needle-dissected gonads of F3 adult worms in 4 replicates in each treatment group (BPA or DMSO exposed or water). The dissected germlines were processed through the NucleoSpin RNA XS, Macherey Nagel kit. cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing, amplified 10X, and purified using agentcourt AMPure beads.
Nextera XT Library Prep Kit was used to prepare the sequencing libraries from 1 ng of cDNA

treatment_protocol: Worms were exposed to BPA 100uM or DMSO 0.1% or water for 48 hours at the P0 and adult worms at the F3 were then processed for germline dissection.

value: BPA 100uM


title: F3_BPA_sample3


title: Het_DBS_dentate gyrus [HZ11286]


title: L1_I1_LUM_F5

tag: Sex

value: Adult Human Breast Epithelium

tag: location

value: Luminal


title: F3_BPA_sample1


title: WT_Sham_dentate gyrus [HZ11279]


title: F3_BPA_sample2


title: L1_I1_LUM_F4


title: F3_DMSO_sample3

value: DMSO 0.1%


title: WT_Sham_dentate gyrus [HZ11278]


title: F3_DMSO_sample1


title: F3_DMSO_sample2


title: L1_I1_LUM_F3


title: L1_I1_LUM_F2


title: F3_water_sample4

value: Water


title: L1_I1_LUM_F1


title: WT_DBS_dentate gyrus [HZ11276]


title: Het_DBS_dentate gyrus [HZ11275]


title: F3_water_sample2


title: F3_water_sample3


title: F3_water_sample1


title: L1_I1_LUM_E12


title: L1_I1_LUM_E11


title: WT_Sham_dentate gyrus [HZ11274]


title: Het_Sham_dentate gyrus [HZ11273]


title: BR469

city: San Diego

first: YING

last: DING

address: 10777 Science Center Dr.

department: Computational Biology

institute: Pfizer

description:
expression_tpm.txt
The raw data were submitted to EGA
EGA study accession: EGAS00001002621
https://www.ebi.ac.uk/ega/studies/EGAS00001002621

data_processing:
Gene expression (TPM) was predicted from RNA-Seq data of 178 SMC samples (168 tumors, 10 normals) using RSEM, hg19 as the genome reference and the same gene model library as used by Omicsoft
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited data matrix include TPM values with samples as columns and genes as rows

source_name: Primary Tumor

extract_protocol: sequencing libraries were prepared using TruSeq RNA Sample Preparation kit v2 (RS-122-2001 and RS-122-2002, Illumina).

value: Primary Tumor

value: late

tag: ihc

value: ER+

value: pre


title: BR442


title: BR437


title: BR457


title: WT_DBS_dentate gyrus [HZ11272]


title: L1_I1_BAS_E10

value: Basal


title: BR419

value: TN


title: BR431


title: F3_DMSO_sample4


title: BR418


title: PANC-1, control (mRNA, circRNA, lncRNA)

city: Nanning

first: Qiao

last: Yu

address: Shuangyong road, qingxiu district，nanning

institute: First Affiliated Hospital of Guangxi Medical University

description: O

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

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

data_processing:
Raw data were normalized by Quantile algorithm, limma packages in R
Feature Extraction (FE) is the process by which information from probe features is extracted from microarray scan data.

source_name: PANC-1, rapamycin

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

growth_protocol: The human pancreatic cancer cell line PANC-1 was cultured in complete Dulbecco’s modified Eagle’s medium (DMEM).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The PANC-1 cells treated with 100 µM rapamycin were preferred as the autophagy-induced group(group B), and cells cultured by DMEM were selected as the control group(group O)

value: pancreatic cancer cell

tag: agent

value: control


title: Het_Sham_dentate gyrus [HZ11277]

value: MeCP2-heterozygous (Het)

value: female


title: L1_I1_BAS_E8

data_processing:
After demultiplexing sequencing libraries to individual cell FASTQ files (observed average read depth per cell was found to be ~1.6 Million reads), each library was aligned to an indexed GRCh38 RefSeq genome using RSEM version 1.2.1242, and bowtie2 version 2.2.3 with the following options enabled: rsem-calculate- expression -p $CORES -- bowtie2 -- paired-end -output- genome-bam. Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were quantified and concatenated into a resulting gene expression matrix for each library
Genome_build: GrCH38
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts expression matrices corresponding to each of the libraries generated from the 3 individuals in this study

extract_protocol:
Viable organoids were thawed and washed using DMEM, and digested with 0.05% trypsin (Corning 25-052-CI) containing DNase (Sigma Aldrich D4263-5VL) to generate single cell suspension. Cells were stained for FACS using fluorescently labeled antibodies for CD31 (eBiosciences 48-0319-42), CD45 (eBiosciences 48-9459-42), EpCAM (eBiosciences 50-9326-42), CD49f (eBiosciences 12-0495-82), SytoxBlue (Life Technologies S34857). We only proceeded with samples showing at least 80% viability as measured using SytoxBlue in FACS
Sorted cells were washed and resuspended at a concentration of approximately 500 cells/µl. For microfluidics-enabled scRNAseq, cell suspensions were mixed with Fluidigm C1 Suspension Reagents (Fluidigm 100-5315) at a ratio of 8:2 before loading mix onto C1 chip (Fluidigm 100-5760). Bright field images of captured cells were collected using a Keyence BZ-X710 microscope (Keyence Corporation, Itasca, Illinois, USA). Single-cell RNA isolation and amplification were performed using the Fluidigm C1 Single Cell Auto Prep IFC following the Fluidigm Protocol: 100-7168 I1. RNA spike-in controls were omitted. cDNA library preparation were performed following the Fluidigm C1 Protocol: 100-7168 I1. Reagents Kits v2 User Guide: CG00052 Rev B.     Quantification of cDNA libraries was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA chips (Agilent. 5067-4626). Quantification of library construction was performed using KAPA qPCR (Kapa Biosystems KK4824). For microfluidics-enabled scRNAseq libraries, we generally multiplexed 96 cells per lane on an Illumina HiSeq2500 resulting in a calculated depth of ~1.6 million reads per cell (Illumina Rapid PE kit v2 402-4002 and Rapid SBS kit v2 FC 401-4022).


title: PANC-1, rapamycin (mRNA, circRNA, lncRNA)

description: B

value: rapamycin


title: BR414


title: BR412


title: BR413


title: BR395


title: BR408


title: L1_I1_BAS_E7


title: TSC1KO3

city: Albany

first: Yunfei

last: Huang

state: New York

address: 47 New Scotland Ave

department: Neuroscience and Experimental Therapeutics

institute: Albany Medical College

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted pvalue threshold of 0.05 on each set of raw expression measures.
Genome_build: Mapping each sample Individually to the mouse reference genome (GRCm38.p5 primary assembly + gencode M12 annotation) with done using STAR 2.5.2 b
Supplementary_files_format_and_content: DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING

source_name: Microglia

extract_protocol:
Microglia were purified from the mouse brain and RNA was extracted using Trizol.
One nanogram of RNA was used for low input RNAseq library construction and sequencing using NexteraXT library prep kit (Illumina).

treatment_protocol: TSC1Cx3cr1CKO mice were generated by crossing TSC1f/f mouse line with Cx3cr1-cre line.

value: Microglia purified from mice

value: Brain

value: Postnatal  day 25


title: TSC1KO4


title: L1_I1_BAS_E6

city: Irvine

first: Kai

last: Kessenbrock

address: 839 Health Sciences Road

institute: UC Irvine

source_name: Mammoplasty Reduction

value: Adult Human Breast Epithelium


title: TSC1KO2


title: L1_I1_BAS_E9


title: BR393


title: L1_I1_BAS_E5


title: L1_I1_BAS_E4


title: Het_DBS_dentate gyrus [HZ11271]

value: deep brain stimulation (DBS)

value: dentate gyrus


title: BR391

value: Primary Tumor


title: BR374

value: late


title: BR371

value: ER+


title: BR367

value: pre


title: WT4


title: L1_I1_BAS_E3

value: Basal


title: TCS1KO1


title: BR356


title: BR366


title: WT2


title: L1_I1_BAS_E2


title: BR355


title: WT3


title: L1_I1_BAS_D12


title: BR331


title: BR309


title: L1_I1_BAS_D11


title: WT1


title: BR303


title: BR307


title: BR386


title: BR300


title: BR383


title: L1_I1_BAS_E1


title: BR301

value: TN


title: L1_I1_BAS_D10


title: BR259


title: L1_I1_BAS_D9


title: BR255


title: L1_I1_BAS_D8


title: BR248


title: L1_I1_BAS_D7


title: BR251


title: BR316


title: BR233


title: BR313


title: L1_I1_BAS_D6


title: L1_I1_BAS_D5


title: BR226


title: BR212


title: BR205


title: L1_I1_BAS_D4


title: BB01_130


title: L1_I1_BAS_D3


title: BB01_124


title: BB01_051

value: early

value: post


title: BB01_116


title: BB01_120


title: L1_I1_BAS_D2


title: BB01_111


title: L1_I1_BAS_D1


title: L1_I1_BAS_C12


title: BR246


title: BB01_110


title: BB01_108


title: BB01_105


title: L1_I1_BAS_C11


title: BB01_104


title: L1_I1_BAS_C10


title: BR235


title: BB01_103


title: BB01_099


title: BB01_090


title: L1_I1_BAS_C8


title: BB01_128


title: BB01_088


title: BB01_086


title: BB01_125


title: BB01_079


title: L1_I1_BAS_C9


title: BB01_094


title: BB01_068


title: L1_I1_BAS_C7


title: BB01_081


title: BB01_067


title: L1_I1_BAS_C5


title: L1_I1_BAS_C4


title: BB01_059


title: BB01_053


title: BB01_049


title: L1_I1_BAS_C3


title: BB01_046


title: L1_I1_BAS_C2


title: BB01_047


title: BB01_045


title: L1_I1_BAS_C1


title: BB01_040


title: BB01_041


title: L1_I1_BAS_C6


title: L1_I1_BAS_B12


title: BB01_037


title: BB01_035


title: L1_I1_BAS_B10


title: BB01_036


title: BB01_061


title: BB01_034


title: BB01_039


title: BB01_030


title: L1_I1_BAS_B11


title: BB01_031


title: L1_I1_BAS_B8


title: L1_I1_BAS_B9


title: BB01_027


title: L1_I1_BAS_B7


title: BB01_029


title: BB01_024


title: BB01_062


title: L1_I1_BAS_B6


title: BB01_023


title: L1_I1_BAS_B4


title: L1_I1_BAS_B5


title: BB01_026


title: L1_I1_BAS_B3


title: BB01_018


title: BB01_028


title: BB01_016


title: BB01_017


title: Flavum_elderly_83 year old

city: Tokushima

first: Masatoshi

last: Morimoto

address: 3-18-15 Kuramoto

country: Japan

institute: Institute of Biomedical Sciences Tokushima University Graduate School

description: Gene expression in whole ligament

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Flavum_Lumbar Spinal Stenosis_83 year old

extract_protocol: RNA was prepared using RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden Germany)) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: ligamentum flavum

value: male


title: BB01_015


title: L1_I1_BAS_B1

value: female


title: L1_I1_BAS_A12


title: Flavum_elderly_75 year old

description: Gene expression in whole ligament

source_name: Flavum_Lumbar Spinal Stenosis_75 year old


title: BB01_014


title: Flavum_elderly_80 year old

description: Gene expression in whole ligament

source_name: Flavum_Lumbar Spinal Stenosis_80 year old


title: BB01_013


title: BB01_011


title: BB01_022


title: L1_I1_BAS_A9


title: L1_I1_BAS_A10


title: Flavum_elderly_82 year old

description: Gene expression in whole ligament

source_name: Flavum_Lumbar Spinal Stenosis_82 year old


title: BB01_010

value: peri


title: BB01_009


title: Flavum_young_20 year old_2

description: Gene expression in whole ligament

source_name: Flavum_lumbar disc herniation_20 year old


title: L1_I1_BAS_B2


title: Flavum_young_24 year old

description: Gene expression in whole ligament

source_name: Flavum_lumbar disc herniation_24 year old


title: Flavum_young_20 year old_1

description: Gene expression in whole ligament


title: A549res-34µM_5

city: Bonn

first: Ganna

last: Kalayda

address: An der Immenburg 4

department: Clinical Pharmacy

institute: University of Bonn

description: gene expression in res. cells after treatment with 34µM

hyb_protocol: After purifying the labelled/amplified complementary RNA (cRNA) using silica-membrane RNeasy spin columns from the RNeasy® Mini Kit (Qiagen, Venlo, the Netherlands), cRNA was quantified spectrophotometrically using NanoDropTM ND-1000 (Thermo Fisher Scientific Inc., Waltham, MA, USA). 40 µL of equivalent amounts of Cy3-labelled cRNA in 10x Blocking Agent and 25x Fragmentation Buffer, diluted with 2x GEx HI-RPM Hybridization Buffer were loaded on the gaskets of the microarray slide and kept at 65 °C for 17 h with 10 rpm of agitation.

scan_protocol: After washing twice with different washing buffers, the microarray was read out with the SureScan Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA) to obtain immunofluorescence intensity.

data_processing: Array data were pre-processed via background correction (exponential convolution method) and quantile normalization. Statistical significances of dose- and resistance-induced gene expression changes were analysed using limma, a linear model-based technique. Differential expression was declared at a 5 % false discovery rate (FDR) cut-off together with an at least twofold up- or downregulation. The overall significance of the signature of differentially expressed genes was assessed via a global test. VALUE contains quantile normalized data for probes with REFSEQ IDs only (29,729)

source_name: NSCLC, cisplatin resistant, 24h cisplatin, 34uM

label_protocol: Transcriptome was then analysed using One-Color Whole Genome Array SurePrint G3 Human GE V2 8x60K Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. Briefly, total RNA was transcribed to complementary deoxyribonucleic acid (cDNA) using AffinityScript-RT, Oligo dT-Promoter Primer and T7 RNA Polymerase and labelled using the One Colour RNA Spike-In Kit (positive controls) including Cyanin 3-CTP (Cy3) dye.

growth_protocol: The human NSCLC cell line A549 was obtained from American Type Culture Collection (ATCC) (Manassas, VA, USA). Its cisplatin-resistant sub-line A549rCDDP2000 derived from the Resistant Cancer Cell Line (RCCL) collection (www.kent.ac.uk/stms/cmp/RCCL/RCCLabout.html) had been established by adapting the growth of A549 cells in the presence of increasing concentrations of cisplatin until a final concentration of 2000 ng/mL cisplatin. A549 cells were grown in IMDM medium (PAN-Biotech, Aidenbach, Germany) containing 4 mM L-glutamine supplemented with 10 % foetal calf serum, 100 I.E./mL penicillin and 0.1 mg/mL streptomycin. The medium of the A549rCDDP2000 cells additionally contained 2 µg/mL cisplatin. Cells were cultivated as monolayers in a humidified atmosphere at 37 °C and 5 % CO2.

extract_protocol: Total ribonucleic acid (RNA) was isolated from the cells with my-Budget RNA Mini Kit (Bio-Budget, Krefeld, Germany) through different spin columns according to the manufacturer’s instructions. Isolated RNA was stored at -80 °C until analysis was performed.

treatment_protocol: For all experiments, cells were allowed to attach overnight, experienced 4 h of serum starvation and were subsequently treated with cisplatin for 24 h in IMDM medium without any supplements. The parental cells were treated with 11 µM cisplatin. The resistant sub-line was exposed to 11 µM cisplatin and additionally treated with 34 µM cisplatin. The control cells were treated with the drug-free medium.

tag: sensitivity

value: resistant

tag: treatment conc


title: L1_I1_BAS_A7

tag: tissue


title: Flavum_young_19 year old

description: Gene expression in whole ligament

source_name: Flavum_lumbar disc herniation_19 year old


title: L1_I1_BAS_A11


title: L1_I1_BAS_A5


title: L1_I1_BAS_A6


title: BB01_007


title: BB01_008


title: BB01_006


title: A549res-ctrl_5

description: gene expression in untreated res. cells

source_name: NSCLC, cisplatin resistant, control


title: A549res-11µM_5

description: gene expression in res. cells after treatment with 11µM

source_name: NSCLC, cisplatin resistant, 24h cisplatin, 11uM


title: BB01_005


title: L1_I1_BAS_A3


title: L1_I1_BAS_A4


title: L1_I1_BAS_A8


title: A549res-34µM_4


title: BB01_004


title: BB01_002


title: L1_I1_BAS_A2


title: L1_I1_BAS_A1


title: BB01_074


title: A549res-ctrl_4

description: gene expression in untreated res. cells


title: A549sens-ctrl_4

description: gene expression in untreated sens. cells

source_name: NSCLC, cisplatin sensitive, control

value: sensitive


title: Pat. C CpG+

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

hyb_protocol: 15ug of fragmented and biotin-labeled ss-cDNA was hybridized at 45C for 16 hours at 60rpm. GeneChips were then washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 7G.  Data files were generated and processed with Affymetrix software and Expression Console.

data_processing: The data were normalized by RMA method with Affymetrix Expression Console software. Linear model and moderated t-test was used for testing differentially expressed genes by using SAS and R packages.

source_name: B-Chronic Lymphocytic Leukemia (CLL) cells

label_protocol: 100ng RNA was used to generate fragmented and biotin-labeled ss-cDNA according to the manufacturer s protocol in the GeneChip  WT PLUS Reagent Kit Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays

growth_protocol: RPMI 10% FBS

extract_protocol: TRIZOL purification and MiRVANA columns

treatment_protocol: [1] baseline (Vehicle); [2] 4 hours stimulation with 3.2uM of CpG oligonucleotide; [3] 4 hours stimulation with 3.2uM of CpG oligonucleotide + 1 uM of BET inhibitor (PLX51107)

tag: patient id

value: C

value: Primary B-CLL cells


title: A549res-11µM_2


title: Pat. C PLX05 / CpG+


title: BB01_080


title: Pat. B CpG+

value: B


title: BB01_131

value: Primary Tumor


title: Patient C  Vehicle (-)


title: Pat. A PLX05 / CpG+

value: A


title: Immunocompetent Patient P1

city: Fuzhou

first: junjun

last: sang

address: No.168 Xierhuanbei Road

institute: Fuzhou General Hospital

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the hg38 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using HTSeq 0.9.1; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 2.10.0.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: blood cells

extract_protocol:
Total RNA was isolated using PAXgene Blood RNA Kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration.

value: Female

tag: infection

value: Cryptococcal osteomyelitis

value: blood


title: Normal control C1

value: normal control


title: A549res-11µM_4


title: Pat. B PLX05 / CpG+


title: A549res-34µM_3


title: A549res-34µM_2


title: BB01_078

source_name: Primary Tumor

value: late

value: pre


title: LD_ZT11_B (XR-seq)

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

data_processing:
Library strategy: XR-seq
adapter trimming with cutadapt ath 3' end. The adapter is TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG
genome alignment onto TAIR10 by using Bowtie with the following parameters: : --nomaqround --phred33-quals -e 70
read deduplication
read count for each gene for both strands distinctly using bedtools
RPKM normalization
Genome_build: TAIR10
Supplementary_files_format_and_content: tab separated gene tables (txt) of the normalized TS (transcribed strand) and NTS (non-transcribed strand) repair (RPKM).

source_name: LD_ZT11, whole plant

growth_protocol: 10-days-old seedlings of Arabidopsis thaliana ecotype Columbia (Col-0) were used. Plants were grown under a long-day condition (16 h light /8 h dark) with a cool white fluorescent light at 24°C. 8 mg of seeds for each sample were surface-sterilized, and stratified for 2 days at 4°C, and then planted on a Murashige and Skoog (MS) plate. For circadian clock experiments, seedlings were collected in 3-h intervals (ZT1, ZT4, ZT7, ZT10, ZT13, ZT16, ZT19, and ZT22).

extract_protocol:
After 30-min incubation in the dark at 24°C, the seedlings were frozen with liquid nitrogen, and were ground using mortar and pestle. The resulting powder was resuspended in 400 µl of STES buffer (200 mM Tris⋅HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 10 mM EDTA) and 400 µl of phenol:chloroform (20:1). The sample was homogenized by vortexing with acid-washed glass beads for 30 min at 4°C, followed by centrifugation at 14000 rpm for 10 min at room temperature. The supernatant was treated with 10 µl of RNAseA (R4642; Sigma) for 1 hour at 37°C, then with 10 µl of proteinase K (P8107S; NEB) for 1 hour at 60°C. The excision products were precipitated by ethanol precipitation, and purified by immunoprecipitation with a CPD-specific antibody. These fragments were 3′ end radiolabeled with [α- 32P]-3′-deoxyadenosine 5′-triphosphate (cordycepin 5′-triphosphate) (Perkin-Elmer) by terminal deoxynucleotidyl transferase (NEB), and visualized on an 11% sequencing gel.
Excision products were purified as above. 5’ and 3’ adapters compatible with the Illumina TruSeq Small RNA protocol were ligated to excision products. Ligation products were immunoprecipitated with CPD antibodies, then photoreversed with photolyase. Analytical PCR was performed using one percent of the sample to decide the minimum number of cycles required for preparative scale PCR amplification (fig S2B). The repaired ligation products were PCR-amplified using 50- and 63-nt-long primers adding specific barcodes compatible with the Illumina TruSeq Small RNA kit. The correct size PCR products representing the library were gel purified, and then sequenced in the Illumina HiSeq 4000 (experiment 1) and 2500 (experiment 2) platforms, and single-end 50-nt reads were generated.

treatment_protocol: 10-days old seedlings were irradiated with 120 J/m2 UVC (254 nm).

tag: ecotype

tag: experiment

tag: time

value: seedlings


title: LD_ZT8_B (XR-seq)

source_name: LD_ZT8, whole plant


title: A549res-ctrl_3

description: gene expression in untreated res. cells


title: A549sens-11µM_3

description: gene expression in sens. cells after treatment with 11µM

source_name: NSCLC, cisplatin sensitive, 24h cisplatin, 11uM


title: Patient A  Vehicle (-)

tag: cell type


title: BB01_019

value: ER+


title: Pat. A CpG+


title: BB01_112


title: LD_ZT5_B (XR-seq)

source_name: LD_ZT5, whole plant


title: A549res-ctrl_2

description: gene expression in untreated res. cells


title: Patient B  Vehicle (-)


title: BB01_119

value: TN


title: A549sens-ctrl_3


title: A549sens-11µM_2


title: LD_ZT2_B (XR-seq)

source_name: LD_ZT2, whole plant


title: BB01_109


title: BB01_055


title: BB01_126


title: LD_ZT23_B (XR-seq)

source_name: LD_ZT23, whole plant


title: LD_ZT17_B (XR-seq)

source_name: LD_ZT17, whole plant


title: LD_ZT20_B (XR-seq)

source_name: LD_ZT20, whole plant


title: BB01_044


title: BB01_012