title: HNSCC25_P20_D03_S327_comb


title: HNSCC25_P2_H06_S90_comb

status: Public on Nov 30 2017

type: SRA

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

library_source: transcriptomic

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by   RSEM v1.2.3 in paired-end mode  using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted.
For each cell, we quantified two quality measures: the number of genes for which at least one  read was mapped, and the average expression level of a curated list of housekeeping genes. We then conservatively excluded all cells with either fewer than 2,000 detected genes or an average housekeeping expression (E, as defined above) below 2.5.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing TPM values ( transcript-per-million reads) for 23,686 analyzed genes (rows), across 5902  cells (columns, sample names indicated at the top row). Headers indicate the enzyme being used for reverse transcription, the sample site (Primary vs. lymph node), the classification into cancer and non-cancer cells and the inferred non-cancer cell types.

molecule: polyA RNA

organism: Homo sapiens

source_name: Head and neck cancer single cell

extract_protocol:
RNA was purified using Agencourt RNAClean XP  beads (Beckman Coulter, Brea, CA),
Libraries for isolated single cells were  generated based on the SMART-Seq2 protocol (Picelli et al., 2013; Picelli et al., 2014)  with the following modifications:purified RNA was subjected to reverse transcription with Superscript II  (ThermoFisher Scientific) or Maxima (ThermoFisher Scientific) reverse transcriptase  and whole transcriptome amplification using KAPA HiFi HotStart ReadyMix (KAPA  Biosystems, Wilmington, MA). Full length cDNA libraries were tagmented using the  Nextera XT Library Prep Kit (Illumina, San Diego, CA). 384 samples were pooled and  sequenced as paired-end 38 base reads on a NextSeq 500 instrument (Illumina).

treatment_protocol: Tumor Dissociation:  Fresh biopsy samples of oral cavity HNSCC were minced,  washed with phosphate buffered saline (PBS; ThermoFisher Scientific, Waltham, MA),  and dissociated using a Human Tumor Dissociation Kit (Miltenyi Biotec, Bergisch  Gladbach, Germany) per manufacturer guidelines. Viability was confirmed to be >90%  in all samples using trypan blue (ThermoFisher Scientific) exclusion. Cell suspensions  were filtered using a 70 ?m filter (ThermoFisher Scientific), and dissociated cells were  pelleted and re-suspended in PBS with 1% bovine serum albumin (BSA; Sigma-Aldrich,  St. Louis, MO). Cells were stained with CD45-vioblue (Miltenyi Biotec), along with either  the combination of CD90-PE (BD Biosciences, Franklin Lakes, NJ) and CD31-PE-cy7  (BD Biosciences) or CD3-PE-cy7 (ThermoFisher Scientific), then washed with cold  PBS, and re-suspended for flow cytometry analyses.    Sorting of Patient Samples:  Cells were stained for viability with 1 ?M calcein AM  (ThermoFisher Scientific) and 0.33 ?M TO-PRO-3 iodide (ThermoFisher Scientific)  immediately prior to sorting. Fluorescence-activated cell sorting (FACS) was performed  on FACSAria Fusion Special Order System (BD Biosciences) using 488 nm (calcein  AM, 530/30 filter), 640 nm (TO-PRO-3, 670/14 filter), 405 nm (Vioblue, 450/50 filter),  561 nm (PE, 586/15 filter; PE-Cy7, 780/60 filter) lasers. Standard forward scatter height  versus area criteria were used to discard doublets and capture singlets. Viable cells  45  were identified as calceinhigh and TO-PROlow and additional gates were used to enrich or  deplete specific cell types in each plate. For each tumor, plates were sorted containing  CD45- cells (to deplete immune cells), CD45-/CD90-/CD31- cells (to further deplete  fibroblasts and endothelium and enrich for malignant cells), CD45+ cells (to enrich for  immune cells), and CD45+/CD3+ cells (to enrich specifically for T-cells). Single cells  were sorted into 96-well plates containing TCL buffer (Qiagen, Hilden, Germany) with  1% ?-mercaptoethanol. Plates were briefly centrifuged, snap frozen, and stored at ?80  °C before cDNA synthesis and library construction. For each tumor sample, at least one  CD45- and one CD45+ plate was sequenced.

tag: enzyme used

value: SuperScript II

tag: tumor site

value: Primary (oral cavity)


title: HNSCC25_P2_B01_S13_comb


title: HNSCC25_P2_B11_S23_comb


title: HNSCC25_P2_F10_S70_comb


title: HNSCC25_P2_G01_S73_comb


title: HNSCC25_P2_D10_S46_comb


title: HNSCC25_P20_B05_S305_comb

value: Maxima

value: Lymph node


title: HNSCC25_P2_C09_S33_comb


title: HNSCC25_P20_F09_S357_comb


title: HNSCC25_P20_H02_S374_comb


title: HNSCC25_P20_B06_S306_comb


title: HNSCC25_P2_E04_S52_comb


title: HNSCC25_P2_C01_S25_comb


title: HNSCC25_P20_B03_S303_comb


title: HNSCC25_P2_G02_S74_comb


title: HNSCC25_P20_H01_S373_comb


title: HNSCC25_P20_G01_S361_comb


title: HNSCC25_P2_D11_S47_comb


title: HNSCC25_P20_C02_S314_comb


title: HNSCC25_P20_G07_S367_comb


title: HNSCC25_P2_C06_S30_comb


title: HNSCC25_P2_H01_S85_comb


title: HNSCC25_P2_E02_S50_comb


title: HNSCC25_P2_D12_S48_comb


title: HNSCC25_P2_E08_S56_comb


title: HNSCC25_P2_F09_S69_comb


title: HNSCC25_P2_B10_S22_comb


title: HNSCC25_P20_B08_S308_comb


title: HNSCC25_P2_A04_S4_comb


title: HNSCC25_P2_H08_S92_comb


title: HNSCC25_P20_D11_S335_comb


title: HNSCC25_P2_C05_S29_comb


title: HNSCC25_P2_F07_S67_comb


title: HNSCC25_P20_C05_S317_comb


title: HNSCC25_P2_G09_S81_comb


title: HNSCC25_P20_E07_S343_comb


title: HN25_P13P30_D07_S235_comb


title: HN25_P13P30_F07_S259_comb


title: HN25_P13P30_B05_S209_comb


title: HNSCC25_P20_E09_S345_comb


title: HNSCC25_P20_B02_S302_comb


title: HNSCC25_P2_F05_S65_comb


title: HN25_P13P30_C08_S224_comb


title: HN25_P13P30_A12_S204_comb


title: HN25_P13P30_D10_S238_comb


title: HNSCC25_P2_H09_S93_comb


title: HNSCC25_P20_C01_S313_comb


title: HN25_P13P30_A01_S193_comb


title: HN25_P13P30_A09_S201_comb


title: HN25_P13P30_C04_S220_comb


title: HN25_P13P30_E07_S247_comb


title: HN25_P13P30_E01_S241_comb


title: HN25_P13P30_B08_S212_comb


title: HN25_P13P30_B03_S207_comb


title: HNSCC25_P20_F12_S360_comb


title: HN25_P13P30_F01_S253_comb


title: HN25_P13P30_F12_S264_comb


title: HN25_P13P30_A08_S200_comb


title: HN25_P13P30_B09_S213_comb


title: HN25_P13P30_C06_S222_comb


title: HN25_P13P30_A03_S195_comb


title: HN25_P13P30_H02_S278_comb


title: HN25_P13P30_E05_S245_comb


title: HN25_P13P30_D06_S234_comb


title: HN25_P13P30_B10_S214_comb


title: HN25_P13P30_C11_S227_comb


title: HN25_P13P30_A10_S202_comb


title: HN25_P13P30_D11_S239_comb


title: HN25_P13P30_C10_S226_comb


title: HN25_P13P30_B04_S208_comb


title: HN25_P13P30_D03_S231_comb


title: HN25_P13P30_C03_S219_comb


title: HN25_P13P30_F09_S261_comb


title: HN25_P13P30_G05_S269_comb


title: HN25_P13P30_C07_S223_comb


title: HN28_P5_E11_S251_comb


title: HN25_P13P30_G03_S267_comb


title: HN28_P3P4_F11_S71_comb


title: HN28_P3P4_C07_S31_comb


title: HN28_P5_C02_S218_comb


title: HN28_P5_G02_S266_comb


title: HN28_P3P4_C05_S29_comb


title: HN28_P3P4_B03_S15_comb


title: HN28_P14_F04_S160_comb


title: HN28_P3P4_D03_S39_comb


title: HN28_P14_C12_S132_comb


title: HN28_P14_A05_S101_comb


title: HN28_P5_A04_S196_comb


title: HN28_P5_A03_S195_comb


title: HN25_P13P30_C05_S221_comb


title: HN28_P14_E11_S155_comb


title: HN28_P5_E03_S243_comb


title: HN28_P5_D12_S240_comb


title: HN28_P3P4_C02_S26_comb


title: HN28_P3P4_C03_S27_comb


title: HN23_P11_B06_S18_comb


title: HN28_P14_G06_S174_comb


title: HN28_P14_B03_S111_comb


title: HN23_P11_D03_S39_comb


title: HN28_P14_H12_S192_comb


title: HN28_P5_D06_S234_comb


title: HN28_P3P4_A10_S10_comb


title: HN28_P5_D05_S233_comb


title: HN28_P14_B09_S117_comb


title: HN28_P14_F02_S158_comb


title: HN23_P11_A07_S7_comb


title: HN23_P11_B11_S23_comb


title: HN28_P14_B12_S120_comb


title: HN28_P5_A12_S204_comb


title: HN28_P14_F01_S157_comb


title: HN28_P3P4_G08_S80_comb


title: HN23_P11_H10_S94_comb


title: HN28_P5_G08_S272_comb


title: HN23_P11_G02_S74_comb


title: HN28_P3P4_F07_S67_comb


title: HN28_P3P4_H03_S87_comb


title: HN28_P3P4_G07_S79_comb


title: HN28_P14_G05_S173_comb


title: HN28_P3P4_A04_S4_comb


title: HN23_P11_G10_S82_comb


title: HN28_P5_A08_S200_comb


title: HN28_P14_E01_S145_comb


title: HN28_P14_G01_S169_comb


title: HN28_P3P4_B05_S17_comb


title: HN23_P11_E03_S51_comb


title: HN28_P14_D02_S134_comb


title: HN28_P3P4_C10_S34_comb


title: HN28_P3P4_F01_S61_comb


title: HN28_P3P4_E12_S60_comb


title: HN28_P3P4_A09_S9_comb


title: HN28_P3P4_C09_S33_comb


title: HN28_P5_D01_S229_comb


title: HN28_P5_C01_S217_comb


title: HN28_P5_E06_S246_comb


title: HN28_P3P4_A11_S11_comb


title: HN28_P14_E10_S154_comb


title: HN23_P11_D07_S43_comb


title: HN28_P14_B11_S119_comb


title: HN28_P5_H05_S281_comb


title: HN28_P14_E07_S151_comb


title: HN23_P11_A09_S9_comb


title: HN28_P14_F10_S166_comb


title: HN28_P14_D06_S138_comb


title: HN28_P5_C05_S221_comb


title: HN28_P5_B09_S213_comb


title: HN28_P3P4_C01_S25_comb


title: HN23_P11_C03_S27_comb


title: HN28_P3P4_C08_S32_comb


title: HN28_P3P4_D10_S46_comb


title: HN28_P5_F12_S264_comb


title: HN28_P5_H01_S277_comb


title: HN23_P11_F03_S63_comb


title: HN28_P3P4_G11_S83_comb


title: HN23_P11_E12_S60_comb


title: HN28_P5_B08_S212_comb


title: HN28_P5_A10_S202_comb


title: HN28_P5_H06_S282_comb


title: HN28_P14_G08_S176_comb


title: HN23_P11_G11_S83_comb


title: HN28_P5_F11_S263_comb


title: HN28_P5_E02_S242_comb


title: HN23_P11_D11_S47_comb


title: HN28_P5_F07_S259_comb


title: HN28_P3P4_F04_S64_comb


title: HN28_P3P4_F09_S69_comb


title: HN23_P11_E11_S59_comb


title: HN23_P11_E07_S55_comb


title: HN28_P14_G11_S179_comb


title: HN28_P3P4_A05_S5_comb


title: HN28_P14_H02_S182_comb


title: HN28_P5_A01_S193_comb


title: HN28_P3P4_D01_S37_comb


title: HN23_P11_G06_S78_comb


title: HN28_P5_C07_S223_comb


title: HN28_P14_D10_S142_comb


title: HN28_P14_H07_S187_comb


title: HN28_P3P4_C06_S30_comb


title: HN28_P5_G09_S273_comb


title: HN23_P11_E10_S58_comb


title: HN28_P3P4_F12_S72_comb


title: HN28_P3P4_B07_S19_comb


title: HN23_P11_B12_S24_comb


title: HN28_P14_G10_S178_comb


title: HN28_P5_E05_S245_comb


title: HN28_P14_A04_S100_comb


title: HN28_P3P4_A02_S2_comb


title: HN23_P11_H11_S95_comb


title: HN28_P5_H10_S286_comb


title: HN28_P5_C04_S220_comb


title: HN28_P3P4_D02_S38_comb


title: HN28_P3P4_H04_S88_comb


title: HN28_P3P4_H11_S95_comb


title: HN28_P3P4_B09_S21_comb


title: HN28_P5_B10_S214_comb


title: HN28_P3P4_D06_S42_comb


title: HN28_P5_F04_S256_comb


title: HN28_P14_D09_S141_comb


title: HN28_P3P4_G01_S73_comb


title: HN28_P14_D12_S144_comb


title: HN28_P3P4_E10_S58_comb


title: HN23_P11_H04_S88_comb


title: HN28_P5_C10_S226_comb


title: HN23_P11_C04_S28_comb


title: HN28_P3P4_D08_S44_comb


title: HN28_P3P4_E04_S52_comb


title: HN28_P5_H09_S285_comb


title: HN28_P5_F10_S262_comb


title: HN28_P3P4_D04_S40_comb


title: HN28_P3P4_H02_S86_comb


title: HN28_P3P4_E09_S57_comb


title: HN28_P5_B11_S215_comb


title: HN28_P14_G12_S180_comb


title: HN28_P3P4_E07_S55_comb


title: HN28_P14_C02_S122_comb


title: HN23_P11_F09_S69_comb


title: HN28_P5_H03_S279_comb


title: HN23_P11_E04_S52_comb


title: HN28_P3P4_B08_S20_comb


title: HN28_P3P4_B11_S23_comb


title: HN28_P3P4_G06_S78_comb


title: HN25_P13P30_A05_S197_comb


title: HN23_P11_D04_S40_comb


title: HN28_P5_F03_S255_comb


title: HN28_P5_H02_S278_comb


title: HN23_P11_E08_S56_comb


title: HN28_P5_B05_S209_comb


title: HN28_P5_B04_S208_comb


title: HN28_P3P4_B12_S24_comb


title: HN28_P5_E04_S244_comb


title: HN23_P11_D09_S45_comb


title: HN23_P11_B01_S13_comb


title: HN28_P3P4_B10_S22_comb


title: HN28_P3P4_A06_S6_comb


title: HN23_P11_F01_S61_comb


title: HN28_P3P4_H06_S90_comb


title: HN28_P14_D08_S140_comb


title: HN28_P3P4_B01_S13_comb


title: HN28_P14_A02_S98_comb


title: HN28_P14_A03_S99_comb


title: HN23_P11_E01_S49_comb


title: HN28_P14_E08_S152_comb


title: HN28_P14_C10_S130_comb


title: HN28_P3P4_H09_S93_comb


title: HN28_P3P4_C12_S36_comb


title: HN28_P3P4_F10_S70_comb


title: HN28_P5_E10_S250_comb


title: HN28_P14_F11_S167_comb


title: HN23_P11_A08_S8_comb


title: HN28_P3P4_H05_S89_comb


title: HN28_P5_C09_S225_comb


title: HN28_P14_B10_S118_comb


title: HN28_P5_A09_S201_comb


title: HN28_P5_G01_S265_comb


title: HN28_P14_A10_S106_comb


title: HN28_P14_A07_S103_comb


title: HN23_P11_G09_S81_comb


title: HN28_P14_A08_S104_comb


title: HN28_P3P4_G04_S76_comb


title: HN28_P14_B07_S115_comb


title: HN23_P11_H12_S96_comb


title: HN28_P14_A09_S105_comb


title: HN28_P5_H04_S280_comb


title: HN28_P5_D04_S232_comb


title: HN28_P14_C05_S125_comb


title: HN28_P5_F06_S258_comb


title: HN23_P11_G08_S80_comb


title: HN28_P14_F07_S163_comb


title: HN28_P3P4_E02_S50_comb


title: HN23_P11_G05_S77_comb


title: HN28_P3P4_H12_S96_comb


title: HN28_P14_B08_S116_comb


title: HN28_P5_C08_S224_comb


title: HN28_P14_C09_S129_comb


title: HN28_P14_B04_S112_comb


title: HN28_P14_C07_S127_comb


title: HN28_P3P4_A01_S1_comb


title: HN23_P11_B05_S17_comb


title: HN23_P11_A12_S12_comb


title: HN28_P14_C06_S126_comb


title: HN28_P5_D02_S230_comb


title: HN23_P11_B08_S20_comb


title: HN28_P5_H07_S283_comb


title: HN28_P14_G02_S170_comb


title: HN28_P3P4_F05_S65_comb


title: HN28_P14_D05_S137_comb


title: HN28_P14_C01_S121_comb


title: HN23_P11_G12_S84_comb


title: HN28_P3P4_G02_S74_comb


title: HN28_P5_G07_S271_comb


title: HN28_P5_D07_S235_comb


title: HN28_P3P4_B06_S18_comb


title: HN28_P14_E06_S150_comb


title: HN28_P3P4_D09_S45_comb


title: HN28_P5_B02_S206_comb


title: HN28_P3P4_E03_S51_comb


title: HN28_P14_A06_S102_comb


title: HN28_P5_A07_S199_comb


title: HN28_P5_E09_S249_comb


title: HN28_P3P4_B04_S16_comb


title: HN28_P3P4_B02_S14_comb


title: HN23_P11_B10_S22_comb


title: HN28_P14_E03_S147_comb


title: HN28_P3P4_E06_S54_comb


title: HN28_P3P4_F03_S63_comb


title: HN28_P3P4_G03_S75_comb


title: HN28_P3P4_D12_S48_comb


title: HN28_P14_E09_S153_comb


title: HN28_P5_H08_S284_comb


title: HN28_P5_G04_S268_comb


title: HN28_P5_H11_S287_comb


title: HN28_P3P4_C04_S28_comb


title: HN28_P3P4_C11_S35_comb


title: HN28_P14_B05_S113_comb


title: HN28_P3P4_H10_S94_comb


title: HN23_P11_H03_S87_comb


title: HN23_P11_E09_S57_comb


title: HN28_P3P4_D11_S47_comb


title: HN28_P14_F03_S159_comb


title: HN28_P5_F02_S254_comb


title: HN28_P3P4_G05_S77_comb


title: HN28_P14_C04_S124_comb


title: HN28_P3P4_F06_S66_comb


title: HN28_P5_F08_S260_comb


title: HN28_P3P4_E05_S53_comb


title: HN28_P5_E07_S247_comb


title: HN23_P11_C07_S31_comb


title: HN23_P11_G07_S79_comb


title: HN23_P11_C09_S33_comb


title: HN23_P11_C01_S25_comb


title: HN28_P3P4_E08_S56_comb


title: HN28_P5_B03_S207_comb


title: HN23_P11_B07_S19_comb


title: HN28_P5_G12_S276_comb


title: HN28_P3P4_H01_S85_comb


title: HN28_P5_G05_S269_comb


title: HN23_P11_A04_S4_comb


title: HN28_P5_A05_S197_comb


title: HN28_P14_G04_S172_comb


title: HN28_P3P4_G12_S84_comb


title: HN28_P14_H04_S184_comb


title: HN28_P5_G10_S274_comb


title: HN28_P3P4_F02_S62_comb


title: HN28_P5_A11_S203_comb


title: HN28_P3P4_A03_S3_comb


title: HN28_P3P4_H07_S91_comb


title: HN28_P3P4_A08_S8_comb


title: HN28_P3P4_H08_S92_comb


title: HN23_P11_B04_S16_comb


title: HN28_P3P4_A12_S12_comb


title: HN23_P11_D10_S46_comb


title: HN28_P3P4_D07_S43_comb


title: HN28_P14_D07_S139_comb


title: HN28_P3P4_A07_S7_comb


title: HN28_P3P4_F08_S68_comb


title: HN26_P6_G07_S79_comb


title: HN28_P15_H02_S374_comb


title: HN28_P5_D11_S239_comb


title: HNSCC26_P12_C02_S218_comb


title: HNSCC26_P24_A04_S292_comb


title: HN28_P14_E02_S146_comb


title: HN28_P15_A03_S291_comb


title: HN28_P6_B10_S118_comb


title: HN26_P26_H11_S383_comb


title: HN26_P26_G09_S369_comb


title: HNSCC26_P12_F07_S259_comb


title: HN28_P14_G09_S177_comb


title: HN28_P6_A08_S104_comb


title: HN26_P6_F02_S62_comb


title: HNSCC26_P24_F05_S353_comb


title: HN26_P14_C03_S219_comb


title: HN28_P15_H06_S378_comb


title: HN26_P14_G11_S275_comb


title: HNSCC26_P24_A06_S294_comb


title: HN25_P24_H12_S192_comb


title: HNSCC26_P24_D07_S331_comb


title: HN25_P5_G05_S77_comb


title: HN26_P6_B01_S13_comb


title: HNSCC26_P24_C02_S314_comb


title: HN26_P5_C07_S31_comb


title: HN28_P15_D10_S334_comb


title: HN25_P23_B06_S210_comb


title: HN25_P5_C03_S27_comb


title: HN28_P6_F06_S162_comb


title: HNSCC26_P24_F07_S355_comb


title: HN28_P15_B02_S302_comb


title: HN26_P5_E01_S49_comb


title: HN26_P6_A09_S9_comb


title: HN25_P5_D02_S38_comb


title: HN26_P5_B04_S16_comb


title: HNSCC26_P12_D06_S234_comb


title: HN28_P6_A10_S106_comb


title: HN25_P25_E08_S344_comb


title: HN26_P6_E03_S51_comb


title: HN26_P5_F03_S63_comb


title: HN25_P23_E09_S249_comb


title: HN26_P13_A08_S104_comb


title: HN28_P6_D04_S136_comb


title: HN25_P5_G09_S81_comb


title: HN28_P15_D09_S333_comb


title: HN26_P5_G08_S80_comb


title: HN26_P25_E12_S156_comb


title: HNSCC26_P12_G07_S271_comb


title: HN28_P15_G02_S362_comb


title: HN25_P5_B08_S20_comb


title: HN26_P26_C09_S321_comb


title: HN28_P15_H04_S376_comb


title: HN25_P25_A11_S299_comb


title: HN28_P6_C10_S130_comb


title: HN28_P6_D02_S134_comb


title: HN28_P15_G05_S365_comb


title: HN25_P5_B09_S21_comb


title: HN26_P6_A05_S5_comb


title: HN25_P5_F06_S66_comb


title: HN25_P5_G08_S80_comb


title: HN28_P15_A08_S296_comb


title: HN26_P25_B07_S115_comb


title: HN25_P23_D12_S240_comb


title: HN26_P26_B02_S302_comb


title: HN26_P13_D11_S143_comb


title: HN26_P6_H04_S88_comb


title: HN26_P25_G04_S172_comb


title: HN26_P26_B05_S305_comb


title: HN25_P5_H07_S91_comb


title: HN25_P24_A02_S98_comb


title: HN25_P23_F01_S253_comb


title: HN26_P6_H11_S95_comb


title: HN26_P26_H03_S375_comb


title: HN25_P23_A02_S194_comb


title: HN25_P5_F11_S71_comb


title: HNSCC26_P12_F06_S258_comb


title: HN25_P5_C10_S34_comb


title: HN26_P26_D07_S331_comb


title: HN25_P23_B08_S212_comb


title: HN25_P25_A08_S296_comb


title: HN25_P5_F02_S62_comb


title: HN26_P25_D08_S140_comb


title: HN25_P5_G04_S76_comb


title: HN28_P6_F10_S166_comb


title: HN26_P6_G01_S73_comb


title: HN28_P6_F11_S167_comb


title: HN25_P5_E03_S51_comb


title: HN28_P15_G11_S371_comb


title: HN25_P5_C11_S35_comb


title: HN25_P25_B05_S305_comb


title: HN26_P13_G08_S176_comb


title: HN25_P24_A05_S101_comb


title: HN25_P24_B07_S115_comb


title: HN25_P24_B01_S109_comb


title: HNSCC26_P24_E12_S348_comb


title: HN28_P15_B11_S311_comb


title: HN26_P25_H05_S185_comb


title: HN28_P6_E04_S148_comb


title: HN25_P25_G02_S362_comb


title: HNSCC26_P24_G06_S366_comb


title: HN28_P6_F08_S164_comb


title: HN26_P13_G01_S169_comb


title: HNSCC26_P12_D02_S230_comb


title: HN26_P6_F09_S69_comb


title: HN26_P25_H08_S188_comb


title: HN26_P5_F12_S72_comb


title: HN25_P24_F12_S168_comb


title: HN26_P5_C12_S36_comb


title: HN25_P5_H01_S85_comb


title: HN28_P6_F04_S160_comb


title: HN25_P25_A06_S294_comb


title: HN26_P25_H06_S186_comb


title: HN26_P25_G06_S174_comb


title: HN26_P26_C05_S317_comb


title: HN25_P5_B02_S14_comb


title: HN28_P15_C04_S316_comb


title: HN25_P25_A10_S298_comb


title: HN28_P6_E07_S151_comb


title: HN28_P6_D07_S139_comb


title: HN26_P5_C03_S27_comb


title: HN26_P5_D06_S42_comb


title: HN26_P6_H10_S94_comb


title: HN26_P14_C12_S228_comb


title: HN28_P15_B04_S304_comb


title: HN28_P6_B06_S114_comb


title: HN28_P15_A11_S299_comb


title: HNSCC26_P24_H07_S379_comb


title: HNSCC26_P12_E08_S248_comb


title: HN25_P5_E01_S49_comb


title: HN26_P26_B07_S307_comb


title: HN26_P6_A04_S4_comb


title: HNSCC26_P24_E04_S340_comb


title: HN28_P15_F06_S354_comb


title: HN25_P5_A10_S10_comb


title: HN25_P24_F01_S157_comb


title: HN26_P5_D01_S37_comb


title: HNSCC26_P12_D08_S236_comb


title: HN26_P13_E09_S153_comb


title: HN25_P24_A12_S108_comb


title: HN28_P15_C02_S314_comb


title: HN25_P25_H09_S381_comb


title: HN26_P14_A04_S196_comb


title: HNSCC26_P24_A01_S289_comb


title: HN26_P25_E04_S148_comb


title: HN25_P23_E02_S242_comb


title: HN26_P13_E01_S145_comb


title: HN28_P6_B04_S112_comb


title: HNSCC26_P12_D01_S229_comb


title: HN25_P23_D03_S231_comb


title: HN25_P5_H05_S89_comb


title: HN26_P26_A12_S300_comb


title: HN28_P6_A04_S100_comb


title: HN28_P6_A05_S101_comb


title: HN26_P14_E01_S241_comb


title: HN26_P26_G01_S361_comb


title: HN26_P26_A10_S298_comb


title: HN25_P5_H11_S95_comb


title: HNSCC26_P24_G01_S361_comb


title: HN26_P6_B09_S21_comb


title: HN25_P24_A01_S97_comb


title: HNSCC26_P24_D06_S330_comb


title: HN28_P6_D11_S143_comb


title: HN25_P24_E01_S145_comb


title: HN28_P15_D08_S332_comb


title: HN25_P24_A04_S100_comb


title: HN26_P6_E09_S57_comb


title: HN26_P6_E02_S50_comb


title: HN25_P23_D01_S229_comb


title: HN26_P25_A12_S108_comb


title: HN26_P13_F11_S167_comb


title: HN26_P26_G10_S370_comb


title: HN26_P5_D02_S38_comb


title: HN26_P14_D01_S229_comb


title: HN28_P15_B09_S309_comb


title: HN25_P25_B07_S307_comb


title: HN28_P6_D05_S137_comb


title: HNSCC26_P24_G09_S369_comb


title: HN26_P13_E05_S149_comb


title: HN28_P6_F03_S159_comb


title: HN25_P25_C09_S321_comb


title: HN25_P25_E09_S345_comb


title: HN25_P24_D02_S134_comb


title: HN25_P5_D09_S45_comb


title: HN28_P15_F08_S356_comb


title: HN26_P25_F02_S158_comb


title: HNSCC26_P12_B01_S205_comb


title: HN25_P25_E12_S348_comb


title: HN25_P23_F07_S259_comb


title: HN25_P25_G11_S371_comb


title: HN25_P5_H03_S87_comb


title: HN28_P15_H07_S379_comb


title: HN25_P23_D04_S232_comb


title: HNSCC26_P24_C12_S324_comb


title: HN25_P23_F08_S260_comb


title: HNSCC26_P12_E01_S241_comb


title: HN26_P25_D05_S137_comb


title: HN26_P6_C06_S30_comb


title: HN26_P14_H08_S284_comb


title: HN26_P5_C11_S35_comb


title: HNSCC26_P24_G10_S370_comb


title: HN28_P15_H01_S373_comb


title: HN25_P25_D07_S331_comb


title: HN26_P14_E09_S249_comb


title: T2-HBEC3 50 µg DEP/mL 48 h [200793290121_L]

type: RNA

city: OSLO

first: Steen

last: Mollerup

address: Gydas vei, 8

department: Department of Chemical and Biological Work Environment

country: Norway

institute: National Institute of Occupational Health

description:
Replicate 2
SAMPLE 88

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina iScan System

data_processing: Bead level data were summarized by Illumina GenomeStudio Software v2011.1 Bead summary data was normalized using the quantile method in the Lumi package (R). Only probes with a detection p-value < 0.01 in more than 50 % of the arrays were included for further analyses.

label: biotin

molecule: total RNA

source_name: Human bronchial epithelial cell line

label_protocol: Biotinylated cRNA were prepared with the TargetAmp-Nano Labelig Kit for Illumina arrays

growth_protocol: HBEC3 and T2-HBEC3 were maintained in 1:1 mixture of LHC-9 and RPMI1640.

extract_protocol: RNA was extracted with Isol-RNA Lysis Reagent. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Cells were exposed to different concentrations of DEP (SRM2975) at different time-points.

tag: agent

value: 50 microg DEP/mL

tag: time point

tag: cell line


title: HNSCC26_P12_C11_S227_comb


title: HBEC3 50 µg DEP/mL 48 h [200793290121_K]

description:
Replicate 3
SAMPLE 80


title: HBEC3 200 µg DEP/mL 48 h [200761500031_J]

description:
Replicate 3
SAMPLE 83

value: 200 microg DEP/mL


title: HBEC3 Ctr 48 h [200761500023_I]

description:
Replicate 1
SAMPLE 75


title: HBEC3 50 µg DEP/mL 48 h [200761500023_J]

description:
Replicate 2
SAMPLE 79


title: T2-HBEC3 200 µg DEP/mL 48 h [200761500023_L]

description:
Replicate 2
SAMPLE 91


title: HBEC3 Ctr 48 h [200761500020_H]

description:
Replicate 3
SAMPLE 77


title: HBEC3 50 µg DEP/mL 48 h [200761500033_J]

description:
Replicate 1
SAMPLE 78


title: HBEC3 200 µg DEP/mL 48 h [200761500031_I]

description:
Replicate 1
SAMPLE 81


title: T2-HBEC3 Ctr 48 h [200795790003_L]

description:
Replicate 2
SAMPLE 85


title: HN25_P5_A08_S8_comb


title: HBEC3 200 µg DEP/mL 48 h [200761500020_I]

description:
Replicate 2
SAMPLE 82


title: T2-HBEC3 Ctr 48 h [200761500033_K]

description:
Replicate 1
SAMPLE 84


title: T2-HBEC3 200 µg DEP/mL 48 h [200761500033_L]

description:
Replicate 3
SAMPLE 92


title: T2-HBEC3 Ctr 48 h [200761500023_K]

description:
Replicate 3
SAMPLE 86


title: T2-HBEC3 200 µg DEP/mL 72 h [200793290121_I]

description:
Replicate 3
SAMPLE 68


title: HBEC3 Ctr 48 h [200795790003_K]

description:
Replicate 2
SAMPLE 76


title: T2-HBEC3 50 µg DEP/mL 48 h [200761500018_I]

description:
Replicate 1
SAMPLE 87


title: T2-HBEC3 200 µg DEP/mL 48 h [200761500020_J]

description:
Replicate 1
SAMPLE 90


title: HN25_P24_G08_S176_comb


title: T2-HBEC3 200 µg DEP/mL 24 h [200761500033_H]

description:
Replicate 3
SAMPLE 64


title: HN28_P15_E08_S344_comb


title: T2-HBEC3 Ctr 24 h [200761500018_G]

description:
Replicate 3
SAMPLE 63


title: T2-HBEC3 200 µg DEP/mL 72 h [200761500023_G]

description:
Replicate 2
SAMPLE 62


title: HN25_P5_F08_S68_comb


title: T2-HBEC3 50 µg DEP/mL 48 h [200761500031_K]

description:
Replicate 3
SAMPLE 89


title: HN26_P14_A12_S204_comb


title: HN28_P6_H01_S181_comb


title: HN26_P5_D11_S47_comb


title: HN28_P6_C05_S125_comb


title: HN28_P15_H03_S375_comb


title: HN28_P6_H11_S191_comb


title: HN26_P14_D07_S235_comb


title: HN28_P15_C06_S318_comb


title: HN25_P23_D02_S230_comb


title: HN25_P24_G01_S169_comb


title: HN25_P5_C02_S26_comb


title: HN25_P5_B10_S22_comb


title: HN28_P15_H05_S377_comb


title: HN25_P23_E06_S246_comb


title: HN28_P15_A04_S292_comb


title: HNSCC26_P12_B06_S210_comb


title: T2-HBEC3 Ctr 72 h [200795790003_I]

description:
Replicate 2
SAMPLE 61


title: T2-HBEC3 200 µg DEP/mL 72 h [200793290121_H]

description:
Replicate 1
SAMPLE 56


title: HN25_P5_G03_S75_comb


title: HN26_P13_A11_S107_comb


title: HN28_P6_F07_S163_comb


title: T2-HBEC3 200 µg DEP/mL 24 h [200761500033_G]

description:
Replicate 2
SAMPLE 58


title: T2-HBEC3 Ctr 72 h [200761500031_G]

description:
Replicate 1
SAMPLE 55


title: HN26_P14_B03_S207_comb


title: HNSCC26_P24_A07_S295_comb


title: HN25_P23_G01_S265_comb


title: HN28_P6_H02_S182_comb


title: HN25_P24_B06_S114_comb


title: T2-HBEC3 200 µg DEP/mL 24 h [200795790003_H]

description:
Replicate 1
SAMPLE 52


title: T2-HBEC3 Ctr 24 h [200761500020_F]

description:
Replicate 2
SAMPLE 57


title: HN26_P14_G10_S274_comb


title: HBEC3 200 µg DEP/mL 72 h [200761500018_F]

description:
Replicate 3
SAMPLE 50


title: HBEC3 200 µg DEP/mL 24 h [200761500020_E]

description:
Replicate 3
SAMPLE 46


title: T2-HBEC3 Ctr 24 h [200761500018_J]

description:
Replicate 1
SAMPLE 51


title: HN25_P5_H08_S92_comb


title: HBEC3 Ctr 72 h [200761500023_F]

description:
Replicate 3
SAMPLE 49


title: HN26_P6_H05_S89_comb


title: HN28_P6_B02_S110_comb


title: HN25_P23_C04_S220_comb


title: HN25_P23_H08_S284_comb


title: HN25_P5_C07_S31_comb


title: HBEC3 Ctr 72 h [200761500033_F]

description:
Replicate 2
SAMPLE 43


title: HBEC3 200 µg DEP/mL 72 h [200793290121_G]

description:
Replicate 2
SAMPLE 44


title: HBEC3 200 µg DEP/mL 24 h [200761500018_E]

description:
Replicate 2
SAMPLE 40


title: HN25_P24_B04_S112_comb


title: HBEC3 Ctr 24 h [200761500031_F]

description:
Replicate 3
SAMPLE 45


title: HN25_P24_G07_S175_comb


title: HN26_P26_B04_S304_comb


title: HN28_P15_G12_S372_comb


title: HN28_P15_H09_S381_comb


title: HN26_P5_H10_S94_comb


title: HN26_P26_C10_S322_comb


title: HN25_P24_F08_S164_comb


title: HN26_P25_F10_S166_comb


title: HN26_P13_E12_S156_comb


title: HN25_P25_E02_S338_comb


title: HN26_P26_F02_S350_comb


title: HN26_P25_A08_S104_comb


title: HN28_P15_E01_S337_comb


title: HN25_P24_E10_S154_comb


title: HN26_P14_F10_S262_comb


title: HN26_P6_C01_S25_comb


title: HBEC3 Ctr 24 h [200795790003_G]

description:
Replicate 2
SAMPLE 39


title: HN28_P15_F09_S357_comb


title: HN26_P5_G12_S84_comb


title: HN28_P15_D03_S327_comb


title: HN25_P5_E07_S55_comb


title: HN26_P5_E03_S51_comb


title: HNSCC26_P12_A07_S199_comb


title: HBEC3 200 µg DEP/mL 72 h [200761500031_E]

description:
Replicate 1
SAMPLE 38


title: HN28_P6_G09_S177_comb


title: HBEC3 Ctr 72 h [200793290121_F]

description:
Replicate 1
SAMPLE 37


title: HN26_P25_B10_S118_comb


title: HBEC3 200 µg DEP/mL 24 h [200761500033_E]

description:
Replicate 1
SAMPLE 34


title: HN26_P6_G04_S76_comb


title: HBEC3 Ctr 24 h [200761500020_D]

description:
Replicate 1
SAMPLE 33


title: Type 2 diabetes T2D_2060

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

hyb_protocol: Hybridization of 700 ng of each biotinylated cRNA sample on the BeadChip was performed at 58°C for 16–18 hours

scan_protocol: BeadChips were scanned using the Illumina Bead Array Reader (Illumina, San Diego, USA).

data_processing: raw data were log2 transformed and quantile normalized using the lumi package from bioconductor in the R statistical software

source_name: Type 2 diabetes_duodenum

label_protocol: biotin labeling were performed using the TargetAmp Labeling Kit (Illumina, San Diego, USA)

extract_protocol: Total RNA was isolated from intestinal tissue using the RNeasy lipid tissue extraction kit and on-column DNase treatment following the manufacturer’s recommendations (Qiagen, Valencia, USA). RNA concentration and quality were respectively assessed using the NanoDrop spectrophotometer (Thermo Scientific, Wilmington, USA) and the Agilent Technologies 2100 bioanalyzer (Agilent, Santa Clara, USA). Only total RNA samples with a RIN higher than seven were included in the following experiments.

tag: subject status

value: Type II Diabetes

tag: tissue

value: Duodenum


title: Insulin resistant IR_2129

value: insulin-resistant (HOMA-IR>7) obese individual

tag: pair

value: Pair 9


title: Type 2 diabetes T2D_1916


title: Type 2 diabetes T2D_2063


title: Insulin resistant IR_2054

value: Pair 2


title: Insulin resistant IR_2127

value: Pair 8


title: Type 2 diabetes T2D_1881


title: Insulin resistant IR_2126

value: Pair 6


title: HN28_P6_B11_S119_comb


title: Insulin resistant IR_2021

value: Pair 5


title: Insulin resistant IR_2029

value: Pair 10


title: Insulin resistant IR_2013

value: Pair 3


title: HN26_P25_B05_S113_comb


title: HN28_P15_B03_S303_comb


title: HN28_P15_E11_S347_comb


title: HN26_P14_D03_S231_comb


title: HN26_P14_A05_S197_comb


title: HN25_P24_G05_S173_comb


title: HN26_P25_C07_S127_comb


title: HN25_P5_E04_S52_comb


title: HN26_P13_F12_S168_comb


title: HN25_P25_C03_S315_comb


title: HN25_P23_H10_S286_comb


title: HN26_P5_G02_S74_comb


title: HN28_P6_F01_S157_comb


title: HN25_P23_H04_S280_comb


title: T2-HBEC3 Ctr 72 h [200761500031_H]

description:
Replicate 3
SAMPLE 67


title: HNSCC26_P12_D10_S238_comb


title: HN26_P26_B09_S309_comb


title: HN28_P6_D10_S142_comb


title: Insulin resistant IR_2000

value: Pair 7


title: HN28_P6_B12_S120_comb


title: Insulin resistant IR_1932

value: Pair 1


title: HNSCC26_P24_B02_S302_comb


title: Insulin susceptible IS_2114

value: insulin-sensitive (HOMA-IR<3) obese individual


title: HN25_P23_C05_S221_comb

value: Maxima


title: Insulin resistant IR_1934

value: Pair 4


title: Insulin susceptible IS_2173


title: HN26_P26_B01_S301_comb

value: Lymph node


title: HNSCC26_P24_E01_S337_comb


title: Insulin susceptible IS_2066


title: HNSCC26_P24_H06_S378_comb


title: HN26_P14_E12_S252_comb


title: HN28_P6_A03_S99_comb

value: Primary (oral cavity)


title: HNSCC26_P24_A05_S293_comb


title: Insulin susceptible IS_2062


title: HN25_P23_F04_S256_comb


title: HN26_P26_F04_S352_comb


title: HN26_P14_D04_S232_comb


title: Insulin susceptible IS_2102


title: Insulin susceptible IS_2050


title: HN26_P6_E01_S49_comb


title: Insulin susceptible IS_2052


title: HNSCC26_P12_D04_S232_comb


title: HN26_P14_G04_S268_comb


title: HN25_P5_A12_S12_comb


title: Insulin susceptible IS_1940


title: HN26_P14_C09_S225_comb


title: HN28_P15_C12_S324_comb


title: HNSCC26_P12_H10_S286_comb


title: HN28_P15_D05_S329_comb


title: HN25_P5_A06_S6_comb


title: HN26_P5_A06_S6_comb


title: HN25_P25_C08_S320_comb


title: HNSCC26_P24_D04_S328_comb


title: HN26_P26_G04_S364_comb


title: Insulin susceptible IS_1878


title: HN25_P5_H02_S86_comb


title: HN28_P15_G03_S363_comb


title: HN25_P23_E05_S245_comb


title: Insulin susceptible IS_2043


title: HN25_P25_F11_S359_comb


title: HN28_P15_D02_S326_comb


title: crl1 mutant, 4 hours after auxin treatment, repetition 1

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

country: France

institute: Université Montpellier 2

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant, 4 h after auxin treatment, repetition 1

hyb_protocol: All steps of Microarray hybridization and data processing were performed according manufacturer’s instructions (Affymetrix). Equipments were provided by Affymetrix Company. Twelve μg of biotin-labelled antisens RNAs were fragmented and hybridized to GeneChip Rice Genome Arrays (Affymetrix) for 16h at 45°C and 60rpm in a Hybridization Oven 645.

scan_protocol: Arrays were washed, labeled with phycoerythrin on the Fluidic Station 450 and read with the Scanner 3000 7G.

data_processing:
Data acquisition was done with the GeneChip Command Console. Array pictures were analyzed with MAS5 algorithm of the Expression Console software (Affymetrix).
Default parameters were applied, global scaling method was used to normalize data (TGT value set at 100).

label: Biotin

organism: Oryza sativa

source_name: crl1 mutant, 4h after auxin treatment

label_protocol: Antisense RNA strand were biotynilated according the Affymetrix (Affymetrix, CA, USA) IVT Express protocol.

growth_protocol: Dehulled and surface sterilized seeds of Oryza sativa, cv. Taichung65, from wild type or crl1 mutant, were cultured in sterile closed pots containing half strength Murashige and Skoog (MS) medium  and were incubated at 26°C under a 12h light/12h dark photoperiod. Seven day-old seedlings were transferred in flasks containing half strength MS liquid medium.

extract_protocol: Total RNA was extracted from frozen twenty stem bases using a RNeasy Plant Mini Kit (Quiagen) according to manufacturer’s instructions. Residual genomic DNA was removed with the RNAse-Free DNase Set (Quiagen) during RNA purification. They were quantified with a NanoQuant at 260nm wavelength and analyzed for quality on a BioAnalyzer 2100 (Agilent, CA, USA).

treatment_protocol: One day after transfer of seedlings in liquid culture medium, the medium was supplemented with indole acetic acid (IAA) for a final concentration of 10-6 M. Stem bases were collected just before,  2h and 4 h after auxin treatment and immediately frozen in liquid nitrogen for RNA extraction.

tag: genotype

value: crl1 mutant

tag: treatment

value: auxin

tag: time

value: 4 h

value: stem bases of 8 day old seedlings

tag: cultivar

value: Taichung 65


title: crl1 mutant, 4 hours after auxin treatment, repetition 2

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant, 4 h after auxin treatment, repetition 2


title: Wild Type, 4 hours after auxin treatment, repetition 2

description: Gene expression data from stem bases of 8 days old seedlings of wild type, 4 h after auxin treatment, repetition 2

source_name: Wild type, 4h after auxin treatment

value: Wild type


title: crl1 mutant, untreated, t0, repetition 2

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant, untreated, repetition 2

source_name: crl1 mutant, untreated

value: untreated

value: control


title: crl1 mutant, 2 hours after auxin treatment, repetition 1

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant, 2 h after auxin treatment, repetition 1

source_name: crl1 mutant, 2h after auxin treatment

value: 2 h


title: Wild Type, 2 hours after auxin treatment, repetition 2

description: Gene expression data from stem bases of 8 days old seedlings of wild type, 2 h after auxin treatment, repetition 2

source_name: Wild type, 2h after auxin treatment


title: HN25_P5_E08_S56_comb


title: HN26_P14_F03_S255_comb


title: HN28_P6_H09_S189_comb


title: HN26_P25_A05_S101_comb


title: crl1 mutant, 2 hours after auxin treatment, repetition 2

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant, 2 h after auxin treatment, repetition 2


title: Wild Type, 2 hours after auxin treatment, repetition 1

description: Gene expression data from stem bases of 8 days old seedlings of wild type, 2 h after auxin treatment, repetition 1


title: HNSCC26_P12_C07_S223_comb


title: HN26_P14_F02_S254_comb


title: HN25_P5_H12_S96_comb


title: HN25_P5_G02_S74_comb


title: HN25_P5_D08_S44_comb


title: Wild Type, 4 hours after auxin treatment, repetition 1

description: Gene expression data from stem bases of 8 days old seedlings of wild type, 4 h after auxin treatment, repetition 1


title: HN25_P25_A03_S291_comb


title: HN26_P13_H03_S183_comb


title: HN25_P5_C08_S32_comb


title: HNSCC26_P24_D11_S335_comb


title: Wild Type, untreated, t0, repetition 1

description: Gene expression data from stem bases of 8 days old seedlings of wild type, untreated, repetition 1

source_name: Wild type, untreated


title: HN26_P13_E07_S151_comb


title: crl1 mutant, untreated, t0, repetition 1

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant, untreated, repetition 1


title: Wild Type, untreated, t0, repetition 2

description: Gene expression data from stem bases of 8 days old seedlings of wild type, untreated, repetition 2


title: HNSCC26_P12_G10_S274_comb


title: HN28_P6_C11_S131_comb


title: HNSCC26_P12_E03_S243_comb


title: HN25_P5_C12_S36_comb


title: HN28_P15_E03_S339_comb


title: MDAMB231-siCapG-rep4

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

description: Gene expression after CapG knock-down

hyb_protocol: After fragmentation labelled cRNA was hybridized to Agilent 4x44k Whole Human Genome Microarrays for 17 h at 65 °C according to the manufacturers´ protocol.

scan_protocol: Microarrays were scanned in extended dynamic range (XDR) mode as described in the manufacturers´ protocol (Scanner G2505B; Agilent Technologies). Signal intensities on 16 bit tiff images were calculated by Feature Extraction software (FE, Vers. 9.5; Agilent Technologies).

data_processing: quantile normalization / baseline transformation to the median of all samples (GeneSpring GX, Vers. 11; Agilent Technologies)

source_name: MDA-MB-231, CapG knockdown

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed according to the manufacturers´ protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA.

growth_protocol: Cell lines were grown in complete medium consisting of DMEM basic medium with 1 mg/ml glucose supplemented with 10% Fetal Calf Serum (FCS), 1% glutamic acid, 1% MEM vitamins and 0,1% gentamycin at 37°C and 5% CO2. Passaging was performed every 48h.

extract_protocol: Total RNA was isolated from samples using RNeasy® Mini Kit (Qiagen, Germany) according to the manufactures’ protocol

treatment_protocol:
For stable CapG overexpression in BT-20 cells a PCR-amplified cDNA fragment of human CapG comprising the entire coding region supplemented with flanking NotI and BlnI restriction sites, respectively, was digested with the corresponding enzymes (New England biolabs, UK) and cloned into the retroviral S11IN expression vector. S11IN derives from SFβ11 (kindly provided by Christopher Baum, Hannover Medical School, Hannover, Germany). HEK-239 cells were cultured in DMEM supplemented with 10% FCS, 2 mM K-glutamine, penicillin G (100 U/ml) and streptomycin (100 µg/ml). These cells were cotransfected with 70 µg of helper plasmid pHIT60, 7 µg of pczVSV-G envelope and 7 µg of S11IN (control vector) or S11-CapG-IN by using Fugene 6 (Roche, Germany) following the manufacturers’ instructions. Both vectors are based on SF11 with 3’LTR of the spleen focus-forming virus and internal ribosomal entry site (IRES). Twenty-four hours after transfection, the medium was changed to Iscove’s modified medium. Fourty-eight hours after transfection, supernatants were filtered through a 0.45 µm filter and 1 ml virus supernatant and 5 µl Protamin were used to infect BT-20 cells on 6 well plates with 3.5 x 105 cells/well. Forty-eight hours after infection, cells expressing the S11IN or S11-CapG-IN vector were selected by using G418 to a final concentration of 1 mg/ml. BT-20 overexpressing CapG are called BT-20 CapG.
For siRNA treatment 5 x 104 cells per well were placed in 6-well plates one day before they were transfected with siRNA. MDA-MB-231 cells were transfected with commercial available CapG specific siRNA (Ambion Inc., USA) using HiPerFect (Qiagen, Germany) according to manufacturers’ instructions. Final siRNA concentration was 15 nM and the sequence is: 5’-GGUGGUGUGGAGUCAGCAU-3’, which binds within position 335-373 of CapG coding region. MDA-MB-231 CapG knock-down cell are called MDA-MB-231 siCapG. CapG knock-down was verified by Western blot analysis

value: breast cancer cell line

value: ATCC® HTB-26

value: CapG knock-down


title: MDAMB231-siCapG-rep2

description: Gene expression after CapG knock-down


title: HN25_P25_E07_S343_comb


title: MDAMB231-siCapG-rep1

description: Gene expression after CapG knock-down


title: MDAMB231-control-rep4

description: Gene expression profile as reference

source_name: MDA-MB-231, control


title: MDAMB231-siCapG-rep3

description: Gene expression after CapG knock-down


title: HN28_P15_A07_S295_comb


title: HN25_P5_D07_S43_comb


title: HN26_P5_E12_S60_comb


title: HN25_P5_C09_S33_comb


title: HN25_P23_B03_S207_comb


title: HN26_P25_C04_S124_comb


title: HN26_P14_F05_S257_comb


title: HNSCC26_P12_F11_S263_comb


title: HN25_P24_E04_S148_comb


title: HN26_P25_F05_S161_comb


title: HN26_P5_E02_S50_comb


title: HN25_P25_A09_S297_comb


title: MDAMB231-control-rep2

description: Gene expression profile as reference


title: HNSCC26_P24_F09_S357_comb


title: HN26_P14_D06_S234_comb


title: HN26_P6_B07_S19_comb


title: MDAMB231-control-rep1

description: Gene expression profile as reference


title: MDAMB231-control-rep3

description: Gene expression profile as reference


title: HN25_P25_D05_S329_comb


title: HN26_P14_D10_S238_comb


title: HN26_P5_F05_S65_comb


title: HNSCC26_P12_A02_S194_comb


title: HN26_P26_E08_S344_comb


title: HN25_P5_D01_S37_comb


title: HN26_P6_H06_S90_comb


title: HN25_P5_H06_S90_comb


title: HN28_P6_C02_S122_comb


title: HNSCC26_P24_B08_S308_comb


title: HN28_P6_D06_S138_comb


title: pag1Δ_planta_rep3

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Gene expression of the pag1Δ mutant at 4 hpi on cucumber leaf surfaces

hyb_protocol: 600 ng 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Colletotrichum orbiculare Microarray 8x60K 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 by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) and GeneSpring GX12.1 using default parameters.

organism: Colletotrichum orbiculare

source_name: pag1Δ in planta, 4 hpi, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification 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: Each strains were cultured on potato dextrose agar at 24°C in the dark. Conidia were harvested from 6 day old mycelia.

extract_protocol: RNA was prepared using the Agilent Plant RNA Isolation Mini kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For sampling of immature appressoria in vitro, 10 mL of a conidial suspension [5 × 105 conidia/mL 0.1% (w/v) yeast extract solution] was placed on polystyrene petri dishes and incubated at 24°C in the dark for 1 h. The yeast extract solution was then removed and replaced with distilled water. After incubation for 3 h, the distilled water was removed and cells were harvested using a scraper in 10 mL of RNAlater (Life Technologies) containing 1 mL of 0.01% (v/v) Tween 20. For sampling of immature appressoria in planta, 10 µL of a conidial suspension (5 × 105 conidia/mL distilled water) was spotted onto the abaxial surface of cucumber cotyledons and incubated in a humid box at 24 °C in the dark. After 4 h, the lower epidermises of the cotyledons were peeled off and grinded in liquid nitrogen.

value: germinating conidia

tag: growth surface

value: cucumber leaf surfaces

value: 4 hpi


title: HN26_P14_B11_S215_comb

value: Maxima

value: Lymph node


title: HN26_P25_G05_S173_comb


title: HNSCC26_P24_G05_S365_comb


title: HN25_P25_H06_S378_comb


title: HN26_P25_C03_S123_comb


title: HNSCC26_P24_B12_S312_comb


title: HN25_P5_A09_S9_comb

value: Primary (oral cavity)


title: HN25_P25_F03_S351_comb


title: HN25_P5_B03_S15_comb


title: HN28_P15_D12_S336_comb


title: pag1Δ_planta_rep2

source_name: pag1Δ in planta, 4 hpi, replicate 2


title: WT_planta_rep1

description: Gene expression of the wild type at 4 hpi on cucumber leaf surfaces

source_name: Wild-type in planta, 4 hpi, replicate1

value: wt


title: pag1Δ_planta_rep1

source_name: pag1Δ in planta, 4 hpi, replicate 1


title: Cbk1CA_vitro_rep2

description: Gene expression of the Cbk1-CA strain at 4 hpi on polystyrene petri dishes

source_name: Cbk1-CA in vitro, 4 hpi, replicate2

value: polystyrene petri dishes


title: Cbk1CA_vitro_rep1

source_name: Cbk1-CA in vitro, 4 hpi, replicate1


title: WT_planta_rep3

source_name: Wild-type in planta, 4 hpi, replicate3


title: HN26_P25_D04_S136_comb

source_name: Head and neck cancer single cell


title: WT_planta_rep2

source_name: Wild-type in planta, 4 hpi, replicate2


title: HN25_P24_C08_S128_comb


title: HNSCC26_P24_D12_S336_comb


title: HN26_P6_D05_S41_comb


title: HN25_P24_D09_S141_comb


title: HN28_P15_F10_S358_comb


title: HN28_P6_C07_S127_comb


title: HN26_P6_F07_S67_comb


title: HN25_P23_A08_S200_comb


title: HN26_P6_F08_S68_comb


title: HN28_P6_F09_S165_comb


title: HN25_P25_D09_S333_comb


title: HN28_P15_C07_S319_comb


title: HN25_P25_C10_S322_comb


title: HN28_P15_B05_S305_comb


title: HN28_P15_E02_S338_comb


title: HN28_P15_C05_S317_comb


title: WT_vitro_rep3

description: Gene expression of the wild type at 4 hpi on polystyrene petri dishes

source_name: Wild-type in vitro, 4 hpi, replicate3


title: HNSCC26_P24_E02_S338_comb


title: WT_vitro_rep1

source_name: Wild-type in vitro, 4 hpi, replicate1


title: HN25_P24_D12_S144_comb


title: HNSCC26_P24_B01_S301_comb


title: Cbk1CA_vitro_rep3

source_name: Cbk1-CA in vitro, 4 hpi, replicate3


title: HN26_P5_G06_S78_comb


title: HN28_P6_G11_S179_comb


title: HN28_P6_H12_S192_comb


title: HN28_P15_C11_S323_comb


title: HN25_P5_H04_S88_comb


title: HN25_P23_B02_S206_comb


title: HN25_P5_G12_S84_comb


title: HN25_P5_B07_S19_comb


title: HN26_P13_F01_S157_comb


title: HN26_P5_A07_S7_comb


title: HN25_P23_A12_S204_comb


title: HN26_P26_A03_S291_comb


title: HN26_P6_F03_S63_comb


title: HN28_P6_G08_S176_comb


title: WT_vitro_rep2

source_name: Wild-type in vitro, 4 hpi, replicate2


title: HNSCC26_P24_B11_S311_comb


title: HN26_P6_B08_S20_comb


title: HN26_P5_H04_S88_comb


title: HN28_P6_D08_S140_comb


title: HN26_P5_A09_S9_comb


title: HN28_P6_F05_S161_comb


title: HN25_P25_E01_S337_comb


title: HN25_P5_D04_S40_comb


title: HN28_P6_F12_S168_comb


title: HN28_P6_B09_S117_comb


title: HN28_P15_A02_S290_comb


title: HNSCC26_P12_F08_S260_comb


title: HN25_P5_A07_S7_comb


title: HN25_P5_E05_S53_comb


title: HN25_P23_B01_S205_comb


title: HN26_P13_D01_S133_comb


title: HN26_P14_B09_S213_comb


title: HN25_P24_F05_S161_comb


title: HN26_P13_A02_S98_comb


title: HN25_P25_C02_S314_comb


title: HN25_P24_C10_S130_comb


title: HN28_P6_B07_S115_comb


title: HN28_P6_D12_S144_comb


title: HN26_P5_E08_S56_comb


title: HN26_P14_H11_S287_comb


title: HN26_P26_C04_S316_comb


title: HN26_P25_B08_S116_comb


title: HN28_P6_E10_S154_comb


title: HN26_P26_B08_S308_comb


title: HN25_P23_C06_S222_comb


title: HN25_P24_F02_S158_comb


title: HN25_P23_H03_S279_comb


title: HN25_P5_D10_S46_comb


title: HNSCC26_P24_C10_S322_comb


title: HN26_P26_H09_S381_comb


title: HN26_P14_D05_S233_comb


title: HN26_P14_A01_S193_comb


title: HN28_P6_E02_S146_comb


title: HN28_P15_H08_S380_comb


title: HN25_P23_G06_S270_comb


title: HN25_P23_E12_S252_comb


title: HN25_P24_F07_S163_comb


title: HN25_P24_G10_S178_comb


title: HN26_P25_E11_S155_comb


title: HN26_P25_C12_S132_comb


title: HN26_P13_G06_S174_comb


title: HN25_P24_E11_S155_comb


title: HN26_P25_D02_S134_comb


title: HN25_P5_F09_S69_comb


title: HN28_P15_A06_S294_comb


title: HN28_P15_F12_S360_comb


title: HN25_P23_B11_S215_comb


title: HN28_P15_H11_S383_comb


title: HN25_P24_G09_S177_comb


title: HN26_P26_D12_S336_comb


title: HN28_P15_G07_S367_comb


title: HN26_P26_F07_S355_comb


title: HN28_P6_E09_S153_comb


title: HN25_P24_D08_S140_comb


title: HN28_P6_E06_S150_comb


title: HN26_P25_H04_S184_comb


title: HN25_P5_E06_S54_comb


title: HN26_P26_B12_S312_comb


title: HN26_P14_C04_S220_comb


title: HN25_P5_F12_S72_comb


title: HN25_P5_D12_S48_comb


title: HN26_P6_H12_S96_comb


title: HN26_P26_D10_S334_comb


title: HN28_P15_H10_S382_comb


title: HNSCC26_P24_H08_S380_comb


title: HN26_P5_G03_S75_comb


title: HN26_P14_D08_S236_comb


title: HN26_P14_C10_S226_comb


title: HN28_P15_D01_S325_comb


title: HN25_P25_A07_S295_comb


title: HNSCC26_P24_E10_S346_comb


title: HN26_P5_F02_S62_comb


title: HN25_P25_B08_S308_comb


title: HN28_P15_F05_S353_comb


title: HN26_P6_B05_S17_comb


title: HN28_P15_B10_S310_comb


title: HN25_P23_B12_S216_comb


title: HN26_P26_H04_S376_comb


title: HNSCC26_P12_F04_S256_comb


title: HN26_P14_F07_S259_comb


title: HN26_P25_G08_S176_comb


title: HN25_P5_D05_S41_comb


title: HN28_P6_A11_S107_comb


title: HNSCC26_P24_G03_S363_comb


title: HN26_P5_F01_S61_comb


title: HN25_P25_F05_S353_comb


title: HN26_P14_B04_S208_comb


title: HN25_P5_E09_S57_comb


title: HN26_P14_H03_S279_comb


title: HN28_P6_D03_S135_comb


title: HN26_P26_D03_S327_comb


title: HN26_P13_B04_S112_comb


title: HN26_P6_G03_S75_comb


title: HN25_P24_B12_S120_comb


title: HN28_P6_E12_S156_comb


title: HNSCC26_P24_A09_S297_comb


title: HNSCC26_P24_F11_S359_comb


title: HN25_P5_G10_S82_comb


title: HN25_P25_G12_S372_comb


title: HN26_P6_B02_S14_comb


title: HN26_P25_F09_S165_comb


title: HN28_P15_A01_S289_comb


title: HN26_P5_F06_S66_comb


title: HN25_P5_B01_S13_comb


title: HN26_P25_E03_S147_comb


title: HN25_P23_H02_S278_comb


title: HN28_P6_C01_S121_comb


title: HN26_P13_H09_S189_comb


title: HNSCC26_P24_B09_S309_comb


title: HN28_P15_D11_S335_comb


title: HN26_P13_G10_S178_comb


title: HN25_P24_A08_S104_comb


title: HN26_P13_F07_S163_comb


title: HN26_P13_D06_S138_comb


title: HN25_P5_H09_S93_comb


title: HN26_P13_F04_S160_comb


title: HN26_P25_G03_S171_comb


title: HN26_P14_A02_S194_comb


title: HN28_P6_G06_S174_comb


title: HNSCC26_P24_F08_S356_comb


title: HN25_P25_C07_S319_comb


title: HN28_P6_H10_S190_comb


title: HN26_P25_C02_S122_comb


title: HNSCC26_P12_H07_S283_comb


title: HN26_P25_A07_S103_comb


title: HN25_P24_H04_S184_comb


title: HN28_P15_C09_S321_comb


title: HN26_P14_C05_S221_comb


title: HN26_P13_C04_S124_comb


title: HN25_P25_A12_S300_comb


title: HN28_P15_B12_S312_comb


title: HN25_P24_G02_S170_comb


title: HN25_P5_B12_S24_comb


title: HNSCC26_P24_H10_S382_comb


title: HNSCC26_P12_H11_S287_comb


title: HNSCC26_P24_C09_S321_comb


title: HN26_P5_D09_S45_comb


title: HN25_P5_A05_S5_comb


title: HN26_P6_A08_S8_comb


title: HNSCC26_P24_D02_S326_comb


title: HN26_P26_F06_S354_comb


title: HN26_P25_A01_S97_comb


title: HN25_P5_B04_S16_comb


title: HN26_P25_A03_S99_comb


title: HN28_P6_B03_S111_comb


title: HN25_P5_B06_S18_comb


title: HN25_P24_F06_S162_comb


title: HN25_P24_H02_S182_comb


title: HNSCC26_P12_D11_S239_comb


title: HN26_P25_B03_S111_comb


title: HN28_P6_A02_S98_comb


title: HNSCC26_P24_D01_S325_comb


title: HN25_P23_H09_S285_comb


title: HN26_P5_H08_S92_comb


title: HN25_P25_E06_S342_comb


title: HN28_P6_H07_S187_comb


title: HN28_P6_A09_S105_comb


title: HN25_P23_C01_S217_comb


title: HN26_P6_B04_S16_comb


title: HN26_P14_E08_S248_comb


title: HNSCC26_P12_G11_S275_comb


title: HN26_P26_E10_S346_comb


title: HNSCC26_P12_G04_S268_comb


title: HN26_P5_G11_S83_comb


title: HN25_P25_F01_S349_comb


title: HN25_P23_G05_S269_comb


title: HN26_P25_E02_S146_comb


title: HN26_P13_E03_S147_comb


title: HN25_P5_E11_S59_comb


title: HN25_P5_F01_S61_comb


title: HN25_P25_B12_S312_comb


title: HN26_P5_D12_S48_comb


title: HNSCC26_P24_C01_S313_comb


title: HN25_P5_E12_S60_comb


title: HN26_P6_D08_S44_comb


title: HNSCC26_P24_F12_S360_comb


title: HN26_P13_D07_S139_comb


title: HN25_P5_C05_S29_comb


title: HN26_P26_H05_S377_comb


title: HN28_P6_D09_S141_comb


title: HNSCC26_P24_F03_S351_comb


title: HN26_P5_E06_S54_comb


title: HN25_P24_B02_S110_comb


title: HN25_P25_C01_S313_comb


title: HN26_P6_B06_S18_comb


title: HN28_P15_G06_S366_comb


title: HN25_P5_E10_S58_comb


title: HNSCC26_P24_H05_S377_comb


title: HN25_P25_C11_S323_comb


title: HN26_P25_C09_S129_comb


title: HN26_P25_A11_S107_comb


title: HN26_P14_H05_S281_comb


title: HN26_P14_H06_S282_comb


title: HN26_P14_D11_S239_comb


title: HN28_P6_G05_S173_comb


title: HN28_P15_D06_S330_comb


title: HN26_P5_H01_S85_comb


title: HN26_P25_H09_S189_comb


title: HN25_P25_C04_S316_comb


title: HN26_P25_H01_S181_comb


title: Heart_48h_AngII_control_rep4

description:
Control Ang_04
Transgene: homozygous p38α flox/flox

hyb_protocol: After fragmentation labelled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays for 17 h at 65 °C.

scan_protocol: Microarrays were scanned as described in the manufacturers´ protocol. Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 11.0.1.1; Agilent Technologies).

data_processing: Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.

organism: Mus musculus

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA.

extract_protocol: RNA was isolated using Fibrous Tissue RNeasy Kit, Qiagen according to the manufacturers protocol.

treatment_protocol: Mice were treated with 1.5mg/kg/d Angiotensin II via osmotic mini pumps over 48 hours.

tag: gender

value: male

tag: strain

value: Angiotensin II

tag: genotype/variation

value: Heart apex


title: Heart_48h AngII_KO_rep1

description:
KO Ang_01
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox

source_name: Heart_48h AngII_KO

extract_protocol: RNA was isolated using Fibrous Tissue RNeasy Kit, Qiagen according to the manufacturer's protocol.

treatment_protocol: Mice were either treated with 1.5mg/kg/d Angiotensin II  via osmotic mini pumps over 48 hours (Ang) or organs were harvested from untreated mice (Basal).

value: p38MAPK{alpha} KO in vascular smooth muscle cells and cardiomyocytes


title: Heart_48h_AngII_KO_rep1

description:
KO Ang_01
Transgene: heterozygous: α-MHC mercremer, homozygous p38α flox/flox

value: p38MAPK{alpha} KO in cardiomyocytes


title: Heart_48h_AngII_control_rep2

description:
Control Ang_02
Transgene: homozygous p38α flox/flox

value: control


title: Heart_48h AngII_control_rep3

description:
Control Ang_03
Transgene: homozygous p38α flox/flox

source_name: Heart_48h AngII_control


title: Heart_untreated_KO_rep3

description:
KO Basal_03
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox

value: untreated


title: Heart_48h AngII_control_rep2


title: Heart_48h_AngII_control_rep3


title: Heart_48h AngII_KO_rep3

description:
KO Ang_03
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox


title: Heart_untreated_KO_rep4

description:
KO Basal_04
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox


title: Heart_48h_AngII_KO_rep3

description:
KO Ang_03
Transgene: heterozygous: α-MHC mercremer, homozygous p38α flox/flox


title: Heart_untreated_KO_rep2

description:
KO Basal_02
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox


title: Heart_48h_AngII_control_rep1

description:
Control Ang_01
Transgene: homozygous p38α flox/flox


title: Heart_48h_AngII_KO_rep2

description:
KO Ang_02
Transgene: heterozygous: α-MHC mercremer, homozygous p38α flox/flox


title: Heart_untreated_KO_rep1

description:
KO Basal_01
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox


title: Heart_48h AngII_control_rep4


title: Heart_48h AngII_control_rep1


title: Heart_untreated_control_rep4

description:
Control Basal_04
Transgene: homozygous p38α flox/flox


title: Heart_48h AngII_KO_rep4

description:
KO Ang_04
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox


title: Heart_untreated_control_rep3

description:
Control Basal_03
Transgene: homozygous p38α flox/flox


title: Heart_untreated_control_rep2

description:
Control Basal_02
Transgene: homozygous p38α flox/flox


title: Heart_48h AngII_KO_rep2

description:
KO Ang_02
Transgene: heterozygous: SM22α Cre KI, homozygous p38α flox/flox


city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

description: untreated rat stroma surrounding xenograft tumor, sample 2, array slide 18035

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Human Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used. Arrays were then batch-corrected (using array slide number as the batch variable), using the Combat software. 'signal' a measure of the ratio of transcript abundance of the sample versus a universal RNA reference.

label: Alexa Fluor 647

organism: Rattus norvegicus

source_name: rat stroma

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: Two groups of nude rats each underwent unilateral prostatic intervention of botox chemical denervation prior to VCaP-luc injection (botox group), and physical denervation prior to VCaP-luc injection (major pelvic ganglia (MPG) excision) 2 weeks prior to orthotopic injection.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

tag: cell type

value: stroma

tag: surrounding tumor

label: Alexa Fluor 555

source_name: rat, universal reference RNA

tag: sample type

value: reference

tag: vendor

value: Stratagene, Universal Human Reference RNA

tag: catalog#


description: Botox-treated rat stroma surrounding xenograft tumor, sample 2, array slide 18038

value: botox


title: FVB/N Cd151-/- mouse 1

city: Ourimbah

first: Judith

last: Weidenhofer

state: NSW

address: 10 Chittaway Rd

department: School of Biomedical Sciences & Pharmacy

country: Australia

institute: University of Newcastle

description:
biological replicate 1
Sample 5

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic-spline normalisation with Genome studio ® (Illumina)

source_name: Glomerular isolate

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit and hybridized for 17h to MouseRef-8 v1.1 Expression BeadChip (Illumina)

extract_protocol: RNA was extracted from glomerular isolates with the QIAGEN RNeasy mini kit in accordance with the manufacturer's protocol. RNA was quantified by Quant-It RiboGreen RNA assay kit (Invitrogen) and quality control was performed with the Agilent bioanalyser.

value: FVB/N

value: Male

tag: age

value: 3 week old

value: glomerular isolate


title: Heart_untreated_control_rep1

description:
Control Basal_01
Transgene: homozygous p38α flox/flox


title: FVB/N Cd151-/- mouse 4

description:
biological replicate 4
Sample 8


description: Botox-treated rat epithelium surrounding xenograft tumor, sample 2, array slide 18037

source_name: rat epithelium

value: epithelium


description: MPG-treated rat epithelium surrounding xenograft tumor, sample 3, array slide 18037

value: MPG


title: FVB/N Cd151-/- mouse 3

description:
biological replicate 3
Sample 7


description: untreated rat stroma surrounding xenograft tumor, sample 3, array slide 18038


description: MPG-treated rat epithelium surrounding xenograft tumor, sample 2, array slide 18037


description: Botox-treated rat epithelium surrounding xenograft tumor, sample 1, array slide 18034


title: FVB/N Cd151-/- mouse 2

description:
biological replicate 2
Sample 6


description: MPG-treated rat stroma surrounding xenograft tumor, sample 1, array slide 18035


description: MPG-treated rat stroma surrounding xenograft tumor, sample 3, array slide 18038


description: MPG-treated rat epithelium surrounding xenograft tumor, sample 1, array slide 18034


description: untreated rat stroma surrounding xenograft tumor, sample 1, array slide 18035


description: MPG-treated rat stroma surrounding xenograft tumor, sample 2, array slide 18038


description: Botox-treated rat stroma surrounding xenograft tumor, sample 1, array slide 18035


title: FVB/N Cd151+/+ mouse 3

description:
biological replicate 3
Sample 3


description: untreated rat epithelium surrounding xenograft tumor, sample 3, array slide 18037


description: untreated rat epithelium surrounding xenograft tumor, sample 2, array slide 18034


title: FVB/N Cd151+/+ mouse 2

description:
biological replicate 2
Sample 2


title: FVB/N Cd151+/+ mouse 4

description:
biological replicate 4
Sample 4


title: FVB/N Cd151+/+ mouse 1

description:
biological replicate 1
Sample 1


title: Pancreas_LmnaWT_6days_rep4

city: Ann Arbor

first: Juliana

last: Bragazzi Cunha

state: MI

address: 1137 E Catherine St, MSII, room 7720

department: Molecular & Integrative Physiology

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment v3.1.1. RMA was used to fit log2 transformed expression values

source_name: Pancreas

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 100 ng total RNA

extract_protocol: Combination of Trizol and Qiagen Rneasy protocols

treatment_protocol: Tamoxifen was administed at a dose of 3mg/40g by IP injection

value: C57 BL6

tag: Sex

value: Female

value: LmnaWT


title: Pancreas_LmnaWT_6days_rep2


description: untreated rat epithelium surrounding xenograft tumor, sample 1, array slide 18034


title: Pancreas_LmnaKO_6days_rep3

value: LmnaKO


title: Pancreas_LmnaKO_6days_rep2


title: Pancreas_LmnaKO_6days_rep4


title: VCap xenograft tumor, botox treatment

description: botox-treated VCap xenograft tumor, compared to universal reference RNA

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.

source_name: VCap prostate cell line

growth_protocol: VCap cells were maintained in RPMI-1640 medium (Invitrogen) containing 10% fetal bovine serum.

tag: cell line

value: VCap

tag: tumor

tag: catalog #

source_name: human, universal reference RNA


title: Pancreas_LmnaWT_6days_rep3


description: Prostate tumor from patient with spinal injury, compared to universal reference RNA

tag: tissue

value: Prostate tumor

tag: spinal injury

value: yes


title: Pancreas_LmnaWT_6days_rep1


title: VCap xenograft tumor (untreated), sample 2

description: VCap xenograft tumor (untreated), compared to universal reference RNA

tag: treatment


title: Pancreas_LmnaKO_6days_rep1


description: Normal prostate tissue from patient with spinal injury, compared to universal reference RNA

value: Normal prostate


title: Prostate tumor from patient without spinal injury (intact)

description: Prostate tumor from patient without spinal injury, compared to universal reference RNA

value: no


title: VCap xenograft tumor (untreated), sample 1

value: reference

value: Stratagene, Universal Human Reference RNA


title: Normal prostate tissue from patient without spinal injury (intact)

description: Normal prostate tissue from patient without spinal injury, compared to universal reference RNA


title: VCap xenograft tumor, after MPG excision

description: MPG-treated VCap xenograft tumor, compared to universal reference RNA


title: 14574_07 control

type: genomic

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: normal lung sample

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 iScan Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software (v2011.1; methylation modul 1.9.0; Illumina, Inc.)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: surgery 78

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen QIAmp Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction

value: normal lung tissue


title: 6495_08 control

description: normal lung sample

source_name: surgery 79


title: 1449_08 control

description: normal lung sample

source_name: surgery 80


title: 1439_08 control

description: normal lung sample

source_name: surgery 77


title: 3302_12 control

description: normal lung sample

source_name: surgery 73


title: 6591_11 control

description: normal lung sample

source_name: surgery 67


title: 15020_08 control

description: normal lung sample

source_name: surgery 76


title: 19352_07 control

description: normal lung sample

source_name: surgery 74


title: 15982_07 control

description: normal lung sample

source_name: surgery 72


title: 3139_11 control

description: normal lung sample

source_name: surgery 64


title: 12799_12 control

description: normal lung sample

source_name: surgery 71


title: 20371_07 control

description: normal lung sample

source_name: surgery 62


title: 5622_12 control

description: normal lung sample

source_name: surgery 69


title: 12893_12 control

description: normal lung sample

source_name: surgery 70


title: 14893_08 control

description: normal lung sample

source_name: surgery 75


title: 10708_10 control

description: normal lung sample

source_name: surgery 57


title: 9495_10 control

description: normal lung sample

source_name: surgery 53


title: 16673_10 control

description: normal lung sample

source_name: surgery 61


title: 1888_12 control

description: normal lung sample

source_name: surgery 66


title: 15745_07 control

description: normal lung sample

source_name: surgery 52


title: 8901_10 control

description: normal lung sample

source_name: surgery 55


title: 5161_12 control

description: normal lung sample

source_name: surgery 59


title: 12894_12 control

description: normal lung sample

source_name: surgery 68


title: 17962_10 control

description: normal lung sample

source_name: surgery 54


title: 21417_07 control

description: normal lung sample

source_name: surgery 60


title: 11560_12 control

description: normal lung sample

source_name: surgery 58


title: 7533_11 control

description: normal lung sample

source_name: surgery 63


title: 13230_12 control

description: normal lung sample

source_name: surgery 50


title: 12488_12 control

description: normal lung sample

source_name: surgery 56


title: 19192_08 control

description: normal lung sample

source_name: surgery 49


title: 12097_11 control

description: normal lung sample

source_name: surgery 65


title: 2508_11 control

description: normal lung sample

source_name: surgery 51


title: 21577_08 control

description: normal lung sample

source_name: surgery 46


title: 1799_12 control

description: normal lung sample

source_name: surgery 48


title: 22024_11 control

description: normal lung sample

source_name: surgery 42


title: 18010_08 control

description: normal lung sample

source_name: surgery 47


title: 12928_12 control

description: normal lung sample

source_name: surgery 44


title: 6495_08  tumor

description: lung cancer sample

source_name: surgery 37

value: lung cancer


title: 19338_07 control

description: normal lung sample

source_name: surgery 41


title: 20371_07  tumor

description: lung cancer sample

source_name: surgery 22


title: 14574_07  tumor

description: lung cancer sample

source_name: surgery 36


title: 19352_07 tumor

description: lung cancer sample

source_name: surgery 34


title: 3302_12 tumor

description: lung cancer sample

source_name: surgery 33


title: 12066_10 control

description: normal lung sample

source_name: surgery 43


title: 1439_08  tumor

description: lung cancer sample

source_name: surgery 35


title: 12799_12 tumor

description: lung cancer sample

source_name: surgery 31


title: 5622_12 tumor

description: lung cancer sample

source_name: surgery 29


title: 1888_12 tumor

description: lung cancer sample

source_name: surgery 26


title: 12894_12 tumor

description: lung cancer sample

source_name: surgery 28


title: 5161_12  tumor

description: lung cancer sample

source_name: surgery 19


title: 1449_08  tumor

description: lung cancer sample

source_name: surgery 38


title: 15982_07 tumor

description: lung cancer sample

source_name: surgery 32


title: 15020_08  tumor

description: lung cancer sample

source_name: surgery 40


title: 3139_11 tumor

description: lung cancer sample

source_name: surgery 24


title: 21918_11 control

description: normal lung sample

source_name: surgery 45


title: 16673_10  tumor

description: lung cancer sample

source_name: surgery 21


title: 12097_11 tumor

description: lung cancer sample

source_name: surgery 25


title: 7533_11 tumor

description: lung cancer sample

source_name: surgery 23


title: 21417_07  tumor

description: lung cancer sample

source_name: surgery 20


title: 10708_10  tumor

description: lung cancer sample

source_name: surgery 17


title: 11560_12  tumor

description: lung cancer sample

source_name: surgery 18


title: 6591_11 tumor

description: lung cancer sample

source_name: surgery 27


title: Scribbel-wt#2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from HepG2 cells expressing wildtype Scribble

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using human transcriptome arrays 2.0 (HTA-2_0) from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The human HCC cell lines were cultured in RPMI HepG2 supplemented with 10% fetal bo-vine serum and 1% penicillin/streptomycin at 37°C in a 5% CO2 atmosphere (Sigma-Aldrich, Taufkirchen, Germany). Cell lines were authenticated by STR-analysis (DSMZ, Braunschweig, Germany) and routinely checked for mycoplasma contamination.

extract_protocol: For isolation of total RNA from cultured cells, the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany).

treatment_protocol: For the generation of cell lines stably expressing ScribWT and ScribP305L, HepG2 cells were transfected with 9 µg of pEGFP-ScribWT or pEGFP-ScribP305L on a 10 cm dish using Fugene HD (Promega, Mannheim, Germany). Selection with G418 (Geneticin, 1 mg/ml) was started 72 hours after transfection. Single clones were expanded and Scrib overexpression was analysed by Western blotting and real-time PCR.

tag: transfection

value: wildtype Scribble


title: aza, replicate 4

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

country: Spain

institute: Institut de Ciencies del Mar

description: Gene expression in zebrafish ovaries treated with 75 uM of 5-aza-CdR at 90 dpf

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized to the array in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Danio rerio

source_name: aza

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 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: At 10 days post fertilization, fish were divided in 2.8-liter tanks in static conditions.

extract_protocol: At 90 dpf fish were sacrified and gonads were dissected and flash frozen. RNA was extracted by Trizol (Sigma) and were hybridized individually in 4x44K Agilent platform (G2519F).

treatment_protocol: The 5-aza-CdR effects were studied during gonadal development (10–30 dpf) at a concentration of 75 µM. . 5-aza-CdR was added into the water tank and half of the water with the corresponding 5-aza-CdR concentration was changed three times a week during the period of treatment.

value: ovary


title: untrasfected cells#3

description: Gene expression data from HepG2 cells

source_name: HepG2 cells

value: control


title: aza, replicate 3


title: 17962_10  tumor

description: lung cancer sample

source_name: surgery 14


title: Scribbel-wt#3

source_name: HepG2 cells expressing wildtype Scribble


title: untrasfected cells#2

description: Gene expression data from HepG2 cells


title: 14893_08  tumor

description: lung cancer sample

source_name: surgery 39


title: 8901_10  tumor

description: lung cancer sample

source_name: surgery 15


title: untrasfected cells#1

description: Gene expression data from HepG2 cells


title: 19192_08  tumor

description: lung cancer sample

source_name: surgery 9


title: aza, replicate 1


title: Scribbel-mut#2

description: Gene expression data from HepG2 cells expressing mutated Scribble

source_name: HepG2 cells expressing mutated Scribble

value: mutated Scribble


title: control, replicate 2

description: Gene expression in control zebrafish ovaries at 90 dpf

source_name: control


title: 12893_12 tumor

description: lung cancer sample

source_name: surgery 30


title: control, replicate 3


title: Scribbel-mut#3


title: Scribbel-wt#1


title: 9495_10  tumor

description: lung cancer sample

source_name: surgery 13


title: 1799_12  tumor

description: lung cancer sample

source_name: surgery 8


title: 18010_08  tumor

description: lung cancer sample

source_name: surgery 7


title: 2508_11  tumor

description: lung cancer sample

source_name: surgery 11


title: 15745_07  tumor

description: lung cancer sample

source_name: surgery 12


title: 19338_07  tumor

description: lung cancer sample

source_name: surgery 1


title: 22024_11  tumor

description: lung cancer sample

source_name: surgery 2


title: HCC70_siLRRC26_72h

city: Tokushima

first: Yosuke

last: Matsushita

address: 3-18-15 Kuramoto

department: Institute for Genome Research

institute: Tokushima University

description: SAMPLE 4

hyb_protocol: 0.825 μg of Cy3-labeled cRNA was fragmented and hybridized onto the Agilent SurePrint G3 Hmn GE 8 × 60K V2 slide (design ID-039494, G4851B), with rotating incubation at 65˚C for 17 h.

scan_protocol: Slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation, and scanned by the Agilent Microarray scanner system (G2505B) in an ozone protection fume hood.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded..  The data files were subjected to the GeneSpring (ver. 13.0) for analysis.

label_protocol: For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit (Agilent) according to the manufacture’s guidance.  100 ng of total RNA of each sample was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.

growth_protocol: Human triple negative breast cancer cells HCC70 was maintained in RPMI-1640 medium containing 10% FBS and antibiotics/antimycotics.

extract_protocol: After 48 and 72 h of siRNA transfection, total RNA was extracted using NucleoSpin RNA kit (TaKaRa Bio) according to the instructions. This included an on-column DNase digestion with the RNase-free Dnase (TaKaRa Bio)

treatment_protocol: Cells were seeded at a density 2×10^5/well onto 6-well plate folllowed by transfection of 10 nM siEGFP (SIGMA) or siLRRC26 (Darmacon) using Lipofectamine RNAiMAX (Life Technologies) according to manufacture's guidance.

value: triple negative breast cancer cell line

tag: transfected with

value: 10 nM of siRNA for LRRC26

tag: time point

value: 72hrs post-transfection


title: 12488_12  tumor

description: lung cancer sample

source_name: surgery 16


title: 21918_11  tumor

description: lung cancer sample

source_name: surgery 5


title: HCC70_siEGFP_48h

description: SAMPLE 1

value: 10 nM of siRNA for EGFP (control)

value: 48hrs post-transfection


title: human iPSCs (D0) replicate 3 vs LBs derived from iPSCs (D29) replicate 3

city: Hangzhou

first: Qiuli

last: FU

state: Zhejiang

address: Jiefang road 88#

country: China

institute: Zhejiang University

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: After a filtering procedure, 37,000 human lncRNAs (annotated by GENCODE/ENSEMBL, human lincRNAs Catalog, RefSeq, UCSC  and et al) were selected for the following analysis. We first did quantile normalization for the microarray data (containing the 37,000 lncRNAs and all mRNAs in the microarray) of 3 paired iPSCs vs LBs. Then, the data was log2-scale transformed. The differentially expressed genes were selected as the threshold values of ≥2-fold and ≤2-fold, and a Benjamini-Hochberg–corrected p value of ＜0.05.

source_name: human urinary cell derived iPSCs

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Both iPSCs and LBs were seeded in Matrigel-coated (BD Biosciences) dishes and cultured in mTesR medium (Stemcell).

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) and purified with mirVana miRAN Isolation Kit (Ambion).The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel eletrophoresis.

treatment_protocol: During LB differentiation, iPSCs were first treated with 100ng/ml BMP inhibitor noggin on D6,and then treated with 20ng/ml BMP4+20ng/ml  BMP7 on D11.Finally,  wnt3a was added into the medium on D15. This protocol was named as fried egg method.

value: human urinary cell derived iPSCs

source_name: LBs derived from human iPSCs

value: LBs derived from human iPSCs


title: human iPSCs (D0) replicate 2 vs LBs derived from iPSCs (D28) replicate 2


title: HCC70_siLRRC26_48h

description: SAMPLE 2


title: human iPSCs (D0) replicate 1 vs LB derived from iPSCs (D28) replicate 1


title: Scribbel-mut#1


title: control, replicate 1


title: Patient 12 surgical resection - post treatment

status: Public on Nov 29 2017

city: Chapel Hill

first: Gary

middle: L

last: Johnson

state: NC

address: 4009 Genetic Medicine Building, 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina School of Medicine

description:
130617_UNC15-SN850_0313_AD276PACXX_1_ACTTGA
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx

data_processing:
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using RSEM and upper-quartile normalized.
For DESeq differential expression analysis comparing pre-treatment and post-treatment patient tumors: RSEM gene-level expected read counts were imported into R version 3.2.2. and were analyzed using DESeq2 v1.12.3 to detect genes that were differentially expressed between pre-treatment and post-treatment conditions.  Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain raw or log2-transformed upper-quartile normalized RSEM transcript abundance estimates, organized by official gene symbol and Entrez Gene ID.

source_name: breast carcinoma

extract_protocol:
Total RNA was isolated with Qiagen RNeasy Mini kit.
mRNA libraries were made with Illumina TruSeq RNA Sample Prep Kit starting with 0.5-1 micrograms of total RNA.

tag: disease state

value: TNBC

tag: individual

value: Patient 12

tag: protocol

value: post-treatment surgical resection

tag: tumor sample subtype

value: normal breast


title: Patient 2 needle core biopsy - pre treatment

description:
121129_UNC11-SN627_0261_BC10V7ACXX_1_TGACCA
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx
DESeq2_trametinibresponse.xlsx

value: Patient 2

value: pre-treatment needle core biospy

value: basal


title: Patient 3 Needle Core Biopsy - pre treatment

description:
130311_UNC16-SN851_0225_AD20N6ACXX_3_TAGCTT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx
DESeq2_trametinibresponse.xlsx

value: Patient 3


title: Patient 4 surgical resection - post treatment

description:
130311_UNC16-SN851_0225_AD20N6ACXX_2_GCCAAT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx

value: Patient 4


title: Patient 11 surgical resection - post treatment

description:
130311_UNC16-SN851_0225_AD20N6ACXX_6_GCCAAT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx

value: Patient 11

value: claudin low


title: Patient 10 surgical resection - post treatment

description:
121129_UNC11-SN627_0261_BC10V7ACXX_6_ACAGTG
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx

value: Patient 10


title: Patient 4 Needle Core Biopsy - pre treatment

description:
130311_UNC16-SN851_0225_AD20N6ACXX_1_CGATGT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx


title: Patient 10 needle core biopsy - pre treatment

description:
121129_UNC11-SN627_0261_BC10V7ACXX_5_TGACCA
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx


title: Patient 11 needle core biopsy - pre treatment

description:
130311_UNC16-SN851_0225_AD20N6ACXX_5_CGATGT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx


title: Patient 2 surgical resection - post treatment

description:
121129_UNC11-SN627_0261_BC10V7ACXX_2_ACAGTG
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx
DESeq2_trametinibresponse.xlsx


title: Patient 12 needle core biopsy - pre treatment

description:
130617_UNC15-SN850_0313_AD276PACXX_1_CGATGT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx


title: Patient 9 surgical resection - post treatment

description:
121129_UNC11-SN627_0261_BC10V7ACXX_4_ACAGTG
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx

value: Patient 9


title: Patient 3 surgical resection - post treatment

description:
130311_UNC16-SN851_0225_AD20N6ACXX_4_GGCTAC
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx
DESeq2_trametinibresponse.xlsx


title: Patient 9 needle core biopsy - pre treatment

description:
121129_UNC11-SN627_0261_BC10V7ACXX_3_TGACCA
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx


title: 21577_08  tumor

description: lung cancer sample

source_name: surgery 6

value: lung cancer


title: HCC70_siEGFP_72h

description: SAMPLE 3

tag: cell type

value: triple negative breast cancer cell line

value: 10 nM of siRNA for EGFP (control)

value: 72hrs post-transfection


title: 12066_10  tumor

description: lung cancer sample

source_name: surgery 3


title: Patient 8 surgical resection - post treatment

description:
120925_UNC10-SN254_0382_AC0YBWACXX_2_CGATGT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx

value: TNBC

value: Patient 8


title: Patient 8 needle core biopsy - pre treatment

description:
120925_UNC10-SN254_0382_AC0YBWACXX_1_CGATGT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx


title: Patient 1 needle core biopsy - pre treatment

description:
120925_UNC10-SN254_0382_AC0YBWACXX_3_CGATGT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx
DESeq2_trametinibresponse.xlsx

value: Patient 1


title: 12928_12  tumor

description: lung cancer sample

source_name: surgery 4


title: aza, replicate 2

description: Gene expression in zebrafish ovaries treated with 75 uM of 5-aza-CdR at 90 dpf

source_name: aza

value: ovary


title: Patient 1 surgical resection - post treatment

description:
120925_UNC10-SN254_0382_AC0YBWACXX_4_CGATGT
LCCC1122_rawRSEM.xlsx
LCCC1122_normalizedLog2RSEM.xlsx
DESeq2_trametinibresponse.xlsx

value: post-treatment surgical resection


title: 13230_12  tumor

description: lung cancer sample

source_name: surgery 10


title: Patient 159 mucosa control sample

status: Public on Nov 28 2017

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

hyb_protocol: cRNA was hybridized to the Human 4 × 44 K array platform from Agilent Technologies (G4112F) as recommended by the manufacturer.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed using the Agilent feature extraction software (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol.

source_name: mucosa

label_protocol: 600ng of total RNA was amplified and transcribed into fluorescence labeled cRNA following the Low RNA Input linear Amplification Kit Plus, One Color protocol (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5339).

extract_protocol: Using the Qiagen AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany) according to manufactures recommendation, RNA was isolated from FFPE samples. Using TRIZOL (cat. no. 15596-018, Life Technologies, Rockeville, MD, USA) RNA was extracted from RNAlater biopsies. All samples underwent strict quality assessment, nucleic acid quantity, and purity was determined using the NanoDrop spectrophotometer ND1000 (Thermo Fisher Scientific Inc., Waltham, MA, USA), quality and integrity was assessed by a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: During index rectoscopy several biopsies of tumor and normal mucosa were taken and either directly buffered in 4% formalin, stored overnight and embedded in paraffin the next day or immediately transferred into RNAlater (Qiagen, Hilden, Germany). Tissue in RNAlater was stored over night at 4 °C to allow saturation of the entire biopsy and stored at −20 °C until RNA isolation.

tag: patient

value: Con Patient 159

tag: gender

value: F

value: mucosa

tag: kras mutation

tag: preoperative radiochemotherapy (rct)

value: 5-FU + Oxaliplatin + RT

tag: depth of invasion before rct

tag: lymph node metastasis before rct

tag: metastasis before rct

tag: depth of invasion after rct

tag: lymph node metastasis after rct

tag: metastasis after rct

tag: cancer recurrance after surgery

tag: disease free time (month)

tag: death due to tumor

tag: survival time (month)


title: Patient 155 mucosa control sample

value: Con Patient 155

tag: age

value: M

tag: tissue

value: WT

value: 5-FU + RT


title: Patient 156 mucosa control sample

value: Con Patient 156


title: Patient 160 mucosa control sample

value: Con Patient 160


title: Patient 157 mucosa control sample

value: Con Patient 157


title: Patient 151 mucosa control sample

value: Con Patient 151


title: Patient 154 mucosa control sample

value: Con Patient 154


title: Patient 152 mucosa control sample

value: Con Patient 152


title: Patient 150 mucosa control sample

value: Con Patient 150


title: Patient 149 mucosa control sample

value: Con Patient 149


title: Patient 158 mucosa control sample

value: Con Patient 158


title: Patient 153 mucosa control sample

value: Con Patient 153


title: Patient 148 mucosa control sample

value: Con Patient 148


title: Genomc DNA from 293T-POU5F1

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

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

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

data_processing: GenomeStudio software v2010.3

growth_protocol: 293T cells were provided from RIKEN Bioresource Center (BRC) and were cultured in Dulbecco's modified Eagle's medium (DMEM) (Wako), supplemented with 10% FBS and penicillin/streptomycin (100 U/ml, 100 µg/ml) (Life Technologies) on Poly-D-lysine courted dish (Becton Dickinson).

extract_protocol: genomic DNA was extracted and purified using NucleoSpin Tissue (Macherey-Nagel) according to standard instructions

treatment_protocol: 293T cells were transduced genes of interest by using lentivirus vector system. Transduced cells were purified by antibiotics or by FACS sorting

value: Female

value: Kidney

tag: developmental stage

value: Embryo

tag: transduction


title: Genomc DNA from 293T-GATA2

tag: gender


title: Genomc DNA from 293T-HNF4A


title: Genomic DNA from 293T mock

value: mock lentivirus vector


title: Patient 145 mucosa control sample

tag: patient

value: Con Patient 145

value: M

value: mucosa

tag: kras mutation

value: WT

value: 5-FU + Oxaliplatin + RT


title: Patient 144 mucosa control sample

value: Con Patient 144

tag: preoperative radiochemotherapy (rct)

tag: depth of invasion before rct


title: Patient 143 mucosa control sample

value: Con Patient 143

tag: lymph node metastasis before rct

tag: metastasis before rct


title: Patient 138 mucosa control sample

value: Con Patient 138

value: F

value: 5-FU + RT

tag: depth of invasion after rct

tag: lymph node metastasis after rct


title: Patient 142 mucosa control sample

value: Con Patient 142

tag: metastasis after rct

tag: cancer recurrance after surgery


title: Patient 139 mucosa control sample

value: Con Patient 139

tag: disease free time (month)

tag: death due to tumor


title: Genomc DNA from 293T-SOX2


title: Patient 140 mucosa control sample

value: Con Patient 140

tag: age

tag: survival time (month)


title: Patient 137 mucosa control sample

value: Con Patient 137

tag: tissue


title: Patient 141 mucosa control sample

value: Con Patient 141


title: Genomc DNA from 293T-NR4A2

value: Female

value: Kidney

tag: developmental stage

value: Embryo

tag: transduction


title: Genomc DNA from 293T-TBX5

tag: gender


title: Patient 136 mucosa control sample

tag: patient

value: Con Patient 136

tag: kras mutation


title: Genomc DNA from 293T-HNF1A


title: Patient 134 mucosa control sample

value: Con Patient 134

value: M

value: mucosa

tag: preoperative radiochemotherapy (rct)

value: 5-FU + Oxaliplatin + Cetuximab + RT

tag: depth of invasion before rct


title: Genomc DNA from 293T-SPI1


title: Genomc DNA from 293T-RUNX3


title: Genomc DNA from 293T-CEBPB

value: CEBPB


title: Patient 146 mucosa control sample

value: Con Patient 146

value: 5-FU + Oxaliplatin + RT

tag: lymph node metastasis before rct

tag: metastasis before rct


title: Genomc DNA from 293T-MAFB

value: MAFB


title: Genomc DNA from 293T-NANOG

value: NANOG


title: Patient 133 mucosa control sample

value: Con Patient 133

value: F

value: WT

tag: depth of invasion after rct

tag: lymph node metastasis after rct


title: Genomc DNA from 293T-CEBPA

value: CEBPA


title: Patient 132 mucosa control sample

value: Con Patient 132

tag: metastasis after rct

tag: cancer recurrance after surgery


title: Genomc DNA from 293T-PAX4

value: Female

value: Kidney


title: Patient 147 mucosa control sample

value: Con Patient 147

tag: disease free time (month)

tag: death due to tumor


title: Patient 131 mucosa control sample

value: Con Patient 131

tag: age

tag: survival time (month)


title: Patient 128 mucosa control sample

value: Con Patient 128

tag: tissue

value: 5-FU + RT


title: Genomc DNA from 293T-MYOD1

tag: developmental stage

value: Embryo

tag: transduction


title: Genomc DNA from 293T-NKX2-5

tag: gender


title: Patient 126 mucosa control sample

tag: patient

value: Con Patient 126

value: mucosa

tag: kras mutation


title: Patient 122 mucosa control sample

value: Con Patient 122

value: M

tag: preoperative radiochemotherapy (rct)

tag: depth of invasion before rct


title: Patient 125 mucosa control sample

value: Con Patient 125

tag: lymph node metastasis before rct

tag: metastasis before rct


title: Patient 127 mucosa control sample

value: Con Patient 127

value: 5-FU + Oxaliplatin + Cetuximab + RT

tag: depth of invasion after rct

tag: lymph node metastasis after rct


title: Patient 121 mucosa control sample

value: Con Patient 121

value: 5-FU + Oxaliplatin + RT

tag: metastasis after rct

tag: cancer recurrance after surgery


title: Patient 129 mucosa control sample

value: Con Patient 129

tag: disease free time (month)

tag: death due to tumor


title: Patient 123 mucosa control sample

value: Con Patient 123

tag: age

value: WT

tag: survival time (month)


title: Patient 119 mucosa control sample

value: Con Patient 119

value: F

tag: tissue


title: Patient 117 mucosa control sample

value: Con Patient 117


title: Patient 118 mucosa control sample

value: Con Patient 118

value: 5-FU + RT


title: Patient 115 mucosa control sample

value: Con Patient 115


title: Patient 114 mucosa control sample

value: Con Patient 114

value: mucosa


title: Patient 116 mucosa control sample

value: Con Patient 116