title: MGH54-P2-G05


title: MGH54-P2-F12

status: Public on Nov 06 2016

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", which allows alignment of sequences with single base changes such as point mutation in the IDH1  gene. Expression values were calculated from SAM files using 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.
Expression levels were quantified as Ei,j=log2(TPMi,j/10+1), where TPMi,j refers to transcriptper-million  for gene i in sample j, as calculated by RSEM41. TPM values are divided by 10 since  we estimate the complexity of single cell libraries in the order of 100,000 transcripts and would  like to avoid counting each transcript ~10 times, as would be the case with TPM, which may  inflate the difference between the expression level of a gene in cells in which the gene is detected  and those in which it is not detected.
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 3,000 detected genes or an average housekeeping expression (E, as defined above) below 2.5. We then distinguished oligodendroglioma from non-malignant cells by inferrence of copy number variations and excluded the non-malignant cells. For the remaining cells we calculated  the aggregate expression of each gene as log2(average(TPMi,1...n)+1), and excluded genes with an  aggregate expression below 4, leaving a set of 8008 analyzed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing the normalized expression levels (E) for 8008 analyzed genes across 2,594 oligodendroglioma cells that passed QC.

molecule: total RNA

organism: Homo sapiens

source_name: oligodendroglioma single cell

growth_protocol: no culutring (freshly-resected tumor samples)

extract_protocol:
RNA from single cells was first purified with Agencourt  RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with  Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle  PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent  Agencourt AMPure XP bead purification as described. Libraries were tagmented using the  Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon  request). Libraries from 384 cells with unique barcodes were combined and sequenced using a  NextSeq 500 sequencer (Illumina).

treatment_protocol: Fresh tumor tissue was minced with a scalpel and enzymatically dissociated using a gentle papain-based brain tumor dissociation kit (Miltenyi Biotec). Large pieces of debris were removed with a 100 micron strainer, and dissociated cells were layered carefully onto a 5mL density gradient (Lympholyte-H, Cedar Lane labs), which was centrifuged at 2,000 rpm for 10 min at room temperature to pellet dead cells and red blood cells. The interface containing live cells was saved and used for staining and flow cytometry. Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA /  HBSS), and then stained first with CD45-Vioblue direct antibody conjugate (Miltenyi Biotec) for  30 min at 4C. Cells were washed with cold PBS, and then resuspended in 1 mL of BSA / HBSS  containing 1uM calcein AM (Life Technologies) and 0.33uM TO-PRO-3 iodide (Life  Technologies) to co-stain for 30 min before sorting. Fluorescence-activated cell sorting was  performed on FACSAria Fusion Special Order System (Becton Dickinson) using 488nm (calcein  AM, 530/30 filter), 640nm (TO-PRO-3, 670/14 filter), and 405nm (Vioblue, 450/50 filter) lasers.   Fluorescence-minus-one controls were included with all tumors, as well as heat killed controls in  early pilot experiments, which were crucial to ensure proper identification of the TO-PRO-3  positive compartment and ensure sorting of the live cell population. Standard, strict forward  scatter height versus area criteria were used to discriminate doublets and gate only singlets.  Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3.  Single cells were sorted into 96-well plates containing cold buffer TCL buffer (Qiagen)  containing 1% beta-mercaptoethanol, snap frozen on dry ice, and then stored at -80C prior to  whole transcriptome amplification, library preparation and sequencing.

tag: cell type

value: oligodendroglioma single cell


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title: MGH54-P13-C04


title: MGH54-P13-C01


title: MGH54-P13-C03


title: MGH54-P13-C05


title: MGH54-P13-B09


title: MGH54-P13-B10


title: MGH54-P13-B11


title: MGH54-P13-B08


title: MGH54-P13-B07


title: MGH54-P13-B05


title: MGH54-P13-B04


title: MGH54-P13-A12


title: MGH54-P13-B01


title: MGH54-P13-C11


title: MGH54-P13-A11


title: MGH54-P13-A10


title: MGH54-P13-A08


title: MGH54-P13-A07


title: MGH54-P13-A04


title: MGH54-P13-A06


title: MGH54-P13-A05


title: MGH54-P13-A02


title: MGH54-P13-A03


title: MGH54-P13-A01


title: MGH54-P12-H11


title: MGH54-P12-H10


title: MGH54-P12-H09


title: MGH54-P12-H04


title: MGH54-P12-H07


title: MGH54-P12-H08


title: MGH54-P12-H05


title: MGH54-P13-B06


title: MGH54-P12-H06


title: MGH54-P12-H03


title: MGH54-P13-B02


title: MGH54-P13-B03


title: MGH54-P12-H02


title: MGH54-P12-G12


title: MGH54-P12-G11


title: MGH54-P13-A09


title: MGH54-P12-G10


title: MGH54-P12-G09


title: MGH54-P12-H01


title: MGH54-P12-G07


title: MGH54-P12-G05


title: MGH54-P12-G04


title: MGH54-P12-G01


title: MGH54-P12-G03


title: MGH54-P12-H12


title: MGH54-P12-G02


title: MGH54-P12-F12


title: MGH54-P12-F10


title: MGH54-P12-F11


title: MGH54-P12-F04


title: MGH54-P12-F06


title: MGH54-P12-F05


title: MGH54-P12-F08


title: MGH54-P12-F07


title: MGH54-P12-F09


title: MGH54-P12-F02


title: MGH54-P12-F03


title: MGH54-P12-E12


title: MGH54-P12-G08


title: MGH54-P12-E08


title: MGH54-P12-E10


title: MGH54-P12-E06


title: MGH54-P12-G06


title: MGH54-P12-F01


title: MGH54-P12-E07


title: MGH54-P12-E11


title: MGH54-P12-E09


title: MGH54-P12-E05


title: MGH54-P12-E02


title: MGH54-P12-E01


title: MGH54-P12-D12


title: MGH54-P12-D10


title: MGH54-P12-D06


title: MGH54-P12-D08


title: MGH54-P12-D07


title: MGH54-P12-E04


title: MGH54-P12-D11


title: MGH54-P12-D09


title: MGH54-P12-D04


title: MGH54-P12-D01


title: MGH54-P12-C12


title: MGH54-P12-D05


title: MGH54-P12-D02


title: MGH54-P12-C10


title: MGH54-P12-C11


title: MGH54-P12-C07


title: MGH54-P12-C04


title: MGH54-P12-E03


title: MGH54-P12-C08


title: MGH54-P12-C06


title: MGH54-P12-C09


title: MGH54-P12-C01


title: MGH54-P12-C05


title: MGH54-P12-C03


title: MGH54-P12-C02


title: MGH54-P12-B11


title: MGH54-P12-B10


title: MGH54-P12-B09


title: MGH54-P12-B07


title: MGH54-P12-B08


title: MGH54-P12-B06


title: MGH54-P12-D03


title: MGH54-P12-B04


title: MGH54-P12-B03


title: MGH54-P12-B02


title: MGH54-P12-A10


title: MGH54-P12-A11


title: MGH54-P12-A08


title: MGH54-P12-A09


title: MGH54-P12-A07


title: MGH54-P12-A06


title: MGH54-P12-B12


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title: MGH54-P12-A04


title: MGH54-P11-H09


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title: MGH54-P11-H05


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title: MGH54-P11-H04


title: MGH54-P12-B01


title: MGH54-P12-B05


title: MGH54-P11-H01


title: MGH54-P11-H03


title: MGH54-P12-A12


title: MGH54-P11-H02


title: MGH54-P11-G11


title: MGH54-P11-G10


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title: MGH54-P11-G07


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title: MGH54-P11-G01


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title: MGH54-P11-G12


title: MGH54-P11-E12


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title: MGH54-P11-C10


title: MGH54-P11-C01


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title: MGH54-P11-B11


title: MGH54-P11-C04


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title: MGH54-P11-B07


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title: MGH54-P10-H12


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title: MGH54-P10-H10


title: MGH54-P10-H09


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title: MGH54-P10-H04


title: MGH54-P10-H02


title: MGH54-P10-H03


title: MGH54-P11-A09


title: MGH54-P10-H01


title: MGH54-P10-G12


title: MGH54-P11-A12


title: MGH54-P10-G08


title: MGH54-P10-G10


title: MGH54-P10-G06


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title: MGH54-P10-G04


title: MGH54-P10-G03


title: MGH54-P10-G09


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title: MGH54-P10-C12


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title: MGH53-P9-H12


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title: MGH53-P9-G06


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title: MGH53-P9-G04


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title: MGH53-P9-G02


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title: MGH53-P9-F09


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title: MGH53-P9-D12


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title: MGH53-P9-D06


title: MGH53-P9-D09


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title: MGH53-P9-D04


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title: MGH53-P9-D07


title: MGH53-P9-D01


title: MGH53-P9-D03


title: MGH53-P9-D02


title: MGH53-P9-C11


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title: MGH53-P9-B12


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title: MGH53-P9-B10


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title: MGH53-P9-C01


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title: MGH53-P9-A10


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title: MGH53-P8-H12


title: MGH53-P8-H09


title: MGH53-P8-H10


title: MGH53-P8-H08


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title: MGH53-P9-B02


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title: MGH53-P8-F05


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title: MGH53-P7-A09


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title: MGH53-P7-A07


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title: MGH53-P7-B09


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title: MGH53-P6-H09


title: MGH53-P6-H08


title: MGH53-P6-H12


title: MGH53-P7-A01


title: MGH53-P6-H11


title: MGH53-P6-H06


title: MGH53-P6-H07


title: MGH53-P6-H02


title: MGH53-P6-G10


title: MGH53-P6-H05


title: MGH53-P6-G11


title: MGH53-P6-H03


title: MGH53-P6-G08


title: MGH53-P6-H04


title: MGH53-P6-G09


title: MGH53-P6-G06


title: MGH53-P7-A08


title: MGH53-P6-G07


title: MGH53-P6-G05


title: MGH53-P6-H10


title: MGH53-P6-G12


title: MGH53-P6-G03


title: MGH53-P6-G02


title: MGH53-P6-G01


title: MGH53-P6-F11


title: MGH53-P6-F12


title: MGH53-P6-F05


title: MGH53-P6-F08


title: MGH53-P6-F10


title: MGH53-P6-F06


title: MGH53-P6-F09


title: MGH53-P6-F07


title: MGH53-P6-F04


title: MGH53-P6-F03


title: MGH53-P6-E12


title: MGH53-P6-F02


title: MGH53-P6-F01


title: MGH53-P6-E08


title: MGH53-P6-E09


title: MGH53-P6-E06


title: MGH53-P6-H01


title: MGH53-P6-E07


title: MGH53-P6-E05


title: MGH53-P6-E03


title: MGH53-P6-E04


title: MGH53-P6-E01


title: MGH53-P6-D12


title: MGH53-P6-D11


title: MGH53-P6-E11


title: MGH53-P6-D10


title: MGH53-P6-E02


title: MGH53-P6-G04


title: MGH53-P6-E10


title: MGH53-P6-D08


title: MGH53-P6-D06


title: MGH53-P6-D07


title: MGH53-P6-D05


title: MGH53-P6-D01


title: MGH53-P6-D04


title: MGH53-P6-D02


title: MGH53-P6-C11


title: MGH53-P6-D03


title: MGH53-P6-C12


title: MGH53-P6-C08


title: MGH53-P6-C07


title: MGH53-P6-C05


title: MGH53-P6-C06


title: MGH53-P6-B10


title: MGH53-P6-C01


title: MGH53-P6-B09


title: MGH53-P6-C03


title: MGH53-P6-B06


title: MGH53-P6-C04


title: MGH53-P6-B05


title: MGH53-P6-B12


title: MGH53-P6-B11


title: MGH53-P6-C09


title: MGH53-P6-D09


title: MGH53-P6-B07


title: MGH53-P6-B08


title: MGH53-P6-B04


title: MGH53-P6-A12


title: MGH53-P6-A08


title: MGH53-P6-A10


title: MGH53-P6-B03


title: MGH53-P6-B02


title: MGH53-P6-C10


title: MGH53-P6-A06


title: MGH53-P6-B01


title: MGH53-P6-A05


title: MGH53-P6-C02


title: MGH53-P6-A03


title: MGH53-P6-A04


title: MGH53-P6-A02


title: MGH53-P5-H12


title: MGH53-P5-H11


title: MGH53-P5-H10


title: MGH53-P5-H08


title: MGH53-P5-H07


title: MGH53-P5-H09


title: MGH53-P5-H06


title: MGH53-P6-A11


title: MGH53-P5-H05


title: MGH53-P6-A09


title: MGH53-P5-G11


title: MGH53-P5-H04


title: MGH53-P5-H02


title: MGH53-P5-G10


title: MGH53-P5-G08


title: MGH53-P6-A07


title: MGH53-P5-G07


title: MGH53-P5-G09


title: MGH53-P5-H03


title: MGH53-P5-H01


title: MGH53-P5-G05


title: MGH53-P5-G04


title: MGH53-P5-G06


title: MGH53-P5-G02


title: MGH53-P5-G01


title: MGH53-P5-F12


title: MGH53-P5-F11


title: MGH53-P5-G12


title: MGH53-P6-A01


title: MGH53-P5-F10


title: MGH53-P5-F09


title: MGH53-P5-F08


title: MGH53-P5-F07


title: MGH53-P5-F03


title: MGH53-P5-F05


title: MGH53-P5-E10


title: MGH53-P5-F01


title: MGH53-P5-F06


title: MGH53-P5-E08


title: MGH53-P5-F04


title: MGH53-P5-E11


title: MGH53-P5-F02


title: MGH53-P5-E05


title: MGH53-P5-G03


title: MGH53-P5-E03


title: MGH53-P5-E04


title: MGH53-P5-E01


title: MGH53-P5-E09


title: MGH53-P5-D12


title: MGH53-P5-E02


title: 93_P10_A01

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", which allows alignment of sequences with single base changes such as point mutation in the IDH1  gene. Expression values were calculated from SAM files using 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.
Expression levels were quantified as Ei,j=log2(TPMi,j/10+1), where TPMi,j refers to transcriptper-million  for gene i in sample j, as calculated by RSEM41. TPM values are divided by 10 since  we estimate the complexity of single cell libraries in the order of 100,000 transcripts and would  like to avoid counting each transcript ~10 times, as would be the case with TPM, which may  inflate the difference between the expression level of a gene in cells in which the gene is detected  and those in which it is not detected.
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 3,000 detected genes or an average housekeeping expression (E, as defined above) below 2.5. We then distinguished oligodendroglioma from non-malignant cells by inferrence of copy number variations and excluded the non-malignant cells.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing the normalized expression levels (E) for 23,686 analyzed genes across 4347 oligodendroglioma cells that passed QC.

molecule: polyA RNA

extract_protocol:
RNA from single cells was first purified with Agencourt  RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with  Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle  PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent  Agencourt AMPure XP bead purification as described. Libraries were tagmented using the  Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon  request). Libraries from 384 cells with unique barcodes were combined and sequenced using a  NextSeq 500 sequencer (Illumina).
single cell RNA-seq

tag: tumor


title: MGH53-P5-E06


title: MGH53-P5-E07


title: 93_P10_A05


title: 93_P10_A02


title: 93_P10_A09


title: 93_P10_A10


title: 93_P10_A11


title: 93_P10_B02


title: MGH53-P5-E12


title: 93_P10_B04


title: 93_P10_B06


title: 93_P10_B09


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title: 93_P10_D12


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title: 93_P10_A12


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title: 93_P10_E08


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title: 93_P10_G05


title: 93_P10_G04


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title: 93_P10_G03


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title: 93_P10_H04


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title: 97_P5_H06


title: 97_P5_H07


title: 97_P5_H03


title: 97_P5_H09


title: 97_P6_A01


title: 97_P5_H10


title: 97_P6_A02


title: 97_P5_H11


title: 97_P6_A05


title: 97_P6_A03


title: 97_P5_G03


title: 97_P5_G05


title: 97_P6_A04


title: 97_P6_A08


title: 97_P6_A09


title: 97_P6_A10


title: 97_P6_A07


title: 97_P6_A06


title: 97_P6_A12


title: 97_P6_B02


title: 97_P6_B01


title: 97_P5_H04


title: 97_P6_B04


title: 97_P6_B05


title: 97_P6_B03


title: 97_P6_B09


title: 97_P6_B11


title: 97_P6_B08


title: 97_P6_B10


title: 97_P6_B12


title: 97_P6_C02


title: 97_P6_C01


title: 97_P6_C06


title: 97_P6_C07


title: 97_P6_C08


title: 97_P6_D01


title: 97_P6_D03


title: 97_P6_D02


title: 97_P6_C12


title: 97_P6_A11


title: 97_P6_C10


title: 97_P6_C11


title: 97_P6_D04


title: 97_P6_D05


title: 97_P6_D07


title: 97_P6_B06


title: 97_P6_D08


title: 97_P6_D11


title: 97_P6_D12


title: 97_P6_C03


title: 97_P6_D09


title: 97_P6_E01


title: 97_P6_E02


title: 97_P6_E06


title: 97_P6_E07


title: 97_P6_E05


title: 97_P6_F02


title: 97_P6_E09


title: 97_P6_E08


title: 97_P6_E03


title: 97_P6_C09


title: 97_P6_E12


title: 97_P6_F04


title: 97_P6_F03


title: 97_P6_F05


title: 97_P6_F08


title: 97_P6_F09


title: 97_P6_F07


title: 97_P6_F10


title: 97_P6_F12


title: 97_P6_G01


title: 97_P6_E04


title: 97_P6_G03


title: 97_P6_G04


title: 97_P6_G08


title: 97_P6_G09


title: 97_P6_G10


title: 97_P6_G11


title: 97_P6_G07


title: 97_P6_H01


title: 97_P6_G12


title: 97_P6_H04


title: 97_P6_H02


title: 97_P6_H07


title: 97_P6_H05


title: 97_P6_H03


title: 97_P6_H09


title: 97_P6_H10


title: 97_P6_H12


title: 97_P6_F11


title: MGH60_P3_A01


title: 97_P6_G02


title: MGH60_P3_A03


title: MGH60_P3_A09


title: MGH60_P3_A06


title: MGH60_P3_A07


title: MGH60_P3_A08


title: MGH60_P3_A10


title: MGH60_P3_A11


title: MGH60_P3_B01


title: MGH60_P3_A12


title: MGH60_P3_B07


title: MGH60_P3_B10


title: 97_P6_H06


title: MGH60_P3_B06


title: 97_P6_H08


title: MGH60_P3_B04


title: MGH60_P3_B11


title: MGH60_P3_B12


title: MGH60_P3_C04


title: MGH60_P3_C09


title: MGH60_P3_C03


title: MGH60_P3_D01


title: MGH60_P3_C07


title: MGH60_P3_D03


title: MGH60_P3_A02


title: MGH60_P3_D09


title: MGH60_P3_D04


title: MGH60_P3_D07


title: MGH60_P3_D08


title: MGH60_P3_D10


title: MGH60_P3_D11


title: MGH60_P3_E02


title: MGH60_P3_E04


title: MGH60_P3_E07


title: MGH60_P3_E03


title: MGH60_P3_E06


title: MGH60_P3_E08


title: MGH60_P3_E10


title: MGH60_P3_E11


title: MGH60_P3_E09


title: MGH60_P3_E12


title: MGH60_P3_F02


title: MGH60_P3_C08


title: MGH60_P3_F01


title: MGH60_P3_F07


title: MGH60_P3_F04


title: MGH60_P3_F03


title: MGH60_P3_G02


title: MGH60_P3_G04


title: MGH60_P3_G06


title: MGH60_P3_G08


title: MGH60_P3_G07


title: MGH60_P3_F10


title: MGH60_P3_G05


title: MGH60_P3_G11


title: MGH60_P3_H02


title: MGH60_P3_F11


title: MGH60_P3_G10


title: MGH60_P3_H04


title: MGH60_P3_H03


title: MGH60_P3_H07


title: MGH60_P3_H06


title: MGH60_P3_H08


title: MGH60_P3_H09


title: MGH60_P3_F06


title: MGH60_P3_H12


title: MGH60_P3_F09


title: MGH60_P3_H11


title: MGH60_P4_A02


title: MGH60_P3_H10


title: MGH60_P4_A01


title: MGH60_P4_A03


title: MGH60_P4_A06


title: MGH60_P3_F12


title: MGH60_P4_A04


title: MGH60_P4_A07


title: MGH60_P4_A09


title: MGH60_P4_B05


title: MGH60_P4_A12


title: MGH60_P4_A08


title: MGH60_P4_A11


title: MGH60_P4_B01


title: MGH60_P4_B07


title: MGH60_P4_A10


title: MGH60_P4_B08


title: MGH60_P4_B02


title: MGH60_P4_B03


title: MGH60_P4_B12


title: MGH60_P4_B04


title: MGH60_P4_B09


title: MGH60_P4_C02


title: MGH60_P4_C03


title: MGH60_P4_C01


title: MGH60_P4_B10


title: MGH60_P4_A05


title: MGH60_P4_C07


title: MGH60_P4_C04


title: MGH60_P4_C05


title: MGH60_P4_C06


title: MGH60_P4_C09


title: MGH60_P4_C11


title: MGH60_P4_D01


title: MGH60_P4_C12


title: MGH60_P4_D02


title: MGH60_P4_B06


title: MGH60_P4_D03


title: MGH60_P4_D04


title: MGH60_P4_B11


title: MGH60_P4_D12


title: MGH60_P4_D06


title: MGH60_P4_D08


title: MGH60_P4_D05


title: MGH60_P4_D07


title: MGH60_P4_E02


title: MGH60_P4_D10


title: MGH60_P4_E04


title: MGH60_P4_E09


title: MGH60_P4_E03


title: MGH60_P4_F05


title: MGH60_P4_E08


title: MGH60_P4_E06


title: MGH60_P4_E07


title: MGH60_P4_E11


title: MGH60_P4_F06


title: MGH60_P4_E05


title: MGH60_P4_F01


title: MGH60_P4_F04


title: MGH60_P4_E12


title: MGH60_P4_F10


title: MGH60_P4_F08


title: MGH60_P4_F02


title: MGH60_P4_F03


title: MGH60_P4_F07


title: MGH60_P4_E01


title: MGH60_P4_F09


title: MGH60_P4_F11


title: MGH60_P4_F12


title: MGH60_P4_G01


title: MGH60_P4_G05


title: MGH60_P4_G07


title: MGH60_P4_G10


title: MGH60_P4_G11


title: MGH60_P4_H01


title: MGH60_P4_H08


title: MGH60_P4_H07


title: MGH60_P4_G06


title: MGH60_P4_G04


title: MGH60_P4_H10


title: MGH60_P4_G12


title: MGH60_P4_G09


title: MGH60_P4_H09


title: MGH60_P4_H04


title: MGH60_P4_G08


title: MGH60_P4_H11


title: MGH60_P4_H03


title: MGH60_P4_H06


title: MGH60_P4_H12


title: MGH60_P5_A02


title: MGH60_P5_A05


title: MGH60_P5_A01


title: MGH60_P5_A04


title: MGH60_P4_G02


title: MGH60_P4_G03


title: MGH60_P5_A07


title: MGH60_P5_A06


title: MGH60_P5_A08


title: MGH60_P5_A10


title: MGH60_P5_A03


title: MGH60_P5_B01


title: MGH60_P5_B04


title: MGH60_P5_B03


title: MGH60_P5_A11


title: MGH60_P5_B05


title: MGH60_P5_B12


title: MGH60_P5_B09


title: MGH60_P5_B10


title: MGH60_P5_C02


title: MGH60_P5_C01


title: MGH60_P5_B08


title: MGH60_P5_C06


title: MGH60_P5_B02


title: MGH60_P5_B06


title: MGH60_P5_C10


title: MGH60_P5_C03


title: MGH60_P5_A12


title: MGH60_P5_C07


title: MGH60_P5_C09


title: MGH60_P5_C11


title: MGH60_P5_B07


title: MGH60_P5_A09


title: MGH60_P5_D01


title: MGH60_P5_C08


title: MGH60_P5_C05


title: MGH60_P5_C04


title: MGH60_P5_D03


title: MGH60_P5_D04


title: MGH60_P5_D02


title: MGH60_P5_D07


title: MGH60_P5_D06


title: MGH60_P5_D05


title: MGH60_P5_D10


title: MGH60_P5_D12


title: MGH60_P5_E02


title: MGH60_P5_D08


title: MGH60_P5_D11


title: MGH60_P5_E04


title: MGH60_P5_E01


title: MGH60_P5_E03


title: MGH60_P5_E06


title: MGH60_P5_E05


title: MGH60_P5_C12


title: MGH60_P5_E08


title: MGH60_P5_E07


title: MGH60_P5_E10


title: MGH60_P5_E09


title: MGH60_P5_E11


title: MGH60_P5_F01


title: MGH60_P5_F02


title: MGH60_P5_F03


title: MGH60_P5_F04


title: MGH60_P5_D09


title: MGH60_P5_F06


title: MGH60_P5_F05


title: MGH60_P5_F07


title: MGH60_P5_F08


title: MGH60_P5_F09


title: MGH60_P5_G01


title: MGH60_P5_G03


title: MGH60_P5_G02


title: MGH60_P5_G05


title: MGH60_P5_G08


title: MGH60_P5_G04


title: MGH60_P5_G06


title: MGH60_P5_G07


title: MGH60_P5_H02


title: MGH60_P5_G10


title: MGH60_P5_G11


title: MGH60_P5_E12


title: MGH60_P5_H01


title: MGH60_P5_G12


title: MGH60_P5_H03


title: MGH60_P5_H04


title: MGH60_P5_H05


title: MGH60_P5_G09


title: MGH60_P5_H10


title: MGH60_P5_H07


title: MGH60_P5_F12


title: MGH60_P5_H11


title: MGH60_P5_H12


title: MGH60_P6_A01


title: MGH60_P5_F11


title: MGH60_P5_H09


title: MGH60_P6_A02


title: MGH60_P6_A04


title: MGH60_P6_A09


title: MGH60_P6_A07


title: MGH60_P6_A06


title: MGH60_P6_A10


title: MGH60_P6_A08


title: MGH60_P6_A03


title: MGH60_P6_A11


title: MGH60_P5_H06


title: MGH60_P6_B01


title: MGH60_P6_A12


title: MGH60_P6_B08


title: MGH60_P5_H08


title: MGH60_P6_B07


title: MGH60_P6_B05


title: MGH60_P6_B09


title: MGH60_P6_B03


title: MGH60_P6_B11


title: MGH60_P6_B12


title: MGH60_P6_C03


title: MGH60_P6_C06


title: MGH60_P6_B10


title: MGH60_P6_C02


title: MGH60_P6_A05


title: MGH60_P6_C05


title: MGH60_P6_C07


title: MGH60_P6_C08


title: MGH60_P6_C10


title: MGH60_P6_B04


title: MGH60_P6_C11


title: MGH60_P6_D05


title: MGH60_P6_D01


title: MGH60_P6_D04


title: MGH60_P6_B06


title: MGH60_P6_D06


title: MGH60_P6_D07


title: MGH60_P6_D08


title: MGH60_P6_D12


title: MGH60_P3_F08


title: MGH60_P6_E01


title: MGH60_P6_E03


title: MGH60_P6_D11


title: MGH60_P6_D09


title: MGH60_P6_E04


title: MGH60_P6_E02


title: MGH60_P6_E05


title: MGH60_P6_E09


title: MGH60_P6_E07


title: MGH60_P6_E10


title: MGH60_P6_E08


title: MGH60_P6_E06


title: MGH60_P6_E11


title: MGH60_P6_F03


title: MGH60_P6_C09


title: MGH60_P6_F02


title: MGH60_P6_F04


title: MGH60_P6_D03


title: MGH60_P6_F05


title: MGH60_P6_F10


title: MGH60_P6_F09


title: MGH60_P6_F08


title: MGH60_P6_F11


title: MGH60_P6_F06


title: MGH60_P6_G01


title: MGH60_P6_F12


title: MGH60_P6_G02


title: MGH60_P6_G03


title: MGH60_P6_G05


title: MGH60_P6_G04


title: MGH60_P6_G08


title: MGH60_P6_E12


title: MGH60_P6_G11


title: MGH60_P6_G10


title: MGH60_P6_G06


title: MGH60_P6_H01


title: MGH60_P6_H02


title: MGH60_P6_H03


title: MGH60_P6_G12


title: MGH60_P6_H07


title: MGH60_P6_H08


title: MGH60_P6_H06


title: MGH60_P6_H04


title: MGH60_P6_H09


title: MGH60_P6_H12


title: MGH60_P6_F07


title: MGH60_P6_H11


title: MGH60_P7_A03


title: MGH60_P7_A01


title: MGH60_P7_A06


title: MGH60_P7_A07


title: MGH60_P6_G07


title: MGH60_P7_A05


title: MGH60_P7_A04


title: MGH60_P7_A09


title: MGH60_P7_A08


title: MGH60_P7_A11


title: MGH60_P7_B05


title: MGH60_P7_B03


title: MGH60_P7_B04


title: MGH60_P7_B02


title: MGH60_P7_A10


title: MGH60_P7_A12


title: MGH60_P7_B08


title: MGH60_P7_B09


title: MGH60_P7_B07


title: MGH60_P7_B11


title: MGH60_P6_H10


title: MGH60_P7_B12


title: MGH60_P7_A02


title: MGH60_P7_C01


title: MGH60_P7_C02


title: MGH60_P7_C03


title: MGH60_P7_C05


title: MGH60_P7_C04


title: MGH60_P7_C06


title: MGH60_P7_C08


title: MGH60_P7_C09


title: MGH60_P7_C10


title: MGH60_P7_C12


title: MGH60_P7_C11


title: MGH60_P7_C07


title: MGH60_P7_D02


title: MGH60_P7_D01


title: MGH60_P7_B06


title: MGH60_P7_D04


title: MGH60_P7_D08


title: MGH60_P7_B10


title: MGH60_P7_D05


title: MGH60_P7_D10


title: MGH60_P7_D09


title: MGH60_P7_D03


title: MGH60_P7_E02


title: MGH60_P7_E04


title: MGH60_P7_E01


title: MGH60_P7_D11


title: MGH60_P7_E03


title: MGH60_P7_E06


title: MGH60_P7_E07


title: MGH60_P7_E05


title: MGH60_P7_D12


title: MGH60_P7_E11


title: MGH60_P7_F01


title: MGH60_P7_E08


title: MGH60_P7_E09


title: MGH60_P7_F03


title: MGH60_P7_F04


title: MGH60_P7_F05


title: MGH60_P7_D06


title: MGH60_P7_F10


title: MGH60_P7_F08


title: MGH60_P7_F07


title: MGH60_P7_F11


title: MGH60_P7_F12


title: MGH60_P7_G01


title: MGH60_P7_G02


title: MGH60_P7_G03


title: MGH60_P7_G04


title: MGH60_P7_G05


title: MGH60_P7_E12


title: MGH60_P7_G08


title: MGH60_P7_G09


title: MGH60_P7_G07


title: MGH60_P7_H01


title: MGH60_P7_H02


title: MGH60_P7_G12


title: MGH60_P7_G11


title: MGH60_P7_G10


title: MGH60_P7_H06


title: MGH60_P7_H07


title: MGH60_P7_H03


title: MGH60_P7_H04


title: MGH60_P7_F06


title: MGH60_P7_H05


title: MGH60_P7_H08


title: MGH60_P7_H09


title: MGH93_P7_A01


title: MGH93_P7_A03


title: MGH60_P7_H12


title: MGH60_P7_H10


title: MGH93_P7_A05


title: MGH60_P7_H11


title: MGH93_P7_A06


title: MGH93_P7_A07


title: MGH60_P7_G06


title: MGH93_P7_A08


title: MGH93_P7_A10


title: MGH93_P7_A11


title: MGH93_P7_A12


title: MGH93_P7_B02


title: MGH93_P7_B03


title: MGH93_P7_B04


title: MGH93_P7_B12


title: MGH93_P7_B06


title: MGH93_P7_C02


title: MGH93_P7_C05


title: MGH93_P7_C04


title: MGH93_P7_B11


title: MGH93_P7_B10


title: MGH93_P7_C12


title: MGH93_P7_C09


title: MGH93_P7_C07


title: MGH93_P7_C06


title: MGH93_P7_C10


title: MGH93_P7_D04


title: MGH93_P7_D02


title: MGH93_P7_D05


title: MGH93_P7_D07


title: MGH93_P7_D01


title: MGH93_P7_D10


title: MGH93_P7_D12


title: MGH93_P7_D08


title: MGH93_P7_E04


title: MGH93_P7_E06


title: MGH93_P7_A09


title: MGH93_P7_E05


title: MGH93_P7_E10


title: MGH93_P7_E11


title: MGH93_P7_E12


title: MGH93_P7_F01


title: MGH93_P7_F03


title: MGH93_P7_F04


title: MGH93_P7_F02


title: MGH93_P7_F05


title: MGH93_P7_F06


title: MGH93_P7_D06


title: MGH93_P7_F08


title: MGH93_P7_F07


title: MGH93_P7_G08


title: MGH93_P7_F12


title: MGH93_P7_F10


title: MGH93_P7_F11


title: MGH93_P7_G04


title: MGH93_P7_G09


title: MGH93_P7_G07


title: MGH93_P7_H04


title: MGH93_P7_G06


title: MGH93_P7_H05


title: MGH93_P7_H07


title: MGH93_P7_G10


title: MGH93_P7_E09


title: MGH93_P7_H09


title: MGH93_P7_H11


title: MGH93_P7_H12


title: MGH93_P7_H08


title: MGH93_P7_H10


title: MGH97_P10_A02


title: MGH97_P10_A06


title: MGH97_P10_A03


title: MGH93_P7_G03


title: MGH97_P10_A08


title: MGH97_P10_A05


title: MGH97_P10_A09


title: MGH97_P10_A12


title: MGH97_P10_A04


title: MGH97_P10_B01


title: MGH97_P10_B05


title: MGH97_P10_B06


title: MGH93_P7_H01


title: MGH97_P10_B08


title: MGH97_P10_B09


title: MGH97_P10_B03


title: MGH97_P10_B02


title: MGH97_P10_B10


title: MGH97_P10_C03


title: MGH97_P10_C02


title: MGH97_P10_B11


title: MGH97_P10_C06


title: MGH97_P10_C04


title: MGH97_P10_A01


title: MGH97_P10_C08


title: MGH97_P10_C01


title: MGH97_P10_C09


title: MGH97_P10_C07


title: MGH97_P10_C10


title: MGH97_P10_C11


title: MGH97_P10_C12


title: MGH97_P10_D03


title: MGH97_P10_B07


title: MGH97_P10_D05


title: MGH97_P10_D02


title: MGH97_P10_D04


title: MGH97_P10_D07


title: MGH97_P10_D06


title: MGH97_P10_D11


title: MGH97_P10_D08


title: MGH97_P10_D12


title: MGH97_P10_D10


title: MGH97_P10_E01


title: MGH97_P10_E03


title: MGH97_P10_D09


title: MGH97_P10_E02


title: MGH97_P10_E09


title: MGH97_P10_E05


title: MGH97_P10_E07


title: MGH97_P10_E10


title: MGH97_P10_E08


title: MGH97_P10_E06


title: MGH97_P10_E11


title: MGH97_P10_E04


title: MGH97_P10_F02


title: MGH97_P10_D01


title: MGH97_P10_F04


title: MGH97_P10_E12


title: MGH97_P10_F05


title: MGH97_P10_F07


title: MGH97_P10_F10


title: MGH97_P10_F03


title: MGH97_P10_G01


title: MGH97_P10_G02


title: MGH97_P10_F08


title: MGH97_P10_G06


title: MGH97_P10_G05


title: MGH97_P10_F11


title: MGH36_P5_C02


title: MGH97_P10_F01


title: MGH97_P10_F06


title: MGH36_P5_B11


title: MGH36_P5_B12


title: MGH36_P5_B10


title: MGH36_P5_B09


title: MGH36_P5_B07


title: MGH36_P5_B08


title: MGH36_P5_B06


title: MGH36_P5_B04


title: MGH36_P5_B02


title: MGH36_P5_B03


title: MGH36_P5_B01


title: MGH36_P5_A11


title: MGH97_P10_F12


title: MGH36_P5_A12


title: MGH36_P5_A08


title: MGH36_P5_A10


title: MGH36_P5_A09


title: MGH36_P5_C03


title: MGH36_P5_A07


title: MGH36_P5_A05


title: MGH97_P10_G03


title: MGH36_P5_A04


title: MGH36_P5_A06


title: MGH36_P2_H12


title: MGH36_P5_A02


title: MGH36_P5_A03


title: MGH36_P2_H10


title: MGH36_P5_C01


title: MGH36_P2_H08


title: MGH36_P2_H09


title: MGH36_P2_H06


title: MGH36_P5_B05


title: MGH36_P2_H04


title: MGH36_P2_H03


title: MGH36_P2_H02


title: MGH36_P2_H05


title: MGH36_P2_H01


title: MGH36_P2_G09


title: MGH36_P2_G08


title: MGH36_P2_G10


title: MGH36_P5_A01


title: MGH36_P2_G06


title: MGH36_P2_G05


title: MGH36_P2_H11


title: MGH36_P2_G07


title: MGH36_P2_G04


title: MGH36_P2_G02


title: MGH36_P2_H07


title: MGH36_P2_G03


title: MGH36_P2_F11


title: MGH36_P2_F08


title: MGH36_P2_F10


title: MGH36_P2_G01


title: MGH36_P2_F07


title: MGH36_P2_F12


title: MGH36_P2_F05


title: MGH36_P2_F09


title: MGH36_P2_F04


title: MGH36_P2_G12


title: MGH36_P2_F06


title: MGH36_P2_F02


title: MGH36_P2_F03


title: MGH36_P2_E12


title: MGH36_P2_G11


title: MGH36_P2_E10


title: MGH36_P2_E11


title: MGH36_P2_E09


title: MGH36_P2_E08


title: MGH36_P2_E07


title: MGH36_P2_E06


title: MGH36_P2_E04


title: MGH36_P2_E05


title: MGH36_P2_E03


title: MGH36_P2_E02


title: MGH36_P2_D12


title: MGH36_P2_D11


title: MGH36_P2_D08


title: MGH36_P2_D07


title: MGH36_P2_D05


title: MGH36_P2_D06


title: MGH36_P2_F01


title: MGH36_P2_D09


title: MGH36_P2_D04


title: MGH36_P2_C10


title: MGH36_P2_C08


title: MGH36_P2_D01


title: MGH36_P2_E01


title: MGH36_P2_C07


title: MGH36_P2_D10


title: MGH36_P2_C09


title: MGH36_P2_C05


title: MGH36_P2_C12


title: MGH36_P2_C06


title: MGH36_P2_D02


title: MGH36_P2_C04


title: MGH36_P2_C03


title: MGH36_P2_C01


title: MGH36_P2_C02


title: MGH36_P2_B11


title: MGH36_P2_B12


title: MGH36_P2_B10


title: MGH36_P2_D03


title: MGH36_P2_B09


title: MGH36_P2_B07


title: MGH36_P2_C11


title: MGH36_P2_B06


title: MGH36_P2_B04


title: MGH36_P2_B08


title: MGH36_P2_B03


title: MGH36_P2_B02


title: MGH36_P2_A07


title: MGH36_P2_A10


title: MGH36_P2_B01


title: MGH36_P2_A12


title: MGH36_P2_A05


title: MGH36_P2_A11


title: MGH36_P2_A04


title: MGH36_P2_A09


title: MGH36_P2_A03


title: MGH36_P1_H12


title: MGH36_P2_A02


title: MGH36_P1_H10


title: MGH36_P1_H08


title: MGH36_P1_H07


title: MGH36_P2_A06


title: MGH36_P1_H09


title: MGH36_P1_H06


title: MGH36_P2_B05


title: MGH36_P1_H05


title: MGH36_P1_H04


title: MGH36_P1_H03


title: MGH36_P1_H02


title: MGH36_P1_H01


title: MGH36_P1_G12


title: MGH36_P1_G11


title: MGH36_P2_A08


title: MGH36_P1_G10


title: MGH36_P1_G09


title: MGH36_P1_G06


title: MGH36_P1_G08


title: MGH36_P1_G07


title: MGH36_P1_H11


title: MGH36_P2_A01


title: MGH36_P1_G05


title: MGH36_P1_F12


title: MGH36_P1_G04


title: MGH36_P1_G02


title: MGH36_P1_G01


title: MGH36_P1_F09


title: MGH36_P1_G03


title: MGH36_P1_F05


title: MGH36_P1_F08


title: MGH36_P1_F04


title: MGH36_P1_F07


title: MGH36_P1_F03


title: MGH36_P1_F06


title: MGH36_P1_F02


title: MGH36_P1_E04


title: MGH36_P1_E02


title: MGH36_P1_E03


title: MGH36_P1_F01


title: MGH36_P1_D12


title: MGH36_P1_E05


title: MGH36_P1_D11


title: MGH36_P1_D09


title: MGH36_P1_D08


title: MGH36_P1_F10


title: MGH36_P1_F11


title: MGH36_P1_D05


title: MGH36_P1_D06


title: MGH36_P1_D04


title: MGH36_P1_D07


title: MGH36_P1_D03


title: MGH36_P1_D02


title: MGH36_P1_D01


title: MGH36_P1_C12


title: MGH36_P1_C11


title: MGH36_P1_C08


title: MGH36_P1_C07


title: MGH36_P1_C06


title: MGH36_P1_C05


title: MGH36_P1_C10


title: MGH36_P1_C02


title: MGH36_P1_C03


title: MGH36_P1_C04


title: MGH36_P1_C01


title: MGH36_P1_B11


title: MGH36_P1_D10


title: MGH36_P1_B10


title: MGH36_P1_B12


title: MGH36_P1_B08


title: MGH36_P1_B09


title: MGH36_P1_B06


title: MGH36_P1_B05


title: MGH36_P1_B07


title: MGH36_P1_B02


title: MGH36_P1_B03


title: MGH36_P1_A12


title: MGH36_P1_B01


title: MGH36_P1_B04


title: MGH36_P1_C09


title: MGH36_P1_A10


title: MGH36_P1_A11


title: MGH36_P1_A08


title: MGH36_P1_A09


title: MGH36_P1_A05


title: MGH36_P1_A03


title: MGH36_P1_A02


title: MGH36_P1_A04


title: MGH36_P1_A07


title: MGH36_P1_A06


title: 20863 iBET762- 1uM rep2

status: Public on Aug 22 2016

type: RNA

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

country: USA

institute: NIAID

description:
cervical epithelial cells
G 20863 iBET762- rep 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays. ANOVA was performed on the normalized log2 expression estimates to test for mRNA expression differences.  A p-value of 0.05 was used for the statistical significance cutoff, after adjusting for the familywize error rate (FWER) using Benjamini–Hochberg method to account for multiple testing. Statistical analysis was performed using JMP/Genomics software version 6.0.

label: biotin

source_name: 20863 cells treated with inactive enantiomer

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: 20861 and 20863 were co-cultured in F-medium with irradiated J2-3T3 fibroblast feeders. Fibroblasts were removed before RNA extraction.

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: cells were treated with 1 micromolar iBET762- (the inactive enantiomer) or iBET762+ for 44 hours

tag: gender

value: female

tag: virus

value: HPV16 extrachromosomal

tag: cell line

value: epithelial

tag: tissue

value: cervix


title: 20863 iBET762+ 1uM rep1

description:
cervical epithelial cells
D 20863 iBET762+ rep 1

source_name: 20863 cells treated with BET inhibitor


title: MGH36_P1_A01


title: 20861 iBET762+ 1uM rep3

description:
cervical epithelial cells
J 20861 iBET762+ rep 3

source_name: 20861 cells treated with BET inhibitor

value: HPV16 integrated


title: 20863 iBET762- 1uM rep3

description:
cervical epithelial cells
K 20863 iBET762- rep 3


title: 20863 iBET762+ 1uM rep3

description:
cervical epithelial cells
L 20863 iBET762+ rep 3


title: 20861 iBET762+ 1uM rep1

description:
cervical epithelial cells
B 20861 iBET762+ rep 1


title: 20861 iBET762- 1uM rep2

description:
cervical epithelial cells
E 20861 iBET762- rep 2

source_name: 20861 cells treated with inactive enantiomer


title: 20861 iBET762- 1uM rep3

description:
cervical epithelial cells
I 20861 iBET762- rep 3


title: 20863 iBET762+ 1uM rep2

description:
cervical epithelial cells
H 20863 iBET762+ rep 2


title: 20863 iBET762- 1uM rep1

description:
cervical epithelial cells
C 20863 iBET762- rep 1


title: 20861 iBET762- 1uM rep1

description:
cervical epithelial cells
A 20861 iBET762- rep 1


title: 20861 iBET762+ 1uM rep2

description:
cervical epithelial cells
F 20861 iBET762+ rep 2


title: AOCS_158_ICGC_DBDE_20130904_012

status: Public on May 19 2015

type: genomic

city: Herston

first: Ann-Marie

last: Patch

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Raw data for arrays used for methylation analysis

hyb_protocol: Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on Iscan (Illumina)

data_processing: Data was background corrected, normalized to internal controls and QC was performed at the probe and sample level. COMBAT was used to remove batch effects (Johnson et al., 2007)

molecule: genomic DNA

source_name: Primarytumour

label_protocol: Bisulfite converted genomic DNAwas whole genome amplified and labeled using Illumina protocol

extract_protocol: DNA was extracted from fresh frozen tissues using AllPrep DNA/RNA Mini Kit (Qiagen). Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays

value: Female

value: Primarytumour

value: high grade serous ovarian cancer


title: AOCS_147_ICGC_DBPC_20130205_166

source_name: PrimaryTumour

value: PrimaryTumour


title: AOCS_170_ICGC_DBDE_20131003_008


title: AOCS_163_ICGC_DBDE_20130904_017


title: AOCS_159_ICGC_DBDE_20130904_013


title: AOCS_164_ICGC_DBDE_20130904_018


title: AOCS_153_ICGC_DBPC_20130205_176


title: AOCS_148_ICGC_DBPC_20130205_168


title: AOCS_169_ICGC_DBDE_20131003_006


title: AOCS_130_ICGC_DBPC_20130205_116


title: AOCS_165_ICGC_DBDE_20130904_019


title: AOCS_157_ICGC_DBDE_20130904_011


title: AOCS_161_ICGC_DBDE_20130904_015


title: AOCS_125_ICGC_DBPC_20130205_108


title: AOCS_149_ICGC_DBPC_20130205_170


title: AOCS_126_ICGC_DBPC_20130205_110


title: AOCS_144_ICGC_DBPC_20130205_160


title: AOCS_171_ICGC_DBDE_20131003_011


title: AOCS_168_ICGC_DBDE_20131003_004


title: AOCS_152_ICGC_DBPC_20130205_174


title: AOCS_160_ICGC_DBDE_20130904_014


title: AOCS_097_ICGC_DBPC_20130205_074


title: AOCS_131_ICGC_DBPC_20130205_118


title: AOCS_139_ICGC_DBPC_20130205_150


title: AOCS_113_ICGC_DBPC_20130205_088


title: AOCS_133_ICGC_DBPC_20130607_002


title: AOCS_132_ICGC_DBPC_20130205_120


title: AOCS_124_ICGC_DBPC_20130205_106


title: AOCS_115_ICGC_DBPC_20130205_092


title: AOCS_128_ICGC_DBPC_20130205_112


title: AOCS_123_ICGC_DBPC_20130607_006


title: AOCS_145_ICGC_DBPC_20130205_162


title: AOCS_143_ICGC_DBPC_20130205_158


title: AOCS_116_ICGC_DBPC_20130205_094


title: AOCS_109_ICGC_DBPC_20130205_086


title: AOCS_114_ICGC_DBPC_20130205_090


title: AOCS_146_ICGC_DBPC_20130205_164


title: AOCS_112_ICGC_DBPC_20130205_133


title: AOCS_090_ICGC_DBPC_20130205_055


title: AOCS_122_ICGC_DBPC_20130205_102


title: AOCS_106_ICGC_DBPC_20130607_003


title: AOCS_092_ICGC_DBPC_20130205_061


title: AOCS_107_ICGC_DBPC_20130607_004


title: AOCS_095_ICGC_DBPC_20130607_007


title: AOCS_093_ICGC_DBPC_20130205_064


title: AOCS_111_ICGC_DBPC_20130205_131


title: AOCS_094_ICGC_DBPC_20130205_067


title: AOCS_075_ICGC_DBPC_20130205_033


title: AOCS_108_ICGC_DBPC_20130607_005


title: AOCS_083_ICGC_DBPC_20130205_045


title: AOCS_088_ICGC_DBPC_20130701_004


title: AOCS_086_ICGC_DBPC_20130205_052


title: AOCS_104_ICGC_DBPC_20130205_076


title: AOCS_085_ICGC_DBPC_20130205_049


title: AOCS_096_ICGC_DBPC_20130205_072


title: AOCS_084_ICGC_DBPC_20130205_047


title: AOCS_091_ICGC_DBPC_20130205_058


title: AOCS_080_ICGC_DBPC_20130205_041


title: AOCS_081_ICGC_DBPC_20130205_043


title: AOCS_063_ICGC_DBPC_20130205_025


title: Human epidermal keratinocyte replicate 1

status: Public on Mar 31 2014

description: replicate 1

hyb_protocol: gene expression was analyzed by hybridization to Illumina whole genome HumanHT-12 v4.0 BeadChip.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: epidermis

label_protocol: cDNA was prepared using the Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies).

growth_protocol: Keratinocytes were cultured in F medium [3:1 (v/v) F-12-DMEM, 5% FBS, 0.4μg/ml hydrocortisone, 5μg/ml insulin, 8.4ng/ml cholera toxin, 10ng/ml EGF, 24μg/ml adenine,100U/ml penicillin, 100μg/ml streptomycin] in the presence of irradiated 3T3-J2 feeder cells.

extract_protocol: Total RNA was prepared using RNeasy mini prep kit (Qiagen).

treatment_protocol: keratinocytes were cultured for either three or four passes in the presence or absence of 10μM Y27632.

value: HEK

tag: agent


title: AOCS_105_ICGC_DBPC_20130205_078


title: AOCS_078_ICGC_DBPC_20130205_126


title: AOCS_079_ICGC_DBPC_20130205_039


title: AOCS_077_ICGC_DBPC_20130205_037


title: Human epidermal keratinocyte, Y-27632 replicate 1

description: replicate 1


title: Human epidermal keratinocyte, Y-27632 replicate 2

description: replicate 2


title: AOCS_059_ICGC_DBPC_20130205_019


title: Human epidermal keratinocyte replicate 2

description: replicate 2


title: AOCS_065_ICGC_DBPC_20130205_031


title: AOCS_060_ICGC_DBPC_20130205_021


title: AOCS_004_ICGC_DBPC_20130205_004


title: AOCS_057_ICGC_DBPC_20130205_015


title: AOCS_055_ICGC_DBPC_20130205_011


title: AOCS_061_ICGC_DBPC_20130205_023


title: AOCS_064_ICGC_DBPC_20130205_028


title: AOCS_058_ICGC_DBPC_20130205_017


title: AOCS_056_ICGC_DBPC_20130205_013


title: AOCS_034_ICGC_DBPC_20130205_009


title: AOCS_005_ICGC_DBPC_20130205_006


title: AOCS_001_ICGC_DBPC_20130205_002