title: RNA-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: RNA-IPS-Bipo_I_Y-208.04

status: Public on Jan 28 2018

type: SRA

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the human genome mm9(MGSCv37) using in-house software StrongArm.
We required > 30% of exon have > 30x depth. And raw counts by HTSEQ(version 0.6.1p1) based on GENCODE annotation vM7 have been converted to FPKM.
For Differential Expression analysis, we used Voom packge(R 3.23, edgeR 3.12.1, limma 3.26.9) for statical tests.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: tab-delimited text files include raw counts

molecule: total RNA

organism: Mus musculus

source_name: Cell Line

extract_protocol:
RNA was extracted from each iPS cell lines by using RNeasy Plus Mini kit (Qiagen, 74134) or Direct-zol kit (Zymo Research, R2050).
Libraries were prepared from ~500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina).

tag: strain

tag: cell type

value: iPSCs from immature Bipolar cell MakeRetina 208.04

tag: cell line


title: INPUT-NRL-Rod_M_N-P6

library_source: genomic

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
We required > 10M unique mapped reads for point-source factor (H3K4me2/3, H3K9/14Ac, H3K27Ac, CTCF, RNAPolII, BRD4) and RSC > 1. We required 20M unique mapped reads for broad markers (H3K9me3, H3K27me3, H3K36me3). We required 10M unique mapped reads for INPUTs and RSC < 1. We noticed H3K4me1 is point-source factor in some stages while broad in other stages so we QC H3K4me1 as broad markers. Then upon manually inspection, the cross-correlation plot generated by SPP, the best fragment size estimated (the smallest fragment size estimated by SPP in all our cases) were used to extend each reads and generate bigwig file to view on IGV (version 2.3.40).
All profiles were manually inspected for clear peaks and good signal to noise separation. We followed ENCODE guideline for quality control.
We extended reads and generate the final bigwig track normalized to 30M reads for visualization.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

extract_protocol:
After removal of IRMEFs, iPS cells were collected after washing with PBS. Then cells were subjected to crosslinking in 1% formaldehyde (Thermo scientific, 28906) for 10 minutes at room temperature, followed by the addition of glycine at the final concentration of 0.125 M to quench the reaction. After centrifuge, cells were washed with cold PBS, counted and pelleted as 10 million cells for each nuclei preparation.
The nuclei were isolated and prepared for shearing using TruChIP chromatin shearing kit (Covaris, 520127) according to manufacturer’s protocol. After shearing, ChIP was performed using the iDeal ChIP-seq kit (Diagenode, C01010051). The antibodies used were: anti-H3K4me3 (Diagenode, C15410003-50), anti-H3K4me2 (Abcam, ab7766), anti-H3K4me1 (Abcam, ab8895), anti-H3K9/14ac (Diagenode, C15410200), anti-H3K27ac (Abcam, ab4729), anti-H3K36me3 (Active Motif, 61101), anti-H3K27me3 (Active Motif, 39155), and anti-CTCF (Active Motif, 61311). After de-crosslinking, DNA was extracted using MinElute PCR-purification kit (Qiagen, 28006) or Agencourt AMPure XP beads (Beckman Coulter, A63881) and subjected to library preparation using NEBNext ChIP-Seq Library Prep Master Mix Set for illumina (NEB, E6240L). The ChIP experiments and library preparation for antibodies including anti-RNA polymerase II (Abcam, ab5095), anti-Brd4 (Bethyl Laboratories, A301-985A) and anti-H3K9me3 (Active Motif, 39161), were performed by Active Motif.

tag: strain background

value: NRL-GFP sorted Rod cell postnatal day 6

tag: chip antibody

value: none (input)


title: INPUT-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: INPUT-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: RNAPolII-IPS-Cone_I_Y-209.11

value: RNAPolII (Abcam,ab5095)


title: INPUT-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: INPUT-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: RNAPolII-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: RNAPolII-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: INPUT-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: INPUT-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: INPUT-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: INPUT-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: INPUT-IPS-Bipo_I_Y-208.03


title: RNAPolII-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: INPUT-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: RNAPolII-IPS-Bipo_I_Y-208.04


title: INPUT-IPS-Bipo_I_Y-208.04


title: RNAPolII-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: RNAPolII-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: RNAPolII-IPS-MullFibr_F_N-FCR02


title: INPUT-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: RNAPolII-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: RNAPolII-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: RNAPolII-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: H3K9me3-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04

value: H3K9me3 (ActiveMotif,39161)


title: RNAPolII-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02

value: RNAPolII (Abcam,ab5095)


title: RNAPolII-IPS-AmacFibr_F_N-fG140.02


title: INPUT-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401

value: none (input)


title: RNAPolII-IPS-Cone_I_N-rCh209.04


title: RNAPolII-IPS-Mull_M_Y-rCr33.04


title: RNAPolII-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: H3K9me3-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: RNAPolII-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: H3K9me3-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: H3K9me3-IPS-Cone_I_Y-209.13


title: RNAPolII-IPS-Cone_M_Y-257.03


title: RNAPolII-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: H3K9me3-IPS-Mull_M_Y-rCr33.04


title: H3K9me3-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: H3K9me3-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: RNAPolII-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: H3K9me3-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: H3K9me3-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: RNAPolII-IPS-Bipo_I_Y-rM0401


title: H3K9me3-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: H3K9me3-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: H3K9me3-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602

value: H3K9me3 (ActiveMotif,39161)


title: RNAPolII-IPS-Bipo_I_Y-208.03

value: RNAPolII (Abcam,ab5095)


title: RNAPolII-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: H3K9me3-IPS-Mull_M_N-rCr263.4


title: H3K9me3-IPS-Bipo_I_N-rM0408


title: H3K9me3-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: H3K9me3-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: H3K9-14Ac-IPS-Mull_M_N-rCr263.4


title: H3K9-14Ac-IPS-Mull_M_N-rCr143.02


title: H3K9-14Ac-IPS-AmacFibr_F_N-fG140.02


title: H3K9-14Ac-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: RNAPolII-IPS-Rod_I_Y-8602


title: H3K9me3-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: H3K9me3-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: H3K9me3-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: H3K9me3-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: H3K9-14Ac-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: H3K9me3-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: H3K9-14Ac-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: H3K9-14Ac-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: H3K9me3-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: H3K9me3-IPS-Cone_I_Y-209.12


title: H3K9me3-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04


title: H3K9-14Ac-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: H3K9-14Ac-IPS-Mull_M_Y-263.08


title: H3K9-14Ac-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: H3K9me3-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401

value: H3K9me3 (ActiveMotif,39161)


title: H3K9-14Ac-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: H3K9-14Ac-IPS-RodFibr_F_Y-FNR07


title: H3K9me3-IPS-Amac_M_Y-30.02


title: H3K9-14Ac-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: H3K9-14Ac-IPS-Bipo_I_Y-rM0401


title: H3K9-14Ac-IPS-Mull_M_Y-rCr33.01


title: H3K9-14Ac-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: H3K9-14Ac-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: H3K9-14Ac-IPS-Cone_I_Y-209.11


title: H3K9-14Ac-IPS-Bipo_I_Y-208.04


title: H3K4me3-NRL-Rod_M_N-P6

value: NRL-GFP sorted Rod cell postnatal day 6


title: H3K9-14Ac-IPS-Mull_M_N-rCr33.05


title: H3K9-14Ac-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: H3K9-14Ac-NRL-Rod_M_N-P21

value: NRL-GFP sorted Rod cell postnatal day 21


title: H3K9-14Ac-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: H3K4me3-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: H3K9-14Ac-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: H3K4me3-IPS-Cone_M_N-rCh257.4


title: H3K4me3-IPS-Mull_M_N-rCr33.05


title: H3K9-14Ac-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: H3K4me3-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: H3K4me3-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: H3K4me3-IPS-Cone_I_N-rCh209.04


title: H3K9-14Ac-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: H3K4me3-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: H3K4me3-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: H3K9-14Ac-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: H3K4me3-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: H3K4me3-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: H3K4me3-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: H3K4me3-IPS-Amac_I_N-rG79.04


title: H3K4me3-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: H3K4me3-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: H3K4me3-IPS-Mull_M_Y-Cr143.01


title: H3K4me3-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: H3K4me3-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: H3K4me3-IPS-Mull_M_Y-rCr33.04


title: H3K4me3-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: H3K4me3-IPS-Mull_I_Y-207.11


title: H3K4me3-IPS-Bipo_I_Y-rM0405


title: H3K4me2-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4

value: H3K4me2 (Abcam,ab7766)


title: H3K4me3-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: H3K4me2-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: H3K4me3-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04


title: H3K4me2-NRL-Rod_M_N-P6

value: NRL-GFP sorted Rod cell postnatal day 6


title: H3K4me3-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: H3K4me2-NRL-Rod_M_N-P21

value: NRL-GFP sorted Rod cell postnatal day 21


title: H3K4me3-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: H3K4me2-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: H3K4me3-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: H3K4me2-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: H3K4me2-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: H3K4me2-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: H3K4me2-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: H3K4me2-IPS-MullFibr_F_N-FCR01


title: H3K4me2-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: H3K4me2-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: H3K4me2-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: H3K4me2-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04

value: H3K4me2 (Abcam,ab7766)


title: H3K4me2-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: H3K4me2-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: H3K4me2-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: H3K4me2-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: H3K4me2-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: H3K4me2-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: H3K4me2-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: H3K4me2-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: H3K4me2-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: H3K4me2-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: H3K4me2-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: H3K4me2-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: H3K4me2-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: H3K4me1-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4

value: H3K4me1 (Abcam,ab8895)


title: H3K4me1-NRL-Rod_M_N-P6

value: NRL-GFP sorted Rod cell postnatal day 6


title: H3K4me1-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: H3K4me2-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04

value: H3K4me2 (Abcam,ab7766)


title: H3K4me1-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: H3K4me1-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: H3K4me1-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: H3K4me1-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: H3K4me1-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: H3K4me1-NRL-Rod_M_N-P21

value: NRL-GFP sorted Rod cell postnatal day 21


title: H3K4me1-IPS-Bipo_I_N-rM0408


title: H3K4me1-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: H3K4me1-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: H3K4me1-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: H3K4me1-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: H3K4me1-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: H3K4me1-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: H3K4me1-GRM6-Bipo_M_N

value: GRM6-GFP sorted Bipolar cell

value: H3K4me1 (Abcam,ab8895)


title: H3K4me1-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: H3K4me1-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: H3K4me1-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: H3K4me1-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: H3K36me3-NRL-Rod_M_N-P21

value: H3K36me3 (ActiveMotif,61101)


title: H3K4me1-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: H3K4me1-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: H3K4me1-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04


title: H3K36me3-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: H3K36me3-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: H3K36me3-NRL-Rod_M_N-P6

value: NRL-GFP sorted Rod cell postnatal day 6


title: H3K36me3-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: H3K36me3-IPS-MullFibr_F_N-FCR02


title: H3K4me1-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: H3K36me3-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: H3K36me3-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: H3K4me1-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: H3K4me1-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03

value: H3K4me1 (Abcam,ab8895)


title: H3K4me2-GRM6-Bipo_M_N

value: GRM6-GFP sorted Bipolar cell

value: H3K4me2 (Abcam,ab7766)


title: H3K36me3-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: H3K36me3-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03

value: H3K36me3 (ActiveMotif,61101)


title: H3K36me3-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: H3K36me3-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: H3K36me3-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: H3K36me3-IPS-Mull_I_Y-207.11


title: H3K36me3-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: H3K36me3-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: H3K36me3-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: H3K36me3-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04


title: H3K36me3-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: H3K27me3-NRL-Rod_M_N-P6

value: NRL-GFP sorted Rod cell postnatal day 6

value: H3K27me3 (ActiveMotif,39155)


title: H3K36me3-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: H3K36me3-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: H3K36me3-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: H3K27me3-GRM6-Bipo_M_N

value: GRM6-GFP sorted Bipolar cell


title: H3K27me3-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: H3K36me3-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: H3K27me3-NRL-Rod_M_N-P21

value: NRL-GFP sorted Rod cell postnatal day 21


title: H3K36me3-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03

value: H3K36me3 (ActiveMotif,61101)


title: H3K36me3-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: H3K36me3-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: H3K27me3-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: H3K27me3-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: H3K27me3-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: H3K36me3-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: H3K27me3-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: H3K36me3-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: H3K27me3-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408

value: H3K27me3 (ActiveMotif,39155)


title: H3K27me3-IPS-Cone_I_Y-209.13


title: H3K27me3-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: H3K27me3-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: H3K27me3-IPS-Amac_M_Y-30.02


title: H3K27me3-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: H3K27me3-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: H3K27me3-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: H3K4me1-IPS-RodFibr_F_Y-FNR07

value: H3K4me1 (Abcam,ab8895)


title: H3K27me3-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: H3K27me3-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: H3K27me3-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: H3K27me3-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: H3K27me3-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: H3K27me3-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: H3K27me3-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: H3K27me3-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04


title: H3K27Ac-NRL-Rod_M_N-P6

value: NRL-GFP sorted Rod cell postnatal day 6

value: H3K27Ac (Abcam,ab4729)


title: H3K27Ac-NRL-Rod_M_N-P21

value: NRL-GFP sorted Rod cell postnatal day 21


title: H3K27Ac-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: H3K27Ac-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: H3K27me3-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602

value: H3K27me3 (ActiveMotif,39155)


title: H3K27me3-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: H3K27me3-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: H3K27Ac-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: H3K27me3-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: H3K27me3-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: H3K27Ac-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: H3K27Ac-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: H3K27Ac-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: H3K27Ac-IPS-Mull_M_Y-263.08


title: H3K4me1-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05

value: H3K4me1 (Abcam,ab8895)


title: H3K27Ac-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: H3K27Ac-IPS-Bipo_I_Y-rM0405

value: H3K27Ac (Abcam,ab4729)


title: H3K27Ac-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: H3K27Ac-IPS-Rod_I_Y-8602


title: H3K27Ac-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: H3K27Ac-IPS-Cone_M_Y-257.03


title: H3K27Ac-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: H3K27Ac-GRM6-Bipo_M_N

value: GRM6-GFP sorted Bipolar cell


title: H3K27Ac-IPS-Mull_M_N-rCr33.05


title: CTCF-IPS-Cone_I_N-rCh209.04

value: CTCF (ActiveMotif,61311)


title: H3K27Ac-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: H3K27Ac-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: H3K27Ac-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: H3K27Ac-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: H3K27Ac-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: H3K27Ac-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: CTCF-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: CTCF-IPS-MullFibr_F_N-FCR02


title: H3K27Ac-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: CTCF-IPS-MullFibr_F_N-FCR01


title: H3K27Ac-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04


title: H3K27Ac-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: CTCF-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: CTCF-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: CTCF-IPS-Cone_I_Y-209.11


title: CTCF-IPS-Amac_M_Y-30.02


title: H3K27Ac-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04

value: H3K27Ac (Abcam,ab4729)


title: CTCF-NRL-Rod_M_N-P6

value: NRL-GFP sorted Rod cell postnatal day 6


title: H3K27Ac-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: CTCF-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408

value: CTCF (ActiveMotif,61311)


title: CTCF-IPS-Amac_I_N-rG79.04

value: iPSCs from immature Amacrine cell CanNotMakeRetina rG79.04


title: CTCF-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: CTCF-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: CTCF-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: CTCF-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: BRD4-IPS-Amac_I_N-rG79.04

value: BRD4 (Bethyl,A301-985A)


title: BRD4-IPS-Mull_M_N-rCr143.02

value: iPSCs from mature Muller cell CanNotMakeRetina rCr143.02


title: CTCF-NRL-Rod_M_N-P21

value: NRL-GFP sorted Rod cell postnatal day 21


title: CTCF-IPS-Mull_M_Y-rCr33.04


title: CTCF-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: CTCF-IPS-Mull_M_N-rCr143.02


title: CTCF-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: CTCF-IPS-AmacFibr_F_N-fG140.02

value: iPSCs from fibroblast Amacrine cell CanNotMakeRetina fG140.02


title: CTCF-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: CTCF-IPS-Cone_I_Y-209.12

value: iPSCs from immature Cone cell MakeRetina 209.12


title: BRD4-IPS-MullFibr_F_N-FCR01

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR01


title: BRD4-IPS-AmacFibr_F_N-fG140.02


title: BRD4-IPS-RodFibr_F_Y-FNR07

value: iPSCs from fibroblast Rod cell MakeRetina FNR07


title: BRD4-IPS-Bipo_I_N-rM0408

value: iPSCs from immature Bipolar cell CanNotMakeRetina rM0408


title: BRD4-IPS-Cone_I_Y-209.13

value: iPSCs from immature Cone cell MakeRetina 209.13


title: CTCF-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04

value: CTCF (ActiveMotif,61311)


title: CTCF-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: BRD4-IPS-Amac_M_Y-30.02

value: iPSCs from mature Amacrine cell MakeRetina 30.02


title: CTCF-IPS-Bipo_I_Y-rM0401

value: iPSCs from immature Bipolar cell MakeRetina rM0401


title: BRD4-IPS-Cone_I_Y-209.12

value: BRD4 (Bethyl,A301-985A)


title: BRD4-IPS-Mull_M_N-rCr263.4

value: iPSCs from mature Muller cell CanNotMakeRetina rCr263.4


title: CTCF-IPS-RodFibr_F_Y-FNR07


title: BRD4-IPS-Cone_M_N-rCh257.4

value: iPSCs from mature Cone cell CanNotMakeRetina rCh257.4


title: BRD4-IPS-Mull_M_Y-Cr143.01

value: iPSCs from mature Muller cell MakeRetina Cr143.01


title: CTCF-IPS-Mull_M_N-rCr33.05

value: iPSCs from mature Muller cell CanNotMakeRetina rCr33.05


title: BRD4-IPS-MullFibr_F_N-FCR02

value: iPSCs from fibroblast Muller cell CanNotMakeRetina FCR02


title: BRD4-IPS-Cone_I_N-rCh209.04

value: iPSCs from immature Cone cell CanNotMakeRetina rCh209.04


title: BRD4-IPS-Bipo_I_Y-rM0401


title: BRD4-IPS-Mull_M_Y-263.08

value: iPSCs from mature Muller cell MakeRetina 263.08


title: MT P30 [13_P30MTnt3]

status: Public on Jan 27 2018

city: New York

first: Josephine

last: Galatioto

state: New York

address: 1468 Madison Avenue

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
13_P30MTnt3
processed data file: P30.csv

data_processing:
Sequencing reads were aligned to the mouse reference genome 'mm9' using Tophat 2.0.8, samtools-0.1.7 and bowtie 2.1.0.
DEGs were identified with cufflinks 1.3.0. Tophat was used with the ensemble GTF file as a gene annotation reference and the option ’no-novel-juncs’.
Output BAM files were directly subjected to differential gene expression identification using Cufflinks with the options ’multi-read-correct’, ’upper-quartile-norm’ and ’frag-bias-correct’ against the mm9 genome.
DEGs in mutant (MT) versus wildtype (WT) aortas were identified based on a false discovery rate (FDR) of 10% and a minimum fold change (log2((FPKMcondition1+1)/(FPKMcondition2 + 1)) ≥ ± log2(1.3)).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.csv: Cufflinks output files.

source_name: Aorta

extract_protocol:
RNA was purified from frozen aortic tissues using the RNeasy Fibrous Tissue Kit (Qiagen). RNA amounts were quantitated by Qubit fluorometer (Life Technologies) and RNA quality was assessed using an Agilent 2100 Bioanalyzer. Total RNA preparations with ribosomal integrity numbers >8 were used for RNA-Seq experiments performed using Illumina HiSeq4000.
Libraries were prepared from 1μg of total RNA using TruSeq Stranded mRNA kit protocol (Illumina®) according to the supplier’s recommendation. Briefly, poly-A RNA was isolated using oligo-dTs attached to magnetic beads, fragmented into ~300 bp-long pieces using divalent cations under elevated temperature, used as template for double-stranded cDNA synthesis, Illumina adapters ligation and PCR-mediated cDNA library amplification. Sequencing of random paired-end 75 bp molecules was carried out on Illumina HiSeq4000.

tag: strain/background

tag: genotype/variation

value: fibrillin-1 hypomorphic

tag: age

value: 30 days

tag: gender

value: male

tag: tissue

value: Aorta


title: BRD4-IPS-Mull_M_N-rCr33.05


title: BRD4-IPS-Mull_M_Y-rCr33.04

value: iPSCs from mature Muller cell MakeRetina rCr33.04


title: MT P60 [17_P60MTnt1]

description:
17_P60MTnt1
processed data file: P60.csv

value: 60 days


title: WT P30 [35_P30WTnt4]

description:
35_P30WTnt4
processed data file: P30.csv

value: wildtype


title: BRD4-IPS-Cone_I_Y-209.11

value: iPSCs from immature Cone cell MakeRetina 209.11


title: MT P30 [5_P30MTnt1]

description:
5_P30MTnt1
processed data file: P30.csv


title: BRD4-IPS-Mull_I_Y-207.11

value: iPSCs from immature Muller cell MakeRetina 207.11


title: BRD4-IPS-Bipo_I_Y-208.04

value: iPSCs from immature Bipolar cell MakeRetina 208.04

value: BRD4 (Bethyl,A301-985A)


title: BRD4-IPS-Cone_M_Y-257.03

value: iPSCs from mature Cone cell MakeRetina 257.03


title: WT P60 [21_P60WTnt2]

description:
21_P60WTnt2
processed data file: P60.csv


title: WT P30 [3_P30WTnt1]

description:
3_P30WTnt1
processed data file: P30.csv


title: MT P60 [23_P60MTnt2]

description:
23_P60MTnt2
processed data file: P60.csv


title: BRD4-IPS-Bipo_I_Y-rM0405

value: iPSCs from immature Bipolar cell MakeRetina rM0405


title: MFS P16 [2_P16MT1]

description:
2_P16MT1
processed data file: P16.csv

value: 16 days


title: WT P30  [9_P30WTnt2]

description:
9_P30WTnt2
processed data file: P30.csv


title: MT P30 [33_P30MTnt4]

description:
33_P30MTnt4
processed data file: P30.csv


title: BRD4-IPS-Mull_M_Y-rCr33.01

value: iPSCs from mature Muller cell MakeRetina rCr33.01


title: BRD4-IPS-Rod_I_Y-8602

value: iPSCs from immature Rod cell MakeRetina 8602


title: BRD4-IPS-Bipo_I_Y-208.03

value: iPSCs from immature Bipolar cell MakeRetina 208.03


title: WT P16 [1_P16WT1]

description:
1_P16WT1
processed data file: P16.csv


title: MT P60 [29_P60MTnt3]

description:
29_P60MTnt3
processed data file: P60.csv

value: fibrillin-1 hypomorphic


title: MT P30 [11_P30MTnt2]

description:
11_P30MTnt2
processed data file: P30.csv

value: 30 days


title: MFS P16 [20_P16MT3]

description:
20_P16MT3
processed data file: P16.csv

value: male


title: WT P60 [27_P60WTnt3]

description:
27_P60WTnt3
processed data file: P60.csv

value: Aorta


title: WT P30 [25_P30WTnt3]

description:
25_P30WTnt3
processed data file: P30.csv


title: WT P16 [19_P16WT3]

description:
19_P16WT3
processed data file: P16.csv


title: MFS P16 [8_P16MT2]

description:
8_P16MT2
processed data file: P16.csv


title: LC150N

type: RNA

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Gene expression profile of human liver cancer #LC150, non-tumorous tissue

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The microarray data of 152 tumorous and 91 adjacent liver tissues from HCC patients as well as 14 normal liver were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

label: biotin

organism: Homo sapiens

source_name: Human liver cancer #LC150, non-tumorous tissue

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue specimens by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tissue samples were stored in RNAlater (Thermo Fisher Scientific) at -80°C immediately after dissected.

value: Liver cancer, non-tumorous tissue


title: LC144N

description: Gene expression profile of human liver cancer #LC144, non-tumorous tissue

source_name: Human liver cancer #LC144, non-tumorous tissue


title: LC138N

description: Gene expression profile of human liver cancer #LC138, non-tumorous tissue

source_name: Human liver cancer #LC138, non-tumorous tissue


title: LX2-FABP4 (2)

description: Gene expression profile of LX2-FABP4 (2)

data_processing: The data were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: Human hepatic stellate cell line LX2 constitutively expressing FABP4

extract_protocol: Total RNA was extracted from cells by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human hepatic stellate cell line, LX2, was purchased from Merck Millipore and then grown in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Thermo Fisher Scientific). Cells were cultured in a humidified incubator at 37°C with 5% CO2.

tag: overxpression


title: WT P16 [7_P16WT2]

description:
7_P16WT2
processed data file: P16.csv


title: LC147N

description: Gene expression profile of human liver cancer #LC147, non-tumorous tissue

source_name: Human liver cancer #LC147, non-tumorous tissue


title: LC148N

description: Gene expression profile of human liver cancer #LC148, non-tumorous tissue

source_name: Human liver cancer #LC148, non-tumorous tissue


title: LC146N

description: Gene expression profile of human liver cancer #LC146, non-tumorous tissue

source_name: Human liver cancer #LC146, non-tumorous tissue


title: LX2-control (2)

description: Gene expression profile of LX2-control (2)

source_name: Human hepatic stellate cell line LX2 constitutively expressing eGFP

value: eGFP


title: LC135N

description: Gene expression profile of human liver cancer #LC135, non-tumorous tissue

source_name: Human liver cancer #LC135, non-tumorous tissue


title: LC141N

description: Gene expression profile of human liver cancer #LC141, non-tumorous tissue

source_name: Human liver cancer #LC141, non-tumorous tissue


title: LX2-FABP4 (1)

description: Gene expression profile of LX2-FABP4 (1)


title: HCC3

description: Gene expression profile of hepatocellular carcinoma from C4R-KO mouse #HCC3

hyb_protocol: Hybridization of SurePrint G3 Mouse Gene Expression 8x60K Microarray Kit (G4852A, Agilent) were performed following the manufacturer's instruction by using the Agilent DNA Microarray Hybridization Oven.

scan_protocol: Microarray chips were scanned with Agilent DNA Microarray Scanner.

data_processing: The data were normalized by using Feature Extraction Software (Agilent, ver 10.7.1.1), and then transformed into log 2 base.

source_name: Hepatocelluar carcinoma from MC4R-KO mouse #HCC3

label_protocol: Cyanine-3 labeled complementary RNA was prepared from total RNA for each mouse sample by using the Low Input Quick Amp Labeling kit (Agilent).

treatment_protocol: Tumor samples and normal liver tissues were collected from the MC4R-KO mice fed with high-fat and high-sucrose diets and the wild-type done with standard diets.

value: Hepatocellular carcinoma


title: LC149N

description: Gene expression profile of human liver cancer #LC149, non-tumorous tissue

source_name: Human liver cancer #LC149, non-tumorous tissue


title: LC142N

description: Gene expression profile of human liver cancer #LC142, non-tumorous tissue

source_name: Human liver cancer #LC142, non-tumorous tissue


title: LC151N

description: Gene expression profile of human liver cancer #LC151, non-tumorous tissue

source_name: Human liver cancer #LC151, non-tumorous tissue


title: LC139N

description: Gene expression profile of human liver cancer #LC139, non-tumorous tissue

source_name: Human liver cancer #LC139, non-tumorous tissue


title: LC140N

description: Gene expression profile of human liver cancer #LC140, non-tumorous tissue

source_name: Human liver cancer #LC140, non-tumorous tissue


title: LC137N

description: Gene expression profile of human liver cancer #LC137, non-tumorous tissue

source_name: Human liver cancer #LC137, non-tumorous tissue


title: LC145N

description: Gene expression profile of human liver cancer #LC145, non-tumorous tissue

source_name: Human liver cancer #LC145, non-tumorous tissue


title: LC136N

description: Gene expression profile of human liver cancer #LC136, non-tumorous tissue

source_name: Human liver cancer #LC136, non-tumorous tissue


title: LC130N

description: Gene expression profile of human liver cancer #LC130, non-tumorous tissue

source_name: Human liver cancer #LC130, non-tumorous tissue


title: femur_sham

city: Shanghai

first: Jingyu

last: Zhao

address: 320 Yueyang Road

country: China

institute: Zhaojingyu, Huang Mingjian

description: microRNA expression after sham surgery in mice femurs

hyb_protocol: 0.6 μg Cyanine-3(Cy3) labeled cRNA was fragmented at 60°C for 30 mins in a reaction volume of 22.5 μl containing 1×Aligent fragmentation buffer and 2×Aligent block agent following the manufacture’s instruction. On completion of the fragment reaction, 22.5 μl 2×Aligent hybridization buffer was added to the mix and hybridization to Agilent miRNA Microarray ( 8x60K) for 17hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarray was washed 1 min at room temperature with GE wash buffer and 1 min at 37°C with GE wash buffer 2 (Aligent), and try immedietly.

scan_protocol: Slides were scanned immedietly after washing on the Aligent DNA Microarray Scanner (G2505c) using one color set scan for 4x180K array slides

data_processing: Agilent Feature Extraction software (version 11.0.1.1, Agilent Technologies) was used to export heat map. Quantile normalization was performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: femur tissue , sham group

label_protocol: Cyanine-3(Cy3) labeled cRNA was prepared from 0.2μg RNA using the one-color low RNA input linear amplification plus kit (Agilent) according to the manufacture’s protocol, followed by RNAeasy column purification (QIAGEN). Dye incorporation and Crna yield were checked with the nanoDrop ND-1000 spectrophotometer.

growth_protocol: all the tissue from C57BL/6 background mice with sham and OVX surgery

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem AM1556) following the manufacture's protocol

treatment_protocol: freshly femurs which contains both marrow and bone spices were collected in trizol reagent (invirogen) and homogenated immedietly

value: femur tissue

value: 9 month

value: female


title: LC128N

description: Gene expression profile of human liver cancer #LC128, non-tumorous tissue

source_name: Human liver cancer #LC128, non-tumorous tissue


title: HCC1

description: Gene expression profile of hepatocellular carcinoma from C4R-KO mouse #HCC1

source_name: Hepatocelluar carcinoma from MC4R-KO mouse #HCC1


title: NL6

description: Gene expression profile of normal liver from wild-type mouse #NL6

source_name: Normal liver from wild-type mouse #NL6

value: Normal liver


title: NL2

description: Gene expression profile of normal liver from wild-type mouse #NL2

source_name: Normal liver from wild-type mouse #NL2


title: LC127N

description: Gene expression profile of human liver cancer #LC127, non-tumorous tissue

source_name: Human liver cancer #LC127, non-tumorous tissue


title: femur_OVX

description: microRNA expression after OVX surgery in mice femurs

source_name: femur tissue, OVX group


title: LC134N

description: Gene expression profile of human liver cancer #LC134, non-tumorous tissue

source_name: Human liver cancer #LC134, non-tumorous tissue


title: HCC5

description: Gene expression profile of hepatocellular carcinoma from C4R-KO mouse #HCC5

source_name: Hepatocelluar carcinoma from MC4R-KO mouse #HCC5


title: TRA00028708_umi_15

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

growth_protocol: Live cells were sorted by flow cytometry from the spleen, muscle 1-4 days after cardiotoxin injury, visceral adipose tissue and colon lamina propria of mice carrying a Foxp3 reporter gene.

extract_protocol:
Spleen were mechanically dissociated and the other tissues were digested with collagenase/dispase to single cell suspensions. FoxP3+ and FoxP3- cells were sorted by flow cytometry as DAPI- TCRb+ CD4+ reporter+/- cells. Single cells were then sorted in a 96-well plate and the CEL-seq protocol was performed.
mRNA was reverse transcribed using adapters containing oligo dT in each well. Single-cell cDNA libraries with different barcodes were amplified by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a HiSeq2500.

value: F1 B6 Foxp3-Ires-Gfp 4 days after injury

tag: age (weeks)

tag: Sex

tag: flow cytometry parameters

tag: flow cytometry values

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)

tag: transgene expression (gfp or thy1.1)


title: TRA00028708_umi_9

tag: strain


title: LC133N

description: Gene expression profile of human liver cancer #LC133, non-tumorous tissue

source_name: Human liver cancer #LC133, non-tumorous tissue


title: HCC2

description: Gene expression profile of hepatocellular carcinoma from C4R-KO mouse #HCC2

source_name: Hepatocelluar carcinoma from MC4R-KO mouse #HCC2


title: LX2-control (1)

description: Gene expression profile of LX2-control (1)

source_name: Human hepatic stellate cell line LX2 constitutively expressing eGFP


title: LC121N

description: Gene expression profile of human liver cancer #LC121, non-tumorous tissue

source_name: Human liver cancer #LC121, non-tumorous tissue


title: LC131N

description: Gene expression profile of human liver cancer #LC131, non-tumorous tissue

source_name: Human liver cancer #LC131, non-tumorous tissue


title: NL3

description: Gene expression profile of normal liver from wild-type mouse #NL3

source_name: Normal liver from wild-type mouse #NL3


title: LC129N

description: Gene expression profile of human liver cancer #LC129, non-tumorous tissue

source_name: Human liver cancer #LC129, non-tumorous tissue


title: TRA00028708_umi_12


title: LC117N

description: Gene expression profile of human liver cancer #LC117, non-tumorous tissue

source_name: Human liver cancer #LC117, non-tumorous tissue


title: TRA00028708_umi_16


title: NL1

description: Gene expression profile of normal liver from wild-type mouse #NL1

source_name: Normal liver from wild-type mouse #NL1


title: TRA00028708_ls_8


title: TRA00028708_ls_3


title: TRA00028708_ls_7


title: LC132N

description: Gene expression profile of human liver cancer #LC132, non-tumorous tissue

source_name: Human liver cancer #LC132, non-tumorous tissue


title: TRA00028708_ls_4


title: LC123N

description: Gene expression profile of human liver cancer #LC123, non-tumorous tissue

source_name: Human liver cancer #LC123, non-tumorous tissue


title: LC114N

description: Gene expression profile of human liver cancer #LC114, non-tumorous tissue

source_name: Human liver cancer #LC114, non-tumorous tissue


title: TRA00028708_ls_9


title: TRA00028708_umi_13


title: LC125N

description: Gene expression profile of human liver cancer #LC125, non-tumorous tissue

source_name: Human liver cancer #LC125, non-tumorous tissue


title: TRA00028708_ls_2


title: TRA00028708_umi_11


title: LC110N

description: Gene expression profile of human liver cancer #LC110, non-tumorous tissue

source_name: Human liver cancer #LC110, non-tumorous tissue


title: LC115N

description: Gene expression profile of human liver cancer #LC115, non-tumorous tissue

source_name: Human liver cancer #LC115, non-tumorous tissue


title: LC111N

description: Gene expression profile of human liver cancer #LC111, non-tumorous tissue

source_name: Human liver cancer #LC111, non-tumorous tissue


title: LC109N

description: Gene expression profile of human liver cancer #LC109, non-tumorous tissue

source_name: Human liver cancer #LC109, non-tumorous tissue


title: LC118N

description: Gene expression profile of human liver cancer #LC118, non-tumorous tissue

source_name: Human liver cancer #LC118, non-tumorous tissue


title: LC120N

description: Gene expression profile of human liver cancer #LC120, non-tumorous tissue

source_name: Human liver cancer #LC120, non-tumorous tissue


title: LC124N

description: Gene expression profile of human liver cancer #LC124, non-tumorous tissue

source_name: Human liver cancer #LC124, non-tumorous tissue


title: TRA00028708_umi_10

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: LC122N

description: Gene expression profile of human liver cancer #LC122, non-tumorous tissue

source_name: Human liver cancer #LC122, non-tumorous tissue


title: TRA00028708_umi_14


title: TRA00028708_ls_22


title: TRA00028708_ls_21


title: LC105N

description: Gene expression profile of human liver cancer #LC105, non-tumorous tissue

source_name: Human liver cancer #LC105, non-tumorous tissue


title: LC112N

description: Gene expression profile of human liver cancer #LC112, non-tumorous tissue

source_name: Human liver cancer #LC112, non-tumorous tissue


title: LC103N

description: Gene expression profile of human liver cancer #LC103, non-tumorous tissue

source_name: Human liver cancer #LC103, non-tumorous tissue


title: LC113N

description: Gene expression profile of human liver cancer #LC113, non-tumorous tissue

source_name: Human liver cancer #LC113, non-tumorous tissue


title: TRA00028708_ls_6


title: TRA00028708_ls_23


title: TRA00028708_ls_13


title: TRA00028708_ls_5


title: TRA00028708_ls_1


title: TRA00028708_ls_18


title: LC093N

description: Gene expression profile of human liver cancer #LC093, non-tumorous tissue

source_name: Human liver cancer #LC093, non-tumorous tissue


title: LC094N

description: Gene expression profile of human liver cancer #LC094, non-tumorous tissue

source_name: Human liver cancer #LC094, non-tumorous tissue


title: LC089N

description: Gene expression profile of human liver cancer #LC089, non-tumorous tissue

source_name: Human liver cancer #LC089, non-tumorous tissue


title: LC099N

description: Gene expression profile of human liver cancer #LC099, non-tumorous tissue

source_name: Human liver cancer #LC099, non-tumorous tissue


title: TRA00028708_ls_17


title: LC091N

description: Gene expression profile of human liver cancer #LC091, non-tumorous tissue

source_name: Human liver cancer #LC091, non-tumorous tissue


title: LC090N

description: Gene expression profile of human liver cancer #LC090, non-tumorous tissue

source_name: Human liver cancer #LC090, non-tumorous tissue


title: TRA00028708_ls_24


title: LC102N

description: Gene expression profile of human liver cancer #LC102, non-tumorous tissue

source_name: Human liver cancer #LC102, non-tumorous tissue


title: LC107N

description: Gene expression profile of human liver cancer #LC107, non-tumorous tissue

source_name: Human liver cancer #LC107, non-tumorous tissue


title: LC095N

description: Gene expression profile of human liver cancer #LC095, non-tumorous tissue

source_name: Human liver cancer #LC095, non-tumorous tissue


title: LC100N

description: Gene expression profile of human liver cancer #LC100, non-tumorous tissue

source_name: Human liver cancer #LC100, non-tumorous tissue


title: LC119N

description: Gene expression profile of human liver cancer #LC119, non-tumorous tissue

source_name: Human liver cancer #LC119, non-tumorous tissue


title: TRA00028707_ls_8

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: TRA00028708_ls_16


title: LC101N

description: Gene expression profile of human liver cancer #LC101, non-tumorous tissue

source_name: Human liver cancer #LC101, non-tumorous tissue


title: TRA00028708_ls_14


title: TRA00028707_ls_6


title: LC083N

description: Gene expression profile of human liver cancer #LC083, non-tumorous tissue

source_name: Human liver cancer #LC083, non-tumorous tissue


title: TRA00028707_ls_5


title: LC108N

description: Gene expression profile of human liver cancer #LC108, non-tumorous tissue

source_name: Human liver cancer #LC108, non-tumorous tissue


title: TRA00028708_ls_12


title: TRA00028707_ls_3


title: TRA00028707_ls_2


title: LC079N

description: Gene expression profile of human liver cancer #LC079, non-tumorous tissue

source_name: Human liver cancer #LC079, non-tumorous tissue


title: TRA00028708_ls_15


title: TRA00028707_ls_21


title: TRA00028707_ls_1


title: LC081N

description: Gene expression profile of human liver cancer #LC081, non-tumorous tissue

source_name: Human liver cancer #LC081, non-tumorous tissue


title: TRA00028708_ls_11


title: TRA00028707_umi_9


title: LC086N

description: Gene expression profile of human liver cancer #LC086, non-tumorous tissue

source_name: Human liver cancer #LC086, non-tumorous tissue


title: TRA00028707_ls_15


title: TRA00028707_ls_7


title: TRA00028708_ls_10


title: LC092N

description: Gene expression profile of human liver cancer #LC092, non-tumorous tissue

source_name: Human liver cancer #LC092, non-tumorous tissue


title: LC084N

description: Gene expression profile of human liver cancer #LC084, non-tumorous tissue

source_name: Human liver cancer #LC084, non-tumorous tissue


title: TRA00028707_ls_10


title: TRA00028707_ls_14


title: TRA00028707_ls_13


title: TRA00028707_ls_4


title: TRA00028706_umi_9

value: F1 B6 Foxp3-Ires-Gfp 1 day after injury


title: LC072N

description: Gene expression profile of human liver cancer #LC072, non-tumorous tissue

source_name: Human liver cancer #LC072, non-tumorous tissue


title: TRA00028707_umi_15


title: LC067N

description: Gene expression profile of human liver cancer #LC067, non-tumorous tissue

source_name: Human liver cancer #LC067, non-tumorous tissue


title: TRA00028707_ls_9


title: LC068N

description: Gene expression profile of human liver cancer #LC068, non-tumorous tissue

source_name: Human liver cancer #LC068, non-tumorous tissue


title: TRA00028706_umi_14


title: LC076N

description: Gene expression profile of human liver cancer #LC076, non-tumorous tissue

source_name: Human liver cancer #LC076, non-tumorous tissue


title: LC085N

description: Gene expression profile of human liver cancer #LC085, non-tumorous tissue

source_name: Human liver cancer #LC085, non-tumorous tissue


title: LC060N

description: Gene expression profile of human liver cancer #LC060, non-tumorous tissue

source_name: Human liver cancer #LC060, non-tumorous tissue


title: TRA00028707_ls_16


title: TRA00028706_umi_11


title: TRA00028707_ls_24


title: LC082N

description: Gene expression profile of human liver cancer #LC082, non-tumorous tissue

source_name: Human liver cancer #LC082, non-tumorous tissue


title: LC056N

description: Gene expression profile of human liver cancer #LC056, non-tumorous tissue

source_name: Human liver cancer #LC056, non-tumorous tissue


title: LC077N

description: Gene expression profile of human liver cancer #LC077, non-tumorous tissue

source_name: Human liver cancer #LC077, non-tumorous tissue


title: LC055N

description: Gene expression profile of human liver cancer #LC055, non-tumorous tissue

source_name: Human liver cancer #LC055, non-tumorous tissue


title: LC075N

description: Gene expression profile of human liver cancer #LC075, non-tumorous tissue

source_name: Human liver cancer #LC075, non-tumorous tissue


title: TRA00028706_ls_9

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: LC071N

description: Gene expression profile of human liver cancer #LC071, non-tumorous tissue

source_name: Human liver cancer #LC071, non-tumorous tissue


title: TRA00028706_ls_7


title: TRA00028707_ls_17


title: LC080N

description: Gene expression profile of human liver cancer #LC080, non-tumorous tissue

source_name: Human liver cancer #LC080, non-tumorous tissue


title: TRA00028706_umi_13


title: LC039N

description: Gene expression profile of human liver cancer #LC039, non-tumorous tissue

source_name: Human liver cancer #LC039, non-tumorous tissue


title: LC062N

description: Gene expression profile of human liver cancer #LC062, non-tumorous tissue

source_name: Human liver cancer #LC062, non-tumorous tissue


title: TRA00028706_umi_12


title: LC069N

description: Gene expression profile of human liver cancer #LC069, non-tumorous tissue

source_name: Human liver cancer #LC069, non-tumorous tissue


title: LC036N

description: Gene expression profile of human liver cancer #LC036, non-tumorous tissue

source_name: Human liver cancer #LC036, non-tumorous tissue


title: LC078N

description: Gene expression profile of human liver cancer #LC078, non-tumorous tissue

source_name: Human liver cancer #LC078, non-tumorous tissue


title: LC050N

description: Gene expression profile of human liver cancer #LC050, non-tumorous tissue

source_name: Human liver cancer #LC050, non-tumorous tissue


title: LC073N

description: Gene expression profile of human liver cancer #LC073, non-tumorous tissue

source_name: Human liver cancer #LC073, non-tumorous tissue


title: TRA00028706_umi_16


title: LC057N

description: Gene expression profile of human liver cancer #LC057, non-tumorous tissue

source_name: Human liver cancer #LC057, non-tumorous tissue


title: TRA00028706_ls_22


title: TRA00028706_umi_15


title: LC048N

description: Gene expression profile of human liver cancer #LC048, non-tumorous tissue

source_name: Human liver cancer #LC048, non-tumorous tissue


title: TRA00028706_ls_23


title: TRA00028706_umi_10


title: TRA00028706_ls_8


title: TRA00028706_ls_5


title: LC064N

description: Gene expression profile of human liver cancer #LC064, non-tumorous tissue

source_name: Human liver cancer #LC064, non-tumorous tissue


title: LC061N

description: Gene expression profile of human liver cancer #LC061, non-tumorous tissue

source_name: Human liver cancer #LC061, non-tumorous tissue


title: TRA00028706_ls_6


title: TRA00028706_ls_18


title: TRA00028706_ls_2


title: LC044N

description: Gene expression profile of human liver cancer #LC044, non-tumorous tissue

source_name: Human liver cancer #LC044, non-tumorous tissue


title: LC150T

description: Gene expression profile of human liver cancer #LC150, tumorous tissue

source_name: Human liver cancer #LC150, tumorous tissue

value: Liver cancer, tumorous tissue


title: TRA00028706_ls_14


title: LC038N

description: Gene expression profile of human liver cancer #LC038, non-tumorous tissue

source_name: Human liver cancer #LC038, non-tumorous tissue


title: LC148T

description: Gene expression profile of human liver cancer #LC148, tumorous tissue

source_name: Human liver cancer #LC148, tumorous tissue


title: LC149T

description: Gene expression profile of human liver cancer #LC149, tumorous tissue

source_name: Human liver cancer #LC149, tumorous tissue


title: LC037N

description: Gene expression profile of human liver cancer #LC037, non-tumorous tissue

source_name: Human liver cancer #LC037, non-tumorous tissue


title: LC146T

description: Gene expression profile of human liver cancer #LC146, tumorous tissue

source_name: Human liver cancer #LC146, tumorous tissue


title: TRA00028706_ls_3

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: TRA00028706_ls_4


title: TRA00028706_ls_17


title: LC042N

description: Gene expression profile of human liver cancer #LC042, non-tumorous tissue

source_name: Human liver cancer #LC042, non-tumorous tissue


title: TRA00028706_ls_12


title: TRA00028706_ls_21


title: LC034N

description: Gene expression profile of human liver cancer #LC034, non-tumorous tissue

source_name: Human liver cancer #LC034, non-tumorous tissue


title: TRA00028706_ls_11


title: LC058N

description: Gene expression profile of human liver cancer #LC058, non-tumorous tissue

source_name: Human liver cancer #LC058, non-tumorous tissue


title: LC147T

description: Gene expression profile of human liver cancer #LC147, tumorous tissue

source_name: Human liver cancer #LC147, tumorous tissue


title: LC143T

description: Gene expression profile of human liver cancer #LC143, tumorous tissue

source_name: Human liver cancer #LC143, tumorous tissue


title: LC152T

description: Gene expression profile of human liver cancer #LC152, tumorous tissue

source_name: Human liver cancer #LC152, tumorous tissue


title: TRA00028706_ls_16


title: LC145T

description: Gene expression profile of human liver cancer #LC145, tumorous tissue

source_name: Human liver cancer #LC145, tumorous tissue


title: TRA00028706_ls_15


title: LC140T

description: Gene expression profile of human liver cancer #LC140, tumorous tissue

source_name: Human liver cancer #LC140, tumorous tissue


title: LC141T

description: Gene expression profile of human liver cancer #LC141, tumorous tissue

source_name: Human liver cancer #LC141, tumorous tissue


title: TRA00028705_ls_9


title: LC137T

description: Gene expression profile of human liver cancer #LC137, tumorous tissue

source_name: Human liver cancer #LC137, tumorous tissue


title: LC144T

description: Gene expression profile of human liver cancer #LC144, tumorous tissue

source_name: Human liver cancer #LC144, tumorous tissue


title: TRA00028706_ls_1


title: LC151T

description: Gene expression profile of human liver cancer #LC151, tumorous tissue

source_name: Human liver cancer #LC151, tumorous tissue


title: TRA00028705_umi_9


title: TRA00028706_ls_13


title: LC032N

description: Gene expression profile of human liver cancer #LC032, non-tumorous tissue

source_name: Human liver cancer #LC032, non-tumorous tissue


title: TRA00028706_ls_10


title: TRA00028705_ls_6


title: LC132T

description: Gene expression profile of human liver cancer #LC132, tumorous tissue

source_name: Human liver cancer #LC132, tumorous tissue


title: TRA00028705_umi_15


title: LC130T

description: Gene expression profile of human liver cancer #LC130, tumorous tissue

source_name: Human liver cancer #LC130, tumorous tissue


title: LC128T

description: Gene expression profile of human liver cancer #LC128, tumorous tissue

source_name: Human liver cancer #LC128, tumorous tissue


title: LC142T

description: Gene expression profile of human liver cancer #LC142, tumorous tissue

source_name: Human liver cancer #LC142, tumorous tissue


title: TRA00028705_umi_12

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: LC134T

description: Gene expression profile of human liver cancer #LC134, tumorous tissue

source_name: Human liver cancer #LC134, tumorous tissue


title: TRA00028705_umi_14


title: TRA00028705_umi_16


title: LC125T

description: Gene expression profile of human liver cancer #LC125, tumorous tissue

source_name: Human liver cancer #LC125, tumorous tissue


title: LC139T

description: Gene expression profile of human liver cancer #LC139, tumorous tissue

source_name: Human liver cancer #LC139, tumorous tissue


title: LC138T

description: Gene expression profile of human liver cancer #LC138, tumorous tissue

source_name: Human liver cancer #LC138, tumorous tissue


title: TRA00028705_umi_11


title: TRA00028705_ls_7


title: TRA00028705_ls_5


title: TRA00028705_ls_8


title: LC136T

description: Gene expression profile of human liver cancer #LC136, tumorous tissue

source_name: Human liver cancer #LC136, tumorous tissue


title: TRA00028705_ls_1


title: LC131T

description: Gene expression profile of human liver cancer #LC131, tumorous tissue

source_name: Human liver cancer #LC131, tumorous tissue


title: LC121T

description: Gene expression profile of human liver cancer #LC121, tumorous tissue

source_name: Human liver cancer #LC121, tumorous tissue


title: TRA00028705_ls_4


title: LC122T

description: Gene expression profile of human liver cancer #LC122, tumorous tissue

source_name: Human liver cancer #LC122, tumorous tissue


title: TRA00028705_ls_3


title: LC135T

description: Gene expression profile of human liver cancer #LC135, tumorous tissue

source_name: Human liver cancer #LC135, tumorous tissue


title: TRA00028705_ls_2


title: TRA00028705_ls_24


title: LC133T

description: Gene expression profile of human liver cancer #LC133, tumorous tissue

source_name: Human liver cancer #LC133, tumorous tissue


title: TRA00028705_ls_13


title: TRA00028705_ls_23


title: TRA00028705_ls_10


title: TRA00028705_ls_12


title: TRA00028704_umi_9


title: LC129T

description: Gene expression profile of human liver cancer #LC129, tumorous tissue

source_name: Human liver cancer #LC129, tumorous tissue


title: TRA00028705_ls_17


title: TRA00028704_umi_16


title: TRA00028705_ls_22


title: TRA00028704_umi_15


title: LC127T

description: Gene expression profile of human liver cancer #LC127, tumorous tissue

source_name: Human liver cancer #LC127, tumorous tissue


title: TRA00028705_ls_21


title: TRA00028705_ls_16


title: TRA00028704_umi_12


title: LC126T

description: Gene expression profile of human liver cancer #LC126, tumorous tissue

source_name: Human liver cancer #LC126, tumorous tissue


title: LC124T

description: Gene expression profile of human liver cancer #LC124, tumorous tissue

source_name: Human liver cancer #LC124, tumorous tissue


title: TRA00028705_ls_14


title: TRA00028704_umi_13


title: LC123T

description: Gene expression profile of human liver cancer #LC123, tumorous tissue

source_name: Human liver cancer #LC123, tumorous tissue


title: TRA00028705_ls_15


title: LC120T

description: Gene expression profile of human liver cancer #LC120, tumorous tissue

source_name: Human liver cancer #LC120, tumorous tissue


title: LC116T

description: Gene expression profile of human liver cancer #LC116, tumorous tissue

source_name: Human liver cancer #LC116, tumorous tissue


title: TRA00028704_ls_9

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: LC112T

description: Gene expression profile of human liver cancer #LC112, tumorous tissue

source_name: Human liver cancer #LC112, tumorous tissue


title: TRA00028704_ls_8


title: LC114T

description: Gene expression profile of human liver cancer #LC114, tumorous tissue

source_name: Human liver cancer #LC114, tumorous tissue


title: TRA00028704_umi_14


title: LC110T

description: Gene expression profile of human liver cancer #LC110, tumorous tissue

source_name: Human liver cancer #LC110, tumorous tissue


title: TRA00028704_umi_10


title: LC118T

description: Gene expression profile of human liver cancer #LC118, tumorous tissue

source_name: Human liver cancer #LC118, tumorous tissue


title: LC113T

description: Gene expression profile of human liver cancer #LC113, tumorous tissue

source_name: Human liver cancer #LC113, tumorous tissue


title: TRA00028704_umi_11


title: LC115T

description: Gene expression profile of human liver cancer #LC115, tumorous tissue

source_name: Human liver cancer #LC115, tumorous tissue


title: LC109T

description: Gene expression profile of human liver cancer #LC109, tumorous tissue

source_name: Human liver cancer #LC109, tumorous tissue


title: LC108T

description: Gene expression profile of human liver cancer #LC108, tumorous tissue

source_name: Human liver cancer #LC108, tumorous tissue


title: LC107T

description: Gene expression profile of human liver cancer #LC107, tumorous tissue

source_name: Human liver cancer #LC107, tumorous tissue


title: LC119T

description: Gene expression profile of human liver cancer #LC119, tumorous tissue

source_name: Human liver cancer #LC119, tumorous tissue


title: LC117T

description: Gene expression profile of human liver cancer #LC117, tumorous tissue

source_name: Human liver cancer #LC117, tumorous tissue


title: TRA00028704_ls_7


title: LC105T

description: Gene expression profile of human liver cancer #LC105, tumorous tissue

source_name: Human liver cancer #LC105, tumorous tissue


title: TRA00028704_ls_6


title: TRA00028704_ls_5


title: TRA00028704_ls_3


title: LC106T

description: Gene expression profile of human liver cancer #LC106, tumorous tissue

source_name: Human liver cancer #LC106, tumorous tissue


title: TRA00028704_ls_4


title: LC111T

description: Gene expression profile of human liver cancer #LC111, tumorous tissue

source_name: Human liver cancer #LC111, tumorous tissue


title: TRA00028704_ls_23


title: LC104T

description: Gene expression profile of human liver cancer #LC104, tumorous tissue

source_name: Human liver cancer #LC104, tumorous tissue


title: LC103T

description: Gene expression profile of human liver cancer #LC103, tumorous tissue

source_name: Human liver cancer #LC103, tumorous tissue


title: TRA00028704_ls_21

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: TRA00028704_ls_18


title: TRA00028704_ls_2


title: LC101T

description: Gene expression profile of human liver cancer #LC101, tumorous tissue

source_name: Human liver cancer #LC101, tumorous tissue


title: LC102T

description: Gene expression profile of human liver cancer #LC102, tumorous tissue

source_name: Human liver cancer #LC102, tumorous tissue


title: TRA00028704_ls_17


title: TRA00028704_ls_16


title: TRA00028704_ls_22


title: TRA00028704_ls_15


title: TRA00028704_ls_1


title: LC092T

description: Gene expression profile of human liver cancer #LC092, tumorous tissue

source_name: Human liver cancer #LC092, tumorous tissue


title: LC100T

description: Gene expression profile of human liver cancer #LC100, tumorous tissue

source_name: Human liver cancer #LC100, tumorous tissue


title: LC099T

description: Gene expression profile of human liver cancer #LC099, tumorous tissue

source_name: Human liver cancer #LC099, tumorous tissue


title: LC098T

description: Gene expression profile of human liver cancer #LC098, tumorous tissue

source_name: Human liver cancer #LC098, tumorous tissue


title: TRA00028704_ls_24


title: LC090T

description: Gene expression profile of human liver cancer #LC090, tumorous tissue

source_name: Human liver cancer #LC090, tumorous tissue


title: LC097T

description: Gene expression profile of human liver cancer #LC097, tumorous tissue

source_name: Human liver cancer #LC097, tumorous tissue


title: LC096T

description: Gene expression profile of human liver cancer #LC096, tumorous tissue

source_name: Human liver cancer #LC096, tumorous tissue


title: TRA00028704_ls_14


title: LC094T

description: Gene expression profile of human liver cancer #LC094, tumorous tissue

source_name: Human liver cancer #LC094, tumorous tissue


title: TRA00028704_ls_13


title: LC091T

description: Gene expression profile of human liver cancer #LC091, tumorous tissue

source_name: Human liver cancer #LC091, tumorous tissue


title: TRA00028704_ls_12


title: TRA00028704_ls_11


title: TRA00028078_umi_16

source_name: VAT

value: B6 Retired Breeder from JAX

value: VAT

value: Retired Breeder


title: TRA00028078_umi_9


title: LC088T

description: Gene expression profile of human liver cancer #LC088, tumorous tissue

source_name: Human liver cancer #LC088, tumorous tissue


title: TRA00028078_umi_15


title: LC089T

description: Gene expression profile of human liver cancer #LC089, tumorous tissue

source_name: Human liver cancer #LC089, tumorous tissue


title: TRA00028704_ls_10


title: TRA00028078_umi_14


title: LC093T

description: Gene expression profile of human liver cancer #LC093, tumorous tissue

source_name: Human liver cancer #LC093, tumorous tissue


title: TRA00028078_umi_13


title: LC095T

description: Gene expression profile of human liver cancer #LC095, tumorous tissue

source_name: Human liver cancer #LC095, tumorous tissue


title: TRA00028078_umi_12


title: TRA00028078_umi_11


title: TRA00028078_umi_10


title: LC084T

description: Gene expression profile of human liver cancer #LC084, tumorous tissue

source_name: Human liver cancer #LC084, tumorous tissue


title: TRA00028078_ls_7

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: TRA00028078_ls_8


title: LC087T

description: Gene expression profile of human liver cancer #LC087, tumorous tissue

source_name: Human liver cancer #LC087, tumorous tissue


title: LC083T

description: Gene expression profile of human liver cancer #LC083, tumorous tissue

source_name: Human liver cancer #LC083, tumorous tissue


title: LC082T

description: Gene expression profile of human liver cancer #LC082, tumorous tissue

source_name: Human liver cancer #LC082, tumorous tissue


title: LC081T

description: Gene expression profile of human liver cancer #LC081, tumorous tissue

source_name: Human liver cancer #LC081, tumorous tissue


title: LC085T

description: Gene expression profile of human liver cancer #LC085, tumorous tissue

source_name: Human liver cancer #LC085, tumorous tissue


title: LC080T

description: Gene expression profile of human liver cancer #LC080, tumorous tissue

source_name: Human liver cancer #LC080, tumorous tissue


title: LC086T

description: Gene expression profile of human liver cancer #LC086, tumorous tissue

source_name: Human liver cancer #LC086, tumorous tissue


title: LC078T

description: Gene expression profile of human liver cancer #LC078, tumorous tissue

source_name: Human liver cancer #LC078, tumorous tissue


title: LC079T

description: Gene expression profile of human liver cancer #LC079, tumorous tissue

source_name: Human liver cancer #LC079, tumorous tissue


title: TRA00028078_ls_2


title: LC077T

description: Gene expression profile of human liver cancer #LC077, tumorous tissue

source_name: Human liver cancer #LC077, tumorous tissue


title: LC076T

description: Gene expression profile of human liver cancer #LC076, tumorous tissue

source_name: Human liver cancer #LC076, tumorous tissue


title: TRA00028077_ls_6

source_name: VAT


title: LC075T

description: Gene expression profile of human liver cancer #LC075, tumorous tissue

source_name: Human liver cancer #LC075, tumorous tissue


title: TRA00028077_umi_12


title: TRA00028078_ls_3


title: TRA00028078_ls_5


title: TRA00028078_ls_4


title: TRA00028078_ls_1


title: LC074T

description: Gene expression profile of human liver cancer #LC074, tumorous tissue

source_name: Human liver cancer #LC074, tumorous tissue


title: TRA00028077_ls_1


title: LC070T

description: Gene expression profile of human liver cancer #LC070, tumorous tissue

source_name: Human liver cancer #LC070, tumorous tissue


title: LC068T

description: Gene expression profile of human liver cancer #LC068, tumorous tissue

source_name: Human liver cancer #LC068, tumorous tissue


title: LC067T

description: Gene expression profile of human liver cancer #LC067, tumorous tissue

source_name: Human liver cancer #LC067, tumorous tissue


title: TRA00028077_ls_3

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: LC072T

description: Gene expression profile of human liver cancer #LC072, tumorous tissue

source_name: Human liver cancer #LC072, tumorous tissue


title: TRA00028077_ls_5


title: LC071T

description: Gene expression profile of human liver cancer #LC071, tumorous tissue

source_name: Human liver cancer #LC071, tumorous tissue


title: TRA00026615_umi_9

source_name: colon LP

value: B6 Foxp3-Ires-Thy1.1

value: colon LP


title: LC066T

description: Gene expression profile of human liver cancer #LC066, tumorous tissue

source_name: Human liver cancer #LC066, tumorous tissue


title: TRA00028077_ls_4

value: male


title: TRA00026615_umi_12


title: TRA00028077_ls_2


title: TRA00026615_umi_14


title: TRA00026615_umi_16


title: LC060T

description: Gene expression profile of human liver cancer #LC060, tumorous tissue

source_name: Human liver cancer #LC060, tumorous tissue


title: LC073T

description: Gene expression profile of human liver cancer #LC073, tumorous tissue

source_name: Human liver cancer #LC073, tumorous tissue


title: TRA00026615_umi_11


title: LC065T

description: Gene expression profile of human liver cancer #LC065, tumorous tissue

source_name: Human liver cancer #LC065, tumorous tissue


title: LC058T

description: Gene expression profile of human liver cancer #LC058, tumorous tissue

source_name: Human liver cancer #LC058, tumorous tissue


title: LC062T

description: Gene expression profile of human liver cancer #LC062, tumorous tissue

source_name: Human liver cancer #LC062, tumorous tissue


title: LC056T

description: Gene expression profile of human liver cancer #LC056, tumorous tissue

source_name: Human liver cancer #LC056, tumorous tissue


title: LC063T

description: Gene expression profile of human liver cancer #LC063, tumorous tissue

source_name: Human liver cancer #LC063, tumorous tissue


title: LC057T

description: Gene expression profile of human liver cancer #LC057, tumorous tissue

source_name: Human liver cancer #LC057, tumorous tissue


title: LC059T

description: Gene expression profile of human liver cancer #LC059, tumorous tissue

source_name: Human liver cancer #LC059, tumorous tissue


title: LC069T

description: Gene expression profile of human liver cancer #LC069, tumorous tissue

source_name: Human liver cancer #LC069, tumorous tissue


title: LC055T

description: Gene expression profile of human liver cancer #LC055, tumorous tissue

source_name: Human liver cancer #LC055, tumorous tissue


title: LC061T

description: Gene expression profile of human liver cancer #LC061, tumorous tissue

source_name: Human liver cancer #LC061, tumorous tissue


title: TRA00026614_umi_11


title: TRA00026614_umi_14


title: TRA00026613_umi_9


title: TRA00026614_umi_13


title: LC064T

description: Gene expression profile of human liver cancer #LC064, tumorous tissue

source_name: Human liver cancer #LC064, tumorous tissue


title: TRA00026613_umi_16

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: TRA00026615_umi_13


title: TRA00026613_umi_12


title: TRA00026614_umi_9


title: TRA00026612_umi_9

source_name: spleen

value: F1 B6 Foxp3-Ires-Gfp X NOD

value: spleen


title: TRA00026612_umi_16


title: TRA00026612_umi_15


title: TRA00026614_umi_12


title: TRA00026613_umi_14


title: TRA00026612_umi_14


title: LC050T

description: Gene expression profile of human liver cancer #LC050, tumorous tissue

source_name: Human liver cancer #LC050, tumorous tissue


title: TRA00026614_umi_16

source_name: colon LP


title: LC049T

description: Gene expression profile of human liver cancer #LC049, tumorous tissue

source_name: Human liver cancer #LC049, tumorous tissue


title: TRA00026612_umi_12


title: LC048T

description: Gene expression profile of human liver cancer #LC048, tumorous tissue

source_name: Human liver cancer #LC048, tumorous tissue


title: LC047T

description: Gene expression profile of human liver cancer #LC047, tumorous tissue

source_name: Human liver cancer #LC047, tumorous tissue


title: LC053T

description: Gene expression profile of human liver cancer #LC053, tumorous tissue

source_name: Human liver cancer #LC053, tumorous tissue


title: LC054T

description: Gene expression profile of human liver cancer #LC054, tumorous tissue

source_name: Human liver cancer #LC054, tumorous tissue


title: LC052T

description: Gene expression profile of human liver cancer #LC052, tumorous tissue

source_name: Human liver cancer #LC052, tumorous tissue


title: TRA00026612_umi_11


title: TRA00026612_ls_8


title: TRA00026612_ls_5


title: LC042T

description: Gene expression profile of human liver cancer #LC042, tumorous tissue

source_name: Human liver cancer #LC042, tumorous tissue


title: TRA00026612_ls_6


title: TRA00026612_ls_4


title: TRA00026612_ls_3


title: LC051T

description: Gene expression profile of human liver cancer #LC051, tumorous tissue

source_name: Human liver cancer #LC051, tumorous tissue


title: TRA00026612_ls_2


title: TRA00026611_umi_9


title: LC043T

description: Gene expression profile of human liver cancer #LC043, tumorous tissue

source_name: Human liver cancer #LC043, tumorous tissue


title: TRA00026612_ls_1


title: LC039T

description: Gene expression profile of human liver cancer #LC039, tumorous tissue

source_name: Human liver cancer #LC039, tumorous tissue


title: LC035T

description: Gene expression profile of human liver cancer #LC035, tumorous tissue

source_name: Human liver cancer #LC035, tumorous tissue


title: LC044T

description: Gene expression profile of human liver cancer #LC044, tumorous tissue

source_name: Human liver cancer #LC044, tumorous tissue


title: LC045T

description: Gene expression profile of human liver cancer #LC045, tumorous tissue

source_name: Human liver cancer #LC045, tumorous tissue


title: LC038T

description: Gene expression profile of human liver cancer #LC038, tumorous tissue

source_name: Human liver cancer #LC038, tumorous tissue


title: TRA00026611_umi_16

source_name: spleen


title: LC040T

description: Gene expression profile of human liver cancer #LC040, tumorous tissue

source_name: Human liver cancer #LC040, tumorous tissue


title: LC046T

description: Gene expression profile of human liver cancer #LC046, tumorous tissue

source_name: Human liver cancer #LC046, tumorous tissue


title: LC041T

description: Gene expression profile of human liver cancer #LC041, tumorous tissue

source_name: Human liver cancer #LC041, tumorous tissue


title: LC037T

description: Gene expression profile of human liver cancer #LC037, tumorous tissue

source_name: Human liver cancer #LC037, tumorous tissue


title: LC036T

description: Gene expression profile of human liver cancer #LC036, tumorous tissue

source_name: Human liver cancer #LC036, tumorous tissue


title: LC034T

description: Gene expression profile of human liver cancer #LC034, tumorous tissue

source_name: Human liver cancer #LC034, tumorous tissue


title: LC032T

description: Gene expression profile of human liver cancer #LC032, tumorous tissue

source_name: Human liver cancer #LC032, tumorous tissue


title: TRA00026611_umi_14

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: LC033T

description: Gene expression profile of human liver cancer #LC033, tumorous tissue

source_name: Human liver cancer #LC033, tumorous tissue


title: TRA00026611_umi_12


title: TRA00026611_umi_13


title: TRA00026611_umi_11


title: TRA00026611_ls_7


title: TRA00026611_ls_8


title: TRA00026611_ls_6


title: TRA00026611_ls_5


title: LC029T

description: Gene expression profile of human liver cancer #LC029, tumorous tissue

source_name: Human liver cancer #LC029, tumorous tissue


title: LC030T

description: Gene expression profile of human liver cancer #LC030, tumorous tissue

source_name: Human liver cancer #LC030, tumorous tissue


title: TRA00026611_ls_3


title: LC028T

description: Gene expression profile of human liver cancer #LC028, tumorous tissue

source_name: Human liver cancer #LC028, tumorous tissue


title: LC031T

description: Gene expression profile of human liver cancer #LC031, tumorous tissue

source_name: Human liver cancer #LC031, tumorous tissue


title: LC026T

description: Gene expression profile of human liver cancer #LC026, tumorous tissue

source_name: Human liver cancer #LC026, tumorous tissue


title: TRA00026611_ls_2


title: LC027T

description: Gene expression profile of human liver cancer #LC027, tumorous tissue

source_name: Human liver cancer #LC027, tumorous tissue


title: TRA00026610_umi_9


title: TRA00026610_umi_16


title: TRA00026611_ls_1


title: TRA00026610_umi_15


title: TRA00026610_umi_10


title: TRA00026610_umi_14


title: TRA00026610_ls_7


title: LC024T

description: Gene expression profile of human liver cancer #LC024, tumorous tissue

source_name: Human liver cancer #LC024, tumorous tissue


title: LC021T

description: Gene expression profile of human liver cancer #LC021, tumorous tissue

source_name: Human liver cancer #LC021, tumorous tissue


title: LC025T

description: Gene expression profile of human liver cancer #LC025, tumorous tissue

source_name: Human liver cancer #LC025, tumorous tissue


title: LC018T

description: Gene expression profile of human liver cancer #LC018, tumorous tissue

source_name: Human liver cancer #LC018, tumorous tissue


title: LC017T

description: Gene expression profile of human liver cancer #LC017, tumorous tissue

source_name: Human liver cancer #LC017, tumorous tissue


title: LC020T

description: Gene expression profile of human liver cancer #LC020, tumorous tissue

source_name: Human liver cancer #LC020, tumorous tissue


title: TRA00026610_ls_8

source_name: spleen


title: LC023T

description: Gene expression profile of human liver cancer #LC023, tumorous tissue

source_name: Human liver cancer #LC023, tumorous tissue


title: LC015T

description: Gene expression profile of human liver cancer #LC015, tumorous tissue

source_name: Human liver cancer #LC015, tumorous tissue


title: LC019T

description: Gene expression profile of human liver cancer #LC019, tumorous tissue

source_name: Human liver cancer #LC019, tumorous tissue


title: LC014T

description: Gene expression profile of human liver cancer #LC014, tumorous tissue

source_name: Human liver cancer #LC014, tumorous tissue


title: TRA00026610_umi_13

description: singlecellRNAseq_MouseTregTconvs_CelSeq_counts.txt


title: LC016T

description: Gene expression profile of human liver cancer #LC016, tumorous tissue

source_name: Human liver cancer #LC016, tumorous tissue


title: LC013T

description: Gene expression profile of human liver cancer #LC013, tumorous tissue

source_name: Human liver cancer #LC013, tumorous tissue


title: LC022T

description: Gene expression profile of human liver cancer #LC022, tumorous tissue

source_name: Human liver cancer #LC022, tumorous tissue


title: TRA00026610_ls_4


title: TRA00026610_umi_12


title: TRA00026610_ls_5


title: LC012T

description: Gene expression profile of human liver cancer #LC012, tumorous tissue

source_name: Human liver cancer #LC012, tumorous tissue


title: TRA00026610_ls_6


title: LC011T

description: Gene expression profile of human liver cancer #LC011, tumorous tissue

source_name: Human liver cancer #LC011, tumorous tissue


title: TRA00026610_ls_1


title: TRA00026610_ls_2


title: TRA00026610_ls_3


title: LC008T

description: Gene expression profile of human liver cancer #LC008, tumorous tissue

source_name: Human liver cancer #LC008, tumorous tissue


title: LC003T

description: Gene expression profile of human liver cancer #LC003, tumorous tissue

source_name: Human liver cancer #LC003, tumorous tissue


title: LC004T

description: Gene expression profile of human liver cancer #LC004, tumorous tissue

source_name: Human liver cancer #LC004, tumorous tissue


title: LC005T

description: Gene expression profile of human liver cancer #LC005, tumorous tissue

source_name: Human liver cancer #LC005, tumorous tissue


title: NL012

description: Gene expression profile of human normal liver #NL012

source_name: Human normal liver #NL012


title: NL011

description: Gene expression profile of human normal liver #NL011

source_name: Human normal liver #NL011


title: LC006T

description: Gene expression profile of human liver cancer #LC006, tumorous tissue

source_name: Human liver cancer #LC006, tumorous tissue


title: LC010T

description: Gene expression profile of human liver cancer #LC010, tumorous tissue

source_name: Human liver cancer #LC010, tumorous tissue


title: LC009T

description: Gene expression profile of human liver cancer #LC009, tumorous tissue

source_name: Human liver cancer #LC009, tumorous tissue


title: Dync_flow2

city: Nijmegen

first: Joost

last: Hoenderop

state: Gelderland

address: Geert Grooteplein Zuid 30

department: Physiology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

data_processing:
FastQC version 0.11.5 was used to assess sequencing read quality
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Bowtie2 version 2.1.0
Relative abundance were calculated in terms of transcripts per million (TPM) using RSEM version 1.2.31 ( Li and Dewey et al., BMC Bioinformatics, 2011).
Genome_build: GRCm38.p5 mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Dync2h1 knockout_IMCD3_Fluid flow

growth_protocol: IMCD3 cells were cultured in DMEM/F-12 1:1 v/v medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 1 mM sodium pyruvate, 10 % v/v fetal calf serum, and 10 μg/ml ciproxin, at 37oC and 5 % v/v CO2.

extract_protocol:
After cells were incubated under static or fluid flow condition, RNA was harvested using the RNAesy Micro kit (QIAGEN, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IMCD3 cells, with or without cilia, were seeded onto microslide VI ibiTreat chambers and subjected to either static or physiologically relevant fluid shear stress (~0.7 dyne/cm2) conditions for 3 h at 37 C

tag: strain background

value: Dync2h1 knockout

tag: cell type

value: Inner-medullary collecting duct 3 (IMCD3)

tag: passage

tag: culture condition

value: Fluid flow


title: Dync_flow1

tag: genotype/variation


title: Dync_static2

source_name: Dync2h1 knockout_IMCD3_Static

value: Static


title: Dync_static3


title: LC001T

description: Gene expression profile of human liver cancer #LC001, tumorous tissue

source_name: Human liver cancer #LC001, tumorous tissue


title: NL007

description: Gene expression profile of human normal liver #NL007

source_name: Human normal liver #NL007


title: Dync_flow3


title: NL009

description: Gene expression profile of human normal liver #NL009

source_name: Human normal liver #NL009


title: NL006

description: Gene expression profile of human normal liver #NL006

source_name: Human normal liver #NL006


title: Ift_flow3

source_name: Ift140 knockout_IMCD3_Fluid flow

value: Ift140 knockout


title: Ift_flow1


title: NL008

description: Gene expression profile of human normal liver #NL008

source_name: Human normal liver #NL008

value: Normal liver


title: LC002T

description: Gene expression profile of human liver cancer #LC002, tumorous tissue

source_name: Human liver cancer #LC002, tumorous tissue


title: Dync_static1


title: NL014

description: Gene expression profile of human normal liver #NL014

source_name: Human normal liver #NL014


title: Ift_static2

source_name: Ift140 knockout_IMCD3_Static


title: NL010

description: Gene expression profile of human normal liver #NL010

source_name: Human normal liver #NL010


title: Ift_flow2


title: LC007T

description: Gene expression profile of human liver cancer #LC007, tumorous tissue

source_name: Human liver cancer #LC007, tumorous tissue


title: NL013

description: Gene expression profile of human normal liver #NL013

source_name: Human normal liver #NL013


title: Ctr_flow3

source_name: WT_IMCD3_Fluid flow

value: wild type (WT)


title: BRK098

city: colombo

first: Aruna Dharshan

last: De Silva

address: Kandawala Road, Ratmalana

country: Sri Lanka

institute: Kotelawala Defense University

description: control

data_processing:
18srRNA was the house keeping gene used for normalization
The statistical significance of the Relative expression ratios are taken from a paired T-test. For each subject the value of the
expression ratio = log( Etarget )( Ctarget ) – log( Eref )( Cref) is computed. A paired t-test compares the mean of theses values between select subpopulations.
The resulting test is the parametric equivalent of randomization tests  implemented in the ‘REST’ PCR analysis software, where Relative expression ratio (R)= (E target) ΔCT target/(E ref) ΔCT ref
where ΔCT target = Average control samples – Average experimental samples of the relevant target gene
ΔCT ref = Average control samples – Average experimental samples of the reference house keeping gene
Analysis is carried out with SAS version 9.4, SAS PROC MIXED.

label: SYBR Green

source_name: PBMC

label_protocol: Real Time qPCR was performed in a 25ml reaction mixture containing 12.5ml of RT2 SYBR green ROX qPCR master mix (catalog no: 330520), 1ml each of 10uM forward and reverse primers, 9.5ml of nuclease free water and 1ml of cDNA template, on the Qiagen Q5 plex thermal cycler. The PCR conditions were 94°C-2 min of initial denaturation followed by 35 cycles of 94°C-30 sec, 63°C-1 min, 72°C-1 min.

extract_protocol: Total RNA was extracted with Qiagen RNeasy Mini Kit

tag: disease state

value: Healthy controls

value: PBMC


title: Ctr_flow2


title: NL005

description: Gene expression profile of human normal liver #NL005

source_name: Human normal liver #NL005

tag: tissue


title: NL002

description: Gene expression profile of human normal liver #NL002

source_name: Human normal liver #NL002


title: NL003

description: Gene expression profile of human normal liver #NL003

source_name: Human normal liver #NL003


title: Ctr_flow1


title: Ctr_static2


title: NL004

description: Gene expression profile of human normal liver #NL004

source_name: Human normal liver #NL004


title: BRK090

description: control


title: BRK099

description: control


title: Ift_static1


title: BRK093

description: control


title: BRK094

description: control


title: BRK089

description: control


title: Ctr_static3


title: Ctr_static1


title: BRK087

description: control


title: Ift_static3


title: BRK081

description: control

value: Sepsis cases


title: BRK079

description: control


title: BRK082

description: control


title: BRK085

description: control


title: BRK091

description: control


title: BRK086

description: control


title: NL001

description: Gene expression profile of human normal liver #NL001

source_name: Human normal liver #NL001


title: BRK067

description: control


title: BRK064

description: control


title: BRK075

description: control


title: BRK044

description: control


title: BRK129

description: Test

value: Melioidosis cases


title: Limousin - differentiated bovine satellite cells (6th day)_rep 7

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 7 of 8. Differentiated bovine satellite cells (6th day) from Limousin

hyb_protocol: For hybridization, Microarray Hybridization Chamber (Agilent, USA) and Hyb-Buffer (Agilent, USA) were used according to manufacturer protocol.

scan_protocol: Microarray Scanner (model G2565CA) with SureScan High-Resolution Technology (Agilent, USA). Microarray data were extracted, the background subtracted and LOWESS normalisation performed using the standard procedures contained in the Agilent Feature Extraction (FE) Software Version 10.7.3.1.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>2.0. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

organism: Bos taurus

source_name: musculus semitendinosus

label_protocol: MiRNA Complete Labeling and Hyb Kit (Version 2.3, December 2010) (Agilent) was used for labeling, according to manufacturer protocol.

growth_protocol: Bovine satellite cells (BSC) were isolated from semitendinosus muscle of bulls of different performance based on the protocol using pronase from Streptomyces griseus. Next, BSC were cultured in Primaria culture flask (BD, USA) using the growth medium (10%FBS//DMEM/AB), which was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate (BD, USA). After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB) and maintain through 6 days, changed every 48h. FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,5 were included into the analysis.

tag: cattle breed

value: LIM

tag: day of differentiation

value: 6th day of differentiation

value: semitendinosus


title: Limousin - differentiated bovine satellite cells (6th day)_rep 8

description: Biological replicate 8 of 8. Differentiated bovine satellite cells (6th day) from Limousin