title: Cjun-RV-Nr4a1

status: Public on Mar 24 2018

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

institute: Tsinghua university

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 with the default parameters.Duplicate reads were removed after the alignment with samtools command-line tools.
peaks were called using SICER_V1.1 after filtering with input or IgG isotype control sequence with the following setting:Window size 200 and FDR 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using SICER_V1.1 by a moving window of size 200bp and the tag count in the windown was further normalized by library size per million.

source_name: Spleen and peripheral lymoh organs

growth_protocol: FACS Sorted CD4+ T cells were stimulated by plate-coated anti-CD3 plus anti-CD28 in the medium of RPMI 1640 with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone or transcriptional factors-DNA complexes were isolated with antibody or isotype IgG.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit. Briefly, DNA was end-repaired  using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: FACS Sorted CD4+ T cells were stimulated by plate-coated anti-CD3 plus anti-CD28, or followed with retroviral infection.

tag: cell type

value: CD4+ T cell

tag: activation

value: in vitro activation by TCR/Co-stimulation

value: C-Jun (sc-45x, Santa Cruz)


title: FFPE_X219016692 [X89_X.172_plate2NHSII]

status: Public on Aug 31 2017

type: RNA

city: Boston

first: Rulla

middle: M

last: Tamimi

state: MA

address: 181 Longwood Avenue

department: Medicine

country: USA

institute: Brigham and Women's Hospital

hyb_protocol: Hybridization was performed according to standard protocols.

scan_protocol: Scanning was performed according to standard protocols.

data_processing:
Gene expression data were normalized and summarized using Robust Multiarray Average (RMA; Affymetrix Power Tools [APT] v1.18.0). Differential expression was determined using Limma with multiple hypothesis testing (Benjamini and Hochberg); Bioconductor, R.
GSE93601_ER*_tumor_*_alcohol.xlsx: Limma analyses outputs.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: breast tissue

label_protocol: Labeling was performed according to standard Affymetrix protocols.

extract_protocol: Qiagen AllPrep RNA isolation kit was used to isolate total RNA.

treatment_protocol: Formalin-fixed paraffin-embedded tissue blocks.

tag: tissue

value: breast tumor-adjacent normal

tag: age at diagnosis

tag: year of diagnosis

tag: estrogen receptor status

value: Negative

tag: alcohol intake

tag: microarray batch

tag: patient id


title: FFPE_X216760020 [X28_X.285_NHSIIplate4]

value: breast tumor

value: Positive

value: 0 g/day


title: FFPE_X216299546 [X44_X.301_NHSIIplate4]

value: >10 g/day


title: FFPE_X217999436 [X19_X.276_NHSIIplate4]


title: FFPE_X211947925 [X49_X.306_NHSIIplate4]


title: FFPE_X216547328 [X88_X.345_NHSIIplate4]


title: FFPE_X216819144 [X68_X.415_NHSIIplate5]


title: FFPE_X219882409 [X20_X.277_NHSIIplate4]


title: FFPE_X211947925 [X48_X.305_NHSIIplate4]


title: pancreatic_acinar_cells_rep2

status: Public on Nov 04 2018

type: genomic

city: Jerusalem

first: Joshua

last: Moss

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

description: Acinar 2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing: Methylation array data were processed with the minfi package in R. For each sample analyzed on the Illumina Methylation array, CpG sites were filtered out if they were represented by less than 3 beads on the array, if the detection p-value (representing total fluorescence of the relevant probes) was greater than 0.01, or if they mapped to a sex chromosome. Background correction and normalization were performed with the preprocessIllumina function, which removes background calculated based on internal control probes and normalizes all samples to a predetermined control sample.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: pancreatic acinar cells

label_protocol: Standard Illumina Protocol

extract_protocol: cfDNA extraction from plasma was performed with the QIAsymphony liquid handling robot. cfDNA was treated with the Illumina Infinium FFPE  473 restoration kit. DNA from other samples was obtained as detailed in Moss et al., 2018.

tag: sample type

value: Pancreatic acinar cells

tag: disease state

value: Normal

tag: gender

value: Male

tag: age


title: FFPE_X219882409 [X21_X.278_NHSIIplate4]


title: FFPE_X221428357 [X86_X.343_NHSIIplate4]


title: FFPE_X217999436 [X18_X.275_NHSIIplate4]


title: FFPE_X216547328 [X89_X.346_NHSIIplate4]


title: FFPE_X213281248 [X47_X.304_NHSIIplate4]


title: FFPE_X215547418 [X33_X.290_NHSIIplate4]


title: FFPE_X215547418 [X32_X.289_NHSIIplate4]


title: pancreatic_duct_cells_rep2

description: Duct 2

source_name: pancreatic duct cells

value: Pancreatic duct cells


title: FFPE_X221428357 [X87_X.344_NHSIIplate4]


title: FFPE_X216819144 [X69_X.416_NHSIIplate5]


title: pancreatic_acinar_cells_rep3

description: Acinar 3

value: Female


title: FFPE_X213579114 [X83_X.430_NHSIIplate5]


title: FFPE_X212297890 [X31_X.288_NHSIIplate4]


title: FFPE_X213281248 [X46_X.303_NHSIIplate4]


title: FFPE_X212297890 [X30_X.287_NHSIIplate4]


title: FFPE_X216299546 [X45_X.302_NHSIIplate4]


title: FFPE_X216760020 [X29_X.286_NHSIIplate4]


title: FFPE_X219721345 [X16_X.273_NHSIIplate4]


title: pancreatic_duct_cells_rep3

description: Duct 3


title: FFPE_X219721345 [X17_X.274_NHSIIplate4]


title: FFPE_X211688719 [X69_X.152_plate2NHSII]


title: FFPE_X210720732 [X75_X.158_plate2NHSII]


title: FFPE_X219651767 [X14_X.271_NHSIIplate4]


title: FFPE_X216618323 [X85_X.342_NHSIIplate4]


title: FFPE_X214653506 [X65_X.148_plate2NHSII]


title: FFPE_X219103269 [X13_X.270_NHSIIplate4]


title: FFPE_X212943609 [X10_X.267_NHSIIplate4]


title: FFPE_X211688719 [X68_X.151_plate2NHSII]


title: FFPE_X212943609 [X11_X.268_NHSIIplate4]


title: FFPE_X214437793 [X82_X.339_NHSIIplate4]


title: FFPE_X221004582 [X60_X.143_plate2NHSII]


title: FFPE_X211841672 [X62_X.145_plate2NHSII]


title: FFPE_X212551453 [X80_X.337_NHSIIplate4]


title: FFPE_X221004582 [X61_X.144_plate2NHSII]


title: FFPE_X214653506 [X64_X.147_plate2NHSII]


title: FFPE_X219651767 [X15_X.272_NHSIIplate4]


title: FFPE_X214437793 [X83_X.340_NHSIIplate4]


title: FFPE_X211841672 [X63_X.146_plate2NHSII]


title: FFPE_X220286354 [X67_X.150_plate2NHSII]


title: FFPE_X216497867 [X9_X.266_NHSIIplate4]


title: FFPE_X213984655 [X59_X.142_plate2NHSII]


title: FFPE_X214459411 [X89_X.259_NHSIIplate3]


title: FFPE_X216497867 [X8_X.265_NHSIIplate4]


title: FFPE_X213984655 [X58_X.141_plate2NHSII]


title: FFPE_X210368035 [X90_X.173_plate2NHSII]


title: FFPE_X219103269 [X12_X.269_NHSIIplate4]


title: FFPE_X210368035 [X91_X.174_plate2NHSII]


title: FFPE_X214459411 [X90_X.260_NHSIIplate3]


title: FFPE_X216440173 [X57_X.140_plate2NHSII]


title: FFPE_X212597414 [X40_X.297_NHSIIplate4]


title: FFPE_X213464477 [X54_X.137_plate2NHSII]


title: FFPE_X213676522 [X26_X.196_NHSIIplate3]


title: FFPE_X211191939 [X36_X.293_NHSIIplate4]


title: FFPE_X211191939 [X37_X.294_NHSIIplate4]


title: FFPE_X219786521 [X25_X.282_NHSIIplate4]


title: FFPE_X212832168 [X7_X.264_NHSIIplate4]


title: FFPE_X212832168 [X6_X.263_NHSIIplate4]


title: FFPE_X212597414 [X41_X.298_NHSIIplate4]


title: FFPE_X211663571 [X85_X.255_NHSIIplate3]


title: FFPE_X216192809 [X5_X.262_NHSIIplate4]


title: FFPE_X213676522 [X25_X.195_NHSIIplate3]


title: FFPE_X221261843 [X38_X.295_NHSIIplate4]


title: FFPE_X218972291 [X53_X.136_plate2NHSII]


title: FFPE_X213464477 [X55_X.138_plate2NHSII]


title: FFPE_X218972291 [X52_X.135_plate2NHSII]


title: FFPE_X214618915 [X59_X.316_NHSIIplate4]


title: FFPE_X216192809 [X91_X.261_NHSIIplate3]


title: FFPE_X212432124 [X26_X.283_NHSIIplate4]


title: FFPE_X218320380 [X51_X.134_plate2NHSII]


title: FFPE_X221261843 [X39_X.296_NHSIIplate4]


title: FFPE_X211192120 [X11_X.181_NHSIIplate3]


title: FFPE_X214436891 [X88_X.258_NHSIIplate3]


title: FFPE_X211192120 [X12_X.182_NHSIIplate3_2]


title: FFPE_X218320380 [X50_X.133_plate2NHSII]


title: FFPE_X219786521 [X24_X.281_NHSIIplate4]


title: FFPE_X211663571 [X86_X.256_NHSIIplate3]


title: FFPE_X215747028 [X86_X.169_plate2NHSII]


title: FFPE_X212432124 [X27_X.284_NHSIIplate4]


title: FFPE_X212551453 [X81_X.338_NHSIIplate4]


title: FFPE_X212890618 [X79_X.336_NHSIIplate4]


title: FFPE_X213165037 [X23_X.280_NHSIIplate4]


title: FFPE_X210609134 [X49_X.132_plate2NHSII]


title: FFPE_X219499195 [X13_X.183_NHSIIplate3]


title: FFPE_X210609134 [X48_X.131_plate2NHSII]


title: FFPE_X215343473 [X76_X.333_NHSIIplate4]


title: FFPE_X218111665 [X15_X.185_NHSIIplate3]


title: FFPE_X217512289 [X82_X.252_NHSIIplate3]


title: FFPE_X213721982 [X74_X.331_NHSIIplate4]


title: FFPE_X217512289 [X81_X.251_NHSIIplate3]


title: FFPE_X215343473 [X77_X.334_NHSIIplate4]


title: FFPE_X218111665 [X16_X.186_NHSIIplate3]


title: FFPE_X213782211 [X46_X.129_plate2NHSII]


title: FFPE_X213721982 [X75_X.332_NHSIIplate4]


title: FFPE_X219499195 [X14_X.184_NHSIIplate3]


title: FFPE_X216307272 [X66_X.413_NHSIIplate5]


title: FFPE_X210355940 [X82_X.165_plate2NHSII]


title: FFPE_X213782211 [X47_X.130_plate2NHSII]


title: FFPE_X218193943 [X81_X.428_NHSIIplate5]


title: FFPE_X215747028 [X87_X.170_plate2NHSII]


title: FFPE_X216307272 [X67_X.414_NHSIIplate5]


title: FFPE_X213165037 [X22_X.279_NHSIIplate4]


title: FFPE_X214514157 [X68_X.325_NHSIIplate4]


title: FFPE_X218193943 [X80_X.427_NHSIIplate5]


title: FFPE_X219546259 [X73_X.420_NHSIIplate5]


title: FFPE_X216652424 [X66_X.323_NHSIIplate4]


title: FFPE_X213851608 [X83_X.253_NHSIIplate3]


title: FFPE_X214514157 [X69_X.326_NHSIIplate4]


title: FFPE_X211177955 [X73_X.330_NHSIIplate4]


title: FFPE_X211034174 [X45_X.128_plate2NHSII]


title: FFPE_X211034174 [X44_X.127_plate2NHSII]


title: FFPE_X211967836 [X40_X.123_plate2NHSII]


title: FFPE_X216664750 [X43_X.126_plate2NHSII]


title: FFPE_X211023368 [X34_X.117_plate2NHSII]


title: FFPE_X212867323 [X33_X.116_plate2NHSII]


title: FFPE_X211592576 [X38_X.121_plate2NHSII]


title: FFPE_X211592576 [X39_X.122_plate2NHSII]


title: FFPE_X221081526 [X36_X.119_plate2NHSII]


title: FFPE_X214558520 [X78_X.248_NHSIIplate3]


title: FFPE_X221081526 [X37_X.120_plate2NHSII]


title: FFPE_X214478523 [X28_X.111_plate2NHSII]


title: FFPE_X217638453 [X64_X.321_NHSIIplate4]


title: FFPE_X211967836 [X41_X.124_plate2NHSII]


title: FFPE_X215976375 [X31_X.114_plate2NHSII]


title: FFPE_X216664750 [X42_X.125_plate2NHSII]


title: FFPE_X217194214 [X62_X.319_NHSIIplate4]


title: FFPE_X212867323 [X32_X.115_plate2NHSII]


title: FFPE_X214558520 [X77_X.247_NHSIIplate3]


title: FFPE_X214478523 [X29_X.112_plate2NHSII]


title: FFPE_X217194214 [X63_X.320_NHSIIplate4]


title: FFPE_X211023368 [X35_X.118_plate2NHSII]


title: FFPE_X217638453 [X65_X.322_NHSIIplate4]


title: FFPE_X215439095 [X80_X.250_NHSIIplate3]


title: FFPE_X215976375 [X30_X.113_plate2NHSII]


title: FFPE_X216518312 [X64_X.234_NHSIIplate3]


title: FFPE_X215439095 [X79_X.249_NHSIIplate3]


title: FFPE_X217403482 [X26_X.109_plate2NHSII]


title: FFPE_X217403482 [X27_X.110_plate2NHSII]


title: FFPE_X213188375 [X73_X.243_NHSIIplate3]


title: FFPE_X213188375 [X74_X.244_NHSIIplate3]


title: FFPE_X214077983 [X24_X.107_plate2NHSII]


title: FFPE_X217485760 [X91_X.348_NHSIIplate4]


title: FFPE_X212179669 [X35_X.292_NHSIIplate4]


title: FFPE_X214077983 [X25_X.108_plate2NHSII]


title: FFPE_X212130796 [X69_X.239_NHSIIplate3]


title: FFPE_X212179669 [X34_X.291_NHSIIplate4]


title: FFPE_X214371471 [X22_X.105_plate2NHSII]


title: FFPE_X217485760 [X90_X.347_NHSIIplate4]


title: FFPE_X213092238 [X22_X.366_NHSIIplate5]


title: FFPE_X211269042 [X10_X.180_NHSIIplate3]


title: FFPE_X217695068 [X24_X.368_NHSIIplate5]


title: FFPE_X212130796 [X70_X.240_NHSIIplate3]


title: FFPE_X213023915 [X25_X.369_NHSIIplate5]


title: FFPE_X217808763 [X75_X.245_NHSIIplate3]


title: FFPE_X214371471 [X23_X.106_plate2NHSII]


title: FFPE_X217695068 [X23_X.367_NHSIIplate5]


title: FFPE_X217808763 [X76_X.246_NHSIIplate3]


title: FFPE_X218212887 [X5_X.175_NHSIIplate3]


title: FFPE_X213092238 [X21_X.365_NHSIIplate5]


title: FFPE_X213708700 [X7_X.177_NHSIIplate3]


title: FFPE_X213023915 [X26_X.370_NHSIIplate5]


title: FFPE_X212452447 [X75_X.422_NHSIIplate5]


title: FFPE_X218212887 [X6_X.176_NHSIIplate3]


title: FFPE_X216353602 [X78_X.161_plate2NHSII]


title: FFPE_X213708700 [X8_X.178_NHSIIplate3]


title: FFPE_X212452447 [X74_X.421_NHSIIplate5]


title: FFPE_X215767351 [X68_X.238_NHSIIplate3]


title: FFPE_X210665568 [X80_X.163_plate2NHSII]


title: FFPE_X211269042 [X9_X.179_NHSIIplate3]


title: FFPE_X216353602 [X79_X.162_plate2NHSII]


title: FFPE_X216518312 [X63_X.233_NHSIIplate3]


title: FFPE_X216118880 [X65_X.235_NHSIIplate3]


title: FFPE_X210458039 [X76_X.159_plate2NHSII]


title: FFPE_X216118880 [X66_X.236_NHSIIplate3]


title: FFPE_X211142079 [X61_X.231_NHSIIplate3]


title: FFPE_X210458039 [X77_X.160_plate2NHSII]


title: FFPE_X213754818 [X18_X.101_plate2NHSII]


title: FFPE_X214487937 [X20_X.103_plate2NHSII]


title: FFPE_X221148853 [X8_X.91_plate2NHSII]


title: FFPE_X213023291 [X73_X.156_plate2NHSII]


title: FFPE_X213310102 [X11_X.94_plate2NHSII_2]


title: FFPE_X219086438 [X70_X.153_plate2NHSII]


title: FFPE_X210691260 [X20_X.364_NHSIIplate5]


title: FFPE_X217785175 [X5_X.88_plate2NHSII]


title: FFPE_X219656792 [X12_X.95_plate2NHSII]


title: FFPE_X213337254 [X14_X.97_plate2NHSII]


title: FFPE_X214487937 [X21_X.104_plate2NHSII]


title: FFPE_X210244814 [X16_X.360_NHSIIplate5]


title: FFPE_X219656792 [X13_X.96_plate2NHSII]


title: FFPE_X220120677 [X17_X.361_NHSIIplate5]


title: FFPE_X213337254 [X15_X.98_plate2NHSII]


title: FFPE_X213754818 [X19_X.102_plate2NHSII]


title: FFPE_X215043337 [X71_X.241_NHSIIplate3]


title: FFPE_X213310102 [X10_X.93_plate2NHSII]


title: FFPE_X210244814 [X15_X.359_NHSIIplate5]


title: FFPE_X210691260 [X19_X.363_NHSIIplate5]


title: FFPE_X219853078 [X7_X.90_plate2NHSII]


title: FFPE_X220120677 [X18_X.362_NHSIIplate5]


title: FFPE_X215243359 [X89_X.85_plate1NHSII]


title: FFPE_X215243359 [X90_X.86_plate1NHSII]


title: FFPE_X213222829 [X19_X.189_NHSIIplate3]


title: FFPE_X213023291 [X72_X.155_plate2NHSII]


title: FFPE_X218119917 [X61_X.318_NHSIIplate4]


title: FFPE_X219129319 [X60_X.230_NHSIIplate3]


title: FFPE_X211092212 [X73_X.69_plate1NHSII]


title: FFPE_X221541965 [X82_X.78_plate1NHSII]


title: FFPE_X212580057 [X57_X.227_NHSIIplate3]


title: FFPE_X211092212 [X74_X.70_plate1NHSII]


title: FFPE_X221541965 [X81_X.77_plate1NHSII]


title: FFPE_X215716517 [X88_X.84_plate1NHSII]


title: FFPE_X216435191 [X72_X.68_plate1NHSII]


title: FFPE_X218935072 [X80_X.76_plate1NHSII]


title: FFPE_X220183431 [X84_X.431_NHSIIplate5]


title: FFPE_X215043337 [X72_X.242_NHSIIplate3]


title: FFPE_X218540525 [X84_X.80_plate1NHSII]


title: FFPE_X218119917 [X60_X.317_NHSIIplate4]


title: FFPE_X216697168 [X51_X.221_NHSIIplate3]


title: FFPE_X215716517 [X87_X.83_plate1NHSII]


title: FFPE_X211019912 [X53_X.223_NHSIIplate3]


title: FFPE_X221615254 [X55_X.225_NHSIIplate3]


title: FFPE_X213385279 [X50_X.220_NHSIIplate3]


title: FFPE_X221615254 [X56_X.226_NHSIIplate3]


title: FFPE_X213385279 [X49_X.219_NHSIIplate3]


title: FFPE_X218935072 [X79_X.75_plate1NHSII]


title: FFPE_X216697168 [X52_X.222_NHSIIplate3]


title: FFPE_X212101986 [X48_X.218_NHSIIplate3]


title: FFPE_X212101986 [X47_X.217_NHSIIplate3]


title: FFPE_X211042583 [X14_X.358_NHSIIplate5]


title: FFPE_X211042583 [X13_X.357_NHSIIplate5]


title: FFPE_X220336433 [X69_X.65_plate1NHSII]


title: FFPE_X220336433 [X70_X.66_plate1NHSII]


title: FFPE_X211362224 [X12_X.356_NHSIIplate5]


title: FFPE_X210255826 [X63_X.59_plate1NHSII]


title: FFPE_X210255826 [X64_X.60_plate1NHSII]


title: FFPE_X216458020 [X58_X.54_plate1NHSII]


title: FFPE_X219298374 [X62_X.58_plate1NHSII]


title: FFPE_X213952521 [X65_X.61_plate1NHSII]


title: FFPE_X210186429 [X67_X.63_plate1NHSII]


title: FFPE_X213978359 [X86_X.82_plate1NHSII]


title: FFPE_X211362224 [X11_X.355_NHSIIplate5]


title: FFPE_X214108538 [X60_X.56_plate1NHSII]


title: FFPE_X219506334 [X42_X.299_NHSIIplate4]


title: FFPE_X219506334 [X43_X.300_NHSIIplate4]


title: FFPE_X215326680 [X9_X.353_NHSIIplate5]


title: FFPE_X210186429 [X68_X.64_plate1NHSII]


title: FFPE_X212462763 [X52_X.48_plate1NHSII]


title: FFPE_X212462763 [X51_X.47_plate1NHSII]


title: FFPE_X212706053 [X56_X.52_plate1NHSII]


title: FFPE_X213752390 [X54_X.50_plate1NHSII]


title: FFPE_X215666026 [X70_X.417_NHSIIplate5]


title: FFPE_X216457839 [X49_X.45_plate1NHSII]


title: FFPE_X215326680 [X10_X.354_NHSIIplate5]


title: FFPE_X215666026 [X71_X.418_NHSIIplate5]


title: FFPE_X214757743 [X56_X.313_NHSIIplate4]


title: FFPE_X216457839 [X50_X.46_plate1NHSII]


title: FFPE_X218966722 [X48_X.44_plate1NHSII]


title: FFPE_X214757743 [X57_X.314_NHSIIplate4]


title: FFPE_X216822219 [X76_X.72_plate1NHSII]


title: FFPE_X213857226 [X45_X.41_plate1NHSII]


title: FFPE_X213857226 [X46_X.42_plate1NHSII]


title: FFPE_X217703933 [X43_X.39_plate1NHSII]


title: FFPE_X217703933 [X44_X.40_plate1NHSII]


title: FFPE_X212836709 [X43_X.213_NHSIIplate3]


title: FFPE_X212139538 [X40_X.36_plate1NHSII]


title: FFPE_X215349612 [X45_X.215_NHSIIplate3]


title: FFPE_X212139538 [X39_X.35_plate1NHSII]


title: FFPE_X210467247 [X54_X.311_NHSIIplate4]


title: FFPE_X220876934 [X5_X.349_NHSIIplate5]


title: FFPE_X210467247 [X55_X.312_NHSIIplate4]


title: FFPE_X219033382 [X37_X.33_plate1NHSII]


title: FFPE_X219033382 [X38_X.34_plate1NHSII]


title: FFPE_X212836709 [X44_X.214_NHSIIplate3]


title: FFPE_X210417212 [X36_X.32_plate1NHSII]


title: FFPE_X215349612 [X46_X.216_NHSIIplate3]


title: FFPE_X221613038 [X34_X.30_plate1NHSII]


title: FFPE_X211478890 [X29_X.25_plate1NHSII]


title: FFPE_X220876934 [X6_X.350_NHSIIplate5]


title: FFPE_X221613038 [X33_X.29_plate1NHSII]


title: FFPE_X210650433 [X42_X.212_NHSIIplate3]


title: FFPE_X211478890 [X30_X.26_plate1NHSII]


title: FFPE_X210650433 [X41_X.211_NHSIIplate3]


title: FFPE_X212811767 [X31_X.27_plate1NHSII]


title: FFPE_X217553637 [X27_X.23_plate1NHSII]


title: FFPE_X214193576 [X65_X.412_NHSIIplate5]


title: FFPE_X220368773 [X25_X.21_plate1NHSII]


title: FFPE_X212811767 [X32_X.28_plate1NHSII]


title: FFPE_X220368773 [X26_X.22_plate1NHSII]


title: FFPE_X214193576 [X64_X.411_NHSIIplate5]


title: FFPE_X217553637 [X28_X.24_plate1NHSII]


title: FFPE_X212333736 [X35_X.205_NHSIIplate3]


title: FFPE_X215167176 [X40_X.210_NHSIIplate3]


title: FFPE_X217841344 [X34_X.204_NHSIIplate3]


title: FFPE_X217841344 [X33_X.203_NHSIIplate3]


title: FFPE_X212311300 [X27_X.197_NHSIIplate3]


title: FFPE_X215167176 [X39_X.209_NHSIIplate3]


title: FFPE_X221219745 [X30_X.200_NHSIIplate3]


title: FFPE_X219129319 [X59_X.229_NHSIIplate3]


title: FFPE_X214564816 [X32_X.202_NHSIIplate3]


title: FFPE_X217979525 [X52_X.309_NHSIIplate4]


title: FFPE_X221219745 [X29_X.199_NHSIIplate3]


title: FFPE_X213645702 [X38_X.208_NHSIIplate3]


title: FFPE_X217979525 [X53_X.310_NHSIIplate4]


title: FFPE_X215166377 [X7_X.351_NHSIIplate5]


title: FFPE_X213645702 [X37_X.207_NHSIIplate3]


title: FFPE_X219271119 [X23_X.193_NHSIIplate3]


title: FFPE_X217632526 [X21_X.17_plate1NHSII]


title: FFPE_X214858553 [X51_X.308_NHSIIplate4]


title: FFPE_X219271119 [X24_X.194_NHSIIplate3]


title: FFPE_X212333736 [X36_X.206_NHSIIplate3]


title: FFPE_X212564887 [X5_X.1_plate1NHSII]


title: FFPE_X213975550 [X19_X.15_plate1NHSII]


title: FFPE_X211762886 [X21_X.191_NHSIIplate3]


title: FFPE_X212311300 [X28_X.198_NHSIIplate3]


title: FFPE_X215215245 [X24_X.20_plate1NHSII]


title: FFPE_X215215245 [X23_X.19_plate1NHSII]


title: FFPE_X212564887 [X6_X.2_plate1NHSII]


title: FFPE_X220769210 [X17_X.187_NHSIIplate3]


title: FFPE_X215166377 [X8_X.352_NHSIIplate5]


title: FFPE_X213975550 [X20_X.16_plate1NHSII]


title: FFPE_X220769210 [X18_X.188_NHSIIplate3]


title: FFPE_X210545749 [X17_X.13_plate1NHSII]


title: FFPE_X219138424 [X71_X.328_NHSIIplate4]


title: FFPE_X215524692 [X15_X.11_plate1NHSII]


title: FFPE_X219138424 [X70_X.327_NHSIIplate4]


title: FFPE_X218287658 [X13_X.9_plate1NHSII]


title: FFPE_X211644253 [X12_X.8_plate1NHSII]


title: FFPE_X218287658 [X14_X.10_plate1NHSII]


title: FFPE_X211644253 [X11_X.7_plate1NHSII]


title: FFPE_X220356035 [X8_X.4_plate1NHSII]


title: FFPE_X119542857 [X40_1017]


title: FFPE_X117344407 [X9_431_plate5]


title: FFPE_X119555879 [X88_969]


title: FFPE_X117381832 [X27_729_FFPE_Plate8]


title: FFPE_X116207673 [X21_211_plate2]


title: FFPE_X215524692 [X16_X.12_plate1NHSII]


title: FFPE_X110772983 [X87_208_FFPE_PLATE1]


title: FFPE_X116207673 [X22_212_plate2]


title: FFPE_X111137206 [X95_705]


title: FFPE_X111686291 [X38_1015]


title: FFPE_X110576878 [X10_987]


title: FFPE_X218694694 [X9_X.5_plate1NHSII]


title: FFPE_X218694694 [X10_X.6_plate1NHSII]


title: FFPE_X210545749 [X18_X.14_plate1NHSII]


title: FFPE_X110772983 [X25_207_plate2]


title: FFPE_X117381832 [X28_730_FFPE_Plate8]


title: FFPE_X117776482 [X83_953]


title: FFPE_X220356035 [X7_X.3_plate1NHSII]


title: FFPE_X111137206 [X96_706]


title: FFPE_X117776482 [X84_954]


title: FFPE_X117344407 [X10_432_plate5]


title: FFPE_X121305523 [X92_977]


title: FFPE_X119242412 [X91_516_plate5]


title: FFPE_X112949536 [X44_1021]


title: FFPE_X114938138 [X26_728_FFPE_Plate8]


title: FFPE_X112217628 [X20_815_plate9]


title: FFPE_X118575056 [X91_976]


title: FFPE_X115118558 [X18_813_plate9]


title: FFPE_X114938138 [X25_727_FFPE_Plate8]


title: FFPE_X112217628 [X21_816_plate9]


title: FFPE_X115118558 [X19_814_plate9]


title: FFPE_X112013374 [X16_811_plate9]


title: FFPE_X112013374 [X17_812_plate9]


title: FFPE_X116156486 [X36_842_plate9]


title: FFPE_X116156486 [X41_841_plate9]


title: FFPE_X114141737 [X85_951]


title: FFPE_X112168348 [X80_950]


title: FFPE_X112544770 [X43_843_plate9]


title: FFPE_X111565570 [X15_810_plate9]


title: FFPE_X121534561 [X70_940_plate9]


title: FFPE_X111565570 [X14_809_plate9]


title: FFPE_X121280337 [X78_948]


title: FFPE_X112544770 [X44_844_plate9]


title: FFPE_X112481257 [X87_968]


title: FFPE_X118670866 [X75_945]


title: FFPE_X118670866 [X76_946]


title: FFPE_X113217950 [X74_944]


title: FFPE_X121593810 [X71_941_plate9]


title: FFPE_X118305500 [X75_177_plate2]


title: FFPE_X118305500 [X76_178_plate2]


title: FFPE_X117356733 [X55_907_plate9]


title: FFPE_X121534561 [X69_939_plate9]


title: FFPE_X118622738 [X71_173_plate2]


title: FFPE_X118622738 [X72_174_plate2]


title: FFPE_X116750322 [X11_433_plate5]


title: FFPE_X112481051 [X13_435_plate5_2]


title: FFPE_X110954801 [X13_808_plate9]


title: FFPE_X116305983 [X25_C1_plate6_3]


title: FFPE_X119968230 [X11_806_plate9]


title: FFPE_X110954801 [X12_807_plate9]


title: FFPE_X117356733 [X56_908_plate9]


title: FFPE_X114141222 [X6_428_plate5]


title: FFPE_X112481051 [X14_436_plate5]


title: FFPE_X114215850 [X95_395_PLATE4]


title: FFPE_X110313902 [X70_172_plate2]


title: FFPE_X114215850 [X96_396_PLATE4]


title: FFPE_X114141222 [X5_427_plate5]


title: FFPE_X110313902 [X69_171_plate2]


title: FFPE_X113799356 [X67_169_plate2]


title: FFPE_X117463633 [X29_639]


title: FFPE_X119482668 [X18_B6_plate6_3]


title: FFPE_X117171694 [X91_391_PLATE4]


title: FFPE_X117171694 [X92_392_PLATE4]


title: FFPE_X113786334 [X66_168_plate2]


title: FFPE_X117084608 [X8_803_plate9]


title: FFPE_X119968230 [X10_805_plate9]


title: FFPE_X111576376 [X7_802_plate9]


title: FFPE_X111576376 [X6_801_plate9]


title: FFPE_X117084608 [X9_804_plate9]


title: FFPE_X113786334 [X65_167_plate2]


title: FFPE_X117463633 [X30_640]


title: FFPE_X113799356 [X68_170_plate2]


title: FFPE_X113922912 [X94_394_PLATE4]


title: FFPE_X111076939 [X22_230_FFPE_PLATE3]


title: FFPE_X110327002 [X72_799]


title: FFPE_X121291967 [X68_938_plate9]


title: FFPE_X116193814 [X84_1061]


title: FFPE_X121291967 [X67_937_plate9]


title: FFPE_X110327002 [X5_800_plate9]


title: FFPE_X111343009 [X23_725_FFPE_Plate8]


title: FFPE_X111872601 [X7_429_plate5]


title: FFPE_X111343009 [X24_726_FFPE_Plate8]


title: FFPE_X110439133 [X57_909_plate9]


title: FFPE_X120657279 [X12_989]


title: FFPE_X111076939 [X21_229_FFPE_PLATE3]


title: FFPE_X113922912 [X93_393_PLATE4]


title: FFPE_X116458741 [X10_712_FFPE_Plate8]


title: FFPE_X116458741 [X9_711_FFPE_Plate8]


title: FFPE_X111847708 [X65_935_plate9]


title: FFPE_X118717561 [X96_980]


title: FFPE_X110439133 [X58_910_plate9]


title: FFPE_X115764336 [X60_E12_plate6_3]


title: FFPE_X112228228 [X19_227_FFPE_PLATE3]


title: FFPE_X119612847 [X71_798]


title: FFPE_X115546104 [X69_796]


title: FFPE_X115988913 [X17_225_FFPE_PLATE3]


title: FFPE_X115764336 [X61_578_plate_6]


title: FFPE_X115546104 [X68_795]


title: FFPE_X115655941 [X39_649]


title: FFPE_X119612847 [X70_797]


title: FFPE_X115655941 [X40_650]


title: FFPE_X116155481 [X83_1060]


title: FFPE_X114099601 [X81_1058]


title: FFPE_X115988913 [X18_226_FFPE_PLATE3]


title: FFPE_X112518769 [X16_224_FFPE_PLATE3]


title: FFPE_X113688539 [X89_389_PLATE4]


title: FFPE_X111514839 [X33_643]


title: FFPE_X112518769 [X15_223_FFPE_PLATE3]


title: FFPE_X117972902 [X53_663]


title: FFPE_X117972902 [X54_664]


title: FFPE_X111990616 [X35_645]


title: FFPE_X111990616 [X36_646]


title: FFPE_X111514839 [X34_644]


title: FFPE_X113688539 [X90_390_PLATE4]


title: FFPE_X121712971 [X82_1059]


title: FFPE_X120077536 [X50_X.407_NHSIIplate5]


title: FFPE_X121117518 [X11_219_FFPE_PLATE_3]


title: FFPE_X120077536 [X63_X.408_NHSIIplate5]


title: FFPE_X111785091 [X13_221_FFPE_PLATE3]


title: FFPE_X121890622 [X22_B10_plate6_3]


title: FFPE_X121019826 [X38_648]


title: FFPE_X121890622 [X23_B11_plate6_3]


title: FFPE_X111785091 [X14_222_FFPE_PLATE3]


title: FFPE_X121117518 [X12_220_FFPE_PLATE_3]


title: FFPE_X119350832 [X31_641]


title: FFPE_X119106181 [X9_217_FFPE_PLATE_3]


title: FFPE_X111954608 [X87_387_PLATE4]


title: FFPE_X115608406 [X87_1064]


title: FFPE_X119350832 [X32_642]


title: FFPE_X114402438 [X66_793]


title: FFPE_X111954608 [X88_388_PLATE4]


title: FFPE_X114402438 [X67_794]


title: FFPE_X111797217 [X77_87_FFPE_PLATE1]


title: FFPE_X112592280 [X63_921_plate9]


title: FFPE_X117630413 [X88_513_plate5]


title: FFPE_X112592280 [X64_922_plate9]


title: FFPE_X116905746 [X86_511_plate5]


title: FFPE_X116905746 [X87_512_plate5]


title: FFPE_X114152955 [X26_636]


title: FFPE_X117404796 [X65_792]


title: FFPE_X114716292 [X56_X.401_NHSIIplate5]


title: FFPE_X114152955 [X25_635]


title: FFPE_X117170689 [X28_825_plate9_.hGlue_3_0_v1.]


title: FFPE_X119758716 [X86_1063]


title: FFPE_X113316235 [X54_906_plate9]


title: FFPE_X121963936 [X88_1065]


title: FFPE_X117170689 [X29_826_plate9]


title: FFPE_X116725017 [X34_134_plate2]


title: FFPE_X120757811 [X59_X.404_NHSIIplate5]


title: FFPE_X117094615 [X39_1016]


title: FFPE_X117630413 [X89_514_plate5]


title: FFPE_X117404796 [X64_791]


title: FFPE_X121375366 [X8_985]


title: FFPE_X119696311 [X22_724_FFPE_Plate8]


title: FFPE_X114716292 [X57_X.402_NHSIIplate5]


title: FFPE_X119696311 [X21_723_FFPE_Plate8]


title: FFPE_X116725017 [X33_133_plate2]


title: FFPE_X120757811 [X58_X.403_NHSIIplate5]


title: FFPE_X110841350 [X40_840_plate9]


title: FFPE_X118159636 [X48_470_plate5]


title: FFPE_X113316235 [X53_905_plate9]


title: FFPE_X118159636 [X47_469_plate5]


title: FFPE_X122133422 [X30_130_plate2]


title: FFPE_X110841350 [X39_839_plate9]


title: FFPE_X116881874 [X47_1024]


title: FFPE_X119611945 [X29_120_plate2]


title: FFPE_X119611945 [X24_634]


title: FFPE_X115545093 [X27_127_plate2]


title: FFPE_X110511502 [X27_824_plate9_.hGlue_3_0_v1.]


title: FFPE_X118445436 [X17_121_plate2]


title: FFPE_X113982439 [X15_119_plate2]


title: FFPE_X122133319 [X44_D8_plate6_3]


title: FFPE_X112994958 [X19_123_plate2]


title: FFPE_X116132143 [X20_124_plate2]


title: FFPE_X112994958 [X18_122_plate2]


title: FFPE_X115703283 [X26_91_plate2]


title: FFPE_X117303883 [X81_93_FFPE_PLATE1]


title: FFPE_X117897827 [X78_503_plate5]


title: FFPE_X113982439 [X62_920_plate9]


title: FFPE_X119722041 [X13_117_plate2]


title: FFPE_X119722041 [X14_118_plate2]


title: FFPE_X115703283 [X80_92_FFPE_PLATE1]


title: FFPE_X110511502 [X26_823_plate9_.hGlue_3_0_v1.]


title: FFPE_X121876123 [X76_501_plate5_2]


title: FFPE_X114640272 [X12_116_plate2]


title: FFPE_X110901127 [X37_1014]


title: FFPE_X118011242 [X73_114_FFPE_PLATE1]


title: FFPE_X117935059 [X74_499_plate5]


title: FFPE_X118445436 [X16_120_plate2]


title: FFPE_X113131196 [X93_703]


title: FFPE_X118011242 [X11_115_plate2]


title: FFPE_X121724576 [X72_497_plate5]


title: FFPE_X121724576 [X73_498_plate5]


title: FFPE_X117303883 [X82_94_FFPE_PLATE1]


title: FFPE_X111111568 [X51_661]


title: FFPE_X117935059 [X75_500_plate5]


title: FFPE_X119154006 [X88_101_FFPE_PLATE1]


title: FFPE_X117120860 [X89_970]


title: FFPE_X113131196 [X94_704]


title: FFPE_X119903775 [X41_1018]


title: FFPE_X119154006 [X86_100_FFPE_PLATE1]


title: FFPE_X117714430 [X46_1023]


title: FFPE_X111111568 [X52_662]


title: FFPE_X119844488 [X84_96_FFPE_PLATE1]


title: FFPE_X118643448 [X60_918_plate9]


title: FFPE_X115320753 [X92_103_FFPE_PLATE1]


title: FFPE_X113042821 [X46_846_plate9]


title: FFPE_X118219928 [X22_631]


title: FFPE_X113042821 [X45_845_plate9]


title: FFPE_X115320753 [X90_102_FFPE_PLATE1]


title: FFPE_X112303303 [X91_701]


title: FFPE_X119807990 [X76_105_FFPE_PLATE1]


title: FFPE_X118219928 [X23_632]


title: FFPE_X122008518 [X45_1022]


title: FFPE_X112303303 [X92_702]


title: FFPE_X114251549 [X20_629]


title: FFPE_X114251549 [X21_630]


title: FFPE_X119420095 [X51_473_plate5]


title: FFPE_X119420095 [X52_474_plate5]


title: FFPE_X119276041 [X89_699]


title: FFPE_X118571963 [X94_107_FFPE_PLATE1]


title: FFPE_X118850462 [X9_110_plate2]


title: FFPE_X121252738 [X87_697]


title: FFPE_X119153928 [X85_695]


title: FFPE_X117885501 [X42_559_plate_6]


title: FFPE_X120655784 [X61_161_plate2]


title: FFPE_X114873439 [X16_625]


title: FFPE_X118837277 [X54_1031]


title: FFPE_X121252738 [X88_698]


title: FFPE_X110537340 [X74_112_FFPE_PLATE1]


title: FFPE_X115022421 [X10_111_plate2]


title: FFPE_X116328085 [X18_627]


title: FFPE_X114138250 [X53_475_plate5]


title: FFPE_X113614876 [X56_478_plate5]


title: FFPE_X116328085 [X19_628]


title: FFPE_X119276041 [X90_700]


title: FFPE_X122083446 [X72_106_FFPE_PLATE1]


title: FFPE_X117885501 [X43_560_plate_6]


title: FFPE_X114138250 [X54_476_plate5]


title: FFPE_X118850462 [X96_109_FFPE_PLATE1]


title: FFPE_X110227403 [X59_481_plate5]


title: FFPE_X119153928 [X86_696]


title: FFPE_X110537340 [X75_113_FFPE_PLATE1]


title: FFPE_X120655784 [X60_160_plate2]


title: FFPE_X113614876 [X55_477_plate5]


title: FFPE_X114873439 [X17_626]


title: FFPE_X121875221 [X37_837_plate9]


title: FFPE_X110227403 [X60_482_plate5]


title: FFPE_X121875221 [X38_838_plate9]


title: FFPE_X119709268 [X42_836_plate9]


title: FFPE_X111365239 [X82_692]


title: FFPE_X118501496 [X56_156_plate2]


title: FFPE_X113340432 [X84_694]


title: FFPE_X120439768 [X53_153_plate2]


title: FFPE_X117340587 [X58_480_plate5]


title: FFPE_X119709268 [X35_835_plate9]


title: FFPE_X115270056 [X51_151_plate2]


title: FFPE_X120187554 [X15_624]


title: FFPE_X118121981 [X40_557_plate_6]


title: FFPE_X121962622 [X58_158_plate2]


title: FFPE_X118121981 [X41_558_plate_6]


title: FFPE_X121962622 [X59_159_plate2]


title: FFPE_X110722330 [X79_689]


title: FFPE_X118022769 [X6_523_plate_6]


title: FFPE_X112022376 [X36_1013]


title: FFPE_X117340587 [X57_479_plate5]


title: FFPE_X112068955 [X55_155_plate2]


title: FFPE_X118022769 [X7_524_plate_6]


title: FFPE_X120063200 [X52_904_plate9]


title: FFPE_X115457105 [X49_149_plate2]


title: FFPE_X120187554 [X14_623]


title: FFPE_X118501496 [X57_157_plate2]


title: FFPE_X110722330 [X80_690]


title: FFPE_X112579616 [X47_147_plate2]


title: FFPE_X120063200 [X51_903_plate9]


title: FFPE_X120439768 [X52_152_plate2]


title: FFPE_X115270056 [X50_150_plate2]


title: FFPE_X111023471 [X93_1070]


title: FFPE_X115457105 [X48_148_plate2]


title: FFPE_X120560652 [X44_144_plate2]


title: FFPE_X113416040 [X40_140_plate2]


title: FFPE_X117522296 [X71_371_PLATE4]


title: FFPE_X113416040 [X41_141_plate2]


title: FFPE_X117522296 [X72_372_PLATE4]


title: FFPE_X111905572 [X38_138_plate2]


title: FFPE_X115653622 [X69_369_PLATE4]


title: FFPE_X119891205 [X22_999]


title: FFPE_X116340059 [X62_789]


title: FFPE_X117302775 [X49_659]


title: FFPE_X119879849 [X37_137_plate2]


title: FFPE_X116673237 [X35_135_plate2]


title: FFPE_X115761012 [X34_1011]


title: FFPE_X116340059 [X63_790]


title: FFPE_X115653622 [X70_370_PLATE4]


title: FFPE_X110509638 [X75_685]


title: FFPE_X119879849 [X34_834_plate9]


title: FFPE_X116503480 [X47_657]


title: FFPE_X116503480 [X48_658]


title: FFPE_X116868380 [X65_365_PLATE4]


title: FFPE_X120680471 [X45_655]


title: FFPE_X116868380 [X66_366_PLATE4]


title: FFPE_X110509638 [X76_686]


title: FFPE_X120389071 [X68_368_PLATE4]


title: FFPE_X116673237 [X36_136_plate2]


title: FFPE_X117302775 [X50_660]


title: FFPE_X121481776 [X63_164_plate2]


title: FFPE_X115761012 [X35_1012]


title: FFPE_X114785754 [X74_684]


title: FFPE_X110459353 [X33_1010]


title: FFPE_X120087028 [X32_1009]


title: FFPE_X113340432 [X83_693]


title: FFPE_X114785754 [X73_683]


title: FFPE_X118326622 [X85_1062]


title: FFPE_X117822232 [X29_1006]


title: FFPE_X115258288 [X46_146_plate2]


title: FFPE_X119756809 [X30_1007]


title: FFPE_X115258288 [X45_145_plate2]


title: FFPE_X113649928 [X54_154_plate2]


title: FFPE_X120300273 [X20_722_FFPE_Plate8]


title: FFPE_X115307259 [X31_1008]


title: FFPE_X116782353 [X8_216_FFPE_PLATE_3]


title: FFPE_X116782353 [X7_215_FFPE_PLATE_3]


title: FFPE_X113079156 [X28_1005]


title: FFPE_X117472223 [X38_D2_plate6_3]


title: FFPE_X115456100 [X13_622]


title: FFPE_X111882505 [X10_619]


title: FFPE_X115456100 [X12_621]


title: FFPE_X117472223 [X39_556_plate_6]


title: FFPE_X120300273 [X19_721_FFPE_Plate8]


title: FFPE_X119372444 [X5_213_FFPE_PLATE_3]


title: FFPE_X119372444 [X15_B3_plate6_3]


title: FFPE_X117958609 [X60_X.405_NHSIIplate5]


title: FFPE_X111882505 [X11_620]


title: FFPE_X112654994 [X25_325_PLATE4]


title: FFPE_X117507931 [X63_363_PLATE4]


title: FFPE_X112654994 [X26_326_PLATE4]


title: FFPE_X117507931 [X64_364_PLATE4]


title: FFPE_X110446640 [X41_341_PLATE4]


title: FFPE_X117290411 [X18_995]


title: FFPE_X113626069 [X71_681]


title: FFPE_X110446640 [X42_342_PLATE4]


title: FFPE_X112528158 [X23_323_PLATE4]


title: FFPE_X113626069 [X72_682]


title: FFPE_X121051814 [X11_202_FFPE_PLATE1]


title: FFPE_X112564784 [X79_181_plate2]


title: FFPE_X121004273 [X57_200_FFPE_PLATE1]


title: FFPE_X121051814 [X19_201_FFPE_PLATE1]


title: FFPE_X112564784 [X80_182_plate2]


title: FFPE_X118799221 [X49_891_plate9]


title: FFPE_X112528158 [X24_324_PLATE4]


title: FFPE_X110850867 [X37_554_plate_6]


title: FFPE_X118799221 [X50_892_plate9]


title: FFPE_X116829357 [X85_385_PLATE4]


title: FFPE_X113613150 [X84_384_PLATE4]


title: FFPE_X113326139 [X54_X.399_NHSIIplate5]


title: FFPE_X113128848 [X34_C10_plate6_3]


title: FFPE_X113613150 [X83_383_PLATE4]


title: FFPE_X116829357 [X86_386_PLATE4]


title: FFPE_X113128848 [X35_890_plate6_3]


title: FFPE_X110850867 [X36_893_plate6_3]


title: FFPE_X113326139 [X55_X.400_NHSIIplate5]


title: FFPE_X111952180 [X53_X.397_NHSIIplate5]


title: FFPE_X121937111 [X9_618]


title: FFPE_X117243076 [X77_179_plate2]


title: FFPE_X121937111 [X8_617]


title: FFPE_X111905778 [X42_142_plate2]


title: FFPE_X114921508 [X79_379_PLATE4]


title: FFPE_X118488994 [X45_345_PLATE4]


title: FFPE_X118071908 [X5_614]


title: FFPE_X115736840 [X65_1042]


title: FFPE_X112187769 [X6_615]


title: FFPE_X118488994 [X46_346_PLATE4]


title: FFPE_X113846214 [X85_187_plate2]


title: FFPE_X110768079 [X25_447_plate5]


title: FFPE_X111718572 [X82_382_PLATE4]


title: FFPE_X111718572 [X81_381_PLATE4]


title: FFPE_X121924083 [X53_1030]


title: FFPE_X118691370 [X82_184_plate2]


title: FFPE_X110359033 [X84_186_plate2]


title: FFPE_X113846214 [X86_188_plate2_.hGlue_3_0_v1.]


title: FFPE_X110768079 [X26_448_plate5]


title: FFPE_X118071908 [X96_H12_plate6_3]


title: FFPE_X110359033 [X83_185_plate2]


title: FFPE_X114921508 [X80_380_PLATE4]


title: FFPE_X119371851 [X47_347_PLATE4]


title: FFPE_X118691370 [X81_183_plate2]


title: FFPE_X120002456 [X5_210_plate2]


title: FFPE_X119371851 [X48_348_PLATE4]


title: FFPE_X112861808 [X21_998]


title: FFPE_X116879392 [X44_344_PLATE4]


title: FFPE_X116879392 [X43_343_PLATE4]


title: FFPE_X115354176 [X94_H10_plate6_3]


title: FFPE_X120002456 [X23_209_plate2]


title: FFPE_X115796058 [X32_C8_plate6_3]


title: FFPE_X119890406 [X80_1057]


title: FFPE_X115796058 [X33_C9_plate6_3]


title: FFPE_X120050378 [X92_H8_plate6_3_2]


title: FFPE_X120679103 [X49_349_PLATE4]


title: FFPE_X120050378 [X93_610_plate_6]


title: FFPE_X111741661 [X52_X.396_NHSIIplate5]


title: FFPE_X120679103 [X50_350_PLATE4]


title: FFPE_X116239401 [X70_680]


title: FFPE_X118325617 [X30_547_plate_6]


title: FFPE_X110558977 [X91_608_plate_6]


title: FFPE_X118325617 [X31_C7_plate6_3]


title: FFPE_X116840223 [X40_340_PLATE4]


title: FFPE_X113027729 [X37_337_PLATE4]


title: FFPE_X116239401 [X69_679]


title: FFPE_X116128681 [X68_678]


title: FFPE_X113027729 [X38_338_PLATE4]


title: FFPE_X121861400 [X20_997]


title: FFPE_X116128681 [X67_677]


title: FFPE_X115008334 [X94_196_plate2]


title: FFPE_X110558668 [X78_1055]


title: FFPE_X110558977 [X90_607_plate_6]


title: FFPE_X111255530 [X95_197_plate2]


title: FFPE_X119550236 [X91_193_plate2]


title: FFPE_X117845364 [X79_1056]


title: FFPE_X116082579 [X58_358_PLATE4]


title: FFPE_X115008334 [X93_195_plate2]


title: FFPE_X116082579 [X57_357_PLATE4]


title: FFPE_X116840223 [X39_339_PLATE4]


title: FFPE_X110520710 [X29_329_PLATE4]


title: FFPE_X110520710 [X30_330_PLATE4]


title: FFPE_X119719584 [X43_1020]


title: FFPE_X119513223 [X87_189_plate2]


title: FFPE_X119550236 [X92_194_plate2]


title: FFPE_X110249942 [X60_360_PLATE4]


title: FFPE_X119513223 [X88_190_plate2]


title: FFPE_X112186764 [X65_675]


title: FFPE_X116338092 [X53_353_PLATE4]


title: FFPE_X117020128 [X20_537_plate6_3_2]


title: FFPE_X116338092 [X54_354_PLATE4]


title: FFPE_X112186764 [X66_676]


title: FFPE_X111412612 [X89_191_plate2]


title: FFPE_X111571866 [X62_412_PLATE4]


title: FFPE_X117020128 [X21_B9_plate6_3]


title: FFPE_X120363336 [X77_1054]


title: FFPE_X112588309 [X29_546_plate_6]


title: FFPE_X113549190 [X30_X.374_NHSIIplate5]


title: FFPE_X111412612 [X90_192_plate2]


title: FFPE_X116337505 [X17_719_FFPE_Plate8]


title: FFPE_X111571866 [X61_411_PLATE4]


title: FFPE_X113549190 [X29_X.373_NHSIIplate5]


title: FFPE_X112588309 [X28_545_plate_6]


title: FFPE_X117674770 [X64_674]


title: FFPE_X115875874 [X27_327_PLATE4]


title: FFPE_X113721982 [X36_410_PLATE4]


title: FFPE_X113721982 [X35_409_PLATE4]


title: FFPE_X116924652 [X51_351_PLATE4]


title: FFPE_X114466815 [X88_605_plate_6]


title: FFPE_X116337505 [X18_720_FFPE_Plate8]


title: FFPE_X114466815 [X89_H5_plate6_3]


title: FFPE_X115875874 [X28_328_PLATE4]


title: FFPE_X116924652 [X52_352_PLATE4]


title: FFPE_X120777516 [X31_405_PLATE4]


title: FFPE_X119730450 [X86_H2_plate6_3]


title: FFPE_X119730450 [X87_H3_plate6_3]


title: FFPE_X117447124 [X58_668]


title: FFPE_X120777310 [X51_286_plate6_3]


title: FFPE_X117447124 [X57_667]


title: FFPE_X114148257 [X51_259_FFPE_PLATE3]


title: FFPE_X121236435 [X33_407_PLATE4]


title: FFPE_X111486166 [X64_1041]


title: FFPE_X112714874 [X26_C2_plate6_3]


title: FFPE_X114148257 [X52_260_FFPE_PLATE3]


title: FFPE_X113708694 [X49_257_FFPE_PLATE3]


title: FFPE_X120978852 [X70_495_plate5]


title: FFPE_X113941818 [X75_1052]


title: FFPE_X120978852 [X71_496_plate5]


title: FFPE_X119063615 [X22_322_PLATE4]


title: FFPE_X120777310 [X77_285_FFPE_PLATE3]


title: FFPE_X119222501 [X16_404_PLATE4]


title: FFPE_X113708694 [X50_258_FFPE_PLATE3]


title: FFPE_X116732318 [X61_671]


title: FFPE_X115444077 [X96_304_FFPE_PLATE3]


title: FFPE_X118846485 [X84_G12_plate6_3]


title: FFPE_X116732318 [X62_672]


title: FFPE_X119222501 [X15_403_PLATE4]


title: FFPE_X111741661 [X51_X.395_NHSIIplate5]


title: FFPE_X112714874 [X27_C3_plate6_3]


title: FFPE_X121861503 [X19_996]


title: FFPE_X121099161 [X76_1053]


title: FFPE_X121236435 [X34_408_PLATE4]


title: FFPE_X119063615 [X21_321_PLATE4]


title: FFPE_X115444077 [X52_E4_plate6_3]


title: FFPE_X116419615 [X78_595_plate_6]


title: FFPE_X113906815 [X61_X.393_NHSIIplate5]


title: FFPE_X121198682 [X16_718_FFPE_Plate8]


title: FFPE_X120714865 [X74_1051]


title: FFPE_X116419615 [X79_596_plate_6]


title: FFPE_X118393141 [X6_306_PLATE4]


title: FFPE_X113906815 [X62_X.394_NHSIIplate5]


title: FFPE_X117650633 [X74_591_plate_6]


title: FFPE_X118452840 [X76_593_plate_6]


title: FFPE_X117650633 [X75_592_plate_6]


title: FFPE_X121198682 [X15_717_FFPE_Plate8]


title: FFPE_X118191315 [X61_1038]


title: FFPE_X116275409 [X8_402_PLATE4]


title: FFPE_X118393141 [X5_305_PLATE4]


title: FFPE_X118381227 [X27_X.371_NHSIIplate5]


title: FFPE_X111879121 [X73_373_PLATE4]


title: FFPE_X117423708 [X30_827_plate9]


title: FFPE_X117553637 [X12_312_PLATE4]


title: FFPE_X119644672 [X23_1000]


title: FFPE_X121859639 [X49_471_plate5]


title: FFPE_X117553637 [X11_311_PLATE4]


title: FFPE_X111448869 [X46_254_FFPE_PLATE3]


title: FFPE_X111448869 [X45_253_FFPE_PLATE3]


title: FFPE_X117423708 [X31_828_plate9]


title: FFPE_X119645059 [X80_G8_plate6_3]


title: FFPE_X118381227 [X28_X.372_NHSIIplate5]


title: FFPE_X111879121 [X74_374_PLATE4]


title: FFPE_X118452840 [X77_G5_plate6_3]


title: FFPE_X121859639 [X50_472_plate5]


title: FFPE_X110705743 [X77_377_PLATE4]


title: FFPE_X122151014 [X47_869_plate9]


title: FFPE_X121014486 [X73_G1_plate6_3]


title: FFPE_X110705743 [X78_378_PLATE4]


title: FFPE_X111546149 [X68_F8_plate6_3]


title: FFPE_X121611852 [X20_320_PLATE4]


title: FFPE_X114968983 [X73_1050]


title: FFPE_X121014486 [X72_F12_plate6_3]


title: FFPE_X120592374 [X10_310_PLATE4]


title: FFPE_X113817507 [X68_493_plate5]


title: FFPE_X122151014 [X48_870_plate9]


title: FFPE_X122150833 [X75_375_PLATE4]


title: FFPE_X117624735 [X67_492_plate5]


title: FFPE_X122150833 [X76_376_PLATE4]


title: FFPE_X111546149 [X69_F9_plate6_3]


title: FFPE_X117624735 [X66_491_plate5]


title: FFPE_X113817507 [X69_494_plate5]


title: FFPE_X116743845 [X65_490_plate5]


title: FFPE_X116743845 [X64_489_plate5]


title: FFPE_X111853277 [X24_1001]


title: FFPE_X121820155 [X39_247_FFPE_PLATE3]


title: FFPE_X117077513 [X59_669]


title: FFPE_X117077513 [X60_670]


title: FFPE_X121744178 [X65_582_plate_6]


title: FFPE_X121744178 [X64_581_plate_6]


title: FFPE_X112749823 [X43_653]


title: FFPE_X114610457 [X67_F7_plate6_3]


title: FFPE_X112749823 [X44_654]


title: FFPE_X121807279 [X62_487_plate5]


title: FFPE_X119814776 [X14_531_plate_6]


title: FFPE_X115863445 [X48_X.392_NHSIIplate5]


title: FFPE_X114208858 [X45_X.389_NHSIIplate5]


title: FFPE_X121085752 [X9_986]


title: FFPE_X119899554 [X62_579_plate_6]


title: FFPE_X119814776 [X15_532_plate_6]


title: FFPE_X121946422 [X72_1049]


title: FFPE_X121048430 [X5_522_plate_6]


title: FFPE_X115863445 [X47_X.391_NHSIIplate5]


title: FFPE_X113472989 [X57_E9_plate6_3]


title: FFPE_X114208858 [X46_X.390_NHSIIplate5]


title: FFPE_X120568486 [X88_296_FFPE_PLATE3]


title: FFPE_X119899554 [X63_F3_plate6_3]


title: FFPE_X110284224 [X58_E10_plate6_3]


title: FFPE_X113472989 [X56_855_plate6_3_2]


title: FFPE_X114069471 [X49_1026]


title: FFPE_X118298258 [X94_519_plate5]


title: FFPE_X113001988 [X17_534_plate_6]


title: FFPE_X121048430 [X96_521_plate5]


title: FFPE_X117128179 [X23_485_FFPE_PLATE1]


title: FFPE_X111386052 [X51_1028]


title: FFPE_X120568486 [X87_295_FFPE_PLATE3]


title: FFPE_X113001988 [X16_533_plate_6]


title: FFPE_X111594901 [X70_1047]


title: FFPE_X116983071 [X55_E7_plate6_3]


title: FFPE_X118846485 [X85_602_plate_6]


title: FFPE_X114782430 [X13_715_FFPE_Plate8]


title: FFPE_X118475251 [X5_484_FFPE_PLATE1]


title: FFPE_X114782430 [X14_716_FFPE_Plate8]


title: FFPE_X115315565 [X69_1046]


title: FFPE_X116983071 [X54_571_plate6_3]


title: FFPE_X120988756 [X48_1025]


title: FFPE_X111802340 [X86_294_FFPE_PLATE3]


title: FFPE_X113436878 [X82_290_FFPE_PLATE3]


title: FFPE_X110776700 [X61_788]


title: FFPE_X112610946 [X76_284_FFPE_PLATE3]


title: FFPE_X118475251 [X61_483_plate5]


title: FFPE_X110776700 [X60_787]


title: FFPE_X120532229 [X56_1033]


title: FFPE_X112610946 [X75_283_FFPE_PLATE3]


title: FFPE_X120156425 [X17_317_PLATE4]


title: FFPE_X120156425 [X18_318_PLATE4]


title: FFPE_X118794711 [X71_279_FFPE_PLATE3]


title: FFPE_X118794711 [X72_280_FFPE_PLATE3]


title: FFPE_X112348253 [X19_441_plate5]


title: FFPE_X116620284 [X24_446_plate5]


title: FFPE_X112348253 [X20_442_plate5]


title: FFPE_X120941790 [X42_652]


title: FFPE_X113767943 [X73_281_FFPE_PLATE3]


title: FFPE_X117941355 [X57_1034]


title: FFPE_X116620284 [X23_445_plate5]


title: FFPE_X113321835 [X21_443_plate5]


title: FFPE_X119073725 [X84_509_plate5]


title: FFPE_X113767943 [X74_282_FFPE_PLATE3]


title: FFPE_X120941790 [X41_651]


title: FFPE_X113321835 [X22_444_plate5]


title: FFPE_X116958178 [X57_265_FFPE_PLATE3]


title: FFPE_X117635438 [X61_269_FFPE_PLATE3]


title: FFPE_X111495065 [X45_268_plate6_3]


title: FFPE_X116958178 [X58_266_FFPE_PLATE3]


title: FFPE_X118757589 [X49_E1_plate6_3]


title: FFPE_X117372006 [X70_F10_plate6_3]


title: FFPE_X121957022 [X56_264_FFPE_PLATE3]


title: FFPE_X112384364 [X12_714_FFPE_Plate8]


title: FFPE_X113110074 [X13_313_PLATE4]


title: FFPE_X119448670 [X17_439_plate5]


title: FFPE_X119448670 [X18_440_plate5]


title: FFPE_X118757589 [X48_D12_plate6_3]


title: FFPE_X112384364 [X11_713_FFPE_Plate8]


title: FFPE_X110196127 [X64_67_FFPE_PLATE1]


title: FFPE_X119813462 [X46_D10_plate6_3]


title: FFPE_X115476217 [X65_70_FFPE_PLATE1]


title: FFPE_X115476217 [X66_71_FFPE_PLATE1]


title: FFPE_X119874103 [X95_1072]


title: FFPE_X115816528 [X7_709_FFPE_Plate8]


title: FFPE_X112396896 [X47_271_plate6_3]


title: FFPE_X113371870 [X52_54_FFPE_PLATE1]


title: FFPE_X121957022 [X55_263_FFPE_PLATE3]


title: FFPE_X111763994 [X61_63_FFPE_PLATE1]


title: FFPE_X111763994 [X60_62_FFPE_PLATE1]


title: FFPE_X117372006 [X71_F11_plate6_3]


title: FFPE_X110246000 [X51_53_FFPE_PLATE1]


title: FFPE_X113110074 [X14_314_PLATE4]


title: FFPE_X114645921 [X27_1004]


title: FFPE_X120987030 [X55_1032]


title: FFPE_X110246000 [X50_52_FFPE_PLATE1]


title: FFPE_X115695351 [X15_437_plate5]


title: FFPE_X117707644 [X59_61_FFPE_PLATE1]


title: FFPE_X115695351 [X16_438_plate5]


title: FFPE_X113568411 [X44_X.388_NHSIIplate5]


title: FFPE_X121573481 [X26_1003]


title: FFPE_X116005023 [X69_75_FFPE_PLATE1]


title: FFPE_X110245716 [X43_465_plate5]


title: FFPE_X117707644 [X58_60_FFPE_PLATE1]


title: FFPE_X118720842 [X59_1036]


title: FFPE_X120857204 [X71_77_FFPE_PLATE1]


title: FFPE_X113568411 [X43_X.387_NHSIIplate5]


title: FFPE_X120857204 [X70_76_FFPE_PLATE1]


title: FFPE_X117502179 [X83_508_plate5]


title: FFPE_X119801960 [X81_506_plate5]


title: FFPE_X116428102 [X62_64_FFPE_PLATE1]


title: FFPE_X117634536 [X68_73_FFPE_PLATE1]


title: FFPE_X110858604 [X19_536_plate_6]


title: FFPE_X113422027 [X8_5_plate2]


title: FFPE_X112171526 [X56_58_FFPE_PLATE1]


title: FFPE_X113035623 [X44_46_FFPE_PLATE1]


title: FFPE_X117502179 [X82_507_plate5]


title: FFPE_X119256542 [X11_988]


title: FFPE_X113422027 [X12_14_FFPE_PLATE1]


title: FFPE_X119738805 [X92_517_plate5]


title: FFPE_X111041372 [X13_990]


title: FFPE_X117634536 [X67_72_FFPE_PLATE1]


title: FFPE_X119738805 [X93_518_plate5]


title: FFPE_X116428102 [X9_A9_plate6_3]


title: FFPE_X111593272 [X81_955]


title: FFPE_X118998753 [X46_48_FFPE_PLATE1]


title: FFPE_X118998753 [X47_49_FFPE_PLATE1]


title: FFPE_X121791822 [X56_783]


title: FFPE_X110882280 [X59_786]


title: FFPE_X115904625 [X9_11_FFPE_PLATE1]


title: FFPE_X112622551 [X5_982]


title: FFPE_X118127187 [X39_41_FFPE_PLATE1]


title: FFPE_X114031822 [X54_781]


title: FFPE_X118127187 [X38_40_FFPE_PLATE1]


title: FFPE_X112073731 [X42_464_plate5]


title: FFPE_X121791822 [X57_784]


title: FFPE_X121583803 [X14_991]


title: FFPE_X121716270 [X15_992]


title: FFPE_X118065091 [X6_708_FFPE_Plate8]


title: FFPE_X112085645 [X53_780]


title: FFPE_X119413109 [X6_2_plate2]


title: FFPE_X118708559 [X36_38_FFPE_PLATE1]


title: FFPE_X118065091 [X5_707_FFPE_Plate8]


title: FFPE_X119762275 [X39_461_plate5]


title: FFPE_X119762275 [X40_462_plate5]


title: FFPE_X118708559 [X37_39_FFPE_PLATE1]


title: FFPE_X117902744 [X7_984]


title: FFPE_X112085645 [X52_779]


title: FFPE_X114901906 [X51_778]


title: FFPE_X112073731 [X41_463_plate5]


title: FFPE_X116568759 [X34_36_FFPE_PLATE1]


title: FFPE_X119353950 [X40_42_FFPE_PLATE1]


title: FFPE_X117790672 [X17_994]


title: FFPE_X113973746 [X10_A10_plate6_3]


title: FFPE_X117039695 [X95_981]


title: FFPE_X117802424 [X13_530_plate_6]


title: FFPE_X113134938 [X40_X.384_NHSIIplate5]


title: FFPE_X121511223 [X35_457_plate5]


title: FFPE_X113973746 [X11_A11_plate6_3]


title: FFPE_X119579192 [X70_773_FFPE_Plate8]


title: FFPE_X113134938 [X39_X.383_NHSIIplate5]


title: FFPE_X119484575 [X45_467_plate5]


title: FFPE_X119579192 [X71_774_FFPE_Plate8]


title: FFPE_X115096078 [X50_1027]


title: FFPE_X114619508 [X68_771_FFPE_Plate8]


title: FFPE_X114767029 [X48_50_FFPE_PLATE1]


title: FFPE_X117790157 [X32_454_plate5]


title: FFPE_X114619508 [X69_772_FFPE_Plate8]


title: FFPE_X117790157 [X31_453_plate5]


title: FFPE_X118353834 [X29_451_plate5]


title: FFPE_X115025436 [X28_450_plate5]


title: FFPE_X121511223 [X36_458_plate5]


title: FFPE_X114767029 [X49_51_FFPE_PLATE1]


title: FFPE_X110602614 [X62_764_FFPE_Plate8]


title: FFPE_X112230607 [X6_983]


title: FFPE_X111653152 [X16_993]


title: FFPE_X117741745 [X65_768_FFPE_Plate8]


title: FFPE_X117741745 [X89_1_FFPE_PLATE1]


title: FFPE_X115025436 [X27_449_plate5]


title: FFPE_X119484575 [X46_468_plate5]


title: FFPE_X120215294 [X60_762_FFPE_Plate8]


title: FFPE_X119048111 [X32_34_FFPE_PLATE1]


title: FFPE_X117320161 [X63_765_FFPE_Plate8]


title: FFPE_X118353834 [X30_452_plate5_2]


title: FFPE_X110123057 [X7_8_FFPE_PLATE1]


title: FFPE_X112319958 [X94_979]


title: FFPE_X121954110 [X54_756_FFPE_Plate8]


title: FFPE_X114679447 [X52_1029]


title: FFPE_X115881758 [X38_X.382_NHSIIplate5]


title: FFPE_X121510630 [X50_752_FFPE_Plate8]


title: FFPE_X121510630 [X49_751_FFPE_Plate8]


title: FFPE_X112634362 [X27_29_FFPE_PLATE1]


title: FFPE_X110726041 [X42_744_FFPE_Plate8]


title: FFPE_X112049534 [X45_747_FFPE_Plate8]


title: FFPE_X113194053 [X43_745_FFPE_Plate8]


title: FFPE_X121510527 [X25_27_FFPE_PLATE1]


title: FFPE_X112634362 [X26_28_FFPE_PLATE1]


title: FFPE_X121009716 [X58_760_FFPE_Plate8]


title: FFPE_X121205615 [X51_753_FFPE_Plate8]


title: FFPE_X113368801 [X25_1002]


title: FFPE_X121954110 [X53_755_FFPE_Plate8]


title: FFPE_X119823572 [X55_757_FFPE_Plate8]


title: FFPE_X115449211 [X93_978]


title: FFPE_X114390892 [X47_749_FFPE_Plate8]


title: FFPE_X112782507 [X37_739_FFPE_Plate8]


title: FFPE_X112782507 [X38_740_FFPE_Plate8]


title: FFPE_X115881758 [X37_X.381_NHSIIplate5]


title: FFPE_X113752287 [X55_665]


title: FFPE_X112049534 [X46_748_FFPE_Plate8]


title: FFPE_X121205615 [X52_754_FFPE_Plate8]


title: FFPE_X110726041 [X41_743_FFPE_Plate8]


title: FFPE_X110725860 [X91_1068]


title: FFPE_X112570050 [X23_818_plate9]


title: FFPE_X113752287 [X56_666]


title: FFPE_X120253833 [X36_738_FFPE_Plate8]


title: FFPE_X111565982 [X38_460_plate5]


title: FFPE_X120253833 [X35_737_FFPE_Plate8]


title: rec8 delta input rep2

status: Public on Jul 18 2017

type: SRA

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
H7660_H7772_Red1_ChIP_reps.wig
H7660_H7772_Hop1_ChIP_reps.wig

library_source: genomic

data_processing:
Sequencing reads were mapped to SacCer3 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). The one condition adjusted was to only collect information about reads that mapped to a single position in the genome.
Reads from two biological replicates were extended towards 3’ ends to a final length of 150 bp using MACS-2.1.0 (https://github.com/taoliu/MACS). MACS2 was also used to remove predicted PCR duplicates.
Bedgraph files from MACS2 were converted into variableStep wiggle files.
To create normalized wiggle files: Median coverage of all base positions in the ChIP sample was calculated. The coverage at each position was then divided by the calculated median. The same division was also performed for the input sample, followed by subtraction of the input from the ChIP sample at each position.
Genome_build: SacCer3
Supplementary_files_format_and_content: Wiggle file: ChIP enrichment at each base position

organism: Saccharomyces cerevisiae

source_name: input for rec8 delta anti-Red1 rep2 and rec8 delta anti-Hop1 rep2

growth_protocol: To induce synchronous meiosis, strains were inoculated at OD600 = 0.3 in BYTA medium for 16.5 hours at 30°C. Then cultures were washed twice with water and resuspended into SPO medium at OD600 = 1.9 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013).
Library preparation was performed using Illumina TruSeq DNA Sample Prep Kits v1 but adaptors were used at 1:20 dilution. Amplified ChIP DNA between 300 and 500bp was gel purified on 1.8% agarose and sequentially quantified using the Qubit assay HS kit as well as an Agilent 2100 Bioanalyzer. Fragments were sequenced on an Illumina HiSeq 2500 instrument using a 51-bp single-end sequencing protocol.

tag: strain

tag: meiotic time point

value: 3 hour

tag: genotype


title: FFPE_X112570050 [X22_817_plate9]


title: FFPE_X119206089 [X33_735_FFPE_Plate8]


title: FFPE_X111565982 [X37_459_plate5]


title: FFPE_X119206089 [X34_736_FFPE_Plate8]


title: FFPE_X113368486 [X30_732_FFPE_Plate8]


title: FFPE_X113368486 [X29_731_FFPE_Plate8]


title: rec8 delta anti-Red1 rep2

source_name: ChIP for rec8 delta input rep2

tag: antibody


title: FFPE_X110614116 [X33_455_plate5]


title: H6200 Red1 ChIP in rec8 delta biological replicate 1

status: Public on Aug 06 2015

data_processing:
Sequencing reads were mapped to the S288C (sacCer2) genome using Bowtie unless specified otherwise, only perfect matches across all 51bp were considered during mapping. Multiple alignments were not taken into account, which means each read only mapped to one location in the genome. Reads were also mapped to the SK1 genome with similar results. Reads were extended towards 3’ ends to a final length of 200bp in MACS (http://liulab.dfci.harvard.edu/MACS/) (Zhang et al., 2008).
To identify axis protein enriched regions (peaks), the observed sequence read tag density along the chromosome was normalized against the measured background (INPUT DNA). Median coverage of all base positions in the ChIP sample was calculated. The coverage at each position was then divided by the calculated median. The same division was also performed for the input sample, followed by subtraction of the input from the ChIP sample at each position. Peak identification was performed using MACS (http://liulab.dfci.harvard.edu/MACS/) (Zhang et al., 2008) using a P-value of 1e-15. Peak summits were defined as the local maximum of read coverage within Red1 peaks.
Genome_build: SacCer2
Supplementary_files_format_and_content: Wiggle file: ChIP enrichment at each base position.

tag: meiotic timepoint

value: rec8 delta

value: Anti-Red1 (S. Roeder)


title: FFPE_X121988357 [X34_X.378_NHSIIplate5]


title: FFPE_X110110241 [X28_30_FFPE_PLATE1]


title: H7660 Input

source_name: Input of H7660


title: Infected_rep2

status: Public on Mar 15 2017

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 20 µm/pixel resolution and analyzed with GenePix software V5.2 (MDS).

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47)

source_name: A549, infected

label_protocol: Purified total RNA was amplified and Cy-labeled using the dual-color QuickAmp kit (Agilent Technologies, Palo Alto, CA) following the kit instructions.

growth_protocol: A549 cells were seeded in culture vessels in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% Glutamax, 100 U/ml penicillin, 100 μg/ml streptomycin GibcoBRL 24 hours before infection with Human coronavirus 229E with an MOI of 1.

extract_protocol: ARCTURUS® PicoPure® RNA Isolation Kit (life technologies)

treatment_protocol: For the infection, cells were incubated with DMEM (supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% Glutamax, 100 U/ml penicillin, 100 μg/ml streptomycin) containing HCoV-229E at a multiplicity of infection (MOI) of 1 and incubated  at 33°C.  1 hour post inoculation the supernatant was removed and replaced with the according fresh growth medium and incubated at 33°C for 48 hours. Control cells were mock infected and also incubated at 33°C. For the Laser Micro Dissection (LMD) cells were stained with antibodies raised against the viral N protein as well as human DNA Polymerase II phosporylated at Serin 2. Afterwards 4 different cell populations (indicated under Treatment groups) have been separated with an Leica LMD6000 system, followed by RNA isolation.

tag: cell type

value: A549 cells

tag: position

value: Infected


title: H6200 Input

source_name: Input of H6200


title: FFPE_X110110241 [X29_31_FFPE_PLATE1]

tag: tissue

tag: age at diagnosis


title: FFPE_X110614116 [X34_456_plate5_2]

tag: year of diagnosis

tag: estrogen receptor status


title: FFPE_X115976993 [X39_741_FFPE_Plate8]

tag: alcohol intake

tag: microarray batch


title: FFPE_X121988357 [X33_X.377_NHSIIplate5]

tag: patient id


title: Uninfected_rep2

source_name: A549, uninfected

value: Uninfected


title: Distant_rep1

source_name: A549, distant

value: Distant


title: Infected_rep1


title: FFPE_X116437722 [X79_89_FFPE_PLATE1]


title: Distant_rep2


title: Adjacent_rep2

source_name: A549, adjacent

value: Adjacent


title: H4471 Input biological replicate 2

source_name: Input of H4471 biological replicate 2


title: H4471 Rec8 ChIP biological replicate 2

source_name: Red1 ChIP of H4471 biological replicate 2

value: Anti-3HA (Cat#:11867431001, Roche Applied Science)


title: H4471 Rec8 ChIP biological replicate 1

source_name: Red1 ChIP of H4471 biological replicate 1


title: Uninfected_rep1


title: FFPE_X115976993 [X40_742_FFPE_Plate8]

value: breast tumor-adjacent normal

value: Positive


title: H4471 Input biological replicate 1

source_name: Input of H4471 biological replicate 1


title: H7660 Red1 ChIP in rec8 delta biological replicate 2


title: H6408 Hop1 ChIP biological replicate 1

source_name: Hop1 ChIP of H6408 biological replicate 1

value: wild type

value: Anti-Hop1 (N. Hollingsworth)


title: H119 Input biological replicate 2

source_name: Input of H119 biological replicate 2


title: H119 Red1 ChIP biological replicate 1

source_name: Red1 ChIP of H119 biological replicate 1


title: H119 Input biological replicate 1

source_name: Input of H119 biological replicate 1


title: Adjacent_rep1


title: H119 Red1 ChIP biological replicate 2

source_name: Red1 ChIP of H119 biological replicate 2


title: H6408 Input biological replicate 1

source_name: Input of H6408 biological replicate 1


title: Obese 3

status: Public on Feb 11 2015

city: Kajang

first: Hien Fuh

last: Ng

state: SELANGOR

country: Malaysia

institute: UTAR

description: Sal

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-Seq reads were aligned to hg19 genome build, with gene location information from NCBI, using Tophat version 2.0.4 with the following options --b2-very-sensitive --library-type fr-firststrand --transcriptome-index gene_index/gene and the first stage aligner software is using Bowtie version 2.0.0.6
Aligned BAM files generated from Tophat was imported into Genespring (Agilent Technologies) version 12.5 for PCR duplicates removal and quality score filtering, whereby reads with average PHRED score less than 30 is removed
Reads passing the filter were used to perform quantification of gene expression in Genespring (Agilent Technologies) version 12.5
After quantification, normalization with DESeq is performed in Genespring (Agilent Technologies) version 12.5
Genome_build: hg19
Supplementary_files_format_and_content: Log2 normalized expression values of known genes and novel genes identified by Genespring (Agilent Technologies) version 12.5 on default setting for identification of novel genes from imported BAM files
Supplementary_files_format_and_content: Transcript and Exon reads count with chromosomal location and annotation

source_name: Omental adipose tissue

extract_protocol:
Omental adipose tissues were obtained from the patients. The tissue specimens were preserved in Allprotect Tissue Reagent (Qiagen). RNA purification was performed using RNeasy Lipid Tissue Mini Kit (Qiagen); on-column DNase digestion was carried out with RNase-free DNase (Qiagen).
One-µg of total RNA from each sample was used for library preparation for RNA-Seq, using the SureSelect Strand-specific RNA Library Prep Kit (Agilent).
Strand-specific, Illumina HiSeq 2000 2 X 100 protocol

value: F

tag: grouping

value: Obese


title: Obese 1

description: Hoh

tag: gender

value: M


title: Obese 2

description: Har

tag: age


title: Lean 4

description: Mal

value: Lean


title: Lean 3

description: Goh


title: Lean 2

description: Hz


title: Lean 1

description: Yap


title: LSEC

status: Public on Jan 01 2015

city: Leuven

first: Marc

last: Jacquemin

address: O&N I Herestraat 49 - bus 913

country: Belgium

institute: KU Leuven

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.6 with default settings
The abundance data was generated with cufflinks v.2.0.2 using the tool cuffcompare.
Genome_build: hg19 (NCBI Homo sapiens build 37.2)
Supplementary_files_format_and_content: the tmap files (output of cufflinks) with abundance measurements.

source_name: LSEC

growth_protocol: primary cells

extract_protocol:
To prepare cell extracts, the cells were pelleted by centrifugation and immediately lysed in variable amounts of CelLytic M cell lysis reagent (lysis buffer; Sigma-Aldrich) containing 1x protease inhibitor (Halt Protease inhibitor Single-use Cocktail; Thermo Scientific; Belgium) for 15 minutes on ice followed by 5 minutes centrifugation at 18,000g (13,000 rpm) at 4°C to remove the debris. The lysate was then used for further analysis.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kits v2  RS-122-2001

treatment_protocol: Human LSECs and hepatocytes were purified from normal liver cell suspension discarded during isolation of hepatocytes collected for transplantation. Briefly, liver cells were dispersed with collagenase and hepatocytes were isolated by filtration and low speed centrifugation.18 The cells remaining in the supernatant were collected and cryopreserved. In addition, LSECs at passage 1 were purchased from ScienCell (San Diego, CA) and human umbilical vein endothelial cells (HUVECs-passage 1) and hepatocytes from Promocell (Heidelberg, Germany). CHO cells transduced with an expression vector for FVIII were kindly provided by A. Benhida (University of Leuven, Belgium).19 The study was approved by the University of Louvain Ethics committee.

value: Liver sinusoidal endothelial cells

tag: passages


title: islet preparation 5 under palmitate exposure

status: Public on Jan 09 2014

city: Bruxelles

first: Miriam

last: Cnop

address: Route de Lennik 808 CP618

department: Faculté de Medecine

institute: Université Libre de Bruxelles

description: Sample 10

data_processing:
Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCh37
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

molecule: polyA RNA

source_name: islets of Langerhans

growth_protocol: Human islet preparations were obtained from heart-beating organ donors with no medical history of diabetes or metabolic disorders. The islets were isolated using collagenase digestion and density gradient purification. They were cultured in M199 culture medium containing 5.5 mM glucose and shipped within 1-5 days following isolation. Upon arrival, the human islet cells were cultured in Ham's F-10 medium containing 6.1 mM glucose, 10% fetal bovine serum (FBS), 2 mM GlutaMAX, 50 μM 3-isobutyl-1-methylxanthine, 1% BSA, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands), which favors purification of all RNA molecules longer than 200 nucleotides and sample preparation was done as described by the manufacturer (Illumina, Eindhoven, The Netherlands). Briefly, mRNA was purified from two μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 3’-monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bioanalyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 μL cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on one sequencing lane of an Illumina Genome Analyzer II system (GAII, Illumina).

treatment_protocol: The islets were exposed or not to 0.5 mM palmitate in the same medium without FBS for 2 days (8; 13; 31). The serum-free culture conditions have previously been validated (32). Human islet viability, assessed after Hoechst 33342 and propidium iodide staining (see below), was similar in serum-free or 10% FBS-containing medium (respectively 93±1% vs 95±1% viable cells after 72 h, n=8, p=0.3).

value: islets of Langerhans

tag: treatment

value: palmitate


title: islet preparation 3 under palmitate exposure

description: Sample 6


title: islet preparation 4 under control condition

description: Sample 7

value: control


title: islet preparation 4 under palmitate exposure

description: Sample 8


title: islet preparation 5 under control condition

description: Sample 9


title: islet preparation 3 under control condition

description: Sample 5


title: miR-142-3p-1 rep. 2

status: Public on Jul 31 2015

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the default quantile normalisation with R/bioconductor package lumi version 2.15.1

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: 5x10^5 HEK293 cells were seeded in each well of a 6-well plate and grown in DMEM supplemented with 10% fetal bovine serum

extract_protocol: Total RNA was extracted 2 days post transfection using Trizol reagent. RNA was further purified using Qiagen Rneasy MinElute Cleanup Kit.

treatment_protocol: Cells were transfected after 24 h of seeding with 50 pmol of each mirVana miRNA mimic using Lipofectamine RNAiMAX.

tag: cell line

value: Embryonic kidney cells

tag: transfected with


title: miR-K10a rep. 3


title: islet preparation 2 under palmitate exposure

description: Sample 4


title: Ago2 PAR-CLIP BC-3 cells lane 2

status: Public on Nov 16 2011

description:
Ago2 ribonucleoprotein complexes
KSHV (HHV8)

data_processing:
The reads from the Ago2 PAR-CLIP deep sequencing libraries were stripped of the 3’ adapter sequences using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).  Reads that were less than 13nt in length or contained an ambiguous nucleotide were discarded. The remaining reads were aligned to the human (hg19), the KSHV (NC_009333) and/or EBV genomes (NC_009334) genomes, with up to 3 mismatches allowed, by the Bowtie algorithm (Langmead et al., 2009).  Mapped locations were only reported for those with the minimum number of observed mismatches for each read.  All T to C mismatches between the RNA fragment and the genome were subtracted from the mismatch count for each mapped location.  After subtraction only reads that mapped to a single genomic location at the minimum number of mismatches were used for further analysis.  The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1 (Hubbard et al., 2007).  If a read mapped to a location representing multiple categories, it was reported to belong to the category based on the following order of preference: 3’UTR, coding sequence, 5’UTR, intron, non-coding RNA, intergenic. Defining Ago2 binding sites by PARalyzer: Consecutive nucleotides with higher likelihood of T to C conversion than non-conversion and a read depth of at least 5 are considered “interaction sites” and were extended to clusters, which include all adjacent positions with a read depth of at least 5. Clusters were searched for miRNA seed matches to all miRNAs with significant expression in the matched small RNA sequencing samples. Seed matches were designated according to standard nomenclature (Bartel, 2009): for e.g. “7mer1A” seed matches, nts 2-7 of the miRNA are perfectly base paired with the target and the match is followed by an A in the 3’UTR. For e.g. “7mer2-8 seed matches, nts 2-8 of the miRNA are perfectly base paired. We designated different seed types for up to 12mer seed matches. Seed matches that were more extensive were also designated as “12mer” seed matches. PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer
The columns for the small RNA data bed files are the following info for PAR-CLIP clusters defined by PARalyzer:
1. Chromosome
2. Start
3. End
4. Cluster ID
5. Conversion Event Count
6. Strand

source_name: primary effusion lymphoma cell line BC-3

growth_protocol: BC-1 and BC-3 cell lines were cultured in RPMI1640 medium supplemented with 10mM Hepes (pH7.4), 1mM sodium pyruvate, 50 mM b-Mercaptoethanol, 10 mg/ml gentamicin and 10% fetal bovine serum (FBS) for BC-1 or 15% FBS for BC-3.

extract_protocol: Cell pellets were thawed on ice, resuspended in NP40 lysis buffer and incubated on ice for 20 min. The cell lysate was cleared by centrifugation. RNase T1 (Fermentas) was added to the cleared cell lysates and the reaction mixture was incubated at 22ÂºC for 15 min and subsequently cooled for 5 min on ice before addition of antibody-conjugated magnetic beads. Immunoprecipitates were RNase T1-digested and Ago2-complexes were further purified by SDS page and associated RNAs were liberated by protease K digest and carried through a small RNA library preparation protocol with barcoded 5âadaptors (BC-1: TCAAG, BC-3: TTGGC) . Resulting PCR products were purified from 10% TBE gels and each product was sequenced on two lanes on the Illumina GAII platform.

treatment_protocol: ~1.5 x 10^9 BC-3 cells or ~3 x 10^9 BC-1 cells were labeled with 100mM 4-Thiouridine (4SU, Sigma) for ~18 hours. At the time of harvest, cells were at or below 10^6 cells/ml. For UV crosslinking, cells were collected by centrifugation, washed once with ice-cold PBS, resuspended in ice cold PBS, irradiated with 365 nm UV light in a Stratalinker 2400 (Stratagene) and washed with PBS. The resulting cell pellet was snap-frozen.

tag: photoactivatable ribonucleoside and crosslinking wavelength

tag: antibody

value: Millipore anti-Ago2 clone 9E8.2

tag: immunoprecipitated protein

value: Ago2 (EIF2C2)


title: Ago2 PAR-CLIP BC-3 cells lane 1


title: miR-K10a rep. 2

tag: cell type


title: islet preparation 1 under palmitate exposure

description: Sample 2

tag: tissue


title: islet preparation 1 under control condition

description: Sample 1


title: miR-K10a+1 rep. 2


title: miR-K10a+1 rep. 1


title: miR-K10a rep. 1


title: miR-142-3p-1 rep. 3


title: miR-K10a+1 rep. 3


title: islet preparation 2 under control condition

description: Sample 3


title: Ago2 PAR-CLIP BC-1 cells lane 2

description:
Ago2 ribonucleoprotein complexes
KSHV (HHV8), EBV (HHV-4)

source_name: primary effusion lymphoma cell line BC-1


title: miR-142-3p-1 rep. 1


title: Control rep. 2

source_name: HEK293_negative control miRNA mimic

value: negative control miRNA mimic


title: miR-142-3p rep. 2


title: Control rep. 3


title: Control rep. 1


title: BC-1 cells small RNA

description: KSHV (HHV8), EBV (HHV-4)

data_processing:
Resulting reads were pre-processed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) and aligned to the human (hg19), KSHV (NC_009333) and/or EBV genomes (NC_009334) using Bowtie (Langmead et al., 2009). Reads were required to be at least 13nt in length and contain no ambiguous nucleotides after barcode removal and adapter stripping. Reads were aligned to the human and viral genome(s) concurrently. Reads were permitted to contain up to 3 mismatches, however only the locations from the lowest mismatch-stratum were recorded. To ensure that members of miRNA families were not discarded because of sequence identity, each read was permitted to align to up to 25 locations.  Only locations where at least one read mapped with no mismatches were considered for miRNA annotation. miRNAs, as they are identified by miRBase (v16) (Griffiths-Jones et al., 2006), were considered expressed if at least a single read mapped to the mature sequence and the pre-miRNA had at least 5 reads that mapped to it.  Variants of currently annotated miRNAs were only considered expressed if at least 5 reads mapped to the pre-miRNA and their read count was â¥10% of the reads that mapped to the pre-miRNA. In addition, miRNA variants needed to contain at least 90% of the sequence of the known mature sequence. miRNA* sequences not currently annotated as a known mature were considered an expressed mature miRNA if they contained â¥10% of the reads that mapped to the pre-miRNA and contained at least 90% of the predicted miRNA* sequence given the miRBase (v16) defined pre-miRNA foldback structure.  miRNA variants with 5â or 3â offsets from the sequence in miRBase were assigned adjusted names, i.e. â-/+_n_5â or â-/+_n_3â was appended to the miRNA name to designate 5â (_5) or 3â (_3) offsets from the miRBase sequence by n nucleotides.
The columns for the small RNA data bed files are the following info on the read level:
1. Chromosome
2. Start
3. End
4. Gene ID
5. Read Count
6. Strand

extract_protocol: 18-25nt long small RNAs were gel purified from 50 mg total RNA and subjected to small RNA cDNA library preparation protocol with barcoded 5âadaptors (BC-1: TCAAG, BC-3: TTGGC, BCBL-1: GCCTA) . Resulting PCR products were purified from 10% TBE gels, pooled and sequenced on one lanes on the Illumina GAII platform.

treatment_protocol: At the time of harvest, cells were at or below 10^6 cells/ml. Cells were pelleted and total RNA was prepared using TRIZOL.


title: BC-3 cells small RNA

description: KSHV (HHV8)


title: Ago2 PAR-CLIP BC-1 cells lane 1


title: miR-142-3p rep. 3


title: miR-142-3p rep. 1


title: BJAB expressing miR-K4-3p_replicate 3

hyb_protocol: Sample and reference cDNAs were pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5xSSC and 0.1% SDS), COT-1 DNA and polydeoxyadenylic acid to limit  non-specific binding, and heated to 95 °C for 2 min. This mixture was pipetted onto a microarray slide and hybridized overnight at 42 °C on the MAUI hybridization system (BioMicro Systems). Arrays were printed at the Duke Microarray Facility using the Genomics Solutions OmniGrid 300 Arrayer. The arrays contain the Human Operon v3.0.2 arrays (Oligo Source) that possess 34,602 unique optimized 70-mers.

scan_protocol: The array was washed at increasing stringencies and scanned on a GenePix 4000B microarray scanner (Axon Instruments).

data_processing: All arrays were subjected to background subtraction followed by loess normalization within each array and scale normalization across all arrays with the arrayMagic package in R. The KNN impute package in GenePattern was used to impute missing data if a probe had intensity values for at least half the samples. Otherwise the probes were excluded from analysis. Replicate probes were collapsed to one probe corresponding to the median value of all the replicates.

molecule: cytoplasmic RNA

source_name: human B cell line BJAB stably transduced with pNL-SIN-CMV-AcGFP/miR-K4-3p

label_protocol: Cytoplasmic RNA (10 mg) from each sample and the reference (Universal Human Reference RNA; Stratagene) were hybridized to oligo(dT) primers at 65 °C and then incubated at 42 °C for 2 h in the presence of reverse transcriptase, Cy5-dUTP or Cy3-dUTP and Cy5-dCTP or Cy3-dCTP, and a deoxynucleotide mix. In all cases, BJAB-derived RNA samples were labelled with Cy5 and reference samples were labelled with Cy3. NaOH was used to destroy residual RNA.

growth_protocol: BJAB were cultured in RPMI1640 medium supplemented with 10 mg/ml gentamicin and 10% fetal bovine serum (FBS).

extract_protocol: cytoplasmic RNA for microarray analysis was prepared with the RNeasy Mini kit (Qiagen) according to instructions provided with the kit.

treatment_protocol: Lentiviral vectors were produced by transfection of 293T cells and used to transduce about 106 BJAB at a cell concentration of about 5x105/ml. The next day, the growth medium was exchanged; 48 h after transduction, cells were collected by centrifugation and resuspended in medium containing 2mM EDTA. AcGFP-expressing cells were sorted (using the 488-nm line of a 20mW laser) and analyzed with a BD FACSAria cell sorter with DiVa software (BD Biosciences). Cell populations of similar mean fluorescence intensities were collected for all samples. Cell pools were expanded and cytoplasmic RNA for microarray analysis was prepared with the RNeasy Mini kit (Qiagen) and harvested on days 12 or 16 after transduction of BJAB cells.

value: BJAB

source_name: Universal Human Reference RNA, Stratagene

tag: reference


title: BJAB expressing miR-K1_replicate 4

source_name: human B cell line BJAB stably transduced with pNL-SIN-CMV-AcGFP/miR-K1

value: Universal Human Reference RNA, Stratagene


title: BJAB expressing miR-K4-3p_replicate 5


title: colon cancer (GRUBER_CRC_280)

status: Public on Apr 07 2011

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

institute: UT MD Anderson Cancer Center

description: amplified using Nugen WT-Ovation™

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
Expression levels were measured in two batches using Affymetrix U133A and U133A Plus 2.0 arrays (Santa Clara, CA). Expression analyses were carried out in the R-software using the package Bioconductor. Expression data in both batches were first subjected for quality assessment by creating the density plot of the log-intensity and RNA degradation plot corresponding to each sample. After preprocessing and quality assessment the two batches were aligned. Probes of the U133A array present in the U133A Plus 2.0 were selected and quantile normalized to mimic the distribution of the U133A array. Five samples had been hybridize in both arrays and served to verify that the correlation of the expression was adequate for the majority of the probes. A total of 331 samples and 419,473 probe sets were subjected to further analysis. Two class comparison of MSI versus MSS tumors were carried out by two-sample t-test to yield a list of differentially expressed probe sets, discriminating between the two biologic states of interest under consideration. We had information on MSI status available from 300 patients and the data set was subsequently reduced to this 300 patients. Then we examined only the expression levels of those genes integrated in the KEGG pathway hsa03440 corresponding to the homologous recombination (a total of 31 genes and their correponding 49 probe sets) using data from a total of 300 CRCs. The issue of multiple testing was addressed by using adjusted P-values after controlling for the overall false discovery rate by Benjamini and Hochberg method (BH-adjusted P-values). We also evaluated the local false discovery rate associated with our probe selection procedure by using the locfdr package in R.
For all 331 samples, MAS 5.0-calculated signal intensities were normalized using the quantile normalization procedure implemented in robust multiarray analysis and the normalized data were log 2 transformed.  Sample specific median centering and scaling by the standard deviation were additionally applied. Filtering was done to exclude probe sets that were not expressed or probe sets that exhibited low variability across samples. Expression values were required to be above the lower quartile of all expression measurements in at least 25% of samples, and the interquartile range across the samples on  log 2 scale was required to be at least 0.5.

source_name: colon cancer tissue

label_protocol: The RNA samples were labeled with IVT labelling kit according to manufacturer's instructions.

extract_protocol: RNA isolation and Microarray procedures. Primary tumors were obtained at the time of surgical resection, then they were snap frozen in liquid nitrogen at -80C, embedded in optimum cutting temperature freezing media (Miles Scientific, Naperville, IL), cryotome sectioned, stained with H&E, and evaluated by a surgical pathologist. Areas with >70% tumor cellularity were identified for RNA isolation. Selected sections of tumor samples were homogenized in Trizol (Invitrogen, Carlsbad, CA), and total cellular RNA was purified according the instructions of the manufacturer, with additional purification using RNeasy spin columns (Qiagen, Valencia, CA). RNA quality was assessed by 1% agarose gel electrophoresis, and samples were included only if the 18S and 28S bands were discrete and approximately equal.

value: Male

tag: microsatellite instability (msi) status

value: Stable [MSS]


title: BJAB expressing miR-K1_replicate 6


title: BJAB expressing miR-K4-3p_replicate 6


title: colon cancer (GRUBER_CRC_294)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_287)

description: amplified using Nugen WT-Ovation™

value: Female


title: BJAB expressing miR-K1_replicate 2


title: BJAB expressing miR-K1_replicate 3


title: BJAB expressing miR-K1_replicate 5


title: BJAB expressing miR-K4-3p_replicate 4


title: colon cancer (GRUBER_CRC_277)

description: amplified using Nugen WT-Ovation™

value: Unknown


title: colon cancer (GRUBER_CRC_274)

description: amplified using Nugen WT-Ovation™


title: BJAB expressing miR-K4-3p_replicate 2


title: BJAB expressing miR-K4-3p_replicate 1


title: colon cancer (GRUBER_CRC_267)

description: amplified using Nugen WT-Ovation™

value: Low [MSI-L]


title: colon cancer (GRUBER_CRC_282)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_288)

description: amplified using Nugen WT-Ovation™

value: High [MSI-H]


title: colon cancer (GRUBER_CRC_276)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_273)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_269)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_285)

description: amplified using Nugen WT-Ovation™


title: BC-3

description: Gene expression data from human B cell line BC-3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human Genome Array version 1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  The chips were scanned by the Affymetrix scanner.

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

data_processing: Total RNA from BC-1 and BC-3 was analyzed on Affymetrix Human Gene 1.0 ST arrays. Multiple  replicates were not included in this analysis, because the purpose of the experiment was  exclusively to make present/absent calls and to confirm published data (Fan et al., 2005).  The Gene 1.0 ST array data was loaded into R statistical software (R Development Core Team,  2011, http://www.R-project.org), where RMA normalization was performed by functions in the  ‘affy’ library (Gautier et al., 2004). Gene annotations were assigned for the probes based upon  the ‘hugene10sttranscriptcluster .db’ library. An expression present/absent call for each gene  was made based upon if the normalized expression value for that gene was ≥75th percentile of  the probes that were not associated with an annotated gene. The analysis of the Gene 1.0 ST  arrays confirmed the expression of >90% of the mRNAs previously found to be expressed (Fan  et al., 2005).

source_name: KSHV (HHV8)

label_protocol: Total RNA was amplified into sense-strand cDNA using the Ambion WT Expression kit.  5.5 ug of cDNA was fragmented and labeled with biotin using the Affymetrix GeneChip WT Terminal Labeling kit.

extract_protocol: RNA was extracted as described in Chomczynski, P. & Sacchi, N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156–159 (1987).

treatment_protocol: total RNA was harvested from cells grown under standard conditions


title: colon cancer (GRUBER_CRC_271)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_264)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_272)

description: amplified using Nugen WT-Ovation™


title: BC-1

description: Gene expression data from human B cell line BC-1

source_name: KSHV (HHV8), EBV (HHV-4)


title: BJAB expressing miR-K1_replicate 1


title: colon cancer (GRUBER_CRC_266)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_239)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_250)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_258)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_245)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_238)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_251)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_237)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_329)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_256)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_327)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_331)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_233)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_249)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_328)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_260)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_248)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_232)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_330)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_247)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_226)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_225)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_240)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_255)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_223)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_325)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_322)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_324)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_326)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_323)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_230)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_220)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_321)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_320)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_222)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_219)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_318)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_317)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_319)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_316)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_224)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_217)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_212)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_314)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_216)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_313)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_211)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_214)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_213)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_315)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_210)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_215)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_310)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_311)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_309)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_209)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_205)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_206)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_306)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_307)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_308)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_305)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_312)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_202)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_204)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_199)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_304)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_302)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_203)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_207)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_218)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_303)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_252)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_300)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_301)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_298)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_299)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_297)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_192)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_200)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_193)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_197)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_187)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_186)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_296)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_188)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_293)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_189)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_295)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_184)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_291)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_292)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_181)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_182)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_290)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_177)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_286)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_178)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_289)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_281)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_176)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_183)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_279)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_283)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_175)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_278)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_171)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_275)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_172)

description: amplified using Nugen WT-Ovation™