title: Whole genome characterisation of chemoresistant ovarian cancer [Illumina_Omini 2.5-8_SNP]

status: Public on May 19 2015

city: Herston

first: Ann-Marie

last: Patch

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

overall_design:
DNA was assayed with the Omini 2.5-8, V1.0 and V1.1 Illumina Bead Chips as per manufacturer’s instructions (Illumina, San Diego CA). SNP arrays were scanned on an iScan (Illumina, San Diego CA) and data was processed using the Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and LogR ratios. Tumor sample purity was estimated at a molecular level using the R tool, qPure3. 114 samples from 92 cases were estimated to contain at least 50% tumor and progressed to whole genome sequencing. qPure results are detailed in Supplementary Table SX. Genome Alteration Print (GAP)4 was used to call somatic regions of copy number change – gain, loss or copy neutral LOH.

Contributor: The Australian Ovarian Cancer Study Group

first: Ann

first: Elizabeth

last: Christie

first: Dariush

last: Etemadmoghadam

first: Dale

last: Garsed

first: Joshy

last: George

first: Sian

last: Fereday

first: Katia

last: Nones

first: Prue

last: Cowin

first: Kathryn

last: Alsop

first: Peter

last: Bailey

first: Karin

last: Kassahn

first: Felicity

last: Newell

first: Michael

last: Quinn

first: Stephen

last: Kazakoff

first: Kelly

last: Quek

first: Charlotte

last: Wilhelm-Benartzi

first: Ed

last: Curry

first: Huei

last: San

first: San

last: Leong

first: Anne

last: Hamilton

first: Linda

last: Mileshkin

first: George

last: Au-Yeung

first: Catherine

last: Kennedy

first: Jillian

last: Hung

first: Yoke

last: Chiew

first: Paul

last: Harnett

last: Friedlander

first: Jan

last: Pyman

last: Cordner

first: Patricia

last: O'Brien

first: Jodie

last: Leditschke

first: Greg

last: Young

first: Kate

last: Strachan

last: Waring

first: Walid

last: Azar

first: Chris

last: Mitchell

first: Nadia

last: Traficante

first: Joy

last: Hendley

first: Heather

last: Thorne

first: Mark

last: Shackleton

first: David

last: Miller

first: Gisela


title: Whole genome characterisation of chemoresistant ovarian cancer [NanoString miRNA]

first: Ann-Marie

last: Patch

overall_design:
Total RNA was hybridised to NanoString miRNA Human v2.1 probes, immobilized to NanoString cartridge and analysed on the NanoString Digital Analyzer. NanoString nSolver Analysis Software was utilised to check QC metrics and extract raw miRNA counts. Expression was normalised for input using the housekeeping genes.

Contributor: The Australian Ovarian Cancer Study Group

first: Elizabeth

middle: L

last: Christie

first: Dariush

last: Etemadmoghadam

first: Dale

middle: W

last: Garsed

first: Joshy

last: George

first: Sian

last: Fereday

first: Katia

last: Nones

first: Prue

last: Cowin

first: Kathryn

last: Alsop

first: Peter

middle: J

last: Bailey

first: Karin

middle: S

last: Kassahn

first: Felicity

last: Newell

first: Michael

middle: C

last: Quinn

first: Stephen

last: Kazakoff

first: Kelly

last: Quek

first: Charlotte

last: Wilhelm-Benartzi

first: Ed

last: Curry

first: Huei

last: San

first: San

last: Leong

first: Anne

last: Hamilton

first: Linda

last: Mileshkin

first: George

last: Au-Yeung

first: Catherine

last: Kennedy

last: Hung

middle: E

last: Chiew

middle: K

last: Mir Arnau

first: Richard


title: The evolutionary dynamics of meiotic recombination initiation in mice

status: Public on Feb 03 2016

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

country: USA

institute: NIDDK

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. The DNA double strand breaks (DSBs) that initiate meiotic recombination are directed by sequence-specific DNA binding of the PRDM9 protein. Gradual elimination of PRDM9 binding sites by gene conversion is thought to result in the hotspot erosion while mutations affecting DNA binding specificity of PRDM9 will create the new sets of hotspots. To better understand evolutionary turnover of recombination hotspots we mapped DSB hotspots in six inbred mouse strains representing all four major subspecies of Mus musculus and in their F1 hybrids. We found that hotspot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hotspots that become active in the hybrids. As crossovers are disfavored at such hotspots, we propose that sequence divergence generated by hotspot turnover creates impediments for recombination in hybrids, potentially leading to reduction in fertility and eventually, speciation.

overall_design:
Detection of meiotic DNA double strand breaks in testis of 26 mouse strains and F1 hybrids.

Update: [05-30-2023] Sample GSM1954846 was removed because it was incorrectly labeled as CASTfx13Rm (CAST female crossed with a 13R strain male).

first: Fatima

last: Smagulova

first: Yongmei

last: Pu

first: Rafael-Daniel

last: Camerini-Otero

first: Galina

last: Petukhova


title: Single cell RNA sequencing of interneurons of the mouse dorsolateral striatum

status: Public on Aug 22 2018

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data roots of Arabidopsis plants inoculated with Verticillium longisporum

status: Public on Nov 20 2014

city: Uppsala

first: Jonas

last: Roos

address: PO Box 7080

department: Dept. Plant Biology

institute: Swedish University of Agricultural Sciences

summary: Identification of genes differentially expressed in roots of Arabidopsis Col-0 and ndr1-1 mutants 48 h post inoculation with the fungal pathogen Verticillium longisporum.

overall_design: Arabidopsis Col-0 and ndr1-1 seeds were grown in petri dishes with liquid MS medium supplemented with 0.2% sucrose. After two weeks on a horizontal shaker (40 rpm), plants were rinsed twice in sterile distilled water and transferred to liquid 0.5xMS medium without sucrose, supplemented with 200 conidia ml-1 of V. longisporum isolate VL1 (CBS110220). Control plants were grown in 0.5x MS only. At 48 hours post inoculation, materials were harvested in biological replicates (>50 plant roots) and immediately frozen in liquid nitrogen. RNA was extracted with Aurum Total RNA Mini Kit (Bio-Rad) and hybridized to the Arabidopsis ATH1 Genome Array at the DNAVision facility (Gosselies, Belgium). Microarray assays were performed with triplicate biological root samples. Normalization of the microarray data was performed using the Robust Multichip Average (RMA) method as implemented by the “quantile normalization” function in the Bioconductor 1.3 software.

first: Sarosh

last: Bejai

first: Christina

last: Dixelius


title: RNAseq of maize stem at three developmental stages

status: Public on Jun 15 2018

city: Hefei

first: Hengsheng

last: Wang

address: Changjiang Rode 130

country: China

institute: Anhui Agriculture University

summary: Eighteen samples from the low, middle and high hybrid at three development stages were used for RNA sequencing.

overall_design: Three different maize hybrids, with extremely distinct plant height, which were further classified into low (L), middle (M) and high (H) group, were selected for RNA sequencing at three key developmental stages, namely, jointing stage (I), big flare period (II) and tasseling stage (III).

first: Beijiu

last: Cheng


title: Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis

status: Public on Aug 12 2014

city: Cardiff

first: Peter

last: Ghazal

address: Sir Geraint Evans Building, Academic Avenue

department: Systems Immunity University Research Institute

country: United Kingdom

institute: Cardiff University

summary: We aimed to identify the gene network and pathway biology associated with neonatal sepsis by determining genome-wide alterations in host RNA in infected infants

overall_design: Samples were obtained from control and infected human neonates.

first: Paul

last: Dickinson

first: Claire

last: Smith

first: Marie

last: Craigon

first: Alan

last: Ross

first: Mizanur

middle: R

last: Khondoker

first: Thorsten

last: Forster

first: Alasdair

last: Ivens

first: David

last: Lynn

first: Judith

last: Orme

first: Allan

last: Jackson

last: Lacaze

first: Benjamin

last: Stenson


title: DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains;), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale.Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Protocols for generating and quality control for replication timing data from microarray hybridization (Repli-chip) or sequencing (Repli-seq) were performed as previously described. CH12, MEL, Gm12878, Gm12801, Gm12812, Gm12813, HeLa-S3, HepG2, HUVEC, IMR90, MCF-7, Sk-N-Sh and NHEK cells were obtained and grown according to standard ENCODE cell culture protocols. Wild-type control and Suz12 knockout naive mESCs were derived from the previously described strain25 and obtained from Anne Laugesen and Kristian Helin and cultured in 2i+LIF medium as previously described. Previously published Repli-chip and Repli-seq3 data sets were also used in this study.

middle: D

last: Pope

first: Tyrone

last: Ryba

first: Vishnu

last: Dileep

first: Feng

last: Yue

first: Weisheng

last: Wu

first: Olgert

last: Denas

first: Robert

last: Thurman

first: Yong

first: Günhan

last: Gülsoy

first: Michael

last: Snyder

first: John

middle: A

last: Stamatoyannopoulos

first: James

last: Taylor

first: Ross

last: Hardison

first: Tamer

last: Kahveci

first: Bing

last: Ren

middle: M

last: Gilbert


title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

status: Public on May 25 2017

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

summary: The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Further, our data support that CTCF mediates transcriptional insulator function through enhancer-blocking but not direct facultative heterochromatin barrier activity. Beyond defining the functions of CTCF in chromosome folding these results provide new fundamental insights into the rules governing mammalian genome organization.

overall_design: mouse ES cells were engineered to harbor an auxin-inducible degron (AID) tag at both endogenous alleles of CTCF. A transgene encoding the auxin-binding F-box protein Tir1 was subsequently introduce, so that adding auxin to the culture media leads to rapid (hours) and reversible degradation of CTCF. Consequences of acute loss of CTCF and its restoration were investigated using ChIP-seq, RNA-seq and high-throughput Chromosome Conformation Capture (5C and Hi-C).

first: Elphège

middle: P

first: Anton

last: Goloborodko

first: Anne-Laure

last: Valton

first: Johan

middle: H

last: Gibcus

first: Alec

last: Uebersohn

first: Nezar

last: Abdennur

first: Job

last: Dekker

first: Leonid

last: Mirny

first: Benoit

middle: G

last: Bruneau


title: Effect of PLX4720 on melanoma-associated fibroblasts co-cultured with melanoma cells

status: Public on Nov 11 2014

city: Kanazawa

first: Eishu

last: Hirata

state: Ishikawa

address: Kakuma-machi

country: Japan

institute: Kanazawa University

summary: The experiment was designed to assess the effect of PLX4720 on the gene expression in human primary melanoma-associated fibroblast co-cultired with 5555 mouse melanoma cells

overall_design: Total RNA from DMSO or PLX4720-treated melanoma-associated fibroblast (MAF2-mCherry) co-cultured with melanoma cells (5555-mEGFP), FACS sorted

first: Erik

last: Sahai

first: Probir

last: Chakravarty


title: A comparative encyclopedia of DNA elements in the mouse genome

status: Public on Aug 14 2013

first: ENCODE

last: DCC

type: Genome variation profiling by genome tiling array

summary: The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organi- zation. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.


title: Partial urethra obstruction in rat

status: Public on Nov 24 2013

city: Lund

first: Mari

last: Ekman

state: Sverige

address: BMC D12

institute: Lund University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: Urethra was partially ligated and the urinary bladder was removed 10 days or 6 weeks after obstruction. Sham operated rats were used as controls. An addtitonal group of rats were repoerated 6 weeks after surgery and the obstruction was removed. These rats were then sacrificed 10 days after deobstruction. The bladder (including the urothelium) was frozen and used for RNA extraction.

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: Urinary bladders from sham-operated, 10 days and 6 weeks after obstruction and rats 10 days after deobstruction were compared. mRNA and microRNA were both analyzed.

first: Karl

last: Swärd

first: Sebastian

last: Albinsson

first: Bengt

last: Uvelius


title: Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR

status: Public on Apr 19 2012

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yin Shen mailto:y7shen@ucsd.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq (Robertson et al., 2007) to identify transcription factor binding sites and chromatin modification profiles in many mouse (C57Bl/6) tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.
In specific, the Ren lab examined RNA polymerase II (PolII), co-activator protein p300, the insulator protein CTCF, and two chromatin modification marks, H3K4me3 and H3K4me1, due to their demonstrated utilities in identifying promoters, enhancers and insulator elements (Barski et al., 2007; Blow et al., 2010; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005a; Visel et al., 2009). Enrichment of H3K4me3 or PolII signals is a strong indicator of an active promoter, while the presence of p300 or H3K4me1 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million monoclonal, uniquely mapped tags.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://genome.ucsc.edu/ENCODE/protocols/cell/mouse).
Enrichment and Library Preparation
Chromatin immunoprecipitation was performed according to Ren Lab ChIP Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf).
Library construction was performed according to Ren Lab Library Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf).
Sequencing and Analysis
Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead et al., 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts.

first: Bing

last: Ren

first: Yin

last: Shen


title: MCF-7 Fractionated RNA

status: Public on Dec 01 2004

city: Boston

first: Carol

last: Westbrook

state: MA

address: One Boston Medical Center Pl

institute: Boston University

summary:
RNA from MCF-7 cells was fractionated by sucrose density gradient centrifugation to separate RNA associated with membrane-bound polysomes from RNA associated with free polysomes.  These two populations were hybridized in triplicate to U133A microarrays.
Keywords: repeat sample

first: Nathan

middle: O

last: Stitziel

first: Brenton

last: Mar

first: Jie

last: Liang


title: Histone Modifications by ChIP-seq from ENCODE/LICR

status: Public on Jul 30 2011

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yin Shen mailto:y7shen@ucsd.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq (Robertson et al., 2007) to identify transcription factor binding sites and chromatin modification profiles in many mouse (C57Bl/6) tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.
In specific, the Ren lab examined RNA polymerase II (PolII), co-activator protein p300, the insulator protein CTCF, and two chromatin modification marks H3K4me3 and H3K4me1 due to their demonstrated utilities in identifying promoters, enhancers and insulator elements (Barski et al., 2007; Blow et al., 2010; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005a; Visel et al., 2009). Enrichment of H3K4me3 or PolII signals is a strong indicator of active promoter, while the presence of p300 or H3K4me1 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million monoclonal, uniquely mapped tags.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev/ENCODE/protocols/cell/mouse).
Enrichment and Library Preparation: Chromatin immunoprecipitation was performed according to Ren Lab ChIP Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf).
Library construction was performed according to Ren Lab Library Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf).
Sequencing and Analysis: Samples were sequenced on Illumina Genome Analyzer II Genome Analyzer IIx, and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead et al., 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts.


title: Expression data of induced sputum from Unbiased BIOmarkers in Prediction of REspiratory Disease outcomes (U-BIOPRED) Project

status: Public on Dec 31 2016

city: London

first: Chih-hsi

middle: Scott

last: Kuo

address: South Kensington Campus

department: Department of Computing

institute: Imperial College London

summary:
Asthma is a heterogeneous disease requiring understandings at molecular level that characterizes subgroups of patients with specific biomarkers to faciliate the development of targeted thearpies.
We used Affymetrix U133 Plus 2.0 PM only arrays to explore the gene expression profile from induced sputum cells of 118 moderate/severe asthmatic patients and 21 healthy controls.

overall_design:
A cross-sectional study of 118 participants with moderate-to-severe asthma and 21 healthy controls from the U-BIOPRED underwent sputum induction.
contributor: U-BIOPRED Consortium Project Team members