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Items: 15

1.

Archival chromatin sequencing in eastern water dragon museum specimens

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. more...
Organism:
Intellagama lesueurii lesueurii
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL34214
8 Samples
Download data: WIG
Series
Accession:
GSE256157
ID:
200256157
2.

Archival chromatin sequencing in formalin-fixed mouse specimens [FAIRE and Mnase]

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
32 Samples
Download data: WIG
Series
Accession:
GSE261169
ID:
200261169
3.

Effects of formalin-fixation on FAIRE-Seq and MNase-Seq signatures in yeast (RNA-Seq)

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
6 Samples
Download data: FPKM_TRACKING, TXT
Series
Accession:
GSE256160
ID:
200256160
4.

Archival chromatin sequencing in formalin-fixed mouse specimens

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
6 Samples
Download data: TXT
Series
Accession:
GSE256158
ID:
200256158
5.

Effects of formalin-fixation on FAIRE-Seq and MNase-Seq signatures in yeast

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL27812
58 Samples
Download data: WIG
Series
Accession:
GSE256156
ID:
200256156
6.

FFPE-ATAC decodes the chromatin accessibility from the clinical archived FFPE tissues

(Submitter supplied) We present FFPE-ATAC, a new ATAC-seq tool for chromatin accessibility profiling that decodes the chromatin accessibility from mouse FFPE tissue and clinical archived FFPE tissues. The FFPE-ATAC generates the high-quality chromatin accessibility profiles from clinical FFPE tissue sections with 5-20 µm thickness, and reveals the disease-associated regulatory elements in different types of FFPE archived tissue. more...
Organism:
Mus musculus; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13112 GPL11154 GPL24247
68 Samples
Download data: NARROWPEAK, TXT
Series
Accession:
GSE163306
ID:
200163306
7.

Direct Formalin Fixation Induces Widespread Transcriptomic Effects in Archival Tissue Samples

(Submitter supplied) Archival formalin-fixed paraffin-embedded (FFPE) tissue samples hold a wealth of transcriptomic information; however, little is known about potential artifacts. Previously, we identified a consistent shift in global RNA-sequencing profiles between matching frozen and FFPE samples. We hypothesized that this shift was from fixing fresh tissue in formalin. To test this idea, RNA-sequencing was performed on liver samples collected from male mice treated with 600 ppm of a reference chemical (phenobarbital, 600 ppm phenobarbital) or vehicle control for 7 days. more...
Organism:
Mus musculus; Rattus norvegicus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL25029 GPL21626 GPL17021
96 Samples
Download data: CSV, TXT
Series
Accession:
GSE148174
ID:
200148174
8.

Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples

(Submitter supplied) Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-seq offers a novel way to address this problem. In this study we evaluated transcriptomic dose responses using RNA-seq in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one recent (<2 years old) and the other older (>20 years old). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
80 Samples
Download data: TXT
Series
Accession:
GSE78962
ID:
200078962
9.

Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [polyA enrichment]

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using RNA-seq (polyA-enrichment protocol). All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (ribo-depletion protocol) in order to determine the effect of the technology on gene expression profiles.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
24 Samples
Download data: TXT
Series
Accession:
GSE64371
ID:
200064371
10.

Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [ribo-depletion]

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using RNA-seq (ribo-depletion protocol). All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (polyA-enrichment protocol) in order to determine the effect of the technology on gene expression profiles.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
24 Samples
Download data: TXT
Series
Accession:
GSE64370
ID:
200064370
11.

Global gene expression analysis in paired fresh-frozen and FFPE furan-exposed mouse liver samples

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Expression profiling by high throughput sequencing
Platforms:
GPL13112 GPL10787
122 Samples
Download data: TXT, XLSX
Series
Accession:
GSE62843
ID:
200062843
12.

Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using one-colour Agilent microarrays

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays. All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL10787
8 Samples
Download data: TXT
Series
Accession:
GSE62842
ID:
200062842
13.

Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using one-colour Agilent microarrays

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays. To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. All samples (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL10787
50 Samples
Download data: TXT
Series
Accession:
GSE62840
ID:
200062840
14.

Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using two-colour Agilent microarrays

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen (GSE48644) and formalin-fixed paraffin embedded (FFPE; this study) samples using two-colour microarrays. To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL10787
16 Samples
Download data: TXT
Series
Accession:
GSE62838
ID:
200062838
15.

Universal NicE-seq for high resolution accessible chromatin profiling for native and formaldehyde fixed cells and tissues

(Submitter supplied) Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. more...
Organism:
Mus musculus; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL24676 GPL19057
28 Samples
Download data: BW, TXT
Series
Accession:
GSE140276
ID:
200140276

Supplemental Content

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