title: WT E13 CDX2 ChIP-seq replicate 1

description:
E13 MG_CDX2 ChIP rep1
supplementary file: E13_CDX2.bw

extract_protocol:
E13 small intestines were dissected and cross-linked for subsequent ChIP.
Whole cell lysates were sonicated and incubated with 6 uL CDX2  antibody (A300-691A, Bethyl Labs.) overnight for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Embryonic whole tissue from midgut


title: Negative CTR 5 5750

status: Public on Oct 26 2018

type: genomic

city: Cantanhede

first: Helena

last: Vazao

address: Biocant Park Nucleo4, 4A

department: HeartGenetics

country: Portugal

institute: HeartGenetics

description:
5750
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

hyb_protocol: Not applicable

scan_protocol: The status of 171 mutations (by the reading of 61 positions) in 6 genes (OncoAlvo® Panel) was assessed using a high-throughput DNA Microchip platform, the iPLEX® system (Agena Bioscience, Inc). This array platform allows an optimal genetic analysis by combining the benefits of accurate primer extension chemistry with MALDI-TOF mass spectrometry. The different masses of each generated PCR product are then converted into mutational status information.

data_processing: The processed data (attached as 14 .txt files) were generated by software computing analysis. The processing was made by normalizing the peak intensity (converted into fraction of mutant alleles) of each genetic variant of each sample by the peak intensity of the correspondent variant of the average of 96 baseline samples. As the baseline samples serve as the minimum threshold, the computer software does not give a processed data file for them; thus, there are no processed data .txt files for these 96 samples. The processed data files only show the positive results.

molecule: genomic DNA

organism: Homo sapiens

source_name: colorectal healthy sample

label_protocol: Not applicable

growth_protocol: FFPE human colon adenocarcinoma.

extract_protocol: A commercial kit was used to perform DNA extraction and purification from FFPE colon adenocarcinoma. DNA concentration and quality were evaluated with MultiskanGo spectrophotometer (Thermo Scientific).

treatment_protocol: No treatment applied.

tag: tissue

value: FFPE colorectal healthy sample

tag: sample type

value: Negative control


title: WT Villus CDX2 ChIP-seq replicate1

type: SRA

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

country: USA

institute: Dana Farber Cancer Institute

description:
Adult_CDX2_ChIP rep1
supplementary file: WT_AdultVillus_CDX2.bw

library_source: genomic

data_processing:
Alignment: ATAC-seq and ChIP-seq: Bowtie2. RNA-seq: STAR aligner, version 2.5.3a.
ATAC-seq differential region identification: diffReps; Peak calling: MACS2; RNA-seq raw read counts: HTSeq
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: ATAC-Seq & ChIP-seq: bigwig file for visualizing aligned sequence tags (available in tar archives on the series record).
Supplementary_files_format_and_content: RNA-seq:  text file with raw read counts

organism: Mus musculus

source_name: Mouse intestinal villus epithelial cells

extract_protocol:
Villi from middle 1/3rd of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were cross-linked and immediately snap-frozen in liquid nitrogen for subsequent ChIP analysis.
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with beads pre-bound to CDX2 antibody (#12306, Cell Signaling) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: No treatment

tag: strain

value: B6;129 mixed background

tag: cell type

value: Adult differentiated jejunal epithelial cells; middle 1/3 of intestine

tag: genotype

tag: developmental stage

value: adult


title: WT E17 CDX2 ChIP-seq replicate1

description:
E17 MG_CDX2 ChIP rep1
supplementary file: E17_CDX2.bw

source_name: Mouse small intestinal epithelial cells

extract_protocol:
E17 small intestines were dissected and cross-linked for subsequent ChIP.
Whole cell lysates were sonicated and incubated with 6 uL CDX2 antibody (A300-691A, Bethyl Labs.) overnight for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: CD1 wild type

value: Wild-Type


title: Negative CTR 4 5749

description:
5749
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 437 5748

description:
5748
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

source_name: metastatic colorectal carcinoma

value: FFPE colon adenocarcinoma


title: Negative CTR 3 5747

description:
5747
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E11 Small Intestine ATACseq replicate2

description:
E11 MG_ATAC rep2
supplementary file: E11_SmallIntestine_ATAC.bw

source_name: Mouse intestinal epithelial cells

extract_protocol:
E11 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Embryonic epithelial cells from the small intestine


title: WT Villus H3K4me1 ChIP-seq replicate1

description:
Adult villus H3K4me1 ChIP rep1
supplementary file: WT_AdultVillus_H3K4me1.bw

extract_protocol:
Villi from proximal 1/3rd of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were cross-linked and immediately snap-frozen in liquid nitrogen for subsequent ChIP analysis.
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with 2 ug H3K4me1 antibody (C15410194, Diagenode) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Adult differentiated epithelial cells

value: Wild-type


title: WT E11 Small Intestine ATACseq replicate1

description:
E11 MG_ATAC rep1
supplementary file: E11_SmallIntestine_ATAC.bw


title: positive CTRL 4 5756

description:
5756
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: Positive control


title: WT E12 Small Intestine ATACseq replicate2

description:
E12 MG_ATAC rep2
supplementary file: E12_SmallIntestine_ATAC.bw

extract_protocol:
E12 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Patient 436 5745

description:
5745
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Negative CTR 1 5744

description:
5744
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 435 5743

description:
5743
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E12 Small Intestine ATACseq replicate1

description:
E12 MG_ATAC rep1
supplementary file: E12_SmallIntestine_ATAC.bw


title: WT E12 HS ATACseq replicate1

description:
E12 HS_ATAC rep1
supplementary file: E12_HS_ATAC.bw

source_name: Mouse hindstomach epithelial cells

extract_protocol:
E12 hindstomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Embryonic epithelial cells from the hindstomach


title: WT E12 HS ATACseq replicate2

description:
E12 HS_ATAC rep2
supplementary file: E12_HS_ATAC.bw


title: Patient 433 5741

description:
5741
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 432 5740

description:
5740
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E12 FS ATACseq replicate2

description:
E12 FS_ATAC rep2
supplementary file: E12_FS_ATAC.bw

source_name: Mouse forestomach epithelial cells

extract_protocol:
E12 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Embryonic epithelial cells from the forestomach


title: WT E12 FS ATACseq replicate1

description:
E12 FS_ATAC rep1
supplementary file: E12_FS_ATAC.bw


title: Patient 434 5742

description:
5742
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 430 5738

description:
5738
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 429 5737

description:
5737
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 431 5739

description:
5739
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E14 Small Intestine ATACseq replicate2

description:
E14 MG_ATAC rep2
supplementary file: E14_SmallIntestine_ATAC.bw

extract_protocol:
E14 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cellswere immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: WT E14 HS ATACseq replicate3

description:
E14 HS_ATAC rep3
supplementary file: E14_HS_ATAC.bw

extract_protocol:
E14 hindstomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cellswere immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: WT E14 Small Intestine ATACseq replicate1

description:
E14 MG_ATAC rep1
supplementary file: E14_SmallIntestine_ATAC.bw


title: Patient 428 5736

description:
5736
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 427 5735

description:
5735
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E14 HS ATACseq replicate4

description:
E14 HS_ATAC rep4
supplementary file: E14_HS_ATAC.bw


title: WT E14 HS ATACseq replicate2

description:
E14 HS_ATAC rep2
supplementary file: E14_HS_ATAC.bw


title: Patient 426 5734

description:
5734
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 425 5733

description:
5733
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E14 FS ATACseq replicate4

description:
E14 FS_ATAC rep4
supplementary file: E14_FS_ATAC.bw

extract_protocol:
E14 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cellswere immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Negative CTR 2 5746

description:
5746
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E14 HS ATACseq replicate1

description:
E14 HS_ATAC rep1
supplementary file: E14_HS_ATAC.bw


title: Patient 424 5732

description:
5732
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E14 FS ATACseq replicate3

description:
E14 FS_ATAC rep3
supplementary file: E14_FS_ATAC.bw


title: Patient 423 5731

description:
5731
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E14 FS ATACseq replicate2

description:
E14 FS_ATAC rep2
supplementary file: E14_FS_ATAC.bw


title: WT E14 FS ATACseq replicate1

description:
E14 FS_ATAC rep1
supplementary file: E14_FS_ATAC.bw


title: Cdx2-/- (deleted at E13) Small Intestine ATACseq replicate2

description:
E16 MG_E13Cdx2KO_ATAC rep2
supplementary file: E13Cdx2KO_SmallIntestine_ATAC_rep2.bw

extract_protocol:
E16 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were given an oral gavage of 5mg Tamoxifen

value: Cdx2f/f; Villin-Cre


title: Patient 421 5715

description:
5715
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Cdx2-/- (deleted at E13) Small Intestine ATACseq replicate1

description:
E16 MG_E13Cdx2KO_ATAC rep1
supplementary file: E13Cdx2KO_SmallIntestine_ATAC_rep1.bw


title: Patient 420 5714

description:
5714
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 418 5712

description:
5712
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E16 Small Intestine ATACseq replicate2

description:
E16 MG_ATAC rep2
supplementary file: E16_SmallIntestine_ATAC.bw


title: Cdx2-/- (deleted at E10) Small Intestine ATACseq replicate1

description:
E16 MG_E10Cdx2KO_ATAC rep1
supplementary file: E10Cdx2KO_SmallIntestine_ATAC.bw

value: Cdx2f/f; Shh-Cre


title: WT E16 HS ATACseq replicate2

description:
E16 HS_ATAC rep2
supplementary file: E16_HS_ATAC.bw

extract_protocol:
E16 hindstomach were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Patient 416 5710

description:
5710
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 415 5709

description:
5709
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E16 FS ATACseq replicate2

description:
E16 FS_ATAC rep2
supplementary file: E16_FS_ATAC.bw

extract_protocol:
E16 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: WT E16 HS ATACseq replicate1

description:
E16 HS_ATAC rep1
supplementary file: E16_HS_ATAC.bw


title: Patient 414 5708

description:
5708
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E16 FS ATACseq replicate1

description:
E16 FS_ATAC rep1
supplementary file: E16_FS_ATAC.bw


title: Patient 413 5707

description:
5707
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 412 5706

description:
5706
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Cdx2-/- (deleted at E15) Small Intestine ATACseq replicate1

description:
E18 MG_Cdx2KO_ATAC rep1
supplementary file: E15Cdx2KO_SmallIntestine_ATAC_rep1.bw

extract_protocol:
Villi from E18 intestines were isolated by incubation in 5mM EDTA in PBS for 45 minutes at 4°C. Single cells were dissociated with 4X TrypLE in DMEM for 45 minutes at 37°C. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Patient 411 5705

description:
5705
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 422 5730

description:
5730
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Cdx2-/- (deleted at E15) Small Intestine ATACseq replicate2

description:
E18 MG_Cdx2KO_ATAC rep2
supplementary file: E15Cdx2KO_SmallIntestine_ATAC_rep2.bw


title: Patient 410 5704

description:
5704
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT P1 Small Intestine ATACseq replicate2

description:
P1 INTESTINE_ATAC rep2
supplementary file: P1_SmallIntestine_ATAC.bw

extract_protocol:
Villi from P1 intestines were isolated by incubation in 5mM EDTA in PBS for 45 minutes at 4°C. Single cells were dissociated with 4X TrypLE in DMEM for 45 minutes at 37°C. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Post Embryonic Epithelial cells from the intestine


title: Patient 409 5703

description:
5703
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT P1 Small Intestine ATACseq replicate1

description:
P1 INTESTINE_ATAC rep1
supplementary file: P1_SmallIntestine_ATAC.bw


title: Patient 408 5702

description:
5702
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E18 Small Intestine ATACseq replicate1

description:
E18 MG_WT_ATAC rep1
supplementary file: E18_SmallIntestine_WT_ATAC.bw


title: Patient 417 5711

description:
5711
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT P1 HS ATACseq replicate2

description:
P1 HS_ATAC rep2
supplementary file: P1_HS_ATAC.bw

extract_protocol:
P1 hindstomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flowcytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Post Embryonic Epithelial cells from the hindstomach


title: Patient 419 5713

description:
5713
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

extract_protocol: A commercial kit was used to perform DNA extraction and purification from FFPE colon adenocarcinoma. DNA concentration and quality were evaluated with MultiskanGo spectrophotometer (Thermo Scientific).


title: Patient 405 5699

description:
5699
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT P1 FS ATACseq replicate2

description:
P1 FS_ATAC rep2
supplementary file: P1_FS_ATAC.bw

extract_protocol:
P1 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flowcytometry. Cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Post Embryonic Epithelial cells from the forestomach


title: WT P1 FS ATACseq replicate1

description:
P1 FS_ATAC rep1
supplementary file: P1_FS_ATAC.bw

extract_protocol:
P1 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flowcytometry. Cellswere immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: WT E16 Small Intestine ATACseq replicate1

description:
E16 MG_ATAC rep1
supplementary file: E16_SmallIntestine_ATAC.bw


title: Cdx2-/- Adult Ileum Villus ATACseq replicate1

description:
Adult Ileum_Cdx2KO_ATAC rep1
supplementary file: AdultVillus_Ileum_Cdx2KO_ATAC.bw

source_name: Mouse ileal villus epithelial cells

extract_protocol:
Villi from the distal 1/3rd (ileum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Villi were dissociated with 4X TrypLE in DMEM for 45 minutes at 37°C. Cells were counted, lysed and immediately used for transposase reaction.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected i.p. with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre for recombination of conditional alleles, and were sacrificed 3 days after last injection.

value: B6;129 mixed background

value: Adult ileal villi


title: Patient 407 5701

description:
5701
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT Adult Ileum Villus ATACseq replicate1

description:
Adult Ileum_WT_ATAC rep1
supplementary file: AdultVillus_Ileum_WT_ATAC.bw

treatment_protocol: Mice were injected i.p. with sunflower oil (vehicle for tamoxifen) for 5 consecutive days and were sacrificed 3 days after last injection.

value: adult


title: Patient 400 5694

description:
5694
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 399 5693

description:
5693
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 404 5698

description:
5698
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 398 5692

description:
5692
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 402 5696

description:
5696
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: RN2_sgNeg1

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
Sequencing reads were mapped into reference human genome hg38 or mouse genome mm10 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
RNA-seq files of two sgRNAs for each target gene were treated as replicates
Genome_build: hg38, mm10
Supplementary_files_format_and_content: txt, normalized RPKM. Processed data files are included in a tar archive on the series record.

molecule: polyA RNA

source_name: acute myeloid leukemia

growth_protocol: MOLM13, NOMO1, MV4-11, THP1, RN2 were cultured in RPMI with 1XP/S and 10% FBS, OCIAML3 cells were cultured in a-MEM plus 10% FBS and 1XP/S, MLL-AF9/NrasG12D cells were cultured in IMDM with 20%FBS and 1XP/S.

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout

tag: cell line

tag: treatment

value: day9 after sgNeg1 guide RNA infection


title: RN2_sgZfp64e6.3

value: day9 after sgZfp64e6.3 guide RNA infection


title: Patient 397 5691

description:
5691
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma


title: Patient 406 5700

description:
5700
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: RN2_sgZfp64e6.2

value: day9 after sgZfp64e6.2 guide RNA infection


title: WT P1 HS ATACseq replicate1

description:
P1 HS_ATAC rep1
supplementary file: P1_HS_ATAC.bw

value: CD1 wild type

value: Post Embryonic Epithleial cells from the hindstomach

value: Wild-Type


title: Mll-AF9_ZFP64_Rep1

data_processing:
Sequence reads were mapped into reference human genome hg19 or mouse genome mm10 by using Bowtie2.
Peakcalling was done by using MACS2 FDR cut off 5% with narrow peak option for ZFP64.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: bigwig contains normalized tag count calculated by MACS2.0.

growth_protocol: MOLM-13 and NOMO-1 cells were cultured in RPM1 with 10% FBS and penicillin/streptomycin,Mll-AF9 cells were cultrured in IMDM supplemented 10% FBS, 1XP/S, 10ng/ml mSCF, mGM-CSF, mIL3, mIL6 each.

extract_protocol:
Cell lysates were clarified from sonicated nulcei and ZFP64-DNA or histone-DNA complexs were isolated with ZFP64 or histone antibody.
Libraries were prepared using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, ChIP DNA was end-repaired, 3’-adenylated, and then ligated with indexed adaptor. These DNA was size selected (200-400 bp) via agarose gel electrophoresis, and PCR amplified. Final products were purified using AMPure XP beads.

treatment_protocol: For FLAG ChIP-seq, MOLM-13 and NOMO-1 cells were infected with ZFP64 cDNA with fusion to triple FLAG

value: Mll-AF9 knock in

tag: chip antibody

value: ZFP64(Proteintech Group,17187-1-AP)


title: Patient 396 5690

description:
5690
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Mll-AF9_ZFP64_Rep2


title: Patient 395 5688

description:
5688
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 394 5687

description:
5687
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 403 5697

description:
5697
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_WT_r1

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Raw reads were aligned to the mm9 revision of the mouse reference genome using hisat2 with default parameters.
Gene name-level read count quantification was performed with  htseq-count with parameters -I gene_id –stranded=reverse -f bam -m intersection-strict  and a GTF containing transcript positions from Refseq, downloaded 6/6/18.
mm9
Supplementary_files_format_and_content: Counts files represent gene name and gene-level read counts

source_name: V6.5 ESC

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions in 2i media on gelatinized tissue-culture plates.

extract_protocol:
PolyA selected libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) by the Whitehead Institute Genome Technology Core according to manufacturer’s instruction. The cDNA libraries were sequence for 40 bp single at end ends on an Illumina HiSeq 2500 instrument.
Total RNAs were extracted from cells using the Qiagen AllPrep kit using manufacturer's protocol

value: Normal LIF


title: mES_WT_r2


title: Patient 393 5686

description:
5686
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_WT_noLIF_r1

value: LIF withdrawn for 5 days


title: mES_WT_noLIF_r2


title: Patient 392 5685

description:
5685
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_OCT4fkbp_dTAG_r2

source_name: Oct4-Fkbp fusion V6.5 ESC

value: 24 hr dTag9


title: Patient 401 5695

description:
5695
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 391 5684

description:
5684
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 390 5683

description:
5683
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_OCT4fkbp_DMSO_r2

value: 24 hr DMSO


title: mES_OCT4fkbp_dTAG_r1


title: Patient 389 5682

description:
5682
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_OCT4fkbp_DMSO_r1


title: mES_OCT4-FKBP_DMSO_Input

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic stem cells

growth_protocol: V6.5 murine embryonic stem cells were a gift from the Jaenisch lab. Cells were modified to introduce an FKBP tag on the endogenous OCT4 protein. Cells were grown on 0.2% gelatinized (Sigma, G1890) tissue culture plates in 2i media, DMEM-F12 (Life Technologies, 11320082), 0.5X B27 supplement (Life Technologies, 17504044), 0.5X N2 supplement (Life Technologies, 17502048), an extra 0.5mM L-glutamine (Gibco, 25030-081), 0.1mM b-mercaptoethanol (Sigma, M7522), 1% Penicillin Streptomycin (Life Technologies, 15140163), 0.5X nonessential amino acids (Gibco, 11140-050), 1000 U/ml LIF (Chemico, ESG1107), 1μM PD0325901 (Stemgent, 04- 0006-10), 3μM CHIR99021 (Stemgent, 04-0004-10). Cells were grown at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Cells were crosslinked on plate by addition of 10% volume of 11% formaldehyde solution for 15 minutes at room temperature. 50 million cells were used per ChIP reaction. ChIP was performed according to Young lab protocol (Pete Ralh 4.10) and sonication was performed on a QSonica Q700 tip sonicator. Library construction was performed using the Swift Biosciences ChIP kit by the Whitehead Institute Genome Technology Core.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.

treatment_protocol: Control cells were treated with DMSO for 24h.

value: V6.5 OCT4-FKBP

value: DMSO

tag: treatment duration


title: mES_OCT4-FKBP_dTAG_Input

treatment_protocol: To induce degradation of OCT4-FKBP, cells were treated with 100 nM dTAG-47 compound for 24 hours.

tag: system

value: Stem Cell


title: Patient 385 5678

description:
5678
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 384 5677

description:
5677
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_OCT4-FKBP_DMSO_MED1

tag: antibody manu.

value: Bethyl

tag: antibody catalog

tag: antibody lot


title: mES_OCT4-FKBP_dTAG_MED1


title: Patient 383 5675

description:
5675
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_OCT4-FKBP_dTAG_OCT4

value: Santa Cruz


title: Patient 382 5674

description:
5674
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 381 5673

description:
5673
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 379 5671

description:
5671
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 380 5672

description:
5672
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 378 5670

description:
5670
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 377 5669

description:
5669
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 376 5668

description:
5668
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 375 5384

description:
5384
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 371 5380

description:
5380
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 374 5383

description:
5383
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 372 5381

description:
5381
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 373 5382

description:
5382
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 368 5377

description:
5377
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 369 5378

description:
5378
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 370 5379

description:
5379
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 388 5681

description:
5681
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 367 5376

description:
5376
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 366 5375

description:
5375
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 387 5680

description:
5680
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 386 5679

description:
5679
Raw data file: G1139506.xml
Processed data file: G1139506_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 365 5374

description:
5374
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: mES_OCT4-FKBP_DMSO_OCT4


title: Patient 363 5372

description:
5372
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 364 5373

description:
5373
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 359 5368

description:
5368
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 358 5367

description:
5367
Raw data file: G1156558.xml
Processed data file: G1156558_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 360 5369

description:
5369
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 361 5370

description:
5370
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 362 5371

description:
5371
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 357 5366

description:
5366
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 356 5365

description:
5365
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 355 5364

description:
5364
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 351 5360

description:
5360
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 354 5363

description:
5363
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 352 5361

description:
5361
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 349 5358

description:
5358
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 347 5356

description:
5356
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 348 5357

description:
5357
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 346 5355

description:
5355
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 345 5354

description:
5354
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 343 5351

description:
5351
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 342 5350

description:
5350
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 340 5348

description:
5348
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 350 5359

description:
5359
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 341 5349

description:
5349
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 339 5347

description:
5347
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 337 5345

description:
5345
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 353 5362

description:
5362
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 338 5346

description:
5346
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 344 5352

description:
5352
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 333 5341

description:
5341
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 332 5340

description:
5340
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 336 5344

description:
5344
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 330 5338

description:
5338
Raw data file: S0062445.xml
Processed data file: S0062445_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 328 5298

description:
5298
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 331 5339

description:
5339
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 329 5337

description:
5337
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 327 5297

description:
5297
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 326 5296

description:
5296
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 324 5294

description:
5294
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 323 5293

description:
5293
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 321 5291

description:
5291
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 322 5292

description:
5292
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 319 5289

description:
5289
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 318 5288

description:
5288
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 320 5290

description:
5290
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 317 5287

description:
5287
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 316 5286

description:
5286
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 315 5285

description:
5285
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 313 5283

description:
5283
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 335 5343

description:
5343
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 312 5282

description:
5282
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 309 5279

description:
5279
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 310 5280

description:
5280
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 334 5342

description:
5342
Raw data file: G1135675.xml
Processed data file: G1135675_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 308 5278

description:
5278
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 306 5276

description:
5276
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 305 5275

description:
5275
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 307 5277

description:
5277
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 304 5274

description:
5274
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 325 5295

description:
5295
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 302 5272

description:
5272
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 301 5271

description:
5271
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 303 5273

description:
5273
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 299 5269

description:
5269
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 300 5270

description:
5270
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 298 5268

description:
5268
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 293 5261

description:
5261
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 296 5265

description:
5265
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 291 5258

description:
5258
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 292 5259

description:
5259
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 290 5257

description:
5257
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 314 5284

description:
5284
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 289 5256

description:
5256
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 288 5255

description:
5255
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 297 5267

description:
5267
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 287 5254

description:
5254
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 284 5251

description:
5251
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 311 5281

description:
5281
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 285 5252

description:
5252
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 286 5253

description:
5253
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 283 5123

description:
5123
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 280 5119

description:
5119
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 278 5117

description:
5117
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 279 5118

description:
5118
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 281 5120

description:
5120
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 274 5113

description:
5113
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 277 5116

description:
5116
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 273 5112

description:
5112
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 275 5114

description:
5114
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 294 5262

description:
5262
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 295 5263

description:
5263
Raw data file: G1135909.xml
Processed data file: G1135909_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 271 5110

description:
5110
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 269 5108

description:
5108
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 266 5097

description:
5097
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 270 5109

description:
5109
Raw data file: S0075587.xml
Processed data file: S0075587_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 268 5099

description:
5099
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 265 5096

description:
5096
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 263 5093

description:
5093
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 261 5091

description:
5091
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 282 5122

description:
5122
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 259 5089

description:
5089
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 260 5090

description:
5090
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 258 5088

description:
5088
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 256 5086

description:
5086
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 257 5087

description:
5087
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 276 5115

description:
5115
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 254 5084

description:
5084
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 255 5085

description:
5085
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 252 5082

description:
5082
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 253 5083

description:
5083
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 250 5080

description:
5080
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 248 5078

description:
5078
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 272 5111

description:
5111
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 249 5079

description:
5079
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 246 4997

description:
4997
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 245 4996

description:
4996
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 267 5098

description:
5098
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 247 5077

description:
5077
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 243 4994

description:
4994
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 242 4993

description:
4993
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 244 4995

description:
4995
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 262 5092

description:
5092
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 264 5095

description:
5095
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 239 4989

description:
4989
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 238 4988

description:
4988
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 240 4990

description:
4990
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 237 4987

description:
4987
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 236 4986

description:
4986
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 235 4985

description:
4985
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 233 4983

description:
4983
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 234 4984

description:
4984
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 251 5081

description:
5081
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 231 4981

description:
4981
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 230 4980

description:
4980
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 228 4978

description:
4978
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 227 4977

description:
4977
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 226 4976

description:
4976
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 229 4979

description:
4979
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 225 4975

description:
4975
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 232 4982

description:
4982
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 222 4700

description:
4700
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 223 4701

description:
4701
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 221 4699

description:
4699
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 220 4698

description:
4698
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 219 4697

description:
4697
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 241 4992

description:
4992
Raw data file: G1135819.xml
Processed data file: G1135819_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 218 4696

description:
4696
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 216 4694

description:
4694
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 215 4693

description:
4693
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 224 4974

description:
4974
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 217 4695

description:
4695
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 212 4690

description:
4690
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 211 4689

description:
4689
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 214 4692

description:
4692
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 213 4691

description:
4691
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 209 4687

description:
4687
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 207 4685

description:
4685
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 210 4688

description:
4688
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 208 4686

description:
4686
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 205 4683

description:
4683
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 204 4682

description:
4682
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: input APEX-GFP rep2

city: Berkeley

first: Alejandro

last: Padron

state: CA

address: University of California, Berkeley

department: MCB

institute: UC Berkeley

description:
Sample name:
iGFP_2

data_processing:
Library strategy: APEX-seq
Fastq preprocessing performed with cutadapt
reads were aligned using hisat2
count tables were generated using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with counts

molecule: total RNA

extract_protocol:
APEX labeling reaction of RNAs were carried out using 500 µM biotin-phenol and incubating for 30 min followed by a 1 minute 1 mM H2O2 treatment. RNAs were extracted by treating cells with TRIzol. Biotinylated RNAs were enriched using streptavidin beads
Libraries were constructed using NEBnext Ultra II Directional RNA sequencing from NEB

tag: construct

value: APEX-GFP

tag: stress condition

value: Naive


title: Patient 203 4681

description:
4681
Raw data file: G1129200.xml
Processed data file: G1129200_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma