title: T29-Input

description: Input for T29-H3K27ac and T29-H3K4me3


title: T22-Input

status: Public on Aug 26 2021

type: SRA

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

country: China

institute: Wuhan University

description: Input for T22-H3K27ac and T22-H3K4me3

library_source: genomic

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to mouse reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files; Scores represent the RPM value.

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor from colorectal cancer patient

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606).

tag: tissue

value: Colorectal cancer

value: Tumor

tag: chip antibody


title: T23-Input

description: Input for T23-H3K27ac and T23-H3K4me3


title: T27-Input

description: Input for T27-H3K27ac and T27-H3K4me3


title: T9-Input

description: Input for T9-H3K27ac and T9-H3K4me3


title: T18-Input

description: Input for T18-H3K27ac and T18-H3K4me3


title: T20-Input

description: Input for T20-H3K27ac and T20-H3K4me3


title: T10-Input

description: Input for T10-H3K27ac and T10-H3K4me3


title: T17-Input

description: Input for T17-H3K27ac and T17-H3K4me3


title: T7-Input

description: Input for T7-H3K27ac and T7-H3K4me3


title: T5-Input

description: Input for T5-H3K27ac and T5-H3K4me3


title: T2-Input

description: Input for T2-H3K27ac and T2-H3K4me3


title: T3-Input

description: Input for T3-H3K27ac and T3-H3K4me3


title: T29-H3K4me3

value: H3K4me3 (Millipore, 04-745)


title: T4-Input

description: Input for T4-H3K27ac and T4-H3K4me3


title: T6-Input

description: Input for T6-H3K27ac and T6-H3K4me3


title: T1-Input

description: Input for T1-H3K27ac and T1-H3K4me3


title: T26-H3K4me3


title: T27-H3K4me3


title: T24-H3K4me3


title: T23-H3K4me3


title: T28-H3K4me3


title: T22-H3K4me3


title: T8-H3K4me3


title: T17-H3K4me3


title: T18-H3K4me3


title: T10-H3K4me3


title: T20-H3K4me3


title: T5-H3K4me3


title: T4-H3K4me3


title: T16-H3K4me3


title: T7-H3K4me3


title: T9-H3K4me3


title: T19-H3K4me3


title: T6-H3K4me3


title: T21-H3K4me3


title: T3-H3K4me3


title: T1-H3K4me3


title: T2-H3K4me3


title: PTCL_Sample 159

type: RNA

city: Madrid

first: Laura

middle: Jiménez

last: Tomas Roca

state: Madrid

address: Avenue Reyes Catolicos

department: Pathology Department

country: Spain

institute: Research Institute Fundacion Jimenez Diaz

hyb_protocol: Briefly, 208 genes and eight housekeeping gene probes (Supplemental Table 2) were hybridized to 400 ng of the total RNA for 16 h at 65°C, and applied to the nCounter Preparation Station for automated removal of excess probe and immobilization of probe–transcript complexes on a streptavidin-coated cartridge

scan_protocol: Non applicable

data_processing: Gene expression values were normalized through housekeeping genes. Normalized count data were log2 transformed and agglomerative hierarchical clustering of gene expression were performed

label: Non applicable

molecule: total RNA

source_name: Peripheral T-cell lymphoma

label_protocol: Non applicable

extract_protocol: RNA quality and quantity were assessed with an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA) using the TapeStation Systems (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: Formalin-fixed, paraffin-embedded

value: Peripheral T-cell lymphoma

tag: age

value: Adult


title: PTCL_Sample 158


title: PTCL_Sample 157


title: PTCL_Sample 154


title: PTCL_Sample 153


title: PTCL_Sample 155


title: PTCL_Sample 156


title: N79-RNA

description: Colorectal cancer patient 79

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2  v2.1.0 with default  parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: Native tissue from colorectal cancer patient

extract_protocol:
For all CRC patient samples, 50 mg tissue was used for RNA extraction. Total RNA was extracted by using CWBIO Ultrapure RNA Kit (CW0581M).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

tag: diagnosis

value: Native tissue


title: N80-RNA

description: Colorectal cancer patient 80


title: N77-RNA

description: Colorectal cancer patient 77


title: N78-RNA

description: Colorectal cancer patient 78


title: PTCL_Sample 150


title: PTCL_Sample 152


title: PTCL_Sample 144


title: N74-RNA

description: Colorectal cancer patient 74


title: PTCL_Sample 151


title: PTCL_Sample 148


title: N66-RNA

description: Colorectal cancer patient 66


title: N70-RNA

description: Colorectal cancer patient 70


title: N65-RNA

description: Colorectal cancer patient 65


title: N73-RNA

description: Colorectal cancer patient 73


title: PTCL_Sample 146


title: PTCL_Sample 149


title: PTCL_Sample 145


title: N62-RNA

description: Colorectal cancer patient 62


title: N69-RNA

description: Colorectal cancer patient 69


title: N68-RNA

description: Colorectal cancer patient 68


title: N61-RNA

description: Colorectal cancer patient 61


title: PTCL_Sample 143


title: N59-RNA

description: Colorectal cancer patient 59


title: N60-RNA

description: Colorectal cancer patient 60


title: N76-RNA

description: Colorectal cancer patient 76


title: N63-RNA

description: Colorectal cancer patient 63


title: N67-RNA

description: Colorectal cancer patient 67


title: N75-RNA

description: Colorectal cancer patient 75


title: PTCL_Sample 147


title: N72-RNA

description: Colorectal cancer patient 72


title: N64-RNA

description: Colorectal cancer patient 64


title: PTCL_Sample 142


title: N58-RNA

description: Colorectal cancer patient 58


title: N53-RNA

description: Colorectal cancer patient 53


title: N52-RNA

description: Colorectal cancer patient 52


title: N57-RNA

description: Colorectal cancer patient 57


title: N56-RNA

description: Colorectal cancer patient 56


title: GK2

city: Paris

first: Min

last: ZHAO

state: France

address: 15 rue de l'Ecole de Médecine

country: France

institute: INSERM U1138, Centre de Recherche des Cordelier, University Paris Descartes

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files including expecting counts, TPM and FPKM

organism: Rattus norvegicus

source_name: neuroretina

extract_protocol:
Neuroretinas of rats were carefully dissected from enucleated eyes, snap-frozen in liquid nitrogen and stored at -80°C until use. Total RNA was isolated from tissues using the RNeasy Mini Kit including DNase I treatment (Qiagen, Courtaboeuf, France).
Libraries were prepared from the extracted RNA using the KAPA Stranded mRNA-Seq Kit

treatment_protocol: A single intravitreal injection of 5 µL of PLGA microspheres (MSs) containing 6.2 µg spironolactone was performed. After 2 month, retinas were dissected for RNA sequencing. Control rats were injected with non-loaded MSs.

value: neuroretina

value: 14 months

tag: gender

value: male

tag: treatment

value: Non-loaded microspheres


title: Gk10

value: Spironolactone-loaded microspheres


title: N54-RNA

description: Colorectal cancer patient 54


title: GK4


title: GK11


title: pombe_freeMNase_rep1

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
S. pombe with exogenously added MNase
factor-agnostic DNA binding S. pombe protein footprints identified by exogenously added MNase

data_processing:
align using bwa with -n option set to 1; reads that map to more than one location are arbitrarily assigned to one of those locations; in case of mouse, align to both the standard mm10 genome build and to mm10 genome with single nucleotide substitutions from spretus genome (provided here as a fasta file)
picard CleanSam
picard SortSam
picard FixMateInformation
picard AddOrReplaceReadGroups
picard ValidateSamFile
choose only (1) perfect matches to mm10 that do not have perfect matches to mm10musculusSNPStospretusSNPs (musculus); or (2) perfect matches to mm10musculusSNPStospretusSNPs that do not have perfect matches to mm10 (spretus); or (3) restrict fragment length (TLEN designation in sam file format) to appropriate size range, if called for
calculate per-base-pair coverage with BedTools' genomecov with -d and -split options
Genome_build: mm10 (musculus); sacCer3 (S. cerevisiae); mm10 with single nucleotide substitutions from spretus SPRET_EiJ (spretus); Schizosaccharomyces_pombe_ASM294v2 (S. pombe); hg38 (human)
Supplementary_files_format_and_content: bedgraph files or txt files with coverage for single base pairs or intervals, as indicated; 1 fasta format file with musculus genome, except with single nucleotide substitution differences replaced with spretus sequence

organism: Schizosaccharomyces pombe

source_name: Antonio Bedalov

growth_protocol:
Yeast: All S. cerevisiae strains were in S288C background. S. cerevisiae experiments were carried out using standard YPD (yeast peptone dextrose) medium [2% (wt/vol) glucose, 1% yeast extract, 2% (wt/vol) peptone]. S. pombe experiments were carried out in Yeast Extract Dextrose (YES); logarithmically growing cells were arrested in early S-phase by adding 15 mM hydroxyurea and incubating for 3 hours.
Mammalian: Cells were transduced with lentiviral supernatant containing plx302-MCM2-FL-MNase, infected cells were selected out on Puromycin (2.5μg/ml) and expanded for further experiments. The expression of tagged MCM2 in HeLa and Patski cells was confirmed by Western blot using anti- MCM2 rabbit polyclonal antibody (HPA031495 Sigma) at 1:1,000 dilution.

extract_protocol: as described:  Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108(45):18318-23. Epub 2011/10/26. doi: 1110731108 [pii]10.1073/pnas.1110731108. PubMed PMID: 22025700; PubMed Central PMCID: PMC3215028.

treatment_protocol:
Yeast MNase-seq: Cells grown to log phase in rich medium, Yeast Peptone Agar with 2% glucose (YEPD) for S. Cerevisiae or Yeast Extract with Supplements with 3% glucose (YES), from an overnight 25 mL culture were synchronized with 3 μM alpha-factor for 1.5 hrs. at 30° C (S. cerevisiae) or with 15 mM hydroxyurea for 2 hours in S. pombe, which are the same conditions we used to prepare cells for ChEC. Arrested cells were crosslinked with 1% formaldehyde for 30 min at room temperature water bath with shaking. Formaldehyde was quenched with 125 mM glycine and cells were centrifuged at 3000 rpm for 5 min. Cells were washed twice with water and resuspended in 1.5 mL Buffer Z (1 M sorbitol, 50 mM Tris-HCl pH 7.4) with 1 mM beta-mercaptoethanol (1.1 μL of 14.3 M beta-mercaptoethanol diluted 1:10 in Buffer Z) per 25 mL culture. Cells were treated with 100 μL 20 mg/mL zymolyase at 30° C for 20–30 min depending on cell density. Spheroplasts were centrifuged at 5000 rpm for 10 min and resuspended in 5 mL NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) supplemented with 500 μM spermidine, 1 mM beta-mercaptoethanol and 0.075% NP-40. Nuclei were aliquoted in tubes with varying concentrations of micrococcal nuclease (Worthington), mixed via tube inversion, and incubated at room temperature for 20 mins. Chromatin digested with 1.9 U– 7.5 U micrococcal nuclease per 1/5th of spheroplasts from a 25 mL culture yielded appropriate mono-, di-, tri- nucleosome protected fragments for next-generation sequencing. Digestion was stopped with freshly made 5x stop buffer (5% SDS, 50 mM EDTA) and proteinase K was added (0.2 mg/ml final concentration) for an overnight incubation at 65° C to reverse crosslinking. DNA was extracted with phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation.
Yeast MCM-MNase: In budding yeast, ChEC-seq was carried out as previously described [33]. Fission yeast with MNases-tagged MCM2 were transferred from log phase to 15 mM HU for 3 hours, and then processed as in budding yeast. Two biological replicas were prepared for each genotype.
Mammalian MCM-MNase: Cells were grown in 6 well plates until >100% confluent, trypsinized and washed with a Wash Buffer (20mM HEPES, 110mM Potassium Acetate, 5mM Sodium Acetate, pH to 7.3 with NaOH). Cells were permeabilized with 0.02% digitonin in the Wash Buffer along with protease inhibitors (Roche # 04693159001) for 5 mins at RT. CaCl2 was added to a final concentration of 2.5mM for differing amounts of time, as indicated. The MNase activity was stopped by adding equal volume of a 2X Stop Buffer (400mM NaCl, 20mM EDTA, 4mM EGTA, 2% SDS). Proteinase K was added to a final concentration of 0.4mg/ml and samples incubated for 1 hr at 50° C. DNA was isolated using standard Phenol:Chloroform extraction and air dried DNA pellets resuspended in 0.1X TE (pH 8). All samples were treated with RNase A (0.3 μg/ml) before being processed for library preparation. Two biological replicas were prepared for both human and mouse cells.
Mouse replication: Patski cells were stained with propidium iodine and sorted according to DNA content into G1 and S-cells using flow cytometry. DNA was extracted from each cell fraction, fragmented by sonication and sequenced.

tag: sample type

value: MNase-seq

value: free MNase (MNase-seq)


title: PTCL_Sample 139


title: pombe_MCM2ChEC_HU_rep2

description:
S. pombe with MCM2-ChEC construct
MCM2 binding sites in S. pombe determined by MCM2-ChEC in cells arrested hydroxyurea (HU)

value: MCM2-ChEC, HU, rep2

value: calcium-treated DNA (ChEC)


title: GK8


title: N55-RNA

description: Colorectal cancer patient 55


title: PTCL_Sample 138


title: GK3


title: PTCL_Sample 136


title: PTCL_Sample 140


title: PTCL_Sample 141


title: PTCL_Sample 134


title: pombe_MCM2ChEC_G1_rep1

description:
S. pombe with MCM2-ChEC construct
MCM2 binding sites in S. pombe determined by MCM2-ChEC in cells arrested in G1 by nitrogen depletion

value: MCM2-ChEC, G1, rep1


title: PTCL_Sample 137


title: N49-RNA

description: Colorectal cancer patient 49


title: pombe_MCM2ChEC_HU_rep1

value: MCM2-ChEC, HU, rep1


title: N51-RNA

description: Colorectal cancer patient 51

value: Colorectal cancer


title: PTCL_Sample 135


title: N47-RNA

description: Colorectal cancer patient 47


title: N45-RNA

description: Colorectal cancer patient 45


title: N48-RNA

description: Colorectal cancer patient 48


title: PTCL_Sample 132


title: PTCL_Sample 130


title: N50-RNA

description: Colorectal cancer patient 50


title: PTCL_Sample 131


title: N44-RNA

description: Colorectal cancer patient 44


title: N46-RNA

description: Colorectal cancer patient 46


title: PTCL_Sample 133


title: N43-RNA

description: Colorectal cancer patient 43


title: PTCL_Sample 129


title: PTCL_Sample 127


title: N42-RNA

description: Colorectal cancer patient 42


title: PTCL_Sample 128


title: PTCL_Sample 126


title: PTCL_Sample 125


title: N41-RNA

description: Colorectal cancer patient 41


title: HPRT3 ARV-771 3

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HPRT3 ARV-771 3

growth_protocol: Human RT-DLBCL cells collected from mouse PDX models were cultured in 20% FBS containing RPMI1640 media.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility.

treatment_protocol: 1 x 10^6 Human RT-DLBCL cells collected from mouse PDX models were cultured in 20% FBS containing RPMI1640 media and treated for 8 hours with 1000 nM of OTX015 or 250 nM of ARV-771. Cells were harvested by centrifugation and lysed with a Beta-mercaptoethanol containing RNA lysis buffer.

tag: cell type

value: Diffuse Large B cell Lymphoma cells

tag: clonal relationship

value: Clonally related to CLL

tag: agent


title: GC B cells of Tnfrsf13b-KO, biological rep2

city: Ann Arbor

first: Mayara

last: Garcia de Mattos Barbosa

state: Michigan

address: 1150 Medical Science Center Drive MSRB1 room A520-1

department: Transplant Surgery

institute: University of Michigan

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
Tnfrsf13b-KO_GC-2

hyb_protocol: Following labeling procedure, 2.75 ug of cDNA were hybridized at 48°C on Mouse Gene 2.1 ST, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.4.3

label: biotin

organism: Mus musculus

source_name: Germinal center B cells from Tnfrsf13b knockout mice

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico kit protocol (GeneChip® WT Pico Reagent Kit Manual P/N 703262 Rev. 1) from 10 ng total RNA.

extract_protocol: RNA from the sorted GC B cells were extracted with the RNeasy Plus Mini Kit (Qiagen Cat#74134) as recommended by the manufacturer.

treatment_protocol: Splenocytes were isolated from C57BL/6 mice background mice 10 days postimmunization. Cells were stained, and germinal center B cells (FVS780- CD19+ GL7+ CD95+) were sorted in a Synergy SY3200 Cell Sorter.

value: Splenic GC B cells

tag: background strain

tag: genotype

value: C57BL-6 Tnfrsf13b knockout

value: adult


title: HPRT3 OTX015 3

source_name: HPRT3 OTX015 3


title: HPRT3 ARV-771 1

source_name: HPRT3 ARV-771 1


title: HPRT3 ARV-771 2

source_name: HPRT3 ARV-771 2


title: GC B cells of Tnfrsf13b-KO, biological rep3

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
Tnfrsf13b-KO_GC-3


title: PTCL_Sample 124

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 123


title: LAM332-1

city: Chicago

first: Kyle

last: Amber

state: Illinois

address: 1735 W Harrison St. Lab 741

institute: Rush University Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp.
Clean Reads mapped to GRCh38.p13 whole genome using HISAT2 version 2.2.1 with default parameters
Reads count were calculated using Htseq-count with parameters --stranded=no -f bam.
DESeq2 was used to analyze the DEG for samples with biological replicates. During the process, Fold Change ≥ 2 and FDR <0.01 are set as screening criteria.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Primary human keratiniocyte incubated with laminin-332 pemphigoi

growth_protocol: Epilife, low calcium, 5% CO2

extract_protocol:
Qiagan Rneasy
After DNase I treatment and performing quality control (QC), 200 ng of high-quality total RNA was proceed to library construction. Magnetic beads with Oligo (dT) are used to isolate mRNA (for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer after adding dNTPs, RNase H and DNA polymerase I. Short fragments are purified and resolved with EB buffer for end repair and single nucleotide A (adenine) addition. After that, the short fragments are connected with sequencing adapters. The double-stranded cDNA library is completed through size selection and PCR enrichment. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

treatment_protocol: Treated overnight with Laminin-332 IgG or control IgG

value: Primary human keratinocytes

value: IgG from patients with laminin-332 pemphigoi


title: LAM332-3


title: CtrlIgG-2

source_name: Primary human keratiniocyte incubated with IgG

value: IgG from normal healthy control


title: CtrlIgG-1


title: LAM332-2


title: LAM332-4


title: CtrlIgG-3


title: GC B cells of Tnfrsf13b WT, biological rep2

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
WT_GC-2

source_name: Germinal center B cells from Tnfrsf13b wild type mice

value: C57BL-6 Tnfrsf13b wild type-wild type


title: GC B cells of Tnfrsf13b A144E-WT, biological rep1

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
A144E-WT_GC-1

source_name: Germinal center B cells from Tnfrsf13b A144E heterozygous mice

value: C57BL-6 Tnfrsf13b wild type-wild type and A144E-A144E parents


title: GC B cells of Tnfrsf13b WT, biological rep3

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
WT_GC-3


title: GC B cells of Tnfrsf13b-KO, biological rep1

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
Tnfrsf13b-KO_GC-1


title: HPRT3 OTX015 2

source_name: HPRT3 OTX015 2


title: GC B cells of Tnfrsf13b WT, biological rep1

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
WT_GC-1


title: HPRT3 OTX015 1

source_name: HPRT3 OTX015 1


title: N40-RNA

description: Colorectal cancer patient 40

value: Native tissue


title: GC B cells of Tnfrsf13b A144E-A144E, biological rep2

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
A144E-A144E_GC-2

source_name: Germinal center B cells from Tnfrsf13b A144E homozygous mice

value: C57BL-6 Tnfrsf13b A144E-A144E


title: N39-RNA

description: Colorectal cancer patient 39


title: N38-RNA

description: Colorectal cancer patient 38


title: PTCL_Sample 122


title: N37-RNA

description: Colorectal cancer patient 37


title: HPRT3 Control 3

source_name: HPRT3 Control 3

value: Control


title: N36-RNA

description: Colorectal cancer patient 36


title: PTCL_Sample 121

source_name: Peripheral T-cell lymphoma


title: N35-RNA

description: Colorectal cancer patient 35

source_name: Native tissue from colorectal cancer patient


title: HPRT3 Control 2

source_name: HPRT3 Control 2


title: HPRT2 ARV-771 2

source_name: HPRT2 ARV-771 2

value: Clonally unrelated to CLL


title: HPRT2 OTX015 3

source_name: HPRT2 OTX015 3


title: N34-RNA

description: Colorectal cancer patient 34

value: Colorectal cancer


title: PTCL_Sample 120


title: HPRT2 ARV-771 1

source_name: HPRT2 ARV-771 1

value: Diffuse Large B cell Lymphoma cells


title: N33-RNA

description: Colorectal cancer patient 33


title: HPRT3 Control 1

source_name: HPRT3 Control 1

value: Clonally related to CLL


title: PTCL_Sample 117


title: PTCL_Sample 116


title: HPRT2 OTX015 1

source_name: HPRT2 OTX015 1


title: HPRT2 Control 1

source_name: HPRT2 Control 1


title: N31-RNA

description: Colorectal cancer patient 31


title: HPRT2 Control 3

source_name: HPRT2 Control 3


title: HPRT1 ARV-771 2

source_name: HPRT1 ARV-771 2

value: GCB subtype


title: PTCL_Sample 118


title: N32-RNA

description: Colorectal cancer patient 32


title: HPRT1 ARV-771 3

source_name: HPRT1 ARV-771 3


title: HPRT2 ARV-771 3

source_name: HPRT2 ARV-771 3


title: GC B cells of Tnfrsf13b A144E-A144E, biological rep3

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
A144E-A144E_GC-3

value: Splenic GC B cells


title: N30-RNA

description: Colorectal cancer patient 30


title: HPRT2 Control 2

source_name: HPRT2 Control 2


title: HPRT1 OTX015 2

source_name: HPRT1 OTX015 2


title: PTCL_Sample 119


title: N29-RNA

description: Colorectal cancer patient 29


title: HPRT1 OTX015 1

source_name: HPRT1 OTX015 1


title: HPRT1 Control 2

source_name: HPRT1 Control 2


title: HPRT1 Control 3

source_name: HPRT1 Control 3


title: HPRT1 Control 1

source_name: HPRT1 Control 1


title: N27-RNA

description: Colorectal cancer patient 27

source_name: Native tissue from colorectal cancer patient


title: N28-RNA

description: Colorectal cancer patient 28


title: N26-RNA

description: Colorectal cancer patient 26


title: HPRT1 OTX015 3

source_name: HPRT1 OTX015 3


title: human_MCM2ChEC_rep1

description:
human (HeLa) cells with MCM2-Mnase construct
MCM2 binding sites in human HeLa cells determined by MCM2-ChEC in cells grown to confluence

source_name: Antonio Bedalov

value: calcium-treated DNA (ChEC)


title: GM-EDTA-R2

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2 and the iterative mapping approach described in Imakaev et al. 2012
Filtering was carried out using the dekkerlab-cMapping pipeline available on github https://github.com/dekkerlab/cMapping
All sequencing runs from each replicate were mapped separately, then combined for iterative correction and binning performed using method described by Imakaev et al. and implemented in https://github.com/dekkerlab/cMapping
Genome_build: hg19
Supplementary_files_format_and_content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 10 kb, 20 kb, 40 kb, 100 kb, 250 kb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 2.5 Mb bin size

source_name: GM12878 cells

growth_protocol: GM12878 cells were maintained and split according to Coriell SOPs.

extract_protocol:
Hi-C experiments were performed on 10-20 million cells for each condition.  Crosslinking was performed with 1% formaldehyde pre-mixed with the corresponding appropriate buffer (1x HBSS, or 1 mM EDTA + 10 mM HEPES) immediately before addition to the plates of nuclei.  After 10 minutes, crosslinking was quenched with glycine, and plates of crosslinked nuclei were washed in the same buffer corresponding to their expansion or contraction condition.  It was not possible to harvest and collect nuclei by scraping and centrifugation due to the fragility of the nuclei, particularly in the expanded case, so nuclei were lysed directly in plates by aspirating all liquid and then adding 1.8 mL of 0.3% SDS in 1x NEB2 buffer (New England Biolabs) per 10 cm dish. Dishes were incubated with gentle agitation at 37oC for 30 min.  Crosslinked material was then removed the plate by scraping. If more than one plate was to be combined to obtain enough cells, the SDS-cell mixture scraped from the first plate was transferred to the second plate for another round of incubation, so that cells from all plates were combined into a final volume of less than 3 mL.  SDS was sequestered by addition of 1.8% Triton (final concentration).  Crosslinked complexes were then divided into aliquots of 560 uL each to match other Hi-C protocols, and were then subjected to digestion with HindIII overnight (500 U per 560 uL aliquot), biotin fill-in, and dilute ligation as previously described (Belton et al. 2012).
After streptavidin enrichment of biotinylated ligation junctions,  Illumina paired-end adapters were ligated onto the DNA ends and then the fragments were PCR amplified.

treatment_protocol: GM12878 nuclei were isolated with the following approach:  1x10^8 cells were collected by centrifugation (200xg, 5 minutes, room temperature) and then washed twice with 10 mL ice-cold 1X dPBS and then twice with 5 mL ice cold Nuclei Buffer (NB) (10 mM PIPES pH 7.4, 2 mM MgCl2, 10 mM KCl, 1mM DTT, H2O pH 7.4) containing protease inhibitors (Thermo Scientific).  After final wash and spin, the cell pellet was resuspended in 10 mL NB + 0.06% NP-40, vortexed gently, and then allowed to equilibrate on ice for 10 minutes. Cells were then homogenized on ice using a Dounce homogenizer (Pestle A) with 10 slow strokes.  To remove excess cellular material, 5 mL of lysed cell mixture was layered on top of a 20 mL sucrose cushion: 30% sucrose in NB and centrifuged for 10 minutes at 730xg. The supernatant and interface was carefully removed and the pellet containing nuclei was resuspended in either 1x Hank’s Balanced Salt Solution (HBSS: 1.26 mM CaCl2, 0.49 mM MgCl2, 0.41 mM MgSO4, 5 mM KCl, 0.44 mM KH2PO4, 4.17 mM NaHCO3, 137.9 mM NaCl, 0.34 mM Na2HPO4, 5.56 mM D-Glucose) and were allowed to settle and attach to poly-D-lysine coated dishes at 4 C for several hours or overnight.

tag: condition

value: Isolated nuclei expanded by incubation in 10 mM HEPES pH 7.4 + 1 mM EDTA for 1 hour, 4 degrees C

tag: media

value: RPMI, 15 percentFBS, 100 micrograms/mL penicillin-streptomycin

tag: cell line


title: GM-HBSSpostEDTA-R2

value: Isolated nuclei after expansion in 1 mM EDTA for 1 hour, returned to 1xHBSS for 20 minutes


title: GM-1xHBSS-R3

value: Isolated nuclei in 1xHBSS


title: N23-RNA

description: Colorectal cancer patient 23


title: Single cell expression of human CRC samples from patient C172_T [C172_T_0_0_0_c1_v3]

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description: Single cell RNA-Seq (10x)

data_processing:
3' RNAseq (10x kit V2 or V3 chemistry)
Demultiplexing is run using Cell Ranger mkfastq.
Cellranger count is run using cell-ranger v3.1 on firecoud.
R package dropletUtils is used to exclude chimeric reads and identify and exclude empty droplets
Genome_build: GRCh37 hg19 liftover (v28, https://www.gencodegenes.org/human/release_28lift37.html)
Supplementary_files_format_and_content: Raw count matriece are in the HDF5 Feature Barcode Matrix Format used by 10x, and metadata files are comma-delimited text.
Supplementary_files_format_and_content: hdf5 file in 10x cellranger format
Supplementary_files_format_and_content: csv file, cluster subtype assignments

source_name: Human colon tissue

extract_protocol:
Samples were cut by pathology assistants at MGH and BWH hospitals. To preserve the invasive border for clinical pathological evaluation, the pathology assistants did not sample tumor down to the invasive border. The tissue was transported in ice cold RPMI with 5% human serum prior to processing. Tissue was transferred into a petri dish on ice. Fat, necrotic, and fibrous areas were removed. Residual blood and stool were washed off the tissue with cold RPMI. Tissue allocated for dissociation was minced into small pieces (~1 mm^3) using a scalpel prior to enzymatic dissociation. Thereafter tissue was transferred into 1.5 ml Eppendorf tubes, each containing 1 ml of enzymatic digestion mix (Miltenyi, Human Tumor Dissociation kit). 1 ml of digestion mix was used per 50 mg of tissue. The Eppendorf tubes were then transferred to a rotation shaker set to 37 ̊C and 550 rpm and shaken for 20 min. The digestion mix was subsequently filtered through a 70um cell strainer sitting on a 50 ml falcon tube on ice and mechanically dissociated once more with the plunger of a 1ml syringe against the screen. The filter and enzymatic mixture were washed with RPMI containing 2% human serum as needed until the suspension passed through the filter. The cell suspension was spun at 500 g for 7 min in 4 ̊C pre-cooled centrifuge to pellet the cells. The pellet was lysed in 4ml ammonium-chloride-potassium (ACK) buffer for 2 minutes and then stopped with RPMI containing 2% human serum. The cell suspension was then centrifuged at 500 g for 7 min at 4 ̊C. The resulting cell pellet was resuspended in loading buffer (PBS containing 0.04% m/v BSA) and filtered through the cell strainer snap cap (Corning 352235) into a 1.5 ml Eppendorf tube. The cell suspension was centrifuged at 500 g for 2 min at 4 ̊C. The pellet was resuspended in cold loading buffer (PBS containing 0.04% m/w BSA) and counted by trypan exclusion. The suspension was then diluted to 1000 cells / ul. 8000 cells were loaded into each channel of the 10x Chromium controller, following the manufacturer-supplied protocol for the 3’ kit. Additionally, a CD45-enriched sample was run for each specimen. To this end, dissociated and ACK-lysed cells were resuspended in cold PBS with 2 mM EDTA and 0.5% FCS and CD45+ cells were enriched using CD45 MicroBeads, human (Miltenyi) following the manufacturer’s instructions. Cells were resuspended in loading buffer and loaded with 8000 cells per channel as described above.
10x libraries were constructed using the 10x supplied protocol and sequenced at the Broad Institute Genomics Platform.
3' RNAseq (10x kit V2 or V3 chemistry)

value: T

value: unosrted

tag: patienttypeid

tag: histologictypesimple

value: Adenocarcinoma

value: preserved

tag: mmrstatus

value: MMRp

value: RIGHT (ascending)

tag: tissuesitesimple

value: right

value: Grade 2 (Moderately differntiated)

tag: histologicgradesimple

value: low

tag: tumorstage

tag: nodestatussimple

value: Nneg

tag: metastasisstatus

value: not entered (Mx)

tag: tumorsize

tag: sizequantile


title: Single cell expression of human CRC samples from patient C173_T [C173_T_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: LEFT(descending)

value: left

value: Grade 3 (Poorly differentiated. < 50% gland formation).

value: high

value: Npos


title: Single cell expression of human CRC samples from patient C171_TB [C171_TB_1_1_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: RIGHT colon


title: human_MCM2ChEC_rep2

description:
human (HeLa) cells with MCM2-ChEC construct
MCM2 binding sites in human HeLa cells determined by MCM2-ChEC in cells grown to confluence

tag: sample type

value: MCM2-ChEC, rep2

tag: treatment

value: calcium-treated DNA (ChEC)


title: N24-RNA

description: Colorectal cancer patient 24

tag: diagnosis

value: Colorectal cancer

tag: tissue

value: Native tissue


title: N22-RNA

description: Colorectal cancer patient 22


title: Single cell expression of human CRC samples from patient C171_TB [C171_TB_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma

value: preserved

value: MMRp

value: right

value: Grade 2 (Moderately differntiated)


title: N21-RNA

description: Colorectal cancer patient 21


title: GC B cells of Tnfrsf13b A144E-WT, biological rep2

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
A144E-WT_GC-2

source_name: Germinal center B cells from Tnfrsf13b A144E heterozygous mice

value: Splenic GC B cells

tag: background strain

tag: genotype

value: C57BL-6 Tnfrsf13b wild type-wild type and A144E-A144E parents

tag: age

value: adult


title: HPRT2 OTX015 2

source_name: HPRT2 OTX015 2

tag: cell type

value: Diffuse Large B cell Lymphoma cells

tag: clonal relationship

value: Clonally unrelated to CLL

tag: agent


title: Single cell expression of human CRC samples from patient C171_TA [C171_TA_1_1_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

tag: patienttypeid

tag: histologictypesimple

tag: mmrstatus

tag: tissuesitesimple

value: low

value: Nneg

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C170_T [C170_T_0_0_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: Right (ascending)

tag: histologicgradesimple

tag: tumorstage

tag: nodestatussimple

tag: metastasisstatus


title: Single cell expression of human CRC samples from patient C171_TA [C171_TA_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma

value: RIGHT colon

tag: tumorsize

tag: sizequantile


title: HPRT1 ARV-771 1

source_name: HPRT1 ARV-771 1

value: GCB subtype


title: Single cell expression of human CRC samples from patient C170_T [C170_T_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: right

value: Grade 2 (Moderately differntiated)


title: N19-RNA

description: Colorectal cancer patient 19

tag: diagnosis

value: Colorectal cancer

tag: tissue

value: Native tissue


title: Single cell expression of human CRC samples from patient C170_N [C170_N_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: Single cell expression of human CRC samples from patient C169_T [C169_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: MSH2 and MSH6 deficient

value: RIGHT (transverse)

value: Grade 2 (Moderately differentiated. 50-95% gland formation)

value: Npos


title: Single cell expression of human CRC samples from patient C168_T [C168_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma;Mucinous

value: MLH1 and PMS2 deficient

value: MMRd

value: low

value: Nneg

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C167_T [C167_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma

value: PMS2 deficiency and markedly reduced MLH1

value: RIGHT (cecum)

value: right

value: Grade 3 (Poorly differentiated. < 50% gland formation.)

value: high


title: PTCL_Sample 108

source_name: Peripheral T-cell lymphoma

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 109


title: PTCL_Sample 113


title: PTCL_Sample 107


title: PTCL_Sample 111


title: PTCL_Sample 106


title: PTCL_Sample 110


title: PTCL_Sample 115


title: PTCL_Sample 112


title: PTCL_Sample 114


title: N20-RNA

description: Colorectal cancer patient 20

value: Colorectal cancer

value: Native tissue


title: N17-RNA

description: Colorectal cancer patient 17


title: Single cell expression of human CRC samples from patient C165_T [C165_T_0_0_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: Isolated MSH6 deficiency

value: RIGHT colon

value: Grade 3 (poorly differentiated)

value: Npos


title: Single cell expression of human CRC samples from patient C166_T [C166_T_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: LEFT (Sigmoid)

value: left

value: Grade 2 (Moderately differntiated)

value: low

value: not entered (Mx)


title: PTCL_Sample 103


title: Single cell expression of human CRC samples from patient C165_T [C165_T_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma

value: MMRd

value: right

value: high


title: N16-RNA

description: Colorectal cancer patient 16

value: Colorectal cancer

value: Native tissue


title: PTCL_Sample 102

value: Peripheral T-cell lymphoma

value: Adult


title: Single cell expression of human CRC samples from patient C165_N [C165_N_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon

value: RIGHT colon


title: PTCL_Sample 105


title: N10-RNA

description: Colorectal cancer patient 10


title: GC B cells of Tnfrsf13b A144E-WT, biological rep3

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
A144E-WT_GC-3

value: Splenic GC B cells

tag: background strain

tag: genotype

value: C57BL-6 Tnfrsf13b wild type-wild type and A144E-A144E parents

value: adult


title: PTCL_Sample 101

tag: age


title: Single cell expression of human CRC samples from patient C164_T [C164_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: Isolated MSH6 deficiency

value: RIGHT (ascending)

value: Grade 2 (Moderately differentiated. 50-95% gland formation)

value: low

value: Nneg


title: PTCL_Sample 104


title: N18-RNA

description: Colorectal cancer patient 18


title: Single cell expression of human CRC samples from patient C162_T [C162_T_0_0_0_c2_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma

value: preserved

value: MMRp

value: right

value: Grade 2 (Moderately differntiated)

value: Npos

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C162_T [C162_T_0_0_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon


title: Single cell expression of human CRC samples from patient C163_T [C163_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: Medullary

value: MSH2 and MSH6 deficient

value: MMRd

value: RIGHT (transverse)

value: Grade 3 (Poorly differentiated. < 50% gland formation)

value: high


title: Single cell expression of human CRC samples from patient C162_N [C162_N_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: Single cell expression of human CRC samples from patient C162_N [C162_N_0_0_0_c2_v2]

description: Single cell RNA-Seq (10x)

value: unosrted


title: Single cell expression of human CRC samples from patient C162_T [C162_T_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma

value: low


title: Single cell expression of human CRC samples from patient C162_T [C162_T_0_0_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: right


title: PTCL_Sample 99

value: Peripheral T-cell lymphoma

value: Adult


title: Single cell expression of human CRC samples from patient C160_T [C160_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: RIGHT (ascending)

value: Grade 3 (Poorly differentiated. < 50% gland formation) and Grade 2 (Moderately differentiated. 50-95% gland formation)

value: Npos

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C161_T [C161_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: RIGHT colon

value: Grade 2 (Moderately differentiated. 50-95% gland formation)

value: Nneg


title: Single cell expression of human CRC samples from patient C159_T [C159_T_1_1_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: RIGHT (cecum)

value: Grade 3 (Poorly differentiated. < 50% gland formation.)

value: high


title: N6-RNA

description: Colorectal cancer patient 6

value: Colorectal cancer

value: Native tissue


title: PTCL_Sample 98


title: N5-RNA

description: Colorectal cancer patient 5


title: N8-RNA

description: Colorectal cancer patient 8


title: N7-RNA

description: Colorectal cancer patient 7


title: Single cell expression of human CRC samples from patient C159_T [C159_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: unosrted

value: Adenocarcinoma

value: preserved


title: PTCL_Sample 97

value: Peripheral T-cell lymphoma

value: Adult


title: N4-RNA

description: Colorectal cancer patient 4


title: Single cell expression of human CRC samples from patient C158_T [C158_T_1_1_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: right

value: low


title: Single cell expression of human CRC samples from patient C158_T [C158_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: RIGHT colon

value: Grade 2 (Moderately differentiated. 50-95% gland formation)

value: not entered (Mx)


title: N2-RNA

description: Colorectal cancer patient 2


title: Single cell expression of human CRC samples from patient C157_T [C157_T_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: MMRp

value: LEFT(descending)

value: left

value: Grade 2 (Moderately differntiated)

value: Npos


title: N9-RNA

description: Colorectal cancer patient 9

value: Colorectal cancer

value: Native tissue


title: PTCL_Sample 100


title: PTCL_Sample 94


title: T80-RNA

description: Colorectal cancer patient 80

source_name: Tumor from colorectal cancer patient

value: Tumor


title: Single cell expression of human CRC samples from patient C156_T [C156_T_1_1_1_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma

value: Grade 2 (Moderately differentiated. 50-95% gland formation).

value: Nneg


title: Single cell expression of human CRC samples from patient C156_T [C156_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: unosrted

value: MLH1 and PMS2 deficient

value: MMRd

value: right


title: Single cell expression of human CRC samples from patient C157_N [C157_N_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: N1-RNA

description: Colorectal cancer patient 1


title: PTCL_Sample 93

value: Peripheral T-cell lymphoma

value: Adult


title: Single cell expression of human CRC samples from patient C155_T [C155_T_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: RIGHT (ascending)

value: Grade 2 (Moderately differentiated.)

value: low


title: PTCL_Sample 96


title: Single cell expression of human CRC samples from patient C154_T [C154_T_1_1_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: T

value: RIGHT (transverse)

value: Grade 2 (Moderately differentiated. 50-95% gland formation.)

value: Npos

value: not entered (Mx)


title: PTCL_Sample 95


title: Single cell expression of human CRC samples from patient C153_T [C153_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: LEFT (sigmoid)

value: left

value: Grade 2 (Moderately differentiated. 50-95% gland formation)


title: T79-RNA

description: Colorectal cancer patient 79

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C153_T [C153_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted


title: PTCL_Sample 92

value: Peripheral T-cell lymphoma

value: Adult


title: T78-RNA

description: Colorectal cancer patient 78


title: PTCL_Sample 90


title: Single cell expression of human CRC samples from patient C152_T [C152_T_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: RIGHT (hepatic flexure)

value: right

value: Grade 2 (Moderately Differentiated)

value: Nneg


title: PTCL_Sample 91


title: Single cell expression of human CRC samples from patient C152_N [C152_N_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: PTCL_Sample 89


title: Single cell expression of human CRC samples from patient C151_T [C151_T_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma

value: RIGHT (cecum)

value: Grade 3 (but Moderately differentiated)

value: high

value: not entered (Mx)


title: T77-RNA

description: Colorectal cancer patient 77

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C151_N [C151_N_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted


title: GC B cells of Tnfrsf13b A144E-A144E, biological rep1

description:
Gene expression data from sorted splenic germinal center B cells 10 days after immunization with 50 million BALB-c splenocytes and thymocytes
A144E-A144E_GC-1

source_name: Germinal center B cells from Tnfrsf13b A144E homozygous mice

value: Splenic GC B cells

value: C57BL-6 Tnfrsf13b A144E-A144E

value: adult


title: PTCL_Sample 88

value: Peripheral T-cell lymphoma

value: Adult


title: T76-RNA

description: Colorectal cancer patient 76


title: Single cell expression of human CRC samples from patient C149_T [C149_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: RIGHT colon

value: right

value: Grade 2 (Moderately differentiated. 50-95% gland formation)

value: low

value: Npos


title: T75-RNA

description: Colorectal cancer patient 75


title: T74-RNA

description: Colorectal cancer patient 74


title: Single cell expression of human CRC samples from patient C149_T [C149_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma


title: Single cell expression of human CRC samples from patient C150_T [C150_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: LEFT (rectosigmoid)

value: left

value: Nneg

value: not entered (Mx)


title: PTCL_Sample 87


title: Single cell expression of human CRC samples from patient C147_T [C147_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: RIGHT (cecum)


title: T73-RNA

description: Colorectal cancer patient 73

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C146_T [C146_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT (ascending)

value: Grade 1 (Well differentiated. > 95% gland formation)


title: Single cell expression of human CRC samples from patient C147_T [C147_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: right


title: PTCL_Sample 86

value: Peripheral T-cell lymphoma

value: Adult


title: Single cell expression of human CRC samples from patient C145_T [C145_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma;Mucinous;Neuroendocrine

value: preserved

value: MMRp

value: RIGHT colon

value: Grade 3 (Poorly differentiated. < 50% gland formation)

value: high

value: Npos

value: pM1c (Metastases the peritoneal surface, alone or with other site or organ metastases):Sites involved:Liver and peritoneum.


title: T72-RNA

description: Colorectal cancer patient 72

value: Colorectal cancer


title: Single cell expression of human CRC samples from patient C146_T [C146_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: MLH1 and PMS2 deficient

value: MMRd

value: low

value: Nneg

value: not entered (Mx)


title: PTCL_Sample 84

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 85


title: PTCL_Sample 83


title: T70-RNA

description: Colorectal cancer patient 70

value: Tumor


title: Single cell expression of human CRC samples from patient C144_T [C144_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: RIGHT (cecum)

value: right

value: Grade 2 (Moderately differentiated. 50-95% gland formation).


title: Single cell expression of human CRC samples from patient C144_T [C144_T_1_1_12_c1_v2]

description: Single cell RNA-Seq (10x)


title: T69-RNA

description: Colorectal cancer patient 69


title: Single cell expression of human CRC samples from patient C150_T [C150_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: preserved

value: MMRp

value: LEFT (rectosigmoid)

value: left

value: Grade 2 (Moderately differentiated. 50-95% gland formation)


title: Single cell expression of human CRC samples from patient C144_T [C144_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: MLH1 and PMS2 deficient

value: MMRd


title: Single cell expression of human CRC samples from patient C143_T [C143_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: MSH2 and MSH6 deficient

value: low

value: Nneg

value: not entered (Mx)


title: PTCL_Sample 81

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 82


title: T68-RNA

description: Colorectal cancer patient 68

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C143_T [C143_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: unosrted

value: RIGHT (cecum)

value: right

value: Grade 2 (Moderately differentiated. 50-95% gland formation).


title: T67-RNA

description: Colorectal cancer patient 67


title: Single cell expression of human CRC samples from patient C143_N [C143_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: Single cell expression of human CRC samples from patient C142_T [C142_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: RIGHT (hepatic flexure)

value: Grade 1 (Well differentiated. > 95% gland formation)

value: Npos


title: T66-RNA

description: Colorectal cancer patient 66


title: Single cell expression of human CRC samples from patient C142_T [C142_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: MSH2 and MSH6 deficient

value: MMRd

value: low


title: PTCL_Sample 79

value: Peripheral T-cell lymphoma

value: Adult


title: T65-RNA

description: Colorectal cancer patient 65

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C140_T [C140_T_1_1_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: T

value: preserved

value: MMRp

value: LEFT (sigmoid)

value: left

value: Grade 1 (Well differentiated. > 95% gland formation).

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C140_T [C140_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma


title: PTCL_Sample 80


title: Single cell expression of human CRC samples from patient C142_N [C142_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: unosrted

value: Normal colon

value: RIGHT (hepatic flexure)

value: right


title: Single cell expression of human CRC samples from patient C145_T [C145_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma;Mucinous;Neuroendocrine

value: RIGHT colon

value: Grade 3 (Poorly differentiated. < 50% gland formation)

value: high

value: Npos

value: pM1c (Metastases the peritoneal surface, alone or with other site or organ metastases):Sites involved:Liver and peritoneum.


title: T64-RNA

description: Colorectal cancer patient 64

value: Colorectal cancer

value: Tumor


title: T63-RNA

description: Colorectal cancer patient 63


title: Single cell expression of human CRC samples from patient C140_N [C140_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: LEFT (sigmoid)

value: left


title: Single cell expression of human CRC samples from patient C139_T [C139_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: MSI

value: MMRd

value: Grade 2 (Moderately differentiated. 50-95% gland formation).

value: low

value: Nneg

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C140_T [C140_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma

value: preserved

value: MMRp

value: Grade 1 (Well differentiated. > 95% gland formation).


title: Single cell expression of human CRC samples from patient C139_T [C139_T_1_1_0_c2_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon

value: right


title: Single cell expression of human CRC samples from patient C139_T [C139_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: Single cell expression of human CRC samples from patient C139_N [C139_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: T62-RNA

description: Colorectal cancer patient 62

value: Colorectal cancer

value: Tumor


title: T61-RNA

description: Colorectal cancer patient 61


title: Single cell expression of human CRC samples from patient C139_N [C139_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: PTCL_Sample 78

value: Peripheral T-cell lymphoma

value: Adult


title: T60-RNA

description: Colorectal cancer patient 60


title: Single cell expression of human CRC samples from patient C138_T [C138_T_0_0_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma;Mucinous

value: MSH2 and MSH6 deficient

value: MMRd

value: RIGHT colon (transverse)

value: Grade 2 (Moderately differntiated)


title: Single cell expression of human CRC samples from patient C138_T [C138_T_0_0_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: low

value: Nneg

value: not entered (Mx)


title: T59-RNA

description: Colorectal cancer patient 59


title: PTCL_Sample 72


title: Single cell expression of human CRC samples from patient C138_T [C138_T_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted


title: PTCL_Sample 75


title: PTCL_Sample 76


title: PTCL_Sample 73


title: Single cell expression of human CRC samples from patient C138_N [C138_N_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: right


title: PTCL_Sample 77


title: PTCL_Sample 71


title: Single cell expression of human CRC samples from patient C137_T [C137_T_1_1_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: Isolated PMS2 deficiency

value: RIGHT (ascending)

value: Grade 3 (Poorly differentiated. < 50% gland formation).

value: high

value: Npos


title: Single cell expression of human CRC samples from patient C137_T [C137_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T


title: PTCL_Sample 74

value: Peripheral T-cell lymphoma

value: Adult


title: Single cell expression of human CRC samples from patient C137_T [C137_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: MMRd


title: Single cell expression of human CRC samples from patient C138_N [C138_N_0_0_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon

value: RIGHT colon (transverse)


title: Single cell expression of human CRC samples from patient C137_N [C137_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)


title: PTCL_Sample 69


title: Single cell expression of human CRC samples from patient C136_T [C136_T_1_1_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: LEFT (Rectosigmoid)

value: left

value: Grade 2 (Moderately differntiated)

value: low

value: Nneg


title: PTCL_Sample 70


title: Single cell expression of human CRC samples from patient C138_T [C138_T_0_0_0_c2_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma;Mucinous

value: MSH2 and MSH6 deficient

value: right

value: not entered (Mx)


title: T55-RNA

description: Colorectal cancer patient 55

value: Colorectal cancer

value: Tumor


title: T56-RNA

description: Colorectal cancer patient 56


title: Single cell expression of human CRC samples from patient C137_N [C137_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: RIGHT (ascending)


title: T54-RNA

description: Colorectal cancer patient 54


title: T58-RNA

description: Colorectal cancer patient 58


title: Single cell expression of human CRC samples from patient C136_T [C136_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma


title: PTCL_Sample 68

value: Peripheral T-cell lymphoma

value: Adult


title: Single cell expression of human CRC samples from patient C136_T [C136_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: LEFT (Rectosigmoid)

value: left


title: Single cell expression of human CRC samples from patient C136_N [C136_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Normal colon


title: T53-RNA

description: Colorectal cancer patient 53


title: PTCL_Sample 67


title: Single cell expression of human CRC samples from patient C136_N [C136_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted


title: T57-RNA

description: Colorectal cancer patient 57


title: Single cell expression of human CRC samples from patient C135_T [C135_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT (CECUM)

value: Grade 2 (Moderately differentiated. 50-95% gland formation).

value: low

value: Nneg


title: Single cell expression of human CRC samples from patient C135_T [C135_T_1_1_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: right

value: not entered (Mx)


title: PTCL_Sample 66


title: Single cell expression of human CRC samples from patient C135_N [C135_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N


title: T51-RNA

description: Colorectal cancer patient 51

value: Colorectal cancer

value: Tumor


title: PTCL_Sample 65

value: Peripheral T-cell lymphoma


title: Single cell expression of human CRC samples from patient C134_T [C134_T_0_3_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma

value: LEFT (Sigmoid)

value: Moderately differentiated

value: Npos


title: PTCL_Sample 64

value: Adult


title: Single cell expression of human CRC samples from patient C134_T [C134_T_0_3_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: left


title: T50-RNA

description: Colorectal cancer patient 50


title: T49-RNA

description: Colorectal cancer patient 49


title: Single cell expression of human CRC samples from patient C134_T [C134_T_0_3_0_c2_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: low


title: Single cell expression of human CRC samples from patient C134_T [C134_T_0_3_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: PTCL_Sample 63


title: Single cell expression of human CRC samples from patient C134_N [C134_N_0_3_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Normal colon


title: PTCL_Sample 62


title: Single cell expression of human CRC samples from patient C134_N [C134_N_0_3_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: T52-RNA

description: Colorectal cancer patient 52


title: Single cell expression of human CRC samples from patient C135_T [C135_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT (CECUM)

value: right

value: Grade 2 (Moderately differentiated. 50-95% gland formation).

value: Nneg

value: not entered (Mx)


title: PTCL_Sample 61

value: Peripheral T-cell lymphoma


title: Single cell expression of human CRC samples from patient C132_T [C132_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma

value: MLH1 and PMS2 deficient

value: MMRd

value: LEFT colon

value: Grade 3 (Poorly differentiated. < 50% gland formation)

value: high


title: T47-RNA

description: Colorectal cancer patient 47

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C133_T [C133_T_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: Adenocarcinoma;Mucinous

value: preserved

value: MMRp

value: RIGHT colon

value: Moderately differentiated

value: low


title: Single cell expression of human CRC samples from patient C133_N [C133_N_0_0_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon

value: right


title: Single cell expression of human CRC samples from patient C132_T [C132_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma

value: MLH1 and PMS2 deficient

value: left

value: Nneg

value: not entered (Mx)


title: PTCL_Sample 60

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 59


title: PTCL_Sample 58


title: Single cell expression of human CRC samples from patient C130_TB [C130_TB_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma;Mucinous

value: MMRd

value: RIGHT colon (Cecum;  Ileocecal valve)

value: Grade 2 (Moderately differntiated)

value: Npos


title: Single cell expression of human CRC samples from patient C132_N [C132_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: LEFT colon


title: PTCL_Sample 57


title: Single cell expression of human CRC samples from patient C130_TB [C130_TB_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: low


title: Single cell expression of human CRC samples from patient C130_TA [C130_TA_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: right


title: Single cell expression of human CRC samples from patient C130_TA [C130_TA_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T


title: T43-RNA

description: Colorectal cancer patient 43

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C130_N [C130_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: Single cell expression of human CRC samples from patient C130_N [C130_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: T42-RNA

description: Colorectal cancer patient 42


title: PTCL_Sample 56


title: Single cell expression of human CRC samples from patient C133_T [C133_T_0_0_0_c2_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp

value: RIGHT colon

value: Moderately differentiated

value: Nneg

value: not entered (Mx)


title: T46-RNA

description: Colorectal cancer patient 46


title: Single cell expression of human CRC samples from patient C129_T [C129_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: left

value: Grade 2 (Moderately differentiated. 50-95% gland formation).

value: N0 (i+)* (isolated tumor cells)


title: Single cell expression of human CRC samples from patient C129_T [C129_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: LEFT colon

value: low


title: Single cell expression of human CRC samples from patient C129_N [C129_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)


title: Single cell expression of human CRC samples from patient C129_N [C129_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: Single cell expression of human CRC samples from patient C126_T [C126_T_1_1_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma;Mucinous

value: RIGHT colon (cecum)

value: right

value: Low Grade (Moderately differentiated) and mucinous


title: T45-RNA

description: Colorectal cancer patient 45

value: Colorectal cancer

value: Tumor


title: T48-RNA

description: Colorectal cancer patient 48


title: Single cell expression of human CRC samples from patient C126_T [C126_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp


title: Single cell expression of human CRC samples from patient C126_N [C126_N_1_1_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: Single cell expression of human CRC samples from patient C126_T [C126_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Nneg

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C155_N [C155_N_0_0_0_c1_v3]

description: Single cell RNA-Seq (10x)

value: RIGHT (ascending)


title: Single cell expression of human CRC samples from patient C126_N [C126_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)


title: Single cell expression of human CRC samples from patient C125_T [C125_T_1_1_1_c2_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: LEFT colon (Sigmoid colon)

value: left

value: Low-grade (well differentiated to moderately        differentiated)

value: Npos


title: Single cell expression of human CRC samples from patient C125_T [C125_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: low


title: PTCL_Sample 55

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 54


title: PTCL_Sample 53


title: PTCL_Sample 50


title: PTCL_Sample 51


title: Single cell expression of human CRC samples from patient C126_N [C126_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: RIGHT colon (cecum)

value: right


title: Single cell expression of human CRC samples from patient C125_T [C125_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: MMRp


title: PTCL_Sample 49


title: Single cell expression of human CRC samples from patient C125_N [C125_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: PTCL_Sample 48


title: Single cell expression of human CRC samples from patient C125_N [C125_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: T41-RNA

description: Colorectal cancer patient 41

value: Colorectal cancer

value: Tumor


title: T40-RNA

description: Colorectal cancer patient 40


title: T34-RNA

description: Colorectal cancer patient 34


title: T36-RNA

description: Colorectal cancer patient 36


title: T37-RNA

description: Colorectal cancer patient 37


title: T35-RNA

description: Colorectal cancer patient 35


title: PTCL_Sample 52


title: T38-RNA

description: Colorectal cancer patient 38


title: T39-RNA

description: Colorectal cancer patient 39


title: PTCL_Sample 47


title: Single cell expression of human CRC samples from patient C124_T [C124_T_0_3_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: LEFT colon (rectosigmoid)

value: High Grade (poorly diff with signet ring cell features)

value: high

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C124_T [C124_T_0_3_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: left

value: Npos


title: T33-RNA

description: Colorectal cancer patient 33


title: Single cell expression of human CRC samples from patient C124_N [C124_N_0_3_1_c1_v2]

description: Single cell RNA-Seq (10x)


title: Single cell expression of human CRC samples from patient C123_T [C123_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: RIGHT colon (Ascending colon)

value: Low Grade (Moderately differentiated)

value: low

value: Nneg


title: T44-RNA

description: Colorectal cancer patient 44


title: Single cell expression of human CRC samples from patient C124_N [C124_N_0_3_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: unosrted

value: Normal colon


title: Single cell expression of human CRC samples from patient C123_N [C123_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: right


title: Single cell expression of human CRC samples from patient C123_T [C123_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma


title: Single cell expression of human CRC samples from patient C123_N [C123_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)


title: T31-RNA

description: Colorectal cancer patient 31

value: Colorectal cancer

value: Tumor


title: PTCL_Sample 44

value: Peripheral T-cell lymphoma

value: Adult


title: Single cell expression of human CRC samples from patient C122_T [C122_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: RIGHT colon (Cecum/ascending colon)

value: not entered (Mx)


title: T30-RNA

description: Colorectal cancer patient 30


title: T32-RNA

description: Colorectal cancer patient 32


title: Single cell expression of human CRC samples from patient C122_T [C122_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd


title: Single cell expression of human CRC samples from patient C122_N [C122_N_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)


title: PTCL_Sample 45


title: Single cell expression of human CRC samples from patient C122_N [C122_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)


title: PTCL_Sample 43


title: PTCL_Sample 42


title: Single cell expression of human CRC samples from patient C119_N [C119_N_0_2_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon (Cecum/Ascending Colon)


title: T27-RNA

description: Colorectal cancer patient 27


title: Single cell expression of human CRC samples from patient C118_T [C118_T_1_1_2_c1_v2]

description: Single cell RNA-Seq (10x)

value: Low Grade (Moderately differentiated)

value: low


title: T29-RNA

description: Colorectal cancer patient 29


title: T28-RNA

description: Colorectal cancer patient 28


title: Single cell expression of human CRC samples from patient C119_T [C119_T_0_2_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Intact nuclear staining of MLH1, MSH2, MSH6 and PMS2. MSI-H by PCR-MSI testing.

value: High Grade (with mucinous and signet ring cell features)

value: high

value: Npos


title: PTCL_Sample 46


title: PTCL_Sample 40


title: PTCL_Sample 39


title: PTCL_Sample 41


title: Single cell expression of human CRC samples from patient C116_T [C116_T_0_2_2_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: Isolated PMS2 deficiency; confirmed germline PMS2 variant

value: RIGHT colon (Ascending colon)

value: right

value: Low grade

value: Nneg


title: Single cell expression of human CRC samples from patient C116_T [C116_T_0_2_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: unosrted


title: Single cell expression of human CRC samples from patient C116_T [C116_T_0_2_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: not entered (Mx)


title: T24-RNA

description: Colorectal cancer patient 24

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C115_T [C115_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: Low Grade (Well differentiated or Moderately differentiated)


title: Single cell expression of human CRC samples from patient C115_T [C115_T_1_1_2_c1_v2]

description: Single cell RNA-Seq (10x)

value: low


title: Single cell expression of human CRC samples from patient C116_N [C116_N_0_2_2_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: Single cell expression of human CRC samples from patient C118_T [C118_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: RIGHT colon (Cecum/Ascending Colon)

value: Low Grade (Moderately differentiated)


title: T22-RNA

description: Colorectal cancer patient 22


title: Single cell expression of human CRC samples from patient C114_T [C114_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon (transverse)

value: right

value: Low Grade (Moderately differentiated), focally mucin producing

value: Npos


title: PTCL_Sample 38

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 37


title: Single cell expression of human CRC samples from patient C115_N [C115_N_1_1_2_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon (Ascending colon)


title: Single cell expression of human CRC samples from patient C114_N [C114_N_1_1_2_c1_v2]

description: Single cell RNA-Seq (10x)


title: Single cell expression of human CRC samples from patient C114_T [C114_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: not entered (Mx)


title: T21-RNA

description: Colorectal cancer patient 21

value: Colorectal cancer

value: Tumor


title: PTCL_Sample 34


title: T26-RNA

description: Colorectal cancer patient 26


title: T20-RNA

description: Colorectal cancer patient 20


title: T19-RNA

description: Colorectal cancer patient 19


title: Single cell expression of human CRC samples from patient C113_T [C113_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: preserved

value: MMRp

value: RIGHT colon

value: Low Grade (Moderately differentiated).

value: low


title: Single cell expression of human CRC samples from patient C113_N [C113_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: Single cell expression of human CRC samples from patient C113_T [C113_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: right


title: Single cell expression of human CRC samples from patient C112_T [C112_T_0_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon (cecum)

value: Low Grade

value: Nneg


title: Single cell expression of human CRC samples from patient C112_T [C112_T_0_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T


title: T18-RNA

description: Colorectal cancer patient 18


title: T23-RNA

description: Colorectal cancer patient 23


title: Single cell expression of human CRC samples from patient C112_N [C112_N_0_1_2_c1_v2]

description: Single cell RNA-Seq (10x)


title: Single cell expression of human CRC samples from patient C111_T [C111_T_0_2_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: MLH1 and PMS2 deficient

value: MMRd

value: RIGHT colon (hepatic flexure to cecum)

value: not entered (Mx)


title: T17-RNA

description: Colorectal cancer patient 17

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C111_T [C111_T_0_2_0_c2_v2]

description: Single cell RNA-Seq (10x)

value: unosrted


title: PTCL_Sample 33

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 36


title: PTCL_Sample 31


title: PTCL_Sample 30


title: Single cell expression of human CRC samples from patient C111_T [C111_T_0_2_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: low


title: PTCL_Sample 32


title: T10-RNA

description: Colorectal cancer patient 10


title: Single cell expression of human CRC samples from patient C111_N [C111_N_0_2_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: PTCL_Sample 29


title: T16-RNA

description: Colorectal cancer patient 16


title: Single cell expression of human CRC samples from patient C110_T [C110_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma;Medullary (with solid growth pattern)

value: RIGHT colon (hepatic flexure)

value: right

value: High Grade (Poorly differentiated or Undifferentiated), medullary features

value: high

value: Npos


title: Single cell expression of human CRC samples from patient C109_T [C109_T_0_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: Adenocarcinoma

value: MLH1 and PMS2 deficient

value: MMRd

value: RIGHT colon (ascending colon)

value: Low Grade

value: Nneg


title: Single cell expression of human CRC samples from patient C110_N [C110_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted


title: PTCL_Sample 35

value: Peripheral T-cell lymphoma

value: Adult


title: PTCL_Sample 27


title: T7-RNA

description: Colorectal cancer patient 7

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C109_N [C109_N_0_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon


title: PTCL_Sample 26


title: Single cell expression of human CRC samples from patient C111_N [C111_N_0_2_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon (hepatic flexure to cecum)

value: right


title: Single cell expression of human CRC samples from patient C107_T [C107_T_1_1_3_c1_v2]

description: Single cell RNA-Seq (10x)

value: LiveMACS

value: preserved

value: MMRp

value: RIGHT colon (transverse)

value: Low Grade (Moderately differentiated)

value: low

value: Npos

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C109_T [C109_T_0_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: unosrted

value: Adenocarcinoma

value: MLH1 and PMS2 deficient

value: MMRd

value: RIGHT colon (ascending colon)

value: Low Grade

value: Nneg


title: T6-RNA

description: Colorectal cancer patient 6

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C107_T [C107_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: preserved

value: right


title: T5-RNA

description: Colorectal cancer patient 5


title: Single cell expression of human CRC samples from patient C110_T [C110_T_1_1_1_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma;Medullary (with solid growth pattern)

value: RIGHT colon (hepatic flexure)

value: High Grade (Poorly differentiated or Undifferentiated), medullary features

value: high


title: Single cell expression of human CRC samples from patient C107_N [C107_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon

value: RIGHT colon (transverse)


title: Single cell expression of human CRC samples from patient C106_T [C106_T_1_1_3_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: LiveMACS

value: Adenocarcinoma;Mucinous

value: RIGHT colon (cecum)

value: Low Grade (Well differentiated or Moderately differentiated)

value: low

value: not entered (Mx)


title: PTCL_Sample 28

value: Peripheral T-cell lymphoma

value: Adult


title: T9-RNA

description: Colorectal cancer patient 9

value: Colorectal cancer

value: Tumor


title: T2-RNA

description: Colorectal cancer patient 2


title: Single cell expression of human CRC samples from patient C106_N [C106_N_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: unosrted

value: right


title: T8-RNA

description: Colorectal cancer patient 8


title: PTCL_Sample 22


title: PTCL_Sample 25


title: PTCL_Sample 24


title: PTCL_Sample 23


title: Single cell expression of human CRC samples from patient C105_T [C105_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: preserved

value: MMRp

value: RIGHT colon (ascending colon)

value: Npos


title: Single cell expression of human CRC samples from patient C105_T [C105_T_1_1_3_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: LiveMACS


title: Single cell expression of human CRC samples from patient C104_T [C104_T_1_1_3_c1_v2]

description: Single cell RNA-Seq (10x)

value: RIGHT colon (transverse)

value: Low-grade (well differentiated to moderately differentiated)

value: Nneg


title: PTCL_Sample 21


title: WGBS-SEM-CTCF-AID_with_IAA Replicate 27

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
For ATAC-seq, reads were trimmed for Nextera adapter by cutadapt (version 1.9, paired-end mode, default parameter with “ -m 6 -O 20 ”) and aligned to human genome hg19(GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter)26. The duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2)27. After removing mitochondrial DNA reads, the rest of reads were classified into four groups including nucleosome free, mono-, di-, and tri-nucleosome by fragment size. The bigwig files were generated using the center 80-bp of fragments and scaled to 20 million nucleosome free reads.
We observed reasonable nucleosome free peaks and pattern of mono-, di-, tri-nucleosome peaks surrounding nucleosome free peaks on IGV. All samples exhibited twice of ENCODE criterion. Therefore, we concluded the data show enough depth. Given all samples exhibited more than 15 million nucleosome free fragments, we are confidence most strong nucleosome free regions won’t be missed.
For WGBS: The FASTQ  sequencing files were first trimmed for removing adapter sequences by trimgalore and mapped to the human genome (hg19) by BSMAP (v2.74, parameters “-m 17 -x 600 -u -R -z 33 -f 5 -g 3 -r 0 -p 6”). CpGs were then extracted by the methratio.py in the BSMAP package.
We then confirmed good depth (each sample > 900 million reads), good coverage (>95% CpG have more than 5 reads, >90% CpG have more than 10 reads) and good C to T conversion rate ( > 90%).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: SEM cell line

growth_protocol: The human B-ALL cell line SEM (DSMZ) carrying bi-allelic miniAID-mClover3 knockin tags was established in previous study. Three single-cell derived clones (clones 27, 35 and 42) were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (FBS)(Hyclone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific). Cells were tested negative for mycoplasma infection. Authentic cell identity was confirmed by short tandem repeat (STR) analysis.

extract_protocol:
For ATAC: Briefly, 75,000 cells were collected per sample in duplicate and resuspended in cold PBS with protease inhibitors. After centrifugation at 500 rpm for 5 mins at 4 °C (Eppendorf 5417R Refrigerated Centrifuge), cell pellets were resuspended in cold lysis buffer with protease inhibitors (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL), followed by centrifugation. Pellets were resuspended in 25 µl Tagment DNA Buffer (Nextera, FC-121-1030) and then used directly in the transposition reaction. Nextera Tn5 (Nextera, FC-121-1030) was added to the resuspended nuclei and the transposition reaction was incubated at 37 °C for 30 mins. For WGBS: Genomic DNA collected from Clone 27 with or without IAA treatment for 24 hours was extracted by PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific).
For ATAC: After transposition, DNA was purified by using a Qiagen MinElute PCR purification kit (Qiagen, 28004). Indexing PCR was carried out for 12 cycles using NEBNext HiFi 2X PCR Master Mix (NEB, M0541S) and indexing primers as previously described 25. PCR products were purified by using a 1:3 ratio of Agencourt AMPure XP beads (Beckman Coulter, A63881) and samples were sequenced at paired-end 100 bp on the Illumina HiSeq 4000 system. For WGBS: About 2 µg genomic DNA was used for bisulfite DNA conversion and subsequent cleanup of the converted DNA using The EpiTect Fast Bisulfite Conversion Kit (Qiagen), followed with library construction and next-generation sequencing.

treatment_protocol: Three single-cell derived knock-in clones (clones 27, 35 and 42) were treated with complete medium supplemented with 500 μM IAA (natural auxin)(Sigma) for 24 hours to induce degradation of CTCF.

tag: cell line

value: SEM

tag: cell type

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell carrying bi-allelic miniAID-mClover3 knockin tags

tag: treatment

value: IAA treatment 24hr to induce CTCF degradation


title: Single cell expression of human CRC samples from patient C107_T [C107_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

tag: patienttypeid

tag: histologictypesimple

value: Low Grade (Moderately differentiated)

value: low

value: not entered (Mx)


title: V. cholerae hapR+sub-MICTOB_ replicate3 [8TC]

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

institute: Institut Pasteur

description:
Zeynep-8TC_GCCAAT_L001
processed data file: SLX090-01-vibcol3-MHTOB.s8-TOBvss8-MH.complete.txt

data_processing:
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.001 were considered differentially expressed.
Genome_build: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary_files_format_and_content: excel files containing number of reads and differencial expression values

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: bacterial culture

growth_protocol: growth in liquid MH up to OD 0,4

extract_protocol:
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: no treatment or indole 350µM or tobramycin 0,02µg/ml (2% of MIC)

tag: genotype/variation

tag: growth phase

value: exponential phase OD 0.4

value: tobramycin 0,02 µg/ml


title: Single cell expression of human CRC samples from patient C106_N [C106_N_1_1_3_c1_v2]

description: Single cell RNA-Seq (10x)

value: N

value: Normal colon

tag: mmrstatus

value: RIGHT colon (cecum)

tag: tissuesitesimple

value: right

tag: histologicgradesimple

tag: tumorstage


title: PTCL_Sample 20

value: Peripheral T-cell lymphoma

value: Adult


title: WGBS-SEM-CTCF-AID_no_IAA Replicate 27

value: no


title: Single cell expression of human CRC samples from patient C106_T [C106_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: unosrted

value: Adenocarcinoma;Mucinous

value: MLH1 and PMS2 deficient

value: MMRd

value: Low Grade (Well differentiated or Moderately differentiated)

tag: nodestatussimple

tag: metastasisstatus

tag: tumorsize

tag: sizequantile


title: V. cholerae hapR+sub-MICTOB_ replicate2 [8TB]

description:
Zeynep-8TB_AGTCAA_L003
processed data file: SLX090-01-vibcol3-MHTOB.s8-TOBvss8-MH.complete.txt


title: Single cell expression of human CRC samples from patient C104_T [C104_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: Adenocarcinoma

value: preserved

value: MMRp

value: RIGHT colon (transverse)

value: Low-grade (well differentiated to moderately differentiated)

value: low

value: Nneg


title: V. cholerae hapR+sub-MICTOB_ replicate1 [8TA]

description:
Zeynep-8TA_ATGTCA_L002
processed data file: SLX090-01-vibcol3-MHTOB.s8-TOBvss8-MH.complete.txt

value: exponential phase OD 0.4

value: tobramycin 0,02 µg/ml


title: ATAC-SEM-CTCF-AID_with_IAA Replicate 42

value: SEM

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell carrying bi-allelic miniAID-mClover3 knockin tags

value: IAA treatment 24hr to induce CTCF degradation


title: PTCL_Sample 19

tag: tissue

value: Peripheral T-cell lymphoma

value: Adult


title: T1-RNA

description: Colorectal cancer patient 1

tag: diagnosis

value: Colorectal cancer

value: Tumor


title: Single cell expression of human CRC samples from patient C103_T [C103_T_1_1_0_c1_v2]

description: Single cell RNA-Seq (10x)

value: T

value: unosrted

value: LEFT colon (sigmoid colon)

value: left

value: not entered (Mx)


title: Single cell expression of human CRC samples from patient C103_T [C103_T_1_1_3_c1_v2]

description: Single cell RNA-Seq (10x)

value: LiveMACS

value: Adenocarcinoma

value: preserved

value: MMRp

value: Low-grade (well differentiated to moderately differentiated)


title: V. cholerae hapR+ indole_ replicate1 [IA]

description:
Zeynep-IA_AGTCAA_L001
processed data file: SLX090-01-vibcol3-indol.IvsMH.complete.txt

value: exponential phase OD 0.4

value: indole 350µM


title: PTCL_Sample 15

tag: age


title: ATAC-SEM-CTCF-AID_no_IAA Replicate 42

tag: cell line

value: SEM

tag: cell type

value: Human B Lineage Acute Lymphoblastic Leukemia SEM cell carrying bi-allelic miniAID-mClover3 knockin tags

value: no


title: HD-MB03_miR-592_2

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

data_processing:
Illumina bcl2fastq2 was used for base calling
The fastq data was aligned to the Human genome GRCh37-hg19 assembly using HISAT2 aligner
HTseq algorithm was used to derive the raw count of the number of reads per transcript from the aligned sequence file in the BAM format
DESeq2 algorithm was used for normalization of the HTSeq count data using the variance stabilized transformation as well as for identifying genes differentially expressed upon miR-592 expression.
Genome_build: GRCh37-hg19
Supplementary_files_format_and_content: tab-delimited text files containing counts per gene normalized using the variance stabilized transformation

source_name: Medulloblastoma cell line

growth_protocol: D283, D425, HD-MB03 cell lines and their polyclonal populations expressing miR-592 in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium containing 10% fetal bovine serum at 37 °C in a CO2 incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit as per manufacturer's protocol.
Libraries were prepared from Poly-A enriched fraction of total RNA using the Ilumina TruSeq RNA library preparation kit version 2.0
The libraries were sequenced in a 100 nucleotide single-end read run on the Illumina Hiseq platform

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 72 h for the induction of miR-592 expression

tag: disease

value: Group 3 medulloblastoma

tag: genotype/treatment

value: MiR-592 expressing


title: ATAC-SEM-CTCF-AID_with_IAA Replicate 35

tag: treatment

value: IAA treatment 24hr to induce CTCF degradation


title: V. cholerae hapR+ indole_ replicate2 [IB]

description:
Zeynep-IB_GTGAAA_L002
processed data file: SLX090-01-vibcol3-indol.IvsMH.complete.txt

tag: genotype/variation

tag: growth phase


title: ATAC-SEM-CTCF-AID_with_IAA Replicate 27


title: PTCL_Sample 17

value: Peripheral T-cell lymphoma

value: Adult


title: HD-MB03_miR-592_1


title: ATAC-SEM-CTCF-AID_no_IAA Replicate 35


title: PTCL_Sample 14


title: HD-MB03_VC  [re-used]

value: vector control


title: PTCL_Sample 16


title: PTCL_Sample 13


title: V. cholerae hapR+ non tretated_ replicate 3 [8C]

description:
Zeynep-8C_ACAGTG_L001
processed data file: SLX090-01-vibcol3-indol.IvsMH.complete.txt

value: untreated


title: D425_miR-592_2_U0126

value: MiR-592 expressing treated with U0216


title: HD-MB03_C  [re-used]

value: parental cell line


title: D425_miR-592_2_rapamycin

value: MiR-592 expressing, treated with rapamycin


title: ATAC-SEM-CTCF-AID_no_IAA Replicate 27


title: PTCL_Sample 18


title: V. cholerae hapR+ non tretated_ replicate 1 [8A]

description:
Zeynep-8A_AGTTCC_L002
processed data file: SLX090-01-vibcol3-indol.IvsMH.complete.txt


title: V. cholerae hapR+ indole_ replicate3 [IC]

description:
Zeynep-IC_GTGAAA_L003
processed data file: SLX090-01-vibcol3-indol.IvsMH.complete.txt


title: PTCL_Sample 11


title: PTCL_Sample 12


title: T4-RNA

description: Colorectal cancer patient 4

value: Colorectal cancer

value: Tumor


title: D425_VC_U0126

value: vector control treated with U0216


title: D425_VC_rapamycin

value: vector control treated with rapamycin


title: D425_miR-592_2


title: V. cholerae hapR+ non tretated_ replicate 2 [8B]

description:
Zeynep-8B_CTTGTA_L003
processed data file: SLX090-01-vibcol3-indol.IvsMH.complete.txt

value: exponential phase OD 0.4


title: PTCL_Sample 10


title: PTCL_Sample 9


title: D425_miR-592_1


title: PTCL_Sample 8


title: Sperm_methylation_control_Rep8

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

country: Germany

institute: Saarland University

data_processing:
Raw fastq files were quality controlled with FastQC (http://www.bioinformatics.bbsrc. ac.uk/projects/fastqc/) and subsequently processed using the DEEP pipeline for RRBS.
Reads were first trimmed with the cutadapt wrapper Trim Galore! and then mapped with the bwa wrapper MethylCtools58.
Alignments were manipulated and filtered with Picardtools (“Picard Tools - By Broad Institute” 2017) and samtools.
After realignment and recalibration, methylation calls were made with Bis-SNP (bed files). Reference SNPs and InDels from dbSNP v138 (http://www.ncbi.nlm.nih.gov/SNP) were used in this process.
Genome_build: mm10
Supplementary_files_format_and_content: bed files with methylation calls and corresponding CpG coverage

extract_protocol:
DNA from sperm of 10 isogenic control males and 10 infected was isolated.
comprehensive HaeIII restriction based RRBS (reduced representation bisulfite sequencing)

treatment_protocol: Male mice were infected with subletal dose of C. albicans. One month after clearance of the infection, ‘resting’ (mock-infected with PBS, F0R) and the ‘trained’ (C. albicans-infected and recovered, F0T) mice were mated with healthy non-infected females.

tag: infection

value: control

value: Sperm


title: Sperm_methylation_control_Rep7


title: Sperm_methylation_control_Rep10


title: Sperm_methylation_control_Rep6


title: PTCL_Sample 7


title: Sperm_methylation_control_Rep5


title: Sperm_methylation_control_Rep9


title: D425_VC [re-used]

value: Group 3 medulloblastoma


title: PTCL_Sample 6


title: D425_C1 [re-used]


title: Sperm_methylation_control_Rep4


title: PTCL_Sample 5


title: D283_miR-592_2_U0126


title: Sperm_methylation_control_Rep3


title: PTCL_Sample 4


title: D283_miR-592_2_rapamycin


title: Sperm_methylation_control_Rep2


title: D283_VC_U0126


title: PTCL_Sample 2


title: PTCL_Sample 3


title: Sperm_methylation_control_Rep1