title: scRNA-seq of chimpanzee blastoids-derived cell_100

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_101

status: Public on Feb 26 2025

type: SRA

city: Minato-ku

first: Hideki

last: Masaki

state: Tokyo

address: 4-6-1 Shirokanedai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

description: fastq

library_source: transcriptomic single cell

data_processing:
Adaptor sequences and low-quality base calls were trimmed using Trim Galore! v0.6.6 with default parameters. Trimmed reads were aligned to the Chimpanzee reference genome (Pan_tro3.0) using STAR v2.7.7a (Dobin et al., 2013) in paired-end mode with default parameters.
Assembly: Chimpanzee: Pan_tro_3.0-rel109; Human: GRCh38-2020-A
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

molecule: total RNA

organism: Pan troglodytes

source_name: blastoids-derived cell

growth_protocol: Chimpanzee primed or capacitated iPSCs were cultured with AFX medium (N2B27 basal medium supplemented with 20ng/ml Activin-A, 20ng/ml bFGF, and 2-5μM XAV939). Chimp naive iPSCs were cultured with AE6 medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL Activin-A, 20 ng/mL IL6, and 0.5-1 μM EPZ-6438). Capacitated iPSCs were originated from naïve iPSCs following culture with N2B27 supplemented with 2 μM XAV. For TE induction, naive iPSCs were cultured with N2B27 supplemented with 3μM PD032590 and 3μM A83-01.Human naive ESCs, HNES1, was cultured with PXGL medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL) on MEF feeder, or with AE6 on feeder-free.

extract_protocol:
Blastoids were dissociated into single cells enzymatically. Single cells were transferred into individual wells of a 96-well plate containing Smart-seq2 single-cell lysis buffer by using capillary.
cDNA library was synthesized by using SMART-seq2.

tag: tissue

value: blastoids-derived cell

tag: cell type

value: in vitro-differentiated cells from nPSC


title: scRNA-seq of chimpanzee blastoids-derived cell_105

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_102

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_131

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_96

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_126

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_95

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_99

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_98

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_94

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_91

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_93

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_89

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_90

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_87

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_84

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_86

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_83

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_82

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_80

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_104

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_78

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_76

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_73

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_74

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_75

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_72

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_71

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_68

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_67

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_69

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_66

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_65

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_63

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_64

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_88

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_61

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_85

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_62

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_59

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_55

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_56

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_57

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_79

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_54

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_77

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_52

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_53

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_50

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_51

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_70

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_47

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_49

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_43

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_41

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_40

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_38

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_60

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_36

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_42

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_58

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_46

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_35

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_39

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_34

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_33

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_37

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_31

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_30

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_32

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_28

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_25

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_26

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_27

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_29

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_24

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_45

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_23

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_22

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_48

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_21

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_18

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_17

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_15

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_13

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_11

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_12

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_9

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_10

description: fastq


title: TCP cells, feeder-free, scRNAseq

data_processing:
For bulk RNAseq, reads were trimmed using Fastp to remove sequencing adapters and low quality (<Q22) bases from the 3’ end, reads shorter than 75bp were discarded. Trimmed reads were then aligned to the ENSEMBL Mouse and Chimp references (ENSEMBL_Mus_musculus.GRCm39.109 and ENSEMBL_Pan_troglodytes.Pan_tro_3.0-rel109) using STAR Dobin et al. (2013) version=2.7.9a. The aligned reads were processed by XenofilteR Kluin et al. (2018) version 1.6 to remove suspected mouse related transcripts.
For scRNAseq datasets, raw Illumina data were processed using 10x Genomics Cell Ranger 7.1.0.Cell Ranger mkfastq to demultiplex into cellplex pools (utilising bcl2fastq v2.20.0.422 Illumina). Cellranger multi to demultiplex the cellplex pools align and produce count matrices.
Assembly: Chimpanzee: Pan_tro_3.0-rel109; Mouse:GRCm39.109; Human: GRCh38-2020-A
Supplementary files format and content: For bulk RNAseq samples, tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: For scRNAseq samples, each element of the feature-barcode matrix is the number of UMIs associated with a feature (row) and a barcode (column).

source_name: TCP cells

growth_protocol: Chimpanzee primed or capacitated iPSCs were cultured with AFX medium (N2B27 basal medium supplemented with 20ng/ml Activin-A, 20ng/ml bFGF, and 2-5μM XAV939). Chimp naive iPSCs were cultured with AE6 medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL Activin-A, 20 ng/mL IL6, and 0.5-1 μM EPZ-6438). Capacitated iPSCs were originated from naïve iPSCs following culture with N2B27 supplemented with 2 μM XAV. For TE induction, naive iPSCs were cultured with N2B27 supplemented with 3μM PD032590 and 3μM A83-01. Human naive ESCs, HNES1, was cultured with PXGL medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL) on MEF feeder, or with AE6 on feeder-free.

extract_protocol:
For bulk RNAseq, total RNA was extracted from cultures using TRIzol/chloroform, followed by RNA precipitation with isopropanol. Genomic DNA was depleted using TurboDNase and clean-up was performed using Zymogen Clean and Concentrator kit.
For bulk RNAseq, sequencing libraries were prepared using the NEB Next Ultra Library prep kit for Illumina.
For scRNAseq, cells were dissociated and labelled using the 3' CellPlex kit Set A, then multiplexed and single cells were isolated using the Chromium Next Gem Chip G Single Cell kit on the Chromium X.
For scRNAseq, libraries were prepared using the Chromium Next GEM Single Cell 3' v3.1 kit with 3' Feature Barcode Kit.

value: TCP cells

tag: condition

value: feeder-free


title: TCP cells, on feeder, scRNAseq

value: on feeder


title: CP127 cells, feeder-free, scRNAseq

source_name: CP127 cells

value: CP127 cells


title: CP127 cells, on feeder, scRNAseq


title: Chimpanzee iPSC line" Ume4", primed state, replicate 2

library_source: transcriptomic

source_name: iPSC line Ume4

value: iPSC line Ume4

value: primed state


title: Chimpanzee iPSC line" Ume4", naive state, replicate 1

value: naive state


title: Chimpanzee iPSC line" Pen23", primed state, replicate 2

source_name: iPSC line Pen23

value: iPSC line Pen23


title: Chimpanzee iPSC line" Ume4", primed state, replicate 1


title: Chimpanzee iPSC line" Pen23", primed state, replicate 1


title: Chimpanzee iPSC line "Pen23", naive state, replicate 1


title: Chimpanzee iPSC line "Pen23", naive state, replicate 2


title: Chimpanzee iPSC line" Ume4", naive state, replicate 2


title: scRNA-seq of chimpanzee blastoids-derived cell_20

description: fastq


title: Chimpanzee CP127 cells, TE differentiation day3, replicate 2

value: TE differentiation day3


title: Chimpanzee CPR1 cells, TE differentiation day6, replicate 1

source_name: CPR1 cells

value: CPR1 cells

value: TE differentiation day6


title: Chimpanzee CPR1 cells, TE differentiation day4, replicate 2

value: TE differentiation day4


title: Chimpanzee CP127 cells, TE differentiation day5, replicate 2

value: TE differentiation day5


title: Chimpanzee CP127 cells, TE differentiation day3, replicate 1


title: Chimpanzee CPR1 cells, TE differentiation day4, replicate 1


title: Chimpanzee CP127 cells, TE differentiation day5, replicate 1


title: Chimpanzee iPSC line "CPU6", primed state, replicate 2

description: CPU6 AFX P12

source_name: iPSC line CPU6

value: iPSC line CPU6


title: Chimpanzee iPSC line "CPU6", primed state, replicate 1

description: CPU6 AFX P11


title: Chimpanzee iPSC line "CPR1", naive state, replicate 2

description: CPR1 P25 PXGLAE6

source_name: iPSC line CPR1

value: iPSC line CPR1


title: Chimpanzee iPSC line "CPR1", naive state, replicate 1

description: CPR1 P22 PXGLAE6


title: Chimpanzee iPSC line "CP127", capacitated to primed state

description: CP127 capa AFX P4

source_name: iPSC line CP127

value: iPSC line CP127

value: capacitated to primed state


title: Chimpanzee iPSC line "CPR1", capacitated to primed state, replicate 2

description: CPR1 capa AFX P5


title: Chimpanzee iPSC line "CPR1", capacitated to primed state, replicate 1

description: CPR1 capa AFX P4


title: Chimpanzee iPSC line "CP127", naive state, replicate 3

description: CP127 AE6 P8


title: Chimpanzee iPSC line "CP127", naive state, replicate 2

description: CP127 AE6 P25


title: Chimpanzee iPSC line "CP", primed state

description: CP AFX P12

source_name: iPSC line CP

value: iPSC line CP


title: Chimpanzee iPSC line "CP127", naive state, replicate 1

description: CP127 AE6 P18


title: Myogenic cells, differentiated, ROI2, biol rep 2

city: Milan

first: Fabio

last: Martelli

address: Via Olgettina 58

country: Italy

institute: IRCCS Policlinico San Donato

library_source: genomic

data_processing:
Read quality was assessed using PycoQC (2.5.2), applying a filter with a Q score of 9, and concatenating passing reads into a single FASTQ file per sample.
Minimap2 (v 2.24, default settings for ONT) was employed for read alignment, against (a) the human reference (GRCh38) and reference sequences of (b) the non-edited mutated allele, (c) the CTG-repeats excision and (d) the inversion. For construction of the mutated allele reference, an additional 1600 triplets (4800 nt) were inserted within the repeat region, guided by the observed reads. The CTG-repeats excision reference represents the sequence expected for simultaneous, precise sgC3/384 cut followed by repeat removal (double-cut) and perfect re-joining. The inversion reference is the sequence predicted for sgC3/384 cut followed by reinsertion in the reverse orientation.
Samtools (v1.6) was employed to subset the reads aligned to the Region of Interest (ROI), sort and index the alignment files into sorted BAM files.
IGV (v2.16.2) was used for manual examination of all primary read alignments. Alignments against the human reference (GRCh38) were assessed for investigation of non-edited wild type (WT)-alleles and sgC3/384 target sequences in the absence of CTG excision, while the corresponding alignments were examined for the analysis of non-edited mutated alleles, CTG-repeats excision and inversions.
Assembly: GRCh38 and custom
Supplementary files format and content: Binary coverage files (bigWig), created using deepTools bamCoverage, corresponding to the alignment of long-reads on (a) the reference unedited sequence (extension .sorted.bw), (b) the non-edited mutated allele (extension ins.sorted.bw), (c) the CTG-repeats excision (extension del.sorted.bw), and (d) the inversion (extension inv.sorted.bw).

molecule: genomic DNA

organism: Homo sapiens

source_name: Myogenic cells

growth_protocol: DM1 patient-specific myogenic cells were obtained from primary dermal fibroblasts transduced with hTERT and estrogen-inducible MYOD1. Fibroblasts were derived from a DM1 donor carrying 520 CTG amplifications in the 3’ UTR of the DMPK gene. Due to CTG repeat instability, during in vitro culture the number of triplets further increased to >1000, as estimated by Northern blot. Myogenic cells were co-infected with Lenti-CK8-Cas9 and Lenti-H1-sgC3/384, sorted and propagated in growth medium (GM), or induced to differentiate to myotubes with differentiation medium (DM).

extract_protocol:
Genomic DNA dedicated to targeted ONT sequencing was isolated using the MagAttract HMW DNA kit (Qiagen, Venlo, Netherlands), to preserve high molecular weight DNA (100–200 kb). Where necessary, sample concentration was performed with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) following ONT’s protocol “SPRI size selection protocol for fragments >1.5-2 kb”.
For each pool, equal volumes of the four selected crRNA probes (S. pyogenes Cas9 Alt-R™ crRNAs, Integrated DNA Technologies, Coralville, IA, USA) were combined. Equimolar amounts of crRNA pools and tracrRNA were annealed. Cas9 ribonucleoprotein complexes (RNPs) were formed by assembling the previously annealed crRNA-tracrRNA pools with HiFi Cas9 (Alt-R® S. pyogenes HiFi Cas9 nuclease V3, Integrated DNA Technologies, Coralville, IA, USA). Input gDNA (3.3 - 7 μg) was first dephosphorylated to reduce non-specific adapter-ligation, subsequently cleaved with Cas9 RNPs and A-tailed using ATPs and Taq polymerase. AMX adapters (Ligation Sequencing kit, Oxford Nanopore Technologies, Oxford, United Kingdom) were ligated to Cas9 cut sites and the resulting libraries were then purified and concentrated using AMPure XP beads (Beckman Coulter, Brea, CA, USA). R9.4.1 MinION flow cells (Oxford Nanopore Technologies, Oxford, UK) were first primed and then loaded with the processed libraries, according to manufacturer’s instructions. 24 hours of sequencing run were performed on the GridION (Oxford Nanopore Technologies, Oxford, UK). During sequencing, real-time basecalling was enabled using the High-Accuracy model (HAC) of Guppy (v6.5.7).

treatment_protocol: Administration of doxycycline for 5 days induced sgRNA expression leading to the deletion of CTG repeats in the 3’UTR of the DMPK gene, while Cas9 was constitutively expressed.

value: Myogenic cells

tag: genotype

value: DM1 heterozygous

tag: treatment

value: Differentiation medium

tag: targeted locus


title: Chimpanzee iPSC line "Pen23", naive state, replicate 3


title: Myogenic cells, proliferating, ROI2, biol rep 2

value: Growth medium


title: Myogenic cells, differentiated, ROI2, biol rep 1


title: Myogenic cells, proliferating, ROI2, biol rep 1


title: Chimpanzee CPR1 cells, TE differentiation day6, replicate 2


title: Myogenic cells, differentiated, ROI1


title: collect STIC 4 | 009 | Immune

city: Pittsburgh

first: Lan

last: Coffman

state: PA

address: 5051 Centre Ave

country: USA

institute: UPMC Hillman Cancer Center

description: Library name: collect STIC 4 | 009 | Immune

library_source: other

data_processing:
RNA-seq; LOQ 2pct by target, 3rd quartile normalized.
Assembly: GRCh38.p13
Supplementary files format and content: Columns represent individual ROIs with descriptions designating tissue type, cell type, and sample ID. Rows represent genes.
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Immune

growth_protocol: Slides were stored at 4C in a desiccator after sectioning, then DSP was performed within the timeframe specified by Nanostring.

extract_protocol:
Extract was performed according to UPMC Cytometry Facility, UPMC Health Sciences Sequencing Core and Nanostring GeoMx DSP protocols.
direct PCR. Read pattern: 27x27. 8bp index.

value: Immune


title: collect STIC 4 | 010 | Immune

description: Library name: collect STIC 4 | 010 | Immune


title: collect STIC 4 | 011 | PanCK

description: Library name: collect STIC 4 | 011 | PanCK

source_name: PanCK

value: PanCK


title: collect STIC 4 | 004 | PanCK

description: Library name: collect STIC 4 | 004 | PanCK


title: collect STIC 4 | 007 | PanCK

description: Library name: collect STIC 4 | 007 | PanCK


title: collect STIC 4 | 008 | PanCK

description: Library name: collect STIC 4 | 008 | PanCK


title: collect STIC 4 | 005 | Stroma

description: Library name: collect STIC 4 | 005 | Stroma

source_name: Stroma

value: Stroma


title: collect STIC 4 | 007 | Stroma

description: Library name: collect STIC 4 | 007 | Stroma


title: collect STIC 4 | 006 | PanCK

description: Library name: collect STIC 4 | 006 | PanCK


title: collect STIC 4 | 004 | Stroma

description: Library name: collect STIC 4 | 004 | Stroma


title: collect STIC 4 | 006 | Stroma

description: Library name: collect STIC 4 | 006 | Stroma


title: collect STIC 4 | 002 | Stroma

description: Library name: collect STIC 4 | 002 | Stroma


title: collect STIC 4 | 003 | PanCK

description: Library name: collect STIC 4 | 003 | PanCK


title: collect STIC 3 | 011 | Stroma

description: Library name: collect STIC 3 | 011 | Stroma


title: collect STIC 3 | 011 | PanCK

description: Library name: collect STIC 3 | 011 | PanCK


title: collect STIC 3 | 010 | Stroma

description: Library name: collect STIC 3 | 010 | Stroma


title: collect STIC 3 | 010 | PanCK

description: Library name: collect STIC 3 | 010 | PanCK


title: collect STIC 4 | 001 | PanCK

description: Library name: collect STIC 4 | 001 | PanCK


title: collect STIC 3 | 008 | Immune

description: Library name: collect STIC 3 | 008 | Immune


title: collect STIC 3 | 009 | PanCK

description: Library name: collect STIC 3 | 009 | PanCK


title: collect STIC 4 | 008 | Stroma

description: Library name: collect STIC 4 | 008 | Stroma


title: collect STIC 3 | 007 | Immune

description: Library name: collect STIC 3 | 007 | Immune


title: collect STIC 3 | 006 | PanCK

description: Library name: collect STIC 3 | 006 | PanCK


title: collect STIC 3 | 006 | Stroma

description: Library name: collect STIC 3 | 006 | Stroma


title: collect STIC 3 | 005 | Stroma

description: Library name: collect STIC 3 | 005 | Stroma


title: collect STIC 3 | 007 | Stroma

description: Library name: collect STIC 3 | 007 | Stroma


title: collect STIC 3 | 004 | Stroma

description: Library name: collect STIC 3 | 004 | Stroma


title: collect STIC 3 | 005 | PanCK

description: Library name: collect STIC 3 | 005 | PanCK


title: collect STIC 3 | 003 | Stroma

description: Library name: collect STIC 3 | 003 | Stroma


title: collect STIC 3 | 001 | Stroma

description: Library name: collect STIC 3 | 001 | Stroma


title: collect STIC 4 | 003 | Stroma

description: Library name: collect STIC 4 | 003 | Stroma


title: collect STIC 2 | 012 | Stroma

description: Library name: collect STIC 2 | 012 | Stroma


title: collect STIC 3 | 001 | PanCK

description: Library name: collect STIC 3 | 001 | PanCK


title: collect STIC 3 | 002 | PanCK

description: Library name: collect STIC 3 | 002 | PanCK


title: collect STIC 2 | 012 | B Cell

description: Library name: collect STIC 2 | 012 | B Cell

source_name: B Cell

value: B Cell


title: collect STIC 2 | 013 | Immune

description: Library name: collect STIC 2 | 013 | Immune


title: collect STIC 2 | 014 | B Cell

description: Library name: collect STIC 2 | 014 | B Cell


title: collect STIC 2 | 014 | Stroma

description: Library name: collect STIC 2 | 014 | Stroma


title: collect STIC 3 | 002 | Stroma

description: Library name: collect STIC 3 | 002 | Stroma


title: collect STIC 2 | 013 | B Cell

description: Library name: collect STIC 2 | 013 | B Cell


title: collect STIC 2 | 011 | Immune

description: Library name: collect STIC 2 | 011 | Immune


title: collect STIC 2 | 011 | Stroma

description: Library name: collect STIC 2 | 011 | Stroma


title: collect STIC 4 | 002 | PanCK

description: Library name: collect STIC 4 | 002 | PanCK


title: collect STIC 2 | 009 | PanCK

description: Library name: collect STIC 2 | 009 | PanCK


title: collect STIC 2 | 007 | Stroma

description: Library name: collect STIC 2 | 007 | Stroma


title: collect STIC 2 | 008 | Stroma

description: Library name: collect STIC 2 | 008 | Stroma


title: collect STIC 3 | 004 | PanCK

description: Library name: collect STIC 3 | 004 | PanCK


title: collect STIC 2 | 009 | Stroma

description: Library name: collect STIC 2 | 009 | Stroma


title: collect STIC 2 | 010 | PanCK

description: Library name: collect STIC 2 | 010 | PanCK


title: collect STIC 2 | 006 | Stroma

description: Library name: collect STIC 2 | 006 | Stroma


title: collect STIC 2 | 007 | PanCK

description: Library name: collect STIC 2 | 007 | PanCK


title: collect STIC 2 | 005 | Stroma

description: Library name: collect STIC 2 | 005 | Stroma


title: collect STIC 2 | 006 | Immune

description: Library name: collect STIC 2 | 006 | Immune


title: collect STIC 2 | 005 | Immune

description: Library name: collect STIC 2 | 005 | Immune


title: collect STIC 2 | 005 | B Cell

description: Library name: collect STIC 2 | 005 | B Cell


title: collect STIC 2 | 004 | Stroma

description: Library name: collect STIC 2 | 004 | Stroma


title: collect STIC 2 | 004 | PanCK

description: Library name: collect STIC 2 | 004 | PanCK


title: collect STIC 2 | 003 | Stroma

description: Library name: collect STIC 2 | 003 | Stroma


title: collect STIC 2 | 003 | PanCK

description: Library name: collect STIC 2 | 003 | PanCK


title: collect STIC 2 | 003 | Immune

description: Library name: collect STIC 2 | 003 | Immune


title: collect STIC 2 | 008 | PanCK

description: Library name: collect STIC 2 | 008 | PanCK


title: collect STIC 2 | 002 | Stroma

description: Library name: collect STIC 2 | 002 | Stroma


title: collect STIC 2 | 002 | PanCK

description: Library name: collect STIC 2 | 002 | PanCK


title: collect STIC 2 | 001 | PanCK

description: Library name: collect STIC 2 | 001 | PanCK


title: collect STIC 2 | 001 | Immune

description: Library name: collect STIC 2 | 001 | Immune


title: collect STIC 2 | 001 | Stroma

description: Library name: collect STIC 2 | 001 | Stroma


title: collect STIC 1 | 011 | PanCK

description: Library name: collect STIC 1 | 011 | PanCK


title: collect STIC 2 | 005 | PanCK

description: Library name: collect STIC 2 | 005 | PanCK


title: collect STIC 1 | 009 | Stroma

description: Library name: collect STIC 1 | 009 | Stroma


title: collect STIC 1 | 009 | PanCK

description: Library name: collect STIC 1 | 009 | PanCK


title: collect STIC 1 | 008 | Stroma

description: Library name: collect STIC 1 | 008 | Stroma


title: collect STIC 1 | 010 | Stroma

description: Library name: collect STIC 1 | 010 | Stroma


title: collect STIC 1 | 010 | PanCK

description: Library name: collect STIC 1 | 010 | PanCK


title: collect STIC 1 | 007 | Stroma

description: Library name: collect STIC 1 | 007 | Stroma


title: collect STIC 1 | 006 | Stroma

description: Library name: collect STIC 1 | 006 | Stroma


title: collect STIC 1 | 008 | PanCK

description: Library name: collect STIC 1 | 008 | PanCK


title: collect STIC 1 | 007 | PanCK

description: Library name: collect STIC 1 | 007 | PanCK


title: collect STIC 1 | 004 | Stroma

description: Library name: collect STIC 1 | 004 | Stroma


title: collect STIC 1 | 004 | PanCK

description: Library name: collect STIC 1 | 004 | PanCK


title: collect STIC 1 | 005 | Stroma

description: Library name: collect STIC 1 | 005 | Stroma


title: collect STIC 1 | 003 | PanCK

description: Library name: collect STIC 1 | 003 | PanCK


title: collect STIC 1 | 003 | Stroma

description: Library name: collect STIC 1 | 003 | Stroma


title: collect STIC 1 | 002 | Stroma

description: Library name: collect STIC 1 | 002 | Stroma


title: collect STIC 1 | 001 | Stroma

description: Library name: collect STIC 1 | 001 | Stroma


title: collect STIC 1 | 011 | Stroma

description: Library name: collect STIC 1 | 011 | Stroma


title: 72.3 D35 BMP2+iCRT3 4

city: Charleston

first: Jorge

last: Munera

state: SC

address: 173 Ashley Avenue

institute: Medical University of South Carolina

data_processing:
Fastq files provided by BGI were imported into Partek Flow system
Use STAR in Partek Flow for the data alignment
Partek E/M was used for the data quantification
Data normalized to TPM
Assembly: hg38
Supplementary files format and content: Tab-delimited txt file includes TPM value for all samples

source_name: D35 organoid

extract_protocol:
RNA was extracted using NucleoSpin® RNA extraction kit (Macharey-Nagel) according to manufacturer's protocols.
RNA library construction was performed by BGI.

tag: cell line

value: Human iPSC 72.3

value: D35 organoid

value: BPM2+iCRT3 treatment for 3 days, then back to basic gut medium


title: 72.3 D35 BMP2+iCRT3 3


title: 72.3 D35 BMP2+iCRT3 2


title: collect STIC 1 | 001 | PanCK

description: Library name: collect STIC 1 | 001 | PanCK


title: 72.3 D35 BMP2+iCRT3 1


title: RD-LC-008c_COLLECT | 012 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 012 | TUMOR

source_name: TUMOR

value: TUMOR


title: RD-LC-008c_COLLECT | 013 | STROMA

description: Library name: RD-LC-008c_COLLECT | 013 | STROMA

source_name: STROMA

value: STROMA


title: RD-LC-008c_COLLECT | 012 | STROMA

description: Library name: RD-LC-008c_COLLECT | 012 | STROMA


title: collect STIC 1 | 006 | PanCK

description: Library name: collect STIC 1 | 006 | PanCK


title: 72.3 D35 BMP2+CHIR 3

value: BPM2+CHIR treatment for 3 days, then back to basic gut medium


title: 72.3 D35 BMP2+CHIR 2


title: 72.3 D35 BMP2+CHIR 4


title: RD-LC-008c_COLLECT | 011 | STROMA

description: Library name: RD-LC-008c_COLLECT | 011 | STROMA


title: RD-LC-008c_COLLECT | 010 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 010 | TUMOR


title: RD-LC-008c_COLLECT | 009 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 009 | TUMOR


title: 72.3 D10 BMP2+iCRT3 4

source_name: D10 organoid

value: D10 organoid

value: BPM2+iCRT3 treatment for 3 days


title: 72.3 D10 BMP2+iCRT3 3


title: collect STIC 1 | 005 | PanCK

description: Library name: collect STIC 1 | 005 | PanCK


title: 72.3 D10 BMP2+iCRT3 2


title: RD-LC-008c_COLLECT | 008 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 008 | TUMOR


title: RD-LC-008c_COLLECT | 008 | STROMA

description: Library name: RD-LC-008c_COLLECT | 008 | STROMA


title: RD-LC-008c_COLLECT | 007 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 007 | TUMOR


title: 72.3 D10 BMP2+iCRT3 1


title: RD-LC-008c_COLLECT | 013 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 013 | TUMOR


title: RD-LC-008c_COLLECT | 007 | STROMA

description: Library name: RD-LC-008c_COLLECT | 007 | STROMA


title: 72.3 D10 BMP2+CHIR 3

value: BPM2+CHIR treatment for 3 days


title: 72.3 D10 BMP2+CHIR 4


title: 72.3 D10 BMP2+CHIR 2


title: RD-LC-008c_COLLECT | 006 | STROMA

description: Library name: RD-LC-008c_COLLECT | 006 | STROMA


title: 72.3 D10 BMP2+CHIR 1


title: RD-LC-008c_COLLECT | 005 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 005 | TUMOR


title: 72.3 D7 sph 3

source_name: D7 spheroid

value: D7 spheroid

value: Mid-hindgut spheroids differentiation


title: RD-LC-008c_COLLECT | 005 | STROMA

description: Library name: RD-LC-008c_COLLECT | 005 | STROMA


title: 72.3 D35 BMP2+CHIR 1


title: RD-LC-008c_COLLECT | 009 | STROMA

description: Library name: RD-LC-008c_COLLECT | 009 | STROMA


title: 72.3 D7 sph 1


title: RD-LC-008c_COLLECT | 004 | STROMA

description: Library name: RD-LC-008c_COLLECT | 004 | STROMA


title: 850k data from sample 247

type: genomic

city: London

first: Sarah

last: Bowden

address: IRDB 3rd floor, Du cane Road

department: Department Surgery and Cancer

country: United Kingdom

institute: Imperial College London

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina infinium EPIC beadchip using standard illumina protocol.

scan_protocol: Arrays were imaged using beadarray reader and standard recommended illumina scanner setting

data_processing: Bespoke pipeline in R V4

label: Cy3 and Cy5

source_name: Benign cervical sample

label_protocol: Standard Illumina protocol

extract_protocol: cell-free DNA extracted using Qiagen QIAMP DNA mini kit

tag: Sex

value: Female

value: Benign cervical sample


title: RD-LC-008c_COLLECT | 003 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 003 | TUMOR


title: 850k data from sample 246


title: RD-LC-008c_COLLECT | 004 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 004 | TUMOR


title: 72.3 D7 sph 2


title: 850k data from sample 244


title: 850k data from sample 245

source_name: CIN3 or Cancer sample

value: CIN3 or Cancer sample


title: RD-LC-008c_COLLECT | 003 | STROMA

description: Library name: RD-LC-008c_COLLECT | 003 | STROMA


title: RD-LC-008c_COLLECT | 002 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 002 | TUMOR


title: 850k data from sample 243


title: 850k data from sample 242


title: RD-LC-008c_COLLECT | 001 | STROMA

description: Library name: RD-LC-008c_COLLECT | 001 | STROMA


title: RD-LC-008c_COLLECT | 006 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 006 | TUMOR


title: 850k data from sample 241


title: RD-LC-008c_COLLECT | 001 | TUMOR

description: Library name: RD-LC-008c_COLLECT | 001 | TUMOR


title: RD-LC-007_COLLECT | 014 | Full ROI

description: Library name: RD-LC-007_COLLECT | 014 | Full ROI

source_name: Full ROI

value: Full ROI


title: RD-LC-007_COLLECT | 015 | Full ROI

description: Library name: RD-LC-007_COLLECT | 015 | Full ROI


title: 850k data from sample 239


title: 850k data from sample 238


title: 850k data from sample 240


title: RD-LC-007_COLLECT | 012 | Full ROI

description: Library name: RD-LC-007_COLLECT | 012 | Full ROI


title: RD-LC-007_COLLECT | 013 | TUMOR

description: Library name: RD-LC-007_COLLECT | 013 | TUMOR


title: 850k data from sample 236


title: RD-LC-007_COLLECT | 011 | STROMA

description: Library name: RD-LC-007_COLLECT | 011 | STROMA


title: 850k data from sample 235


title: 850k data from sample 234


title: 850k data from sample 233


title: RD-LC-007_COLLECT | 010 | Full ROI

description: Library name: RD-LC-007_COLLECT | 010 | Full ROI


title: 850k data from sample 232


title: RD-LC-007_COLLECT | 009 | Full ROI

description: Library name: RD-LC-007_COLLECT | 009 | Full ROI


title: RD-LC-007_COLLECT | 008 | TUMOR

description: Library name: RD-LC-007_COLLECT | 008 | TUMOR


title: collect STIC 2 | 010 | Stroma

description: Library name: collect STIC 2 | 010 | Stroma

value: Stroma


title: RD-LC-007_COLLECT | 006 | TUMOR

description: Library name: RD-LC-007_COLLECT | 006 | TUMOR


title: RD-LC-007_COLLECT | 007 | TUMOR

description: Library name: RD-LC-007_COLLECT | 007 | TUMOR


title: 850k data from sample 231


title: RD-LC-008c_COLLECT | 002 | STROMA

description: Library name: RD-LC-008c_COLLECT | 002 | STROMA


title: 850k data from sample 230


title: 850k data from sample 229


title: 850k data from sample 227


title: RD-LC-007_COLLECT | 003 | TUMOR

description: Library name: RD-LC-007_COLLECT | 003 | TUMOR


title: RD-LC-007_COLLECT | 004 | TUMOR

description: Library name: RD-LC-007_COLLECT | 004 | TUMOR


title: 850k data from sample 228


title: 850k data from sample 226


title: RD-LC-007_COLLECT | 002 | Full ROI

description: Library name: RD-LC-007_COLLECT | 002 | Full ROI


title: RD-LC-007_COLLECT | 011 | TUMOR

description: Library name: RD-LC-007_COLLECT | 011 | TUMOR


title: 850k data from sample 225


title: 850k data from sample 237


title: 850k data from sample 224


title: RD-LC-007_COLLECT | 001 | Full ROI

description: Library name: RD-LC-007_COLLECT | 001 | Full ROI


title: 850k data from sample 223


title: RD-LC-006_COLLECT | 009 | TUMOR

description: Library name: RD-LC-006_COLLECT | 009 | TUMOR


title: RD-LC-006_COLLECT | 008 | STROMA

description: Library name: RD-LC-006_COLLECT | 008 | STROMA


title: 850k data from sample 222


title: RD-LC-006_COLLECT | 008 | TUMOR

description: Library name: RD-LC-006_COLLECT | 008 | TUMOR


title: RD-LC-006_COLLECT | 007 | TUMOR

description: Library name: RD-LC-006_COLLECT | 007 | TUMOR


title: 850k data from sample 221


title: 850k data from sample 220


title: RD-LC-006_COLLECT | 006 | TUMOR

description: Library name: RD-LC-006_COLLECT | 006 | TUMOR


title: 850k data from sample 218


title: 850k data from sample 219


title: RD-LC-006_COLLECT | 006 | STROMA

description: Library name: RD-LC-006_COLLECT | 006 | STROMA


title: RD-LC-006_COLLECT | 005 | TUMOR

description: Library name: RD-LC-006_COLLECT | 005 | TUMOR


title: RD-LC-006_COLLECT | 005 | STROMA

description: Library name: RD-LC-006_COLLECT | 005 | STROMA


title: 850k data from sample 217


title: 850k data from sample 216


title: RD-LC-006_COLLECT | 004 | STROMA

description: Library name: RD-LC-006_COLLECT | 004 | STROMA


title: RD-LC-006_COLLECT | 003 | TUMOR

description: Library name: RD-LC-006_COLLECT | 003 | TUMOR


title: 850k data from sample 215


title: RD-LC-006_COLLECT | 009 | STROMA

description: Library name: RD-LC-006_COLLECT | 009 | STROMA


title: RD-LC-006_COLLECT | 002 | TUMOR

description: Library name: RD-LC-006_COLLECT | 002 | TUMOR


title: RD-LC-006_COLLECT | 003 | STROMA

description: Library name: RD-LC-006_COLLECT | 003 | STROMA


title: 850k data from sample 213


title: 850k data from sample 212


title: 850k data from sample 211


title: 850k data from sample 209


title: RD-LC-006_COLLECT | 002 | STROMA

description: Library name: RD-LC-006_COLLECT | 002 | STROMA


title: 850k data from sample 210


title: 850k data from sample 214


title: RD-LC-006_COLLECT | 007 | STROMA

description: Library name: RD-LC-006_COLLECT | 007 | STROMA


title: RD-LC-006_COLLECT | 001 | STROMA

description: Library name: RD-LC-006_COLLECT | 001 | STROMA


title: 850k data from sample 208


title: RD-LC-005_COLLECT | 020 | TUMOR

description: Library name: RD-LC-005_COLLECT | 020 | TUMOR


title: RD-LC-006_COLLECT | 001 | TUMOR

description: Library name: RD-LC-006_COLLECT | 001 | TUMOR


title: RD-LC-005_COLLECT | 020 | STROMA

description: Library name: RD-LC-005_COLLECT | 020 | STROMA


title: 850k data from sample 207


title: RD-LC-005_COLLECT | 019 | TUMOR

description: Library name: RD-LC-005_COLLECT | 019 | TUMOR


title: RD-LC-007_COLLECT | 005 | Full ROI

description: Library name: RD-LC-007_COLLECT | 005 | Full ROI


title: 850k data from sample 205


title: RD-LC-005_COLLECT | 019 | STROMA

description: Library name: RD-LC-005_COLLECT | 019 | STROMA


title: 850k data from sample 203


title: RD-LC-005_COLLECT | 018 | TUMOR

description: Library name: RD-LC-005_COLLECT | 018 | TUMOR


title: 850k data from sample 202


title: 850k data from sample 195


title: 850k data from sample 201


title: RD-LC-005_COLLECT | 015 | STROMA

description: Library name: RD-LC-005_COLLECT | 015 | STROMA


title: 850k data from sample 194


title: 850k data from sample 198


title: RD-LC-005_COLLECT | 017 | STROMA

description: Library name: RD-LC-005_COLLECT | 017 | STROMA


title: RD-LC-005_COLLECT | 016 | STROMA

description: Library name: RD-LC-005_COLLECT | 016 | STROMA


title: 850k data from sample 193


title: RD-LC-005_COLLECT | 012 | STROMA

description: Library name: RD-LC-005_COLLECT | 012 | STROMA


title: 850k data from sample 197


title: RD-LC-005_COLLECT | 014 | TUMOR

description: Library name: RD-LC-005_COLLECT | 014 | TUMOR


title: RD-LC-005_COLLECT | 013 | TUMOR

description: Library name: RD-LC-005_COLLECT | 013 | TUMOR


title: 850k data from sample 200


title: RD-LC-005_COLLECT | 014 | STROMA

description: Library name: RD-LC-005_COLLECT | 014 | STROMA


title: 850k data from sample 196


title: 850k data from sample 192


title: 850k data from sample 199


title: 850k data from sample 191


title: 850k data from sample 189


title: RD-LC-005_COLLECT | 010 | TUMOR

description: Library name: RD-LC-005_COLLECT | 010 | TUMOR


title: RD-LC-005_COLLECT | 010 | STROMA

description: Library name: RD-LC-005_COLLECT | 010 | STROMA


title: 850k data from sample 190


title: 850k data from sample 204


title: 850k data from sample 188


title: RD-LC-005_COLLECT | 009 | TUMOR

description: Library name: RD-LC-005_COLLECT | 009 | TUMOR


title: RD-LC-005_COLLECT | 018 | STROMA

description: Library name: RD-LC-005_COLLECT | 018 | STROMA


title: RD-LC-005_COLLECT | 013 | STROMA

description: Library name: RD-LC-005_COLLECT | 013 | STROMA


title: RD-LC-005_COLLECT | 012 | TUMOR

description: Library name: RD-LC-005_COLLECT | 012 | TUMOR


title: RD-LC-005_COLLECT | 011 | TUMOR

description: Library name: RD-LC-005_COLLECT | 011 | TUMOR


title: RD-LC-005_COLLECT | 011 | STROMA

description: Library name: RD-LC-005_COLLECT | 011 | STROMA


title: 850k data from sample 186


title: 850k data from sample 187


title: RD-LC-005_COLLECT | 007 | TUMOR

description: Library name: RD-LC-005_COLLECT | 007 | TUMOR


title: RD-LC-005_COLLECT | 008 | STROMA

description: Library name: RD-LC-005_COLLECT | 008 | STROMA


title: 850k data from sample 180


title: RD-LC-005_COLLECT | 005 | TUMOR

description: Library name: RD-LC-005_COLLECT | 005 | TUMOR


title: RD-LC-005_COLLECT | 007 | STROMA

description: Library name: RD-LC-005_COLLECT | 007 | STROMA


title: 850k data from sample 183


title: 850k data from sample 179


title: 850k data from sample 181


title: RD-LC-005_COLLECT | 003 | TUMOR

description: Library name: RD-LC-005_COLLECT | 003 | TUMOR


title: 850k data from sample 178


title: RD-LC-005_COLLECT | 004 | STROMA

description: Library name: RD-LC-005_COLLECT | 004 | STROMA


title: 850k data from sample 182


title: RD-LC-005_COLLECT | 002 | TUMOR

description: Library name: RD-LC-005_COLLECT | 002 | TUMOR


title: RD-LC-005_COLLECT | 002 | STROMA

description: Library name: RD-LC-005_COLLECT | 002 | STROMA


title: 850k data from sample 176


title: 850k data from sample 177


title: RD-LC-005_COLLECT | 001 | STROMA

description: Library name: RD-LC-005_COLLECT | 001 | STROMA


title: 850k data from sample 175


title: RD-LC-004 | 018 | Stroma

description: Library name: RD-LC-004 | 018 | Stroma


title: 850k data from sample 174


title: RD-LC-005_COLLECT | 008 | TUMOR

description: Library name: RD-LC-005_COLLECT | 008 | TUMOR


title: RD-LC-004 | 017 | Tumor

description: Library name: RD-LC-004 | 017 | Tumor

source_name: Tumor

value: Tumor


title: 850k data from sample 184


title: RD-LC-005_COLLECT | 005 | STROMA

description: Library name: RD-LC-005_COLLECT | 005 | STROMA


title: 850k data from sample 173


title: 850k data from sample 185


title: RD-LC-004 | 017 | Stroma

description: Library name: RD-LC-004 | 017 | Stroma


title: 850k data from sample 171


title: RD-LC-004 | 016 | Tumor

description: Library name: RD-LC-004 | 016 | Tumor


title: 850k data from sample 169


title: RD-LC-004 | 014 | Tumor

description: Library name: RD-LC-004 | 014 | Tumor


title: 850k data from sample 167


title: RD-LC-004 | 016 | Stroma

description: Library name: RD-LC-004 | 016 | Stroma


title: 850k data from sample 168


title: RD-LC-004 | 013 | Tumor

description: Library name: RD-LC-004 | 013 | Tumor


title: RD-LC-004 | 015 | Stroma

description: Library name: RD-LC-004 | 015 | Stroma


title: 850k data from sample 170


title: RD-LC-004 | 013 | Stroma

description: Library name: RD-LC-004 | 013 | Stroma


title: RD-LC-005_COLLECT | 001 | TUMOR

description: Library name: RD-LC-005_COLLECT | 001 | TUMOR


title: 850k data from sample 165


title: 850k data from sample 164


title: RD-LC-004 | 014 | Stroma

description: Library name: RD-LC-004 | 014 | Stroma


title: RD-LC-004 | 012 | Tumor

description: Library name: RD-LC-004 | 012 | Tumor


title: 850k data from sample 163


title: RD-LC-004 | 015 | Tumor

description: Library name: RD-LC-004 | 015 | Tumor


title: 850k data from sample 162


title: RD-LC-004 | 011 | Tumor

description: Library name: RD-LC-004 | 011 | Tumor


title: 850k data from sample 172


title: 850k data from sample 166


title: 850k data from sample 161


title: RD-LC-004 | 011 | Stroma

description: Library name: RD-LC-004 | 011 | Stroma


title: 850k data from sample 160


title: 850k data from sample 159


title: RD-LC-004 | 010 | Tumor

description: Library name: RD-LC-004 | 010 | Tumor


title: RD-LC-004 | 010 | Stroma

description: Library name: RD-LC-004 | 010 | Stroma


title: 850k data from sample 158


title: RD-LC-004 | 009 | Tumor

description: Library name: RD-LC-004 | 009 | Tumor


title: 850k data from sample 157


title: RD-LC-004 | 009 | Stroma

description: Library name: RD-LC-004 | 009 | Stroma


title: 850k data from sample 156


title: 850k data from sample 155


title: 850k data from sample 154


title: 850k data from sample 153


title: 850k data from sample 152


title: RD-LC-004 | 008 | Tumor

description: Library name: RD-LC-004 | 008 | Tumor


title: RD-LC-004 | 007 | Stroma

description: Library name: RD-LC-004 | 007 | Stroma


title: 850k data from sample 151


title: RD-LC-004 | 005 | Stroma

description: Library name: RD-LC-004 | 005 | Stroma


title: RD-LC-004 | 008 | Stroma

description: Library name: RD-LC-004 | 008 | Stroma


title: 850k data from sample 150


title: RD-LC-004 | 007 | Tumor

description: Library name: RD-LC-004 | 007 | Tumor


title: RD-LC-004 | 004 | Stroma

description: Library name: RD-LC-004 | 004 | Stroma


title: RD-LC-004 | 012 | Stroma

description: Library name: RD-LC-004 | 012 | Stroma


title: 850k data from sample 149


title: RD-LC-004 | 003 | Tumor

description: Library name: RD-LC-004 | 003 | Tumor


title: 850k data from sample 148


title: RD-LC-004 | 003 | Stroma

description: Library name: RD-LC-004 | 003 | Stroma


title: 850k data from sample 147


title: RD-LC-004 | 002 | Tumor

description: Library name: RD-LC-004 | 002 | Tumor


title: RD-LC-004 | 002 | Stroma

description: Library name: RD-LC-004 | 002 | Stroma


title: 850k data from sample 146


title: 850k data from sample 145


title: RD-LC-004 | 001 | Tumor

description: Library name: RD-LC-004 | 001 | Tumor


title: 850k data from sample 144


title: RD-LC-003 | 014 | Stroma

description: Library name: RD-LC-003 | 014 | Stroma


title: RD-LC-003 | 013 | Tumor

description: Library name: RD-LC-003 | 013 | Tumor


title: 850k data from sample 143


title: RD-LC-003 | 012 | Immune

description: Library name: RD-LC-003 | 012 | Immune

value: Immune


title: RD-LC-004 | 005 | Tumor

description: Library name: RD-LC-004 | 005 | Tumor


title: 850k data from sample 141


title: 850k data from sample 140


title: RD-LC-003 | 011 | Stroma

description: Library name: RD-LC-003 | 011 | Stroma


title: RD-LC-003 | 010 | Stroma

description: Library name: RD-LC-003 | 010 | Stroma


title: 850k data from sample 138


title: 850k data from sample 139


title: 850k data from sample 137


title: RD-LC-003 | 010 | Tumor

description: Library name: RD-LC-003 | 010 | Tumor


title: RD-LC-003 | 009 | Tumor

description: Library name: RD-LC-003 | 009 | Tumor


title: RD-LC-003 | 009 | Stroma

description: Library name: RD-LC-003 | 009 | Stroma


title: RD-LC-003 | 008 | Tumor

description: Library name: RD-LC-003 | 008 | Tumor


title: 850k data from sample 136


title: 850k data from sample 135


title: 850k data from sample 133


title: RD-LC-003 | 008 | Stroma

description: Library name: RD-LC-003 | 008 | Stroma


title: 850k data from sample 132


title: 850k data from sample 131


title: RD-LC-003 | 007 | Tumor

description: Library name: RD-LC-003 | 007 | Tumor


title: RD-LC-003 | 007 | Stroma

description: Library name: RD-LC-003 | 007 | Stroma


title: 850k data from sample 130


title: RD-LC-003 | 006 | Tumor

description: Library name: RD-LC-003 | 006 | Tumor


title: 850k data from sample 142


title: RD-LC-003 | 006 | Stroma

description: Library name: RD-LC-003 | 006 | Stroma


title: 850k data from sample 129


title: 850k data from sample 128


title: RD-LC-003 | 011 | Tumor

description: Library name: RD-LC-003 | 011 | Tumor


title: 850k data from sample 127


title: RD-LC-003 | 004 | Tumor

description: Library name: RD-LC-003 | 004 | Tumor


title: 850k data from sample 126


title: 850k data from sample 124


title: 850k data from sample 125


title: RD-LC-003 | 003 | Tumor

description: Library name: RD-LC-003 | 003 | Tumor


title: RD-LC-003 | 004 | Stroma

description: Library name: RD-LC-003 | 004 | Stroma


title: RD-LC-003 | 003 | Stroma

description: Library name: RD-LC-003 | 003 | Stroma


title: 850k data from sample 121


title: 850k data from sample 123


title: RD-LC-003 | 002 | Stroma

description: Library name: RD-LC-003 | 002 | Stroma


title: RD-LC-003 | 002 | Tumor

description: Library name: RD-LC-003 | 002 | Tumor


title: 850k data from sample 119


title: RD-LC-003 | 001 | Stroma

description: Library name: RD-LC-003 | 001 | Stroma


title: RD-LC-003 | 005 | Tumor

description: Library name: RD-LC-003 | 005 | Tumor


title: 850k data from sample 118


title: 850k data from sample 117


title: RD-LC-002 | 009 | Stroma

description: Library name: RD-LC-002 | 009 | Stroma


title: 850k data from sample 120


title: RD-LC-003 | 001 | Immune

description: Library name: RD-LC-003 | 001 | Immune


title: RD-LC-002 | 008 | Tumor

description: Library name: RD-LC-002 | 008 | Tumor


title: RD-LC-002 | 008 | Stroma

description: Library name: RD-LC-002 | 008 | Stroma


title: 850k data from sample 115


title: 850k data from sample 114


title: 850k data from sample 122


title: RD-LC-002 | 009 | Tumor

description: Library name: RD-LC-002 | 009 | Tumor


title: 850k data from sample 113


title: 850k data from sample 112


title: 850k data from sample 116


title: RD-LC-002 | 006 | Stroma

description: Library name: RD-LC-002 | 006 | Stroma


title: RD-LC-002 | 007 | Stroma

description: Library name: RD-LC-002 | 007 | Stroma


title: RD-LC-002 | 005 | Stroma

description: Library name: RD-LC-002 | 005 | Stroma


title: RD-LC-002 | 004 | Tumor

description: Library name: RD-LC-002 | 004 | Tumor


title: 850k data from sample 110


title: RD-LC-002 | 003 | Tumor

description: Library name: RD-LC-002 | 003 | Tumor


title: 850k data from sample 109


title: 850k data from sample 108


title: RD-LC-002 | 003 | Stroma

description: Library name: RD-LC-002 | 003 | Stroma


title: 850k data from sample 107


title: RD-LC-002 | 002 | Tumor

description: Library name: RD-LC-002 | 002 | Tumor


title: 850k data from sample 106


title: RD-LC-002 | 002 | Stroma

description: Library name: RD-LC-002 | 002 | Stroma


title: RD-LC-002 | 001 | Tumor

description: Library name: RD-LC-002 | 001 | Tumor


title: 850k data from sample 105


title: 850k data from sample 104


title: 850k data from sample 103


title: RD-LC-002 | 001 | Stroma

description: Library name: RD-LC-002 | 001 | Stroma


title: RD-LC-001 | 009 | Tumor

description: Library name: RD-LC-001 | 009 | Tumor


title: RD-LC-001 | 009 | Stroma

description: Library name: RD-LC-001 | 009 | Stroma


title: 850k data from sample 102


title: 850k data from sample 99


title: 850k data from sample 101


title: RD-LC-001 | 008 | Tumor

description: Library name: RD-LC-001 | 008 | Tumor


title: RD-LC-002 | 004 | Stroma

description: Library name: RD-LC-002 | 004 | Stroma


title: RD-LC-001 | 008 | Stroma

description: Library name: RD-LC-001 | 008 | Stroma


title: 850k data from sample 111


title: RD-LC-001 | 007 | Tumor

description: Library name: RD-LC-001 | 007 | Tumor


title: 850k data from sample 98


title: 850k data from sample 97


title: RD-LC-001 | 007 | Stroma

description: Library name: RD-LC-001 | 007 | Stroma


title: 850k data from sample 94


title: RD-LC-001 | 006 | Stroma

description: Library name: RD-LC-001 | 006 | Stroma


title: RD-LC-001 | 006 | Tumor

description: Library name: RD-LC-001 | 006 | Tumor


title: 850k data from sample 95


title: RD-LC-002 | 003 | Immune

description: Library name: RD-LC-002 | 003 | Immune


title: RD-LC-001 | 005 | Stroma

description: Library name: RD-LC-001 | 005 | Stroma


title: 850k data from sample 93


title: 850k data from sample 92


title: 850k data from sample 91


title: 850k data from sample 89


title: 850k data from sample 88


title: 850k data from sample 90


title: RD-LC-001 | 004 | Tumor

description: Library name: RD-LC-001 | 004 | Tumor


title: RD-LC-001 | 004 | Stroma

description: Library name: RD-LC-001 | 004 | Stroma


title: RD-LC-001 | 005 | CD20

description: Library name: RD-LC-001 | 005 | CD20


title: 850k data from sample 87


title: RD-LC-001 | 003 | Tumor

description: Library name: RD-LC-001 | 003 | Tumor


title: RD-LC-001 | 003 | Stroma

description: Library name: RD-LC-001 | 003 | Stroma


title: 850k data from sample 86


title: 850k data from sample 96


title: 850k data from sample 85


title: 850k data from sample 84


title: RD-LC-001 | 003 | Immune

description: Library name: RD-LC-001 | 003 | Immune


title: RD-LC-001 | 001 | Tumor

description: Library name: RD-LC-001 | 001 | Tumor


title: RD-LC-001 | 002 | Stroma

description: Library name: RD-LC-001 | 002 | Stroma


title: RD-LC-001 | 005 | Tumor

description: Library name: RD-LC-001 | 005 | Tumor


title: RD-LC-001 | 002 | Tumor

description: Library name: RD-LC-001 | 002 | Tumor


title: RD-LC-001 | 001 | Stroma

description: Library name: RD-LC-001 | 001 | Stroma


title: 850k data from sample 82


title: 850k data from sample 81


title: FT-8_Collect | 020 | TUMOR

description: Library name: FT-8_Collect | 020 | TUMOR


title: 850k data from sample 80


title: 850k data from sample 79


title: FT-8_Collect | 020 | STROMA

description: Library name: FT-8_Collect | 020 | STROMA


title: 850k data from sample 78


title: RD-LC-001 | 004 | Immune

description: Library name: RD-LC-001 | 004 | Immune


title: FT-8_Collect | 019 | STROMA

description: Library name: FT-8_Collect | 019 | STROMA


title: 850k data from sample 77


title: 850k data from sample 76


title: 850k data from sample 75


title: FT-8_Collect | 017 | TUMOR

description: Library name: FT-8_Collect | 017 | TUMOR


title: FT-8_Collect | 018 | TUMOR

description: Library name: FT-8_Collect | 018 | TUMOR


title: FT-8_Collect | 017 | STROMA

description: Library name: FT-8_Collect | 017 | STROMA


title: 850k data from sample 74


title: 850k data from sample 72


title: FT-8_Collect | 016 | TUMOR

description: Library name: FT-8_Collect | 016 | TUMOR


title: 850k data from sample 73


title: FT-8_Collect | 015 | TUMOR

description: Library name: FT-8_Collect | 015 | TUMOR


title: 850k data from sample 83


title: FT-8_Collect | 016 | STROMA

description: Library name: FT-8_Collect | 016 | STROMA


title: 850k data from sample 70


title: FT-8_Collect | 015 | STROMA

description: Library name: FT-8_Collect | 015 | STROMA


title: FT-8_Collect | 014 | TUMOR

description: Library name: FT-8_Collect | 014 | TUMOR


title: 850k data from sample 68


title: FT-8_Collect | 014 | STROMA

description: Library name: FT-8_Collect | 014 | STROMA


title: FT-8_Collect | 019 | TUMOR

description: Library name: FT-8_Collect | 019 | TUMOR


title: FT-8_Collect | 013 | TUMOR

description: Library name: FT-8_Collect | 013 | TUMOR


title: 850k data from sample 66


title: 850k data from sample 69


title: FT-8_Collect | 013 | STROMA

description: Library name: FT-8_Collect | 013 | STROMA


title: FT-8_Collect | 012 | TUMOR

description: Library name: FT-8_Collect | 012 | TUMOR


title: 850k data from sample 65


title: 850k data from sample 67


title: FT-8_Collect | 011 | TUMOR

description: Library name: FT-8_Collect | 011 | TUMOR


title: FT-8_Collect | 012 | STROMA

description: Library name: FT-8_Collect | 012 | STROMA


title: 850k data from sample 64


title: 850k data from sample 63


title: 850k data from sample 61


title: FT-8_Collect | 011 | STROMA

description: Library name: FT-8_Collect | 011 | STROMA


title: 850k data from sample 62


title: 850k data from sample 71


title: 850k data from sample 60


title: 850k data from sample 59


title: FT-8_Collect | 007 | TUMOR

description: Library name: FT-8_Collect | 007 | TUMOR


title: 850k data from sample 58


title: 850k data from sample 57


title: FT-8_Collect | 008 | STROMA

description: Library name: FT-8_Collect | 008 | STROMA


title: FT-8_Collect | 007 | STROMA

description: Library name: FT-8_Collect | 007 | STROMA


title: FT-8_Collect | 006 | TUMOR

description: Library name: FT-8_Collect | 006 | TUMOR


title: FT-8_Collect | 006 | STROMA

description: Library name: FT-8_Collect | 006 | STROMA


title: 850k data from sample 55


title: 850k data from sample 56


title: 850k data from sample 54


title: FT-8_Collect | 005 | TUMOR

description: Library name: FT-8_Collect | 005 | TUMOR


title: FT-8_Collect | 005 | STROMA

description: Library name: FT-8_Collect | 005 | STROMA


title: 850k data from sample 53


title: 850k data from sample 52


title: 850k data from sample 51


title: FT-8_Collect | 010 | STROMA

description: Library name: FT-8_Collect | 010 | STROMA


title: 850k data from sample 50


title: FT-8_Collect | 004 | TUMOR

description: Library name: FT-8_Collect | 004 | TUMOR


title: FT-8_Collect | 009 | STROMA

description: Library name: FT-8_Collect | 009 | STROMA


title: FT-8_Collect | 002 | TUMOR

description: Library name: FT-8_Collect | 002 | TUMOR


title: FT-8_Collect | 002 | STROMA

description: Library name: FT-8_Collect | 002 | STROMA


title: 850k data from sample 47


title: 850k data from sample 48


title: FT-8_Collect | 001 | TUMOR

description: Library name: FT-8_Collect | 001 | TUMOR


title: 850k data from sample 46


title: FT-8_Collect | 001 | STROMA

description: Library name: FT-8_Collect | 001 | STROMA


title: 850k data from sample 43


title: FT-7_Collect | 006 | STROMA

description: Library name: FT-7_Collect | 006 | STROMA


title: FT-7_Collect | 005 | TUMOR

description: Library name: FT-7_Collect | 005 | TUMOR


title: 850k data from sample 42


title: FT-7_Collect | 006 | TUMOR

description: Library name: FT-7_Collect | 006 | TUMOR


title: 850k data from sample 44


title: 850k data from sample 41


title: 850k data from sample 45


title: FT-7_Collect | 004 | STROMA

description: Library name: FT-7_Collect | 004 | STROMA


title: FT-8_Collect | 004 | STROMA

description: Library name: FT-8_Collect | 004 | STROMA


title: 850k data from sample 38


title: FT-8_Collect | 003 | TUMOR

description: Library name: FT-8_Collect | 003 | TUMOR


title: FT-7_Collect | 004 | TUMOR

description: Library name: FT-7_Collect | 004 | TUMOR


title: FT-7_Collect | 003 | TUMOR

description: Library name: FT-7_Collect | 003 | TUMOR


title: 850k data from sample 39


title: FT-7_Collect | 003 | STROMA

description: Library name: FT-7_Collect | 003 | STROMA


title: 850k data from sample 36


title: 850k data from sample 40


title: 850k data from sample 37


title: FT-7_Collect | 002 | STROMA

description: Library name: FT-7_Collect | 002 | STROMA


title: 850k data from sample 35


title: FT-7_Collect | 002 | TUMOR

description: Library name: FT-7_Collect | 002 | TUMOR


title: FT-7_Collect | 001 | TUMOR

description: Library name: FT-7_Collect | 001 | TUMOR


title: FT-7_Collect | 001 | STROMA

description: Library name: FT-7_Collect | 001 | STROMA


title: 850k data from sample 33


title: FT-6_Collect | 007 | TUMOR

description: Library name: FT-6_Collect | 007 | TUMOR


title: 850k data from sample 31


title: FT-6_Collect | 007 | STROMA

description: Library name: FT-6_Collect | 007 | STROMA


title: FT-7_Collect | 005 | STROMA

description: Library name: FT-7_Collect | 005 | STROMA


title: 850k data from sample 29


title: 850k data from sample 28


title: FT-6_Collect | 006 | STROMA

description: Library name: FT-6_Collect | 006 | STROMA


title: 850k data from sample 27


title: FT-6_Collect | 004 | TUMOR

description: Library name: FT-6_Collect | 004 | TUMOR


title: 850k data from sample 25


title: 850k data from sample 26


title: FT-6_Collect | 004 | STROMA

description: Library name: FT-6_Collect | 004 | STROMA


title: 850k data from sample 24


title: FT-6_Collect | 003 | TUMOR

description: Library name: FT-6_Collect | 003 | TUMOR


title: 850k data from sample 23


title: 850k data from sample 21


title: FT-6_Collect | 003 | STROMA

description: Library name: FT-6_Collect | 003 | STROMA


title: FT-6_Collect | 002 | TUMOR

description: Library name: FT-6_Collect | 002 | TUMOR


title: 850k data from sample 22


title: 850k data from sample 32


title: FT-6_Collect | 002 | STROMA

description: Library name: FT-6_Collect | 002 | STROMA


title: FT-6_Collect | 005 | STROMA

description: Library name: FT-6_Collect | 005 | STROMA


title: FT-6_Collect | 001 | TUMOR

description: Library name: FT-6_Collect | 001 | TUMOR


title: 850k data from sample 30


title: FT-6_Collect | 001 | STROMA

description: Library name: FT-6_Collect | 001 | STROMA


title: 850k data from sample 18


title: FT-6_Collect | 006 | TUMOR

description: Library name: FT-6_Collect | 006 | TUMOR


title: FT-5_Collect | 019 | STROMA

description: Library name: FT-5_Collect | 019 | STROMA


title: 850k data from sample 16


title: FT-5_Collect | 018 | STROMA

description: Library name: FT-5_Collect | 018 | STROMA


title: 850k data from sample 12


title: FT-5_Collect | 017 | STROMA

description: Library name: FT-5_Collect | 017 | STROMA


title: FT-5_Collect | 016 | TUMOR

description: Library name: FT-5_Collect | 016 | TUMOR


title: 850k data from sample 17


title: 850k data from sample 10


title: 850k data from sample 8


title: 850k data from sample 20


title: 850k data from sample 7


title: FT-5_Collect | 015 | STROMA

description: Library name: FT-5_Collect | 015 | STROMA


title: FT-5_Collect | 014 | TUMOR

description: Library name: FT-5_Collect | 014 | TUMOR


title: 850k data from sample 19


title: FT-6_Collect | 005 | TUMOR

description: Library name: FT-6_Collect | 005 | TUMOR


title: 850k data from sample 13


title: 850k data from sample 6


title: FT-5_Collect | 015 | TUMOR

description: Library name: FT-5_Collect | 015 | TUMOR


title: 850k data from sample 5


title: FT-5_Collect | 013 | STROMA

description: Library name: FT-5_Collect | 013 | STROMA


title: 850k data from sample 4


title: FT-8_Collect | 003 | STROMA

description: Library name: FT-8_Collect | 003 | STROMA


title: FT-5_Collect | 012 | TUMOR

description: Library name: FT-5_Collect | 012 | TUMOR


title: 850k data from sample 3


title: FT-5_Collect | 012 | STROMA

description: Library name: FT-5_Collect | 012 | STROMA


title: 850k data from sample 15


title: FT-5_Collect | 014 | STROMA

description: Library name: FT-5_Collect | 014 | STROMA


title: FT-5_Collect | 011 | STROMA

description: Library name: FT-5_Collect | 011 | STROMA


title: FT-5_Collect | 017 | TUMOR

description: Library name: FT-5_Collect | 017 | TUMOR


title: FT-5_Collect | 016 | STROMA

description: Library name: FT-5_Collect | 016 | STROMA


title: 850k data from sample 2


title: 850k data from sample 1


title: 14583 CSCs

city: Doha

first: Cristina

last: Maccalli

address: Doha

country: Qatar

institute: Sidra Medicine

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Methylated and unmethylated signal intensity data were generated as idat. files
Idat files generated by Infinium MethylationV.1 BeadChip were analyzed using the RnBeads R package
Differential methylation analysis between CIC and FBS cell lines was conducted using limmaR package at the CpG sites and region levels, defined as tiling (5 kb), genes, promoters, and CpG islands.

label: Cy3, Cy5

label_protocol: not provided

growth_protocol: CICs were cultured as colon-spheres in Advanced DMEM/F12 medium  containing 20 ng/ml of EGF , 50 ng/ml FGF-2. Differenciated cells were cultured in the presence of RPMI 1640 supplemented with 10% FBS

extract_protocol: DNA extraction and purification from CICs and FBS cell lines were performed using the AllPrep DNA/RNA Mini Kit

value: CIC


title: 850k data from sample 9


title: FT-5_Collect | 009 | TUMOR

description: Library name: FT-5_Collect | 009 | TUMOR


title: FT-5_Collect | 010 | STROMA

description: Library name: FT-5_Collect | 010 | STROMA


title: FT-5_Collect | 010 | TUMOR

description: Library name: FT-5_Collect | 010 | TUMOR


title: FT-5_Collect | 009 | STROMA

description: Library name: FT-5_Collect | 009 | STROMA


title: CSC_7

description: Methylated and unmethylated signal intensity data were generated as idat. files


title: CSC_8


title: CSC_59


title: CSC_57


title: FT-5_Collect | 007 | TUMOR

description: Library name: FT-5_Collect | 007 | TUMOR


title: FT-5_Collect | 008 | STROMA

description: Library name: FT-5_Collect | 008 | STROMA


title: FT-5_Collect | 007 | STROMA

description: Library name: FT-5_Collect | 007 | STROMA


title: FT-5_Collect | 006 | STROMA

description: Library name: FT-5_Collect | 006 | STROMA


title: CSC_5


title: CSC_3


title: CSC_20


title: FT-5_Collect | 004 | STROMA

description: Library name: FT-5_Collect | 004 | STROMA


title: FT-5_Collect | 005 | TUMOR

description: Library name: FT-5_Collect | 005 | TUMOR


title: CSC_21


title: FT-5_Collect | 003 | TUMOR

description: Library name: FT-5_Collect | 003 | TUMOR


title: CSC_2


title: CSC_13


title: CSC_14


title: FT-5_Collect | 003 | STROMA

description: Library name: FT-5_Collect | 003 | STROMA


title: FT-5_Collect | 002 | STROMA

description: Library name: FT-5_Collect | 002 | STROMA


title: FT-5_Collect | 002 | TUMOR

description: Library name: FT-5_Collect | 002 | TUMOR


title: CSC_9


title: CSC_11


title: FT-5_Collect | 001 | TUMOR

description: Library name: FT-5_Collect | 001 | TUMOR


title: 1076_col

value: FBS


title: FT-5_Collect | 001 | STROMA

description: Library name: FT-5_Collect | 001 | STROMA


title: CSC 33

value: CSC 33


title: Collect STIC FT-9 | 019 | Stroma

description: Library name: Collect STIC FT-9 | 019 | Stroma


title: 1872 col.


title: CSC 3

value: CSC 3


title: FT-5_Collect | 005 | STROMA

description: Library name: FT-5_Collect | 005 | STROMA

value: STROMA


title: 111011 CSC


title: Collect STIC FT-9 | 019 | STIC

description: Library name: Collect STIC FT-9 | 019 | STIC

source_name: STIC

value: STIC


title: Collect STIC FT-9 | 018 | Stroma

description: Library name: Collect STIC FT-9 | 018 | Stroma


title: Collect STIC FT-9 | 017 | Stroma

description: Library name: Collect STIC FT-9 | 017 | Stroma


title: Collect STIC FT-9 | 018 | STIC

description: Library name: Collect STIC FT-9 | 018 | STIC


title: Collect STIC FT-9 | 017 | STIC

description: Library name: Collect STIC FT-9 | 017 | STIC


title: 1247 col.

description: Methylated and unmethylated signal intensity data were generated as idat. files


title: 1247 CSC


title: Collect STIC FT-9 | 016 | Stroma

description: Library name: Collect STIC FT-9 | 016 | Stroma


title: 1076 col.


title: 1076 CSC


title: Collect STIC FT-9 | 015 | Stroma

description: Library name: Collect STIC FT-9 | 015 | Stroma


title: Collect STIC FT-9 | 014 | Stroma

description: Library name: Collect STIC FT-9 | 014 | Stroma


title: ATRT-311-FHTC

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

description: Cell line grown in serum-free media

hyb_protocol: Bisulphite converted DANN was amplified, fragmented and hybridzed to human Infinium MythylationEPIC using stard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommened Illumina scanner settings

data_processing: Samples were processed in GenomeStudio V2011.1 and processed using defaults (no background correction, no normalization)

growth_protocol: Cells were grown in serum-free media

extract_protocol: DNA was isolated from cell pellets using the Bionano Prep Blood and Cell Culture DANN Isolation Kit


title: ATRT-310-FHTC

description: Cell line grown in serum-free media


title: CHLA-266_SF

description: Cell line grown in serum-free media


title: CHLA-06

description: Cell line grown in serum-free media


title: Collect STIC FT-9 | 013 | Stroma

description: Library name: Collect STIC FT-9 | 013 | Stroma


title: CSC 16

value: CSC 16


title: Collect STIC FT-9 | 012 | STIC

description: Library name: Collect STIC FT-9 | 012 | STIC


title: Collect STIC FT-9 | 011 | STIC

description: Library name: Collect STIC FT-9 | 011 | STIC


title: CHLA-05

description: Cell line grown in serum-free media


title: CHLA-02

description: Cell line grown in serum-free media


title: BT-16_SF

description: Cell line grown in serum-free media


title: Collect STIC FT-9 | 009 | Stroma

description: Library name: Collect STIC FT-9 | 009 | Stroma


title: Collect STIC FT-9 | 008 | Full ROI

description: Library name: Collect STIC FT-9 | 008 | Full ROI


title: BT-12_SF

description: Cell line grown in serum-free media


title: Collect STIC FT-9 | 010 | STIC

description: Library name: Collect STIC FT-9 | 010 | STIC


title: Collect STIC FT-9 | 007 | Stroma

description: Library name: Collect STIC FT-9 | 007 | Stroma


title: ATRT13808

description: Cell line grown in serum-free media


title: JC-ATRT

description: Cell line grown in serum-free media

source_name: JC-ATRT

value: JC-ATRT


title: Collect STIC FT-9 | 006 | Stroma

description: Library name: Collect STIC FT-9 | 006 | Stroma


title: Collect STIC FT-9 | 004 | STIC

description: Library name: Collect STIC FT-9 | 004 | STIC


title: VU397

description: Cell line grown in serum-free media


title: Collect STIC FT-9 | 016 | STIC

description: Library name: Collect STIC FT-9 | 016 | STIC


title: Collect STIC FT-9 | 003 | STIC

description: Library name: Collect STIC FT-9 | 003 | STIC


title: HHU-ATRT-01

description: Cell line grown in serum-free media


title: Collect STIC FT-9 | 002 | STIC

description: Library name: Collect STIC FT-9 | 002 | STIC


title: Collect STIC FT-9 | 001 | STIC

description: Library name: Collect STIC FT-9 | 001 | STIC


title: Collect STIC FT-7 | 018 | STIC

description: Library name: Collect STIC FT-7 | 018 | STIC


title: Collect STIC FT-7 | 017 | Stroma

description: Library name: Collect STIC FT-7 | 017 | Stroma


title: CHLA-04

description: Cell line grown in serum-free media


title: Collect STIC FT-7 | 017 | STIC

description: Library name: Collect STIC FT-7 | 017 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206350360153_R08C01]

city: Jacksonville

first: Samuel

middle: O

last: Antwi

state: FL

address: 4500 San Pablo Road South, 756N Stabile Building

department: Quantitative Health Sciences

institute: Mayo Clinic

hyb_protocol: Standard Illumina Protocol; Bisulphite converted DNA was amplified, fragmented and hybridized to Human Infinium MethylationEPIC BeadChip (Illumina)

scan_protocol: Standard Illumina Protocol; Arrays were imaged using BeadArray Reader (iScan) and standard recommended Illumina scanner setting

data_processing:
Data were processed via 'minfi' library and normalized via 'dasen' method in 'watermelon' R library in R environment (v4.2.2). Probes on chromosomes X and Y were excluded.
HCC_matrix_processed.txt contains normalized Beta

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from leukocytes using the Maxwell RSC Instrument with appropriate kits (Promega) and quantitated using a Qubit fluorometer. DNA quantification was performed using the Invitrogen Qubit dsDNA Quantification Assay kit (ThermoFisher Scientific, Inc., Waltham, MA, USA). All sample processing, including DNA extraction and quantification were performed by the Mayo Clinic Special Studies Laboratory.

value: Male

tag: age

tag: diseasestate

value: Control

value: peripheral blood leukocyte


title: blood leukocyte DNA from metabolic HCC case [206350360185_R04C01]

value: Female

value: Case


title: blood leukocyte DNA from HCC control with metabolic liver disease [206350360185_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206350360153_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206350360185_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206350360185_R02C01]


title: Collect STIC FT-7 | 016 | Stroma

description: Library name: Collect STIC FT-7 | 016 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206350360153_R01C01]


title: Collect STIC FT-7 | 015 | STIC

description: Library name: Collect STIC FT-7 | 015 | STIC


title: Collect STIC FT-9 | 005 | Stroma

description: Library name: Collect STIC FT-9 | 005 | Stroma


title: Collect STIC FT-7 | 016 | STIC

description: Library name: Collect STIC FT-7 | 016 | STIC


title: blood leukocyte DNA from metabolic HCC case [206350360153_R05C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206350360153_R02C01]


title: Collect STIC FT-7 | 015 | Stroma

description: Library name: Collect STIC FT-7 | 015 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390119_R07C01]


title: Collect STIC FT-7 | 013 | Stroma

description: Library name: Collect STIC FT-7 | 013 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206272390119_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206272390119_R02C01]


title: Collect STIC FT-7 | 014 | STIC

description: Library name: Collect STIC FT-7 | 014 | STIC


title: Collect STIC FT-7 | 018 | Stroma

description: Library name: Collect STIC FT-7 | 018 | Stroma


title: Collect STIC FT-7 | 013 | STIC

description: Library name: Collect STIC FT-7 | 013 | STIC


title: Collect STIC FT-7 | 012 | Stroma

description: Library name: Collect STIC FT-7 | 012 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390110_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206272390110_R05C01]


title: Collect STIC FT-7 | 014 | Stroma

description: Library name: Collect STIC FT-7 | 014 | Stroma


title: Collect STIC FT-7 | 011 | Stroma

description: Library name: Collect STIC FT-7 | 011 | Stroma


title: Collect STIC FT-7 | 012 | STIC

description: Library name: Collect STIC FT-7 | 012 | STIC


title: 850k data from sample 49

value: Benign cervical sample


title: blood leukocyte DNA from metabolic HCC case [206272390119_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206272390119_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206272390110_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390107_R08C01]


title: Collect STIC FT-7 | 010 | Stroma

description: Library name: Collect STIC FT-7 | 010 | Stroma

value: Stroma


title: blood leukocyte DNA from metabolic HCC case [206272390110_R04C01]


title: Collect STIC FT-7 | 010 | STIC

description: Library name: Collect STIC FT-7 | 010 | STIC


title: blood leukocyte DNA from metabolic HCC case [206272390107_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390107_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206272390107_R04C01]


title: Collect STIC FT-7 | 008 | STIC

description: Library name: Collect STIC FT-7 | 008 | STIC


title: Collect STIC FT-7 | 007 | Stroma

description: Library name: Collect STIC FT-7 | 007 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390107_R02C01]


title: Collect STIC FT-7 | 008 | Stroma

description: Library name: Collect STIC FT-7 | 008 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390087_R05C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390087_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206272390087_R04C01]


title: Collect STIC FT-7 | 005 | Stroma

description: Library name: Collect STIC FT-7 | 005 | Stroma


title: Collect STIC FT-7 | 007 | STIC

description: Library name: Collect STIC FT-7 | 007 | STIC


title: Collect STIC FT-7 | 005 | STIC

description: Library name: Collect STIC FT-7 | 005 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390087_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390087_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206272390083_R07C01]


title: Collect STIC FT-7 | 004 | Stroma

description: Library name: Collect STIC FT-7 | 004 | Stroma


title: Collect STIC FT-7 | 003 | Stroma

description: Library name: Collect STIC FT-7 | 003 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390083_R06C01]


title: Collect STIC FT-7 | 011 | STIC

description: Library name: Collect STIC FT-7 | 011 | STIC


title: Collect STIC FT-7 | 009 | Stroma

description: Library name: Collect STIC FT-7 | 009 | Stroma


title: Collect STIC FT-7 | 004 | STIC

description: Library name: Collect STIC FT-7 | 004 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390083_R05C01]


title: Collect STIC FT-7 | 002 | STIC

description: Library name: Collect STIC FT-7 | 002 | STIC


title: blood leukocyte DNA from metabolic HCC case [206272390083_R03C01]


title: Collect STIC FT-7 | 002 | Stroma

description: Library name: Collect STIC FT-7 | 002 | Stroma


title: Collect STIC FT-7 | 001 | Stroma

description: Library name: Collect STIC FT-7 | 001 | Stroma


title: Collect STIC FT-7 | 001 | STIC

description: Library name: Collect STIC FT-7 | 001 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390079_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390083_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390083_R04C01]


title: Collect STIC FT-7 | 006 | STIC

description: Library name: Collect STIC FT-7 | 006 | STIC


title: Collect STIC FT-7 | 003 | STIC

description: Library name: Collect STIC FT-7 | 003 | STIC


title: Collect STIC FT-6 | 011 | Stroma

description: Library name: Collect STIC FT-6 | 011 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390079_R06C01]


title: Collect STIC FT-6 | 011 | STIC

description: Library name: Collect STIC FT-6 | 011 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390079_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206272390079_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390087_R03C01]


title: Collect STIC FT-6 | 010 | STIC

description: Library name: Collect STIC FT-6 | 010 | STIC


title: blood leukocyte DNA from metabolic HCC case [206272390079_R02C01]


title: Collect STIC FT-6 | 010 | Stroma

description: Library name: Collect STIC FT-6 | 010 | Stroma


title: Collect STIC FT-6 | 009 | Stroma

description: Library name: Collect STIC FT-6 | 009 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206272390079_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206272390074_R08C01]


title: Collect STIC FT-6 | 008 | Stroma

description: Library name: Collect STIC FT-6 | 008 | Stroma


title: Collect STIC FT-6 | 008 | STIC

description: Library name: Collect STIC FT-6 | 008 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390074_R04C01]


title: Collect STIC FT-6 | 007 | STIC

description: Library name: Collect STIC FT-6 | 007 | STIC


title: Collect STIC FT-6 | 006 | Stroma

description: Library name: Collect STIC FT-6 | 006 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390074_R03C01]


title: Collect STIC FT-6 | 006 | STIC

description: Library name: Collect STIC FT-6 | 006 | STIC


title: blood leukocyte DNA from metabolic HCC case [206272390074_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390074_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390073_R06C01]


title: Collect STIC FT-6 | 007 | Stroma

description: Library name: Collect STIC FT-6 | 007 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206272390073_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206272390073_R04C01]


title: Collect STIC FT-6 | 005 | STIC

description: Library name: Collect STIC FT-6 | 005 | STIC


title: blood leukocyte DNA from metabolic HCC case [206272390073_R02C01]


title: Collect STIC FT-6 | 005 | Stroma

description: Library name: Collect STIC FT-6 | 005 | Stroma


title: Collect STIC FT-6 | 004 | STIC

description: Library name: Collect STIC FT-6 | 004 | STIC


title: Collect STIC FT-6 | 003 | Stroma

description: Library name: Collect STIC FT-6 | 003 | Stroma


title: Collect STIC FT-6 | 004 | Stroma

description: Library name: Collect STIC FT-6 | 004 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470195_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206260470195_R08C01]


title: Collect STIC FT-6 | 003 | STIC

description: Library name: Collect STIC FT-6 | 003 | STIC


title: Collect STIC FT-6 | 002 | Stroma

description: Library name: Collect STIC FT-6 | 002 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470195_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206260470195_R05C01]


title: Collect STIC FT-6 | 009 | STIC

description: Library name: Collect STIC FT-6 | 009 | STIC


title: Collect STIC FT-6 | 002 | STIC

description: Library name: Collect STIC FT-6 | 002 | STIC


title: Collect STIC FT-6 | 001 | Stroma

description: Library name: Collect STIC FT-6 | 001 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470195_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206272390073_R08C01]


title: Collect STIC FT-6 | 001 | STIC

description: Library name: Collect STIC FT-6 | 001 | STIC


title: blood leukocyte DNA from metabolic HCC case [206272390073_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470182_R07C01]


title: Collect STIC FT-2 | 032 | Stroma

description: Library name: Collect STIC FT-2 | 032 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470182_R05C01]


title: Collect STIC FT-2 | 032 | STIC

description: Library name: Collect STIC FT-2 | 032 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470182_R06C01]


title: Collect STIC FT-2 | 031 | Stroma

description: Library name: Collect STIC FT-2 | 031 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470182_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470179_R08C01]


title: Collect STIC FT-2 | 031 | STIC

description: Library name: Collect STIC FT-2 | 031 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470182_R04C01]


title: Collect STIC FT-2 | 028 | Stroma

description: Library name: Collect STIC FT-2 | 028 | Stroma


title: Collect STIC FT-2 | 030 | Stroma

description: Library name: Collect STIC FT-2 | 030 | Stroma


title: Collect STIC FT-2 | 026 | Full ROI

description: Library name: Collect STIC FT-2 | 026 | Full ROI

value: Full ROI


title: blood leukocyte DNA from metabolic HCC case [206260470179_R05C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470177_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470179_R02C01]


title: Collect STIC FT-2 | 025 | Full ROI

description: Library name: Collect STIC FT-2 | 025 | Full ROI


title: Collect STIC FT-2 | 027 | Full ROI

description: Library name: Collect STIC FT-2 | 027 | Full ROI


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470177_R06C01]


title: Collect STIC FT-2 | 024 | Stroma

description: Library name: Collect STIC FT-2 | 024 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470177_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470177_R03C01]


title: Collect STIC FT-2 | 024 | STIC

description: Library name: Collect STIC FT-2 | 024 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470177_R02C01]


title: Collect STIC FT-2 | 023 | Stroma

description: Library name: Collect STIC FT-2 | 023 | Stroma


title: Collect STIC FT-2 | 023 | STIC

description: Library name: Collect STIC FT-2 | 023 | STIC


title: blood leukocyte DNA from metabolic HCC case [206260470177_R01C01]


title: Collect STIC FT-2 | 022 | Stroma

description: Library name: Collect STIC FT-2 | 022 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470176_R08C01]


title: Collect STIC FT-2 | 021 | STIC

description: Library name: Collect STIC FT-2 | 021 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470176_R05C01]


title: Collect STIC FT-2 | 018 | Full ROI

description: Library name: Collect STIC FT-2 | 018 | Full ROI


title: Collect STIC FT-2 | 030 | STIC

description: Library name: Collect STIC FT-2 | 030 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470179_R03C01]


title: Collect STIC FT-2 | 017 | Stroma

description: Library name: Collect STIC FT-2 | 017 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470175_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470175_R05C01]


title: Collect STIC FT-2 | 016 | Stroma

description: Library name: Collect STIC FT-2 | 016 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470175_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470175_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470175_R02C01]


title: Collect STIC FT-2 | 015 | Full ROI

description: Library name: Collect STIC FT-2 | 015 | Full ROI


title: Collect STIC FT-2 | 012 | Stroma

description: Library name: Collect STIC FT-2 | 012 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470149_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470149_R06C01]


title: Collect STIC FT-2 | 011 | Full ROI

description: Library name: Collect STIC FT-2 | 011 | Full ROI


title: Collect STIC FT-2 | 013 | Stroma

description: Library name: Collect STIC FT-2 | 013 | Stroma


title: Collect STIC FT-2 | 014 | Stroma

description: Library name: Collect STIC FT-2 | 014 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470149_R02C01]


title: Collect STIC FT-2 | 009 | Full ROI

description: Library name: Collect STIC FT-2 | 009 | Full ROI


title: Collect STIC FT-2 | 008 | Stroma

description: Library name: Collect STIC FT-2 | 008 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470149_R01C01]


title: Collect STIC FT-2 | 007 | Full ROI

description: Library name: Collect STIC FT-2 | 007 | Full ROI


title: blood leukocyte DNA from metabolic HCC case [206260470148_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470148_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206260470176_R04C01]


title: Collect STIC FT-2 | 006 | Stroma

description: Library name: Collect STIC FT-2 | 006 | Stroma


title: Collect STIC FT-2 | 006 | STIC

description: Library name: Collect STIC FT-2 | 006 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470148_R03C01]


title: Collect STIC FT-2 | 005 | Stroma

description: Library name: Collect STIC FT-2 | 005 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470148_R01C01]


title: Collect STIC FT-2 | 005 | STIC

description: Library name: Collect STIC FT-2 | 005 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470142_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206260470142_R07C01]


title: Collect STIC FT-2 | 004 | Stroma

description: Library name: Collect STIC FT-2 | 004 | Stroma


title: Collect STIC FT-2 | 004 | STIC

description: Library name: Collect STIC FT-2 | 004 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470142_R05C01]


title: Collect STIC FT-2 | 010 | Full ROI

description: Library name: Collect STIC FT-2 | 010 | Full ROI


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470138_R07C01]


title: Collect STIC FT-2 | 003 | Stroma

description: Library name: Collect STIC FT-2 | 003 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470149_R03C01]


title: Collect STIC FT-2 | 003 | STIC

description: Library name: Collect STIC FT-2 | 003 | STIC


title: Collect STIC FT-2 | 002 | Stroma

description: Library name: Collect STIC FT-2 | 002 | Stroma


title: Collect STIC FT-2 | 002 | STIC

description: Library name: Collect STIC FT-2 | 002 | STIC


title: Collect STIC FT-2 | 001 | Stroma

description: Library name: Collect STIC FT-2 | 001 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470138_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470138_R02C01]


title: Collect STIC FT-2 | 001 | STIC

description: Library name: Collect STIC FT-2 | 001 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470137_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470137_R07C01]


title: Collect STIC FT-13 | 010 | Stroma

description: Library name: Collect STIC FT-13 | 010 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470137_R05C01]


title: Collect STIC FT-13 | 009 | Stroma

description: Library name: Collect STIC FT-13 | 009 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470137_R06C01]


title: Collect STIC FT-13 | 009 | STIC

description: Library name: Collect STIC FT-13 | 009 | STIC


title: blood leukocyte DNA from metabolic HCC case [206260470137_R03C01]


title: Collect STIC FT-13 | 008 | Stroma

description: Library name: Collect STIC FT-13 | 008 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470136_R08C01]


title: Collect STIC FT-13 | 008 | STIC

description: Library name: Collect STIC FT-13 | 008 | STIC


title: blood leukocyte DNA from metabolic HCC case [206260470136_R06C01]


title: Collect STIC FT-13 | 007 | STIC

description: Library name: Collect STIC FT-13 | 007 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470138_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470136_R04C01]


title: Collect STIC FT-13 | 006 | Stroma

description: Library name: Collect STIC FT-13 | 006 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470136_R03C01]


title: Collect STIC FT-13 | 006 | STIC

description: Library name: Collect STIC FT-13 | 006 | STIC


title: blood leukocyte DNA from metabolic HCC case [206260470136_R02C01]


title: Collect STIC FT-13 | 005 | Stroma

description: Library name: Collect STIC FT-13 | 005 | Stroma


title: Collect STIC FT-13 | 005 | STIC

description: Library name: Collect STIC FT-13 | 005 | STIC


title: blood leukocyte DNA from metabolic HCC case [206260470136_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206260470102_R08C01]


title: LPS_Sal_3

city: Omaha

first: Aaron

middle: D

last: Schwab

state: NE

address: 42nd and Emile St.

institute: University of Nebraska Medical Center

description: Male

data_processing:
The original fastq format reads were trimmed by fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data; available online at:http://www.bioinformatics.babraham.ac.uk/projects/fastqc) for quality control.
The trimmed fastq files were processed by a standard pipeline utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at gene level.
The trimmed fastq files were mapped to mm10 (GRCm38) mouse reference genome
Assembly: mm10 (GRCm38)
Supplementary files format and content: CSV file that gives raw read counts and normalized expression abundance in TPM and FPKM values for all the available genes.

organism: Mus musculus

source_name: Primary mouse lung

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
Sequencing libraries were generated by the UNMC NGS Core using the NuGEN Universal Plus mRNA-Seq library kit from TECAN following the manufacturers recommended procedure (TECAN, USA Redwood City, CA 94063).

treatment_protocol: C57BL/6 male miice were intratracheally instilled under light sedation with isoflurane with 10 μg LPS or sterile saline in a 50 μl volume, followed by 1 μg recombinant IL-10 or vehicle (saline) control in a 50 μl volume 5-hours post exposure and then daily for the following two days. Animals were euthanized 24 hours after the final LPS exposure for lung collection.

value: Primary mouse lung

value: Collagenase treated lung homogenate

value: C57BL/6J (WT)

value: Intratracheal 10ug LPS w/3 Doses of Saline


title: blood leukocyte DNA from metabolic HCC case [206260470102_R06C01]


title: Collect STIC FT-13 | 010 | STIC

description: Library name: Collect STIC FT-13 | 010 | STIC


title: LPS_Sal_2

description: Male


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470142_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470137_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470102_R04C01]


title: Collect STIC FT-13 | 004 | STIC

description: Library name: Collect STIC FT-13 | 004 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470102_R05C01]


title: Collect STIC FT-13 | 007 | Stroma

description: Library name: Collect STIC FT-13 | 007 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470136_R05C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470102_R02C01]


title: Collect STIC FT-13 | 003 | Stroma

description: Library name: Collect STIC FT-13 | 003 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470102_R01C01]


title: LPS_IL10_3

description: Male

value: Intratracheal 10ug LPS w/3 Doses of IL10


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470088_R08C01]


title: Collect STIC FT-13 | 003 | STIC

description: Library name: Collect STIC FT-13 | 003 | STIC


title: Collect STIC FT-13 | 002 | Stroma

description: Library name: Collect STIC FT-13 | 002 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470088_R06C01]


title: LPS_IL10_2

description: Male


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470088_R05C01]


title: Collect STIC FT-13 | 002 | STIC

description: Library name: Collect STIC FT-13 | 002 | STIC


title: LPS_IL10_1

description: Male


title: Collect STIC FT-13 | 004 | Stroma

description: Library name: Collect STIC FT-13 | 004 | Stroma


title: sep1sep2sep3 SEP3Δtet line 3

city: Grenoble

first: Veronique

last: Hugouvieux

address: 17 rue des Martyrs

department: IRIG

country: France

institute: CEA Grenoble

description: sep1sep2sep3SEP3Δtet replicat 3

data_processing:
Mapping onto the Arabidopsis genome was done using STAR (no multimapping mismatch < 10),  available in the Galaxy platform.
Read count per gene was done using FeatureCount (default parameters)  available in the Galaxy platform.
Statistical analysis were done using  EdgeR (default parameters),  available in the Galaxy platform.
Assembly: Arabidopsis_thaliana_TAIR10

organism: Arabidopsis thaliana

source_name: flower

growth_protocol: Description of the Arabidopsis lines , growth condition and RNA extraction protocoles are found in the following paper: Hugouvieux et al, Nucleic Acid Research, 2018:1;46(10):4966-4977. doi: 10.1093/nar/gky205.

extract_protocol: Poly A selection,  Construction of the libraries and  sequencing were perfomed by Genewiz

value: infloresence meristem flower buds up stages 10-13


title: blood leukocyte DNA from metabolic HCC case [206260470088_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206260470002_R08C01]


title: Collect STIC FT-13 | 001 | Stroma

description: Library name: Collect STIC FT-13 | 001 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470002_R07C01]


title: sep1sep2sep3 SEP3Δtet line 2

description: sep1sep2sep3SEP3Δtet replicat 2

value: infloresence meristem flower buds up stages 10-12


title: blood leukocyte DNA from metabolic HCC case [206260470002_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470002_R05C01]


title: Collect STIC FT-13 | 001 | STIC

description: Library name: Collect STIC FT-13 | 001 | STIC

value: STIC


title: LPS_Sal_1

description: Male


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470002_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206260470102_R03C01]


title: sep1sep2sep3 SEP3Δtet line 1

description: sep1sep2sep3SEP3Δtet replicat 1

value: infloresence meristem flower buds up stages 10-11


title: Collect STIC FT-12 | 010 | STIC

description: Library name: Collect STIC FT-12 | 010 | STIC


title: blood leukocyte DNA from metabolic HCC case [206260470001_R07C01]

value: Male


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470088_R07C01]

value: Control