title: 5TIF4-replicate-2

city: Beijing

first: Gang

last: Jin

address: Zhongguancun North street

department: Institute for Immunology

country: China

institute: Tsinghua University

data_processing:
Quality control of raw sequencing reads was determined by FASTQC.
After getting clean reads, HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to get the alignment results.
Differential analysis, DEseq2.
Assembly: mm10
Supplementary files format and content: Matrix table with gene read counts for every gene and every sample

source_name: Spleen

extract_protocol:
One month after cell transfer, CD8+ Thy1.1+ 5TIF, 5TIF4 cells or endogenous CD8+ T cells were sorted by flow cytometry with purity > 95% from spleen of recipient mice. RNA samples were isolated and purified using TIANGEN RNAprep Pure Cell/Bacteria Kit
RNA samples were shipped to BGI and libraries were prepared by BGI company according to DNBSEQ's instructions

value: Spleen

value: CD8 T


title: IPAH-Oblit-VA010-Full ROI-VA010-IPAH_WTA-002

status: Public on Apr 04 2024

type: RNA

city: Aurora

first: Rubin

middle: M

last: Tuder

state: CO

address: 12700 East 19th Avenue

department: Medicine

country: USA

institute: University of Colorado

description: Obliterative Lesion

scan_protocol: GeoMx Digital Spatial Profiler

data_processing: Gene expression was normalised with RUVIII (Molania et al. 2019) (v0.9.7.1, k=5). The set of control genes with lowest variation across pseudobiological replicates was identified in a two-step approach, first running RUVIII across log2 transformed counts with all genes as controls, then choosing the 100 genes with the least variation to use for the normalisation.

molecule: total RNA

organism: Homo sapiens

source_name: IPAH Lung

extract_protocol: rna kit

tag: individuial

tag: batch


title: IPAH-Plx-VA010-Full ROI-VA010-IPAH_WTA-001

description: Plexifirm lesion


title: RNA-Seq of Vk36973 passaged in vivo harvested from spleen

type: SRA

city: Scottsdale

first: Peter

middle: Leif

last: Bergsagel

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

description:
Vk36973_MM_R_EM_F_MYC.CrbnNull.CRBN_37407_rna
Vk36973_MM_R_EM_F_MYC.CrbnNull.CRBN_37407_rna

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequences with fastp version 0.22 and mapped to genome using salmon version 1.8 with parameters  --gcBias --validateMappings  --reduceGCMemory. The salmon index was created using GENCODE m23 GTF
For TPM_filtered the salmon index was created after removing from the GENCODE m23 GTF file mitochondrial gene transcripts, ribosomal RNA transcripts, and immunoglobulin transcripts, and after addition to the GTF  of RNA transcripts for CRE, GFP, human FGFR3, human CRBN, human IL5Ra, human TRNT, and the VkMYC transgene
Assembly: GRCm38 with addition of  DNA sequences for VkMYC transgene, CRE, FGFR3_IRES_GFP, and human CRBN BAC containing IL5Ra, TRNT, CRBN
Supplementary files format and content: Tab deliminated text file containing TPM summarized per gene

organism: Mus musculus

source_name: spleen

extract_protocol:
CD138-selected cells were placed in TriZol (Invitrogen), and following extraction were further purified on Purelink Micro-Minicolumns (Invitrogen) with an on-column DNAse digestion step
cDNA libraries were prepared using NEBNext Ultra II RNA library Prep Kit (New England Biolabs)

tag: strain

tag: Sex

value: female

tag: tissue

value: spleen

tag: tumor type

value: Transplant recipient

tag: cell line

tag: cell type

value: plasma cell

tag: disease

value: multiple myeloma

tag: genotype

tag: myc transgene_stop_codon_reversion

value: yes


title: 5TIF4-replicate-1


title: C.reinhardtii, short Fe timecourse, 0 min post-wash, rep 2

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

data_processing:
Reads were mapped to the C.reinhardtii reference assembly with STAR (v2.4.1.d) using STAR --outFilterMismatchNoverLmax 0.04  --alignIntronMax 10000  --readFilesCommand zcat  --outFilterType BySJout
Normalized expression estimates were calculated with cuffdiff (v2.0.2) with cuffdiff  --multi-read-correct --max-bundle-frags 1000000000
Assembly: The Chlamydomonas reinhardtii reference genome assembly and annotations (v5.6) available from Phytozome at (https://phytozome-next.jgi.doe.gov/)
Supplementary files format and content: The processed data file, Fe_timecourses.FPKMs.tsv, includes normalized expression estimates in terms of fragments per kb of gene per million mapped reads (FPKMs) for all C.reinhardtii nuclear genes in all samples. The mean of two biologicial replicates is presented.

molecule: polyA RNA

organism: Chlamydomonas reinhardtii

source_name: cultured cells

growth_protocol: Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.

extract_protocol:
Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA).
RNA-Seq libraries compatible with the Illumina HiSeq platform were constructed using standard kits and protocols from Illumina.

treatment_protocol: Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times.

value: cultured cells

tag: time point

value: 0 min post-wash

tag: treatment

value: iron deprevation

tag: cultured in

value: TAP medium without Fe-EDTA 0 min post-wash


title: 5TIF-replicate-2


title: C.reinhardtii, short Fe timecourse, 0 min post-wash, rep 1


title: 5TIF-replicate-1


title: IPAH-Adventitia-CC016-Full ROI-CC016-013

description: Adventitia


title: C.reinhardtii, short Fe timecourse, 0 min pre-wash, rep 1

value: 0 min pre-wash

value: TAP medium without Fe-EDTA 0 min pre-wash


title: RNA-Seq of Vk36387 passaged in vivo harvested from spleen

description:
Vk36387_MM_R_EM_F_MYC.CrbnNull.CRBN_39019_rna
Vk36387_MM_R_EM_F_MYC.CrbnNull.CRBN_39019_rna


title: IPAH-Intima+Media-CC016-Full ROI-CC016-011

description: Intima+Media


title: RNA-Seq of Vk36574 passaged in vivo harvested from spleen

description:
Vk36574_MM_R_EM_M_MYC.CrbnNull.CRBN_38942_rna
Vk36574_MM_R_EM_M_MYC.CrbnNull.CRBN_38942_rna

value: male


title: Endo CD8-replicate 1

value: Endo CD8


title: C.reinhardtii, short Fe timecourse, 0 min pre-wash, rep 2


title: Endo CD8-replicate 2


title: Caenorhabditis elegans,20℃,control adult,rep3

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

institute: Henan university

data_processing:
Illumina Casava1.7 software used for base-calling
Sequenced reads were trimmed for adaptor sequence. and masked for low-complexity or low-quality sequence. then mapped to WBcel235 whole genome using bowtie v0.12.2 with parameters
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level was calculated through a protocol from Chepelev et al., Nucleic Acids Research,2009.
Assembly: C. elegans genome version WBcel235 was used as the reference.
Supplementary files format and content: The txt format file contains the FPKM value of  expression gene

organism: Caenorhabditis elegans

source_name: control

growth_protocol: Harvest worms and collect eggs simultaneously. The eggs were cultured in M9 and incubated at 20℃ until L1.

extract_protocol: RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction

treatment_protocol: For the corresponding stages of worms, administer alternate day fasting (ADF) for a period of seven days, followed by the collection of a large number of nematodes for RNA extraction.

value: whole body

value: control

tag: age

value: adult

value: hermaphrodite

value: WT


title: IPAH-Plx-CC016-Full ROI-CC016-010

description: Plexifirm lesion


title: RNA-Seq of Vk36217 passaged in vivo harvested from spleen

description:
Vk36217_MM_R_EM_M_MYC.CrbnNull.CRBN_37771_rna
Vk36217_MM_R_EM_M_MYC.CrbnNull.CRBN_37771_rna

value: spleen

value: Transplant recipient


title: IPAH-Plx-CC016-Full ROI-CC016-009

description: Plexifirm lesion


title: Caenorhabditis elegans,20℃,control adult,rep2


title: C.reinhardtii, short Fe timecourse, 5 min, rep 1

value: 5 min

value: TAP medium without Fe-EDTA 5 min


title: RNA-Seq of Vk36040 passaged in vivo harvested from bone marrow

description:
Vk36040_MM_R_BM_F_MYC.CrbnNull.CRBN_36914_rna
Vk36040_MM_R_BM_F_MYC.CrbnNull.CRBN_36914_rna

value: female

value: plasma cell

value: multiple myeloma

value: yes


title: RNA-Seq of Vk36040 de novo tumor harvested from spleen

description:
Vk36040_MM_O_EM_F_MYC.CrbnNull.CRBN_36063_rna
Vk36040_MM_O_EM_F_MYC.CrbnNull.CRBN_36063_rna

value: original de novo tumor


title: IPAH-Oblit-CC016-Full ROI-CC016-008

description: Obliterative Lesion


title: IPAH-Oblit-CC016-Full ROI-CC016-007

description: Obliterative Lesion


title: Caenorhabditis elegans,20℃,control adult,rep1


title: IPAH-Oblit-CC016-Full ROI-CC016-006

description: Obliterative Lesion


title: RNA-Seq of Vk36844 passaged in vivo harvested from spleen

description:
Vk36844_MM_R_EM_M_MYC.Omo.rtTA_38507_rna
Vk36844_MM_R_EM_M_MYC.Omo.rtTA_38507_rna


title: RNA-Seq of Vk35707 growing in vitro

description:
Vk35707_MM_V_V_F_MYC.CrbnNull.CRBN_39246_rna
Vk35707_MM_V_V_F_MYC.CrbnNull.CRBN_39246_rna

source_name: in vitro

value: in vitro

value: in vitro tumor


title: Caenorhabditis elegans,20℃,middle adult,rep3

source_name: middle stage ADF

value: middle stage ADF


title: Caenorhabditis elegans,20℃,middle adult,rep2

value: whole body


title: RNA-Seq of Vk35633 passaged in vivo harvested from spleen

description:
Vk35633_MM_R_EM_F_MYC.CrbnNull.CRBN_39668_rna
Vk35633_MM_R_EM_F_MYC.CrbnNull.CRBN_39668_rna

value: no


title: RNA-Seq of Vk35628 passaged in vivo harvested from bone marrow

description:
Vk35628_MM_R_BM_F_MYC.Nsd2Null_36916_rna
Vk35628_MM_R_BM_F_MYC.Nsd2Null_36916_rna

source_name: bone marrow

value: bone marrow


title: IPAH-Oblit-VA010-Full ROI-VA010-IPAH_WTA-004

description: Obliterative Lesion


title: IPAH-Intima+Media-CC016-Full ROI-CC016-005

description: Intima+Media


title: Caenorhabditis elegans,20℃,young adult,rep3

source_name: young stage ADF

value: young stage ADF

value: adult

value: hermaphrodite


title: IPAH-Intima+Media-CC016-Full ROI-CC016-004

description: Intima+Media


title: Caenorhabditis elegans,20℃,young adult,rep2

value: WT


title: RNA-Seq of Vk35621 passaged in vivo harvested from spleen

description:
Vk35621_MM_R_EM_M_MYCfl_36909_rna
Vk35621_MM_R_EM_M_MYCfl_36909_rna

value: male

value: spleen

value: Transplant recipient

value: MYCfl


title: colorectal cancer tissue sample AUS2_892_T

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene expression estimates as RMA values on log2-scale.

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene level expression values were estimated according to the robust multi-array average (RMA) approach implemented with the justRMA function in the R package affy and using custom CDF files from Brainarray. A batch effect from different lot numbers of the GeneChip™ WT Plus Reagent Kit was corrected with ComBat in the R package sva using default parameters (the batch of each sample is indicated as analysis batch.

label: biotin

source_name: Colorectal cancer patient

label_protocol: 100 ng total RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer tissue sample

value: T


title: colorectal cancer tissue sample AUS2_892_T2


title: Repliseq_late_K562_LBRLMNAKO_r2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Repli-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-LMNA-KO; experiment: late fraction
K562_dKO.bw

library_source: genomic

data_processing:
1. DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
Assembly: hg38
Supplementary files format and content: 1. DamID: BigWig files of log2-normalized pADamID scores for 25 kb genomic bins; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios (linked to the corresponding *early sample records).

molecule: genomic DNA

growth_protocol: K562 cells (from ATCC) were cultured according to their ATCC guidelines.

extract_protocol:
1. DamID: Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2. RNA-seq: RNA was isolated using the Qiagen RNeasy column purification kit; 3. Repli-Seq: cells were harvested by centrifugation and immediately fixed in ice-cold ethanol.
1. DamID: the full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; 2: RNA-seq: sequencing libraries were prepared using the Illumina TruSeq polyA stranded RNA kit; 3: replicated DNA was enriched for with a BrdU IP, before libraries were prepared as described in Marchal, 2018.
1. OTHER: DamID; 2. RNA-seq; 3. OTHER: Repli-seq

treatment_protocol: 1. DamID: cells were transduced with lentivirus containing Dam constructs. Three days after transduction, genomic DNA was isolated.; 2. Repli-seq: BrdU was added to a final concentration of 100 uM and cells were incubated at 37 °C for another 2 h.

value: LBR/LMNA DKO


title: colorectal cancer tissue sample AUS2_891_T2


title: RNA-Seq of Vk35567 passaged in vivo harvested from bone marrow

description:
Vk35567_MM_R_BM_M_MYC.Nsd2Null_36906_rna
Vk35567_MM_R_BM_M_MYC.Nsd2Null_36906_rna

value: plasma cell

value: multiple myeloma

value: yes


title: Caenorhabditis elegans,20℃,young adult,rep1

value: whole body


title: RNA-Seq of Vk35546 passaged in vivo harvested from spleen

description:
Vk35546_MM_R_EM_M_MYC_38713_rna
Vk35546_MM_R_EM_M_MYC_38713_rna

value: MYC


title: IPAH-Plx-CC016-Full ROI-CC016-001

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_891_T3

value: no


title: Caenorhabditis elegans,20℃,middle adult,rep1

value: middle stage ADF


title: IPAH-Adventitia-CC016-Full ROI-CC016-002

description: Adventitia


title: RNA-Seq of Vk35049 passaged in vivo harvested from spleen

description:
Vk35049_MM_R_EM_F_MYC.CrbnNull.CRBN_36915_rna
Vk35049_MM_R_EM_F_MYC.CrbnNull.CRBN_36915_rna

value: female


title: RNA-Seq of Vk35707 passaged in vivo harvested from bone marrow

description:
Vk35707_MM_R_BM_F_MYC.CrbnNull.CRBN_36912_rna
Vk35707_MM_R_BM_F_MYC.CrbnNull.CRBN_36912_rna

extract_protocol: Cells were placed in TriZol (Invitrogen), and following extraction were further purified on Purelink Micro-Minicolumns (Invitrogen) with an on-column DNAse digestion step

value: bone marrow


title: IPAH-Adventitia-CC016-Full ROI-CC016-003

description: Adventitia


title: colorectal cancer tissue sample AUS2_889_T3


title: IPAH-Intima+Media-BA035-Full ROI-BA035-020

description: Intima+Media


title: IPAH-Adventitia-BA035-Full ROI-BA035-014

description: Adventitia


title: colorectal cancer tissue sample AUS2_889_T2


title: Repliseq_late_K562_wt_r2

description:
Repli-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype; experiment: late fraction
K562_c17.bw

value: WT


title: RNA-Seq of Vk34635 passaged in vivo harvested from spleen

description:
Vk34635_MM_R_EM_M_MYC.CrbnNull.CRBN_36919_rna
Vk34635_MM_R_EM_M_MYC.CrbnNull.CRBN_36919_rna

value: male


title: Repliseq_late_K562_LBRLMNAKO_r1


title: IPAH-Intima+Media-BA035-Full ROI-BA035-021

description: Intima+Media


title: colorectal cancer tissue sample AUS2_889_T


title: RNA-Seq of Vk34638 passaged in vivo harvested from spleen

description:
Vk34638_MM_R_EM_F_MYC.CrbnNull.CRBN_38813_rna
Vk34638_MM_R_EM_F_MYC.CrbnNull.CRBN_38813_rna

value: spleen


title: colorectal cancer tissue sample AUS2_891_T


title: colorectal cancer tissue sample AUS2_886_T3


title: IPAH-Adventitia-BA035-Full ROI-BA035-012

description: Adventitia


title: RNA-Seq of Vk34586 de novo tumor harvested from spleen

description:
Vk34586_MM_O_EM_F_MYC.Nsd2Null_35394_rna
Vk34586_MM_O_EM_F_MYC.Nsd2Null_35394_rna

value: original de novo tumor


title: Repliseq_early_K562_LBRLMNAKO_r2

description:
Repli-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: LBR-LMNA-KO; experiment: early fraction
K562_dKO.bw


title: colorectal cancer tissue sample AUS2_885_T3


title: colorectal cancer tissue sample AUS2_886_T2


title: RNA-Seq of Vk34585 de novo tumor harvested from spleen

description:
Vk34585_MM_O_EM_M_MYC.Nsd2Null_35399_rna
Vk34585_MM_O_EM_M_MYC.Nsd2Null_35399_rna


title: IPAH-Intima+Media-BA035-Full ROI-BA035-010

description: Intima+Media


title: Repliseq_early_K562_wt_r2

description:
Repli-seq on K562 (ATCC CCL-243) cells (DD-Cas9); condition: wildtype; experiment: early fraction
K562_c17.bw


title: Repliseq_early_K562_LBRLMNAKO_r1


title: IPAH-Oblit-BA035-Full ROI-BA035-009

description: Obliterative Lesion


title: IPAH-Oblit-BA035-Full ROI-BA035-008

description: Obliterative Lesion


title: Repliseq_early_K562_wt_r1


title: Repliseq_late_K562_wt_r1


title: RNA-Seq of Vk34306 de novo tumor harvested from spleen

description:
Vk34306_MM_O_EM_F_MYC.Nsd2het_Vk34306_rna
Vk34306_MM_O_EM_F_MYC.Nsd2het_Vk34306_rna


title: RNA-Seq of Vk34286 growing in vitro

description:
Vk34286_MM_V_V_F_MYC.Omo.rtTA_35884_rna
Vk34286_MM_V_V_F_MYC.Omo.rtTA_35884_rna

value: in vitro

value: in vitro tumor


title: Pool 2, 24 months replicate 2

city: Kensington

first: Sara

last: Ballouz

state: NSW

address: High St

country: Australia

institute: UNSW

description:
10x Genomics
ES004_2_2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, and gene counting were done with the Cell Ranger software (version 7.0.0). Each pool was processed individually. cellranger mkfastq was run to demultiplex the dual indexed libraries. Config files were setup with expect-cells 20000, and include-introns as TRUE. Mapping and alignment were done to GRCh38 (GEX: refdata-cellranger-GRCh38-2020-A) using STAR within the Cell Ranger suite. The pipeline was executed on a high-performance cluster with a 3.10.0-1160.42.2.el7.x86_64 operating system.
Each sample was SNP genotyped (data not provided as it is protected) and demuxlet was used to demultiplex the pools and assign cells to individuals. The final output from this proccess is provided in the processed files.
Assembly: GRCh38
Supplementary files format and content: Gene expression: tab separated features and barcodes files, and counts in matrix market file format (.mtx).
Supplementary files format and content: Barcode to sample assignment files: tab separated files (combined_results_w_combined_assignments.tsv)

source_name: PBMC

extract_protocol:
PBMC from 20 individuals from ADAPT cohort (10 LC and 10 MC) were genotyped and had PBMCs sequenced using the 10x genomics platform. For each individual, 1 vial (∼1mL) of biobanked (frozen) PBMCs was retrieved and thawed. Cell density per vial was roughly 7x106 cells/mL. To this end ∼30uL was used for single-cell RNA-sequencing, and another fraction (106) for genotyping.
For each batch, single-cell RNA capture and barcoding with the Single Cell 5’ v2.0 NextGEM single cell RNA seq (GEX + VDJ (TCR+BCR) from 10x Genomics, with a target capture of 20,000 cells was performed.
scRNA-seq 5' 10x genomics

value: PBMC

tag: time

value: 24 months


title: colorectal cancer tissue sample AUS2_886_T

value: colorectal cancer tissue sample

value: T


title: RNA-Seq of Vk33982 passaged in vivo harvested from spleen

description:
Vk33982_MM_R_EM_F_MYC.CrbnNull.CRBN_37048_rna
Vk33982_MM_R_EM_F_MYC.CrbnNull.CRBN_37048_rna

value: Transplant recipient

value: plasma cell

value: multiple myeloma

value: yes


title: IPAH-Plx-BA035-Full ROI-BA035-005

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_885_INV

value: no

value: INV


title: Pool 2, 24 months replicate 1

description:
10x Genomics
ES004_2_1


title: IPAH-Plx-BA035-Full ROI-BA035-004

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_885_T2


title: Pool 1, 24 months replicate 2

description:
10x Genomics
ES004_1_2


title: RNA-Seq of Vk34098 passaged in vivo harvested from spleen

description:
Vk34098_MM_R_EM_M_MYC.Kdm6aNull.CRE_37147_rna
Vk34098_MM_R_EM_M_MYC.Kdm6aNull.CRE_37147_rna


title: IPAH-Plx-BA035-Full ROI-BA035-001

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_884_T

description: Gene expression estimates as RMA values on log2-scale.


title: colorectal cancer tissue sample AUS2_884_T2


title: RNA-Seq of Vk34306 passaged in vivo harvested from bone marrow

description:
Vk34306_MM_R_BM_F_MYC.Nsd2het_36917_rna
Vk34306_MM_R_BM_F_MYC.Nsd2het_36917_rna

value: female

value: bone marrow


title: Pool 1, 24 months replicate 1

description:
10x Genomics
ES004_1_1


title: IPAH-Oblit-BA035-Full ROI-BA035-007

description: Obliterative Lesion


title: IPAH-Plx-BA035-Full ROI-BA035-002

description: Plexifirm lesion


title: IPAH-Adventitia-BA035-Full ROI-BA035-013

description: Adventitia


title: colorectal cancer tissue sample AUS2_885_T


title: Pool 2, 8 months replicate 2

description:
10x Genomics
8_8mths

value: 8 months


title: colorectal cancer tissue sample AUS2_883_T2


title: RNA-Seq of Vk33882 passaged in vivo harvested from spleen

description:
Vk33882_MM_R_EM_M_MYC.CrbnHet_36908_rna
Vk33882_MM_R_EM_M_MYC.CrbnHet_36908_rna

value: male

value: spleen


title: colorectal cancer tissue sample AUS2_883_T3


title: RNA-Seq of Vk33883 passaged in vivo harvested from spleen

description:
Vk33883_MM_R_EM_M_MYC.CrbnNull.CRBN_38053_rna
Vk33883_MM_R_EM_M_MYC.CrbnNull.CRBN_38053_rna


title: IPAH-Adventitia-UA005-Full ROI-UA005-015

description: Adventitia


title: RNA-Seq of Vk33980 passaged in vivo harvested from spleen

description:
Vk33980_MM_R_EM_M_MYC.Omo.rtTA_37674_rna
Vk33980_MM_R_EM_M_MYC.Omo.rtTA_37674_rna


title: colorectal cancer tissue sample AUS2_883_T


title: Pool 2, 8 months replicate 1

description:
10x Genomics
7_8mths


title: Pool 1, 8 months replicate 2

description:
10x Genomics
6_8mths


title: IPAH-Intima+Media-UA005-Full ROI-UA005-012

description: Intima+Media


title: IPAH-Intima+Media-UA005-Full ROI-UA005-013

description: Intima+Media


title: colorectal cancer tissue sample AUS2_879_T2


title: Pool 1, 8 months replicate 1

description:
10x Genomics
5_8mths


title: RNA-Seq of Vk33342 passaged in vivo harvested from bone marrow

description:
Vk33342_MM_R_BM_F_MYC.Nsd2Null_36907_rna
Vk33342_MM_R_BM_F_MYC.Nsd2Null_36907_rna


title: RNA-Seq of Vk33323 passaged in vivo harvested from spleen

description:
Vk33323_MM_R_EM_M_MYC.Nsd2Null_Vk33323_rna
Vk33323_MM_R_EM_M_MYC.Nsd2Null_Vk33323_rna


title: Pool 2, 4 months replicate 2

description:
10x Genomics
4_4mths

value: 4 months


title: colorectal cancer tissue sample AUS2_879_T


title: IPAH-Intima+Media-UA005-Full ROI-UA005-011

description: Intima+Media


title: colorectal cancer tissue sample AUS2_879_T3


title: colorectal cancer tissue sample AUS2_878_T2


title: Pool 1, 4 months replicate 1

description:
10x Genomics
1_4mths


title: RNA-Seq of Vk33059 growing in vitro

description:
Vk33059_MM_V_V_M_MYC.Nsd2Null_38430_rna
Vk33059_MM_V_V_M_MYC.Nsd2Null_38430_rna

value: in vitro

value: in vitro tumor


title: RNA-Seq of Vk33880 passaged in vivo harvested from bone marrow

description:
Vk33880_MM_R_BM_M_MYC.CrbnNull.CRBN_36913_rna
Vk33880_MM_R_BM_M_MYC.CrbnNull.CRBN_36913_rna


title: Pool 2, 4 months replicate 1

description:
10x Genomics
3_4mths

value: PBMC


title: RNA-Seq of Vk33226 passaged in vivo harvested from bone marrow

description:
Vk33226_MM_R_BM_M_MYC.Kdm6aNull.CRE_37853_rna
Vk33226_MM_R_BM_M_MYC.Kdm6aNull.CRE_37853_rna


title: IPAH-Plx-UA005-Full ROI-UA005-009

description: Plexifirm lesion


title: IPAH-Intima+Media-UA005-Full ROI-UA005-010

description: Intima+Media


title: RNA-Seq of Vk33369 passaged in vivo harvested from spleen

description:
Vk33369_MM_R_EM_F_MYC.CrbnHet.CRBN_37288_rna
Vk33369_MM_R_EM_F_MYC.CrbnHet.CRBN_37288_rna


title: colorectal cancer tissue sample AUS2_878_T

value: colorectal cancer tissue sample


title: colorectal cancer tissue sample AUS2_877_T3


title: h5TIF4

data_processing:
The ultimate constructed and purified library with the target recovery of ~ 13,000 single cells was sequenced on Illumina novaseq 6000.
CeleScope (v1.9.0) pipeline was used for scRNA-seq data alignment and quantification.
The generated data files including aligned and filtered reads, barcodes and unique molecular identifiers were processed by Seurat (v4.3.0)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
One month after transfer, GFP+ human 5TIF4 cells from recipient mice were sorted by flow cytometry. And the single cell suspensions were directly loaded on a microfluidic chip (Singleron GEXSCOPETM Single Cell RNA-seq Kit, Singleron Biotechnologies) and processed for scRNA-seq library preparation according to manufacturer’s protocol.
The sample was processed for scRNA-seq library preparation according to manufacturer’s protocol.

value: Spleen

value: human T cell


title: IPAH-Plx-UA005-Full ROI-UA005-007

description: Plexifirm lesion


title: RNA-Seq of Vk32976 passaged in vivo harvested from bone marrow

description:
Vk32976_MM_R_BM_F_MYC_35398_rna
Vk32976_MM_R_BM_F_MYC_35398_rna

value: Transplant recipient

value: plasma cell

value: MYC


title: RNA-Seq of Vk32908 passaged in vivo harvested from spleen 2

description:
Vk32908_MM_R_EM_M_MYC.CrbnNull.CRBN_Vk32908_rna
Vk32908_MM_R_EM_M_MYC.CrbnNull.CRBN_Vk32908_rna

value: multiple myeloma

value: yes


title: IPAH-Plx-UA005-Full ROI-UA005-008

description: Plexifirm lesion


title: IPAH-Plx-UA005-Full ROI-UA005-006

description: Plexifirm lesion


title: Z003TS_fresh

city: Denver

first: Nathan

last: Jackson

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

description:
10X Genomics
Z002KB_3TS_integrated_culled.rds

data_processing:
Sequencing reads were processed with Cell Ranger (version 4) to produce gene UMI count matrix. We required cells to have at least 500 genes expressed and 1,000 UMIs. Additionally, we removed cells with greater than 30% MT reads. Well also filtered out a large population of squamous cells observed upon initial clustersing. Altogether, between the two samples, this resulted in 11,515 remaining cells to use for clustering analysis. We also filtered mitochondrial ("MT-") and ribosomal ("RPL" and "RPS") genes from the dataset. Integration of the two bronchial brushing datasets was carried out with the SCtransform integration approach implemented in Seurat using the top 30 canonical correlates derived from 5,000 most variable genes across the two datasets. We then carried out PCA on the integrated dataset and used the top 30 PC dimensions for UMAP visualization and to perform SNN clustering with the Leiden algorithm (resolution=0.3, k.param=20), resulting in 17 cell clusters. These cell clusters were then assigned a cell type label based on the list of the marker genes produced with Seurat FindMarkers function.
Assembly: hg38
Supplementary files format and content: Z002KB_fresh_raw_counts.txt is the raw counts table exported from Cell Ranger for sample Z002KB_fresh.
Supplementary files format and content: Z003TS_fresh_raw_counts.txt is the raw counts table exported from Cell Ranger for sample Z003TS_fresh.
Supplementary files format and content: Z002KB_3TS_integrated_culled.rds is a saved R object file (RDS format) containing the culled counts (both raw and integrated) used for analysis in the study.

source_name: Bronchial brushing

extract_protocol:
Bronchial cells were dissociated from the bronchial airway brushes from 2 asthmatic children using Bacillus licheniformis cold active protease (10mg/ml), EDTA (0.5mM), and EGTA (0.5mM) at 4°C with vortex mixing, followed by enzyme neutralization with FBS.  Red blood cell lysis was performed and cells were washed twice in 0.04% BSA/PBS.
Targeted capture of 8000 cells was performed using the 10X Genomics Chromium Next GEM Single Cell 3’ reagent kit chemistry.  Sample capture, cDNA synthesis, and library preparation was performed following 10X Genomics Chromium Next GEM Single Cell 3’ chemistry (CG000204 Rev D), and barcoded samples were pooled and sequenced on an Illumina NovaSeq 6000.

value: Bronchial brushing

value: Bronchial airway cells


title: Z002KB_fresh


title: IPAH-Adventitia-UA005-Full ROI-UA005-005

description: Adventitia


title: colorectal cancer tissue sample AUS2_877_T

value: no

value: T


title: RNA-Seq of Vk32829 passaged in vivo harvested from spleen

description:
Vk32829_MM_R_EM_F_MYC.Nsd2Null_Vk32829_rna
Vk32829_MM_R_EM_F_MYC.Nsd2Null_Vk32829_rna

value: female

value: spleen


title: colorectal cancer tissue sample AUS2_877_T2


title: IPAH-Adventitia-UA005-Full ROI-UA005-004

description: Adventitia


title: RNA-Seq of Vk32642 passaged in vivo harvested from spleen

description:
Vk32642_MM_R_EM_M_MYC.CrbnNull_Vk22284_rna
Vk32642_MM_R_EM_M_MYC.CrbnNull_Vk22284_rna

value: male


title: IPAH-Oblit-UA005-Full ROI-UA005-003

description: Obliterative Lesion


title: RNA-Seq of Vk32908 passaged in vivo harvested from spleen 1

description:
Vk32908_MM_R_EM_M_MYC.CrbnNull.CRBN_40629_rna
Vk32908_MM_R_EM_M_MYC.CrbnNull.CRBN_40629_rna


title: NCI_KO_clone_1_untreated_replicate_2

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

data_processing:
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq.gz files into a single-end fastq.gz file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: NCI

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)

treatment_protocol: treatment 16H with 10 µM Nutlin3a for NCI-H929 and JIM3 or 2 µM for XG7

value: E

value: NCI

value: untreated

tag: clone

tag: replicate


title: NCI_KO_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_2

tag: batch

value: treated with 10 microM Nutlin3a for 16H


title: RNA-Seq of Vk32366 de novo tumor harvested from spleen

description:
Vk32366_MM_O_EM_F_MYC.Nsd2het_Vk32366_rna
Vk32366_MM_O_EM_F_MYC.Nsd2het_Vk32366_rna

tag: strain

value: original de novo tumor


title: RNA-Seq of Vk32269 passaged in vivo harvested from spleen

description:
Vk32269_MM_R_EM_M_MYC.CrbnHet.CRBN_36903_rna
Vk32269_MM_R_EM_M_MYC.CrbnHet.CRBN_36903_rna

tag: Sex

value: Transplant recipient


title: NCI_KO_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_1


title: IPAH-Oblit-UA005-Full ROI-UA005-002

description: Obliterative Lesion

tag: individuial


title: NCI_KO_clone_1_untreated_replicate_3


title: RNA-Seq of Vk32245 growing in vitro 1

description:
Vk32245_MM_V_V_M_MYC_Vk30482_rna
Vk32245_MM_V_V_M_MYC_Vk30482_rna

tag: tissue

value: in vitro

tag: tumor type

value: in vitro tumor

value: plasma cell


title: RNA-Seq of Vk32245 growing in vitro 2

description:
Vk32245_MM_V_V_F_MYC_Vk32245_rna
Vk32245_MM_V_V_F_MYC_Vk32245_rna

tag: cell line

tag: cell type

value: multiple myeloma

value: MYC

value: yes


title: NCI_KO_clone_1_untreated_replicate_1


title: IPAH-Oblit-UA005-Full ROI-UA005-001

description: Obliterative Lesion


title: IPAH-Lymph-VA010-Full ROI-VA010-012

description: Lymph


title: colorectal cancer tissue sample AUS2_876_T

description: Gene expression estimates as RMA values on log2-scale.

value: colorectal cancer tissue sample

value: no


title: colorectal cancer tissue sample AUS2_875_T2


title: colorectal cancer tissue sample AUS2_876_INV

value: INV


title: colorectal cancer tissue sample AUS2_874_T3


title: colorectal cancer tissue sample AUS2_875_T

value: T


title: XG7_KO_clone_1_untreated_replicate_2

value: D


title: XG7_KO_clone_3_untreated_replicate_2


title: IPAH-Adventitia-VA010-Full ROI-VA010-011

description: Adventitia


title: NCI_KO_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_3

value: E


title: colorectal cancer tissue sample AUS2_875_T3


title: IPAH-Adventitia-VA010-Full ROI-VA010-008

description: Adventitia


title: colorectal cancer tissue sample AUS2_874_T


title: colorectal cancer tissue sample AUS2_874_INV


title: colorectal cancer tissue sample AUS2_874_T2


title: RNA-Seq of Vk31803 passaged in vivo harvested from bone marrow

description:
Vk31803_MM_R_BM_F_MYC_35397_rna
Vk31803_MM_R_BM_F_MYC_35397_rna

value: female

value: bone marrow

tag: disease

tag: genotype


title: XG7_KO_clone_2_untreated_replicate_2

value: untreated


title: RNA-Seq of Vk31422 passaged in vivo harvested from spleen

description:
Vk31422_MM_R_EM_F_MYC.CRE_Vk31422_rna
Vk31422_MM_R_EM_F_MYC.CRE_Vk31422_rna

value: spleen

tag: myc transgene_stop_codon_reversion


title: RNA-Seq of Vk31507 passaged in vivo harvested from spleen

description:
Vk31507_MM_R_EM_M_MYC.CrbnNull.CRBN_Vk31507_rna
Vk31507_MM_R_EM_M_MYC.CrbnNull.CRBN_Vk31507_rna

value: male

value: Transplant recipient


title: XG7_KO_clone_1_untreated_replicate_1

tag: treatment


title: IPAH-Lymph-VA010-Full ROI-VA010-006

description: Lymph


title: IPAH-Intima+Media-VA010-Full ROI-VA010-007

description: Intima+Media


title: XG7_KO_clone_2_untreated_replicate_1


title: IPAH-Intima+Media-VA010-Full ROI-VA010-010

description: Intima+Media


title: RNA-Seq of Vk32052 passaged in vivo harvested from spleen

description:
Vk32052_MM_R_EM_F_MYC.CrbnNull.CRBN_Vk32052_rna
Vk32052_MM_R_EM_F_MYC.CrbnNull.CRBN_Vk32052_rna


title: colorectal cancer tissue sample AUS2_873_T


title: RNA-Seq of Vk31159 growing in vitro

description:
Vk31159_MM_V_V_F_MYC_39244_rna
Vk31159_MM_V_V_F_MYC_39244_rna

value: in vitro

value: in vitro tumor


title: XG7_control_clone_3_untreated_replicate_2


title: colorectal cancer tissue sample AUS2_873_T2


title: XG7_KO_clone_3_untreated_replicate_1


title: RNA-Seq of Vk31159 passaged in vivo harvested from spleen

description:
Vk31159_MM_R_EM_F_MYC_Vk31159_rna
Vk31159_MM_R_EM_F_MYC_Vk31159_rna

value: plasma cell

value: multiple myeloma


title: RNA-Seq of Vk31080 growing in vitro

description:
Vk31080_MM_V_V_F_MYC.CRE_35402_rna
Vk31080_MM_V_V_F_MYC.CRE_35402_rna


title: IPAH-Adventitia-VA010-Full ROI-VA010-005

description: Adventitia


title: colorectal cancer tissue sample AUS2_871_T2


title: XG7_control_clone_3_treated with 2 µM Nutlin3a for 16H_replicate_2

value: treated with 2 microM Nutlin3a for 16H


title: IPAH-Intima+Media-VA010-Full ROI-VA010-009

description: Intima+Media


title: XG7_control_clone_3_untreated_replicate_1


title: IPAH-Oblit-VA010-Full ROI-VA010-003

description: Obliterative Lesion


title: IPAH-Oblit-VA010-Full ROI-VA010-004

description: Obliterative Lesion


title: RNA-Seq of Vk29790 passaged in vivo harvested from spleen

description:
Vk29790_MM_R_EM_F_MYC.CrbnHet.CRBN_Vk29790_rna
Vk29790_MM_R_EM_F_MYC.CrbnHet.CRBN_Vk29790_rna


title: RNA-Seq of Vk29087 passaged in vivo harvested from spleen

description:
Vk29087_MM_R_EM_M_MYC.CRE_29882_rna
Vk29087_MM_R_EM_M_MYC.CRE_29882_rna

value: yes


title: colorectal cancer tissue sample AUS2_870_T2

value: colorectal cancer tissue sample

value: no


title: XG7_control_clone_3_treated with 2 µM Nutlin3a for 16H_replicate_1


title: IPAH-Oblit-VA010-Full ROI-VA010-002

description: Obliterative Lesion


title: IPAH-Plx-VA010-Full ROI-VA010-001

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_869_T3


title: colorectal cancer tissue sample AUS2_871_T

value: T


title: colorectal cancer tissue sample AUS2_870_T


title: RNA-Seq of Vk28158 passaged in vivo harvested from spleen

description:
Vk28158_MM_R_EM_M_MYC_29880_rna
Vk28158_MM_R_EM_M_MYC_29880_rna

value: MYC


title: RNA-Seq of Vk26784 passaged in vivo harvested from spleen

description:
Vk26784_MM_R_EM_M_MYC_29878_rna
Vk26784_MM_R_EM_M_MYC_29878_rna


title: RNA-Seq of Vk27181 passaged in vivo harvested from spleen

description:
Vk27181_MM_R_EM_M_MYC_29876_rna
Vk27181_MM_R_EM_M_MYC_29876_rna


title: XG7_control_clone_2_untreated_replicate_2

value: D


title: XG7_KO_clone_1_treated with 2 µM Nutlin3a for 16H_replicate_2


title: colorectal cancer tissue sample AUS2_869_T2


title: XG7_control_clone_2_untreated_replicate_1


title: IPAH-Adventitia-AH001-Full ROI-AH001-020

description: Adventitia


title: RNA-Seq of Vk23631 passaged in vivo harvested from spleen

description:
Vk23631_MM_R_EM_M_MYC_Vk23631_rna
Vk23631_MM_R_EM_M_MYC_Vk23631_rna


title: RNA-Seq of Vk23589 de novo tumor harvested from spleen

description:
Vk23589_MM_O_EM_F_MYC.MIRnull_23923_rna
Vk23589_MM_O_EM_F_MYC.MIRnull_23923_rna

value: female

value: original de novo tumor


title: XG7_KO_clone_3_treated with 2 µM Nutlin3a for 16H_replicate_2


title: XG7_KO_clone_2_treated with 2 µM Nutlin3a for 16H_replicate_2


title: colorectal cancer tissue sample AUS2_868_T3


title: IPAH-Intima+Media-AH001-Full ROI-AH001-016

description: Intima+Media


title: colorectal cancer tissue sample AUS2_869_T


title: RNA-Seq of Vk23053 passaged in vivo harvested from spleen 2

description:
Vk23053_MM_R_EM_M_MYC.Traf3Null.CRE.BCL6_Vk12598V_rna
Vk23053_MM_R_EM_M_MYC.Traf3Null.CRE.BCL6_Vk12598V_rna


title: colorectal cancer tissue sample AUS2_868_T2


title: IPAH-Intima+Media-AH001-Full ROI-AH001-015

description: Intima+Media


title: RNA-Seq of Vk23053 passaged in vivo harvested from spleen 1

description:
Vk23053_MM_R_EM_M_MYC.Traf3Null.CRE.BCL6_35400_rna
Vk23053_MM_R_EM_M_MYC.Traf3Null.CRE.BCL6_35400_rna


title: XG7_KO_clone_3_treated with 2 µM Nutlin3a for 16H_replicate_1


title: XG7_KO_clone_1_treated with 2 µM Nutlin3a for 16H_replicate_1


title: IPAH-Plx-AH001-Full ROI-AH001-012

description: Plexifirm lesion


title: XG7_KO_clone_2_treated with 2 µM Nutlin3a for 16H_replicate_1

value: treated with 10 microM Nutlin3a for 16H


title: RNA-Seq of Vk22284 passaged in vivo harvested from spleen

description:
Vk22284_MM_R_EM_M_MYC.CRE_Vk32642_rna
Vk22284_MM_R_EM_M_MYC.CRE_Vk32642_rna

value: spleen


title: IPAH-Plx-AH001-Full ROI-AH001-011

description: Plexifirm lesion


title: IPAH-Plx-AH001-Full ROI-AH001-010

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_867_T2

description: Gene expression estimates as RMA values on log2-scale.


title: RNA-Seq of Vk14750 growing in vitro

description:
Vk14750_MM_V_V_M_MYC_Vk14750_rna
Vk14750_MM_V_V_M_MYC_Vk14750_rna

value: male


title: IPAH-Plx-AH001-Full ROI-AH001-013

description: Plexifirm lesion


title: XG7_control_clone_2_treated with 2 µM Nutlin3a for 16H_replicate_1


title: IPAH-Plx-AH001-Full ROI-AH001-014

description: Plexifirm lesion


title: RNA-Seq of Vk14451 passaged in vivo harvested from spleen

description:
Vk14451_MM_R_EM_M_MYC.EGFP_Vk14451_rna
Vk14451_MM_R_EM_M_MYC.EGFP_Vk14451_rna

value: Transplant recipient


title: XG7_control_clone_1_untreated_replicate_2

value: untreated


title: IPAH-Adventitia-AH001-Full ROI-AH001-008

description: Adventitia


title: RNA-Seq of Vk14153 de novo tumor harvested from spleen

description:
Vk14153_MM_O_EM_M_MYC_23926_rna
Vk14153_MM_O_EM_M_MYC_23926_rna


title: colorectal cancer tissue sample AUS2_867_INV

value: INV


title: XG7_control_clone_1_untreated_replicate_1


title: RNA-Seq of Vk12653 growing in vitro

description:
Vk12653_MM_V_V_M_MYC.AIDhet_36911_rna
Vk12653_MM_V_V_M_MYC.AIDhet_36911_rna

value: in vitro

value: in vitro tumor

value: plasma cell


title: IPAH-Adventitia-AH001-Full ROI-AH001-006

description: Adventitia


title: XG7_control_clone_1_treated with 2 µM Nutlin3a for 16H_replicate_2

value: treated with 2 microM Nutlin3a for 16H


title: IPAH-Intima+Media-AH001-Full ROI-AH001-005

description: Intima+Media


title: IPAH-Adventitia-AH001-Full ROI-AH001-007

description: Adventitia


title: XG7_control_clone_2_treated with 2 µM Nutlin3a for 16H_replicate_2


title: colorectal cancer tissue sample AUS2_866_T2

value: colorectal cancer tissue sample


title: RNA-Seq of Vk21598 de novo tumor harvested from spleen

description:
Vk21598_MM_O_EM_M_MYC.MDRnull_23922_rna
Vk21598_MM_O_EM_M_MYC.MDRnull_23922_rna

value: multiple myeloma

value: yes


title: colorectal cancer tissue sample AUS2_865_T3

value: no


title: colorectal cancer tissue sample AUS2_867_T

value: T


title: XG7_control_clone_1_treated with 2 µM Nutlin3a for 16H_replicate_1

value: D


title: IPAH-Oblit-AH001-Full ROI-AH001-004

description: Obliterative Lesion


title: RNA-Seq of MDR33167 de novo tumor from MDRnull mice harvested from spleen

description:
MDR33167_MM_O_EM_M_MDRnull_MDR33167_rna
MDR33167_MM_O_EM_M_MDRnull_MDR33167_rna

value: original de novo tumor

value: MDRnull


title: colorectal cancer tissue sample AUS2_865_T


title: colorectal cancer tissue sample AUS2_866_T


title: IPAH-Oblit-AH001-Full ROI-AH001-002

description: Obliterative Lesion


title: scRNA_E135_gastrointestinal_tract_EPCAM_Trp53KO

city: Berlin

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 6.0.1, default parameters).
FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("count pipeline", version 6.0.1, default parameters).
Assembly: mm10 (including mCherry and GFP transgenes)
Supplementary files format and content: The tar gz archive contains the raw gene-barcode matrix as produced by the Cell Ranger pipeline and the MEX-formatted UMI count matrix. 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix... Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

source_name: Gastrointestinal tract epithelium

growth_protocol: Wild type CD1 mice were housed under conditions approved by the local authorities, and zygotes were collected from natural mating for electroporation.

extract_protocol:
Extraembryonic tissues were removed, the gastrointestinal tracts were dissected from four single embryos, these were individually dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes.The cells were washed with 10% FBS/DMEM, stained with EPCAM antibody in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 minutes, and then EPCAM+ cells were enriched by magnetic separation (MACS). Finally, the cells were stained with DAPI at 4 ºC for 8 minutes in FACS buffer. Cells were resuspended in FACS buffer and the indicated populations were sorted into PBS using the BD FACSAria Fusion. The sorted populations were labelled with distinct MULTI-seq surface barcodes, four samples from single embryo replicates were pooled, and the cell suspension was filtered with Flowmi Cell Strainers 40 µM before subjected to single-cell RNA sequencing (10x Genomics, Chromium™ Single Cell 3’ v3.1).
Single-cell RNA-seq libraries were generated following the manual instructions of 10x Genomics, Chromium™ Single Cell 3’ v3.1, with the exception of fewer PCR cycles in the cDNA amplification step, where the MULTI-seq surface barcodes were also amplified. MULTI-seq libraries were generated parallel to the single-cell RNA-seq libraries.

treatment_protocol: Electroporation reactions were set up according to the manufacturer’s guidelines (Integrated DNA Technologies: Alt-R CRISPR–Cas9 ribonucleoprotein (RNP) complex protocol), just before the electroporation. The three gRNAs target exons in Trp53. We used the NEPA21 electroporator with a 5mm gap electrode chamber with the following settings: poring pulse 225V, 2 msec pulse length, 50 msec pulse interval, 4 pulses, 10% decay rate and + polarity; transfer pulse 20V, 50 sec pulse length, 50 msec pulse interval, 5 pulses, 40% decay rate and alternating +/-polarity. Electroporated zygotes were washed and cultured in KSOM (Cosmo Bio, R-B074) at 37 ºC and 5% CO2 until they reached the expanded blastocyst stage. Then, they were retransferred into the uterine horns (maximum 15 embryos on each side) of a pseudopregnant CD1 female at 2.5 days post coitus, generated by mating with vasectomized CD1 males.

value: Gastrointestinal tract epithelium

tag: developmental stage

value: Trp53 KO

value: Zygotic electroporation


title: colorectal cancer tissue sample AUS2_862_T3


title: colorectal cancer tissue sample AUS2_862_T2


title: IPAH-Oblit-AH001-Full ROI-AH001-001

description: Obliterative Lesion


title: colorectal cancer tissue sample AUS2_865_T2


title: IPAH-Oblit-AH001-Full ROI-AH001-003

description: Obliterative Lesion


title: colorectal cancer tissue sample AUS2_868_T


title: NCI_control_clone_1_untreated_replicate_2

value: B

value: NCI

value: untreated


title: WGBS_E95_exMidgut_EPCAM_mCherry

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (version 4.1; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read.
The trimmed reads were aligned to the mouse genome (mm10 including GFP and mCherry transgenes) using BSMAP (version 2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R).
Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.3.0.0; --VALIDATION_STRINGENCY=LENIENT --REMOVE_DUPLICATES=true).
Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
Only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.
Assembly: mm10 (including mCherry and GFP transgenes)
Supplementary files format and content: Bigwig file containing methylation rates for CpGs covered by at least 10 and at most 150 reads: <chr> <start> <end> <methylation rate>

source_name: Midgut endoderm

growth_protocol: GFP+ mESCs were cultured on mitotically inactive primary mouse embryo fibroblasts in serum/LIF condition for two days. Aggregated embryos, cultured in KSOM, that progressed to the expanded blastocyst stage were transferred to a pseudo-pregnant CD1 female. Post-implantation embryos were isolated at the indicated stage, including a 24-hour developmental delay due to the uterine transfer procedure.

extract_protocol:
Extraembryonic tissues were removed, and the midgut from the posterior part from lineage-traced embryos were pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained with EPCAM antibody in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 minutes, and then EPCAM+ cells were enriched by magnetic separation (MACS). Finally, the cells were stained with DAPI at 4 ºC for 8 minutes in FACS buffer. Cells were resuspended in FACS buffer, the indicated populations were sorted into Lysis buffer (10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 10 mM EDTA, 0.5% SDS, 300 ug/mL Proteinase K) using the BD FACSAria Fusion. Genomic DNA was isolated by phenol–chloroform extraction.
Genomic DNA was sheared in micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris 520045) followed by phenol–chloroform extraction. The purified DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo D5005), and WGBS libraries were processed using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences 30096) following the manufacturer’s recommendations. Libraries were cleaned using Agencourt AMPure XP beads. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using 150 base pair paired-end sequencing on a NovaSeq 6000 platform.

treatment_protocol: Embryos were generated by diploid complementation assay with aggregation. In each depression of the aggregation plate, one small GFP+ mESC colony of about 8-15 cells was added together with one zona pellucida-free mCherry+ pre-compaction morula.

value: Midgut endoderm

value: mCherry+ morula (CD1/G4) aggregated with GFP+ mESCs (G4)

value: WT


title: NCI_control_clone_1_untreated_replicate_3


title: colorectal cancer tissue sample AUS2_861_T

value: colorectal cancer tissue sample


title: NCI_control_clone_4_untreated_replicate_3


title: NCI_control_clone_2_untreated_replicate_3


title: WGBS_E95_exHindgut_EPCAM_mCherry

source_name: Hindgut endoderm

extract_protocol:
Extraembryonic tissues were removed, and the most posterior part including the hindgut from lineage-traced embryos were pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained with EPCAM antibody in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 minutes, and then EPCAM+ cells were enriched by magnetic separation (MACS). Finally, the cells were stained with DAPI at 4 ºC for 8 minutes in FACS buffer. Cells were resuspended in FACS buffer, the indicated populations were sorted into Lysis buffer (10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 10 mM EDTA, 0.5% SDS, 300 ug/mL Proteinase K) using the BD FACSAria Fusion. Genomic DNA was isolated by phenol–chloroform extraction.
Genomic DNA was sheared in micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris 520045) followed by phenol–chloroform extraction. The purified DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo D5005), and WGBS libraries were processed using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences 30096) following the manufacturer’s recommendations. Libraries were cleaned using Agencourt AMPure XP beads. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using 150 base pair paired-end sequencing on a NovaSeq 6000 platform.

value: Hindgut endoderm


title: NCI_control_clone_4_untreated_replicate_2


title: IPAH-Oblit-UC007-Full ROI-UC007_a-SMA-012

description: Obliterative Lesion


title: scRNA_E135_gastrointestinal_tract_EPCAM_WT

growth_protocol: Wild type CD1 mice were housed under conditions approved by the local authorities, and embryos were collected from natural mating.


title: NCI_control_clone_2_untreated_replicate_2


title: colorectal cancer tissue sample AUS2_861_T2


title: IPAH-Adventitia-UC007-SMA--UC007_a-SMA-009

description: Adventitia


title: IPAH-Plx-UC007-Full ROI-UC007_a-SMA-014

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_861_INV

value: INV


title: colorectal cancer tissue sample AUS2_862_T

value: no


title: IPAH-Intima+Media-UC007-SMA+-UC007_a-SMA-008

description: Intima+Media


title: colorectal cancer tissue sample AUS2_860_T2


title: NCI_control_clone_1_untreated_replicate_1


title: WGBS_E95_emHindgut_EPCAM_GFP_mCherry_dual_low


title: IPAH-Intima+Media-UC007-SMA+-UC007_a-SMA-007

description: Intima+Media


title: WGBS_E95_YsEndo_mCherry

source_name: Yolk sac endoderm

extract_protocol:
Yolk sac tissues were separated from lineage-traced embryos, pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained first with EPCAM antibody then with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 and 8 minutes, respectively. Cells were resuspended in FACS buffer, the indicated population was sorted into Lysis buffer (10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 10 mM EDTA, 0.5% SDS, 300 ug/mL Proteinase K) using the BD FACSAria Fusion. Genomic DNA was isolated by phenol–chloroform extraction.
Genomic DNA was sheared in micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris 520045) followed by phenol–chloroform extraction. The purified DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo D5005), and WGBS libraries were processed using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences 30096) following the manufacturer’s recommendations. Libraries were cleaned using Agencourt AMPure XP beads. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using 150 base pair paired-end sequencing on a NovaSeq 6000 platform.

value: Yolk sac endoderm


title: WGBS_E65_exEndo2_Rep1

source_name: Extraembryonic endoderm (proximal)

extract_protocol:
Embryos were collected into ice-cold M2 medium (Merck MR-015-D), bisected at the embryonic-extraembryonic border, washed in three drops of HBSS and incubated for 15 min at 4º C in 0,5% Trypsin, 2,5% Pancreatin dissolved in PBS. The proximal extraembryonic endoderm (exEndo 2) was manually separated from the extraembryonic ectoderm by drawing the proximal half through a narrow glass capillary. Pooled exEndo 2 tissues were collected in Lysis buffer (10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 10 mM EDTA, 0.5% SDS, 300 ug/mL Proteinase K). Genomic DNA was isolated by phenol–chloroform extraction.
Genomic DNA was sheared in micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris 520045) followed by phenol–chloroform extraction. The purified DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo D5005), and WGBS libraries were processed using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences 30096) following the manufacturer’s recommendations. Libraries were cleaned using Agencourt AMPure XP beads. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using 150 base pair paired-end sequencing on a NovaSeq 6000 platform.

value: Extraembryonic endoderm (proximal)


title: NCI_control_clone_4_untreated_replicate_1


title: NCI_control_clone_2_untreated_replicate_1


title: WGBS_E65_exEndo2_Rep2


title: WGBS_E65_exEndo1_Rep2

source_name: Extraembryonic endoderm (distal)

extract_protocol:
Embryos were collected into ice-cold M2 medium (Merck MR-015-D), bisected at the embryonic-extraembryonic border, washed in three drops of HBSS and incubated for 15 min at 4º C in 0,5% Trypsin, 2,5% Pancreatin dissolved in PBS. The distal extraembryonic endoderm (exEndo 1) was manually separated from the epiblast by drawing the distal half through a narrow glass capillary. Pooled exEndo 1 tissues were collected in Lysis buffer (10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 10 mM EDTA, 0.5% SDS, 300 ug/mL Proteinase K). Genomic DNA was isolated by phenol–chloroform extraction.
Genomic DNA was sheared in micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris 520045) followed by phenol–chloroform extraction. The purified DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo D5005), and WGBS libraries were processed using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences 30096) following the manufacturer’s recommendations. Libraries were cleaned using Agencourt AMPure XP beads. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using 150 base pair paired-end sequencing on a NovaSeq 6000 platform.

value: Extraembryonic endoderm (distal)


title: WGBS_E95_emMidgut_EPCAM_GFP_mCherry_dual_low


title: NCI_control_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_3

value: treated with 10 microM Nutlin3a for 16H


title: IPAH-Adventitia-UC007-SMA--UC007_a-SMA-004

description: Adventitia

source_name: IPAH Lung

extract_protocol: rna kit


title: colorectal cancer tissue sample AUS2_859_T

value: T


title: IPAH-Plx-UC007-Full ROI-UC007_a-SMA-006

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_860_T


title: IPAH-Adventitia-UC007-SMA--UC007_a-SMA-005

description: Adventitia


title: colorectal cancer tissue sample AUS2_859_INV


title: NCI_control_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_3


title: WGBS_E65_exEndo1_Rep1


title: colorectal cancer tissue sample AUS2_859_T2


title: RRBS_E95_exMidgut_EPCAM_mCherry_Rep4

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (version 4.1; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter).
The trimmed reads were aligned to the mouse genome (mm10 including GFP and mCherry transgenes) using BSMAP (version 2.90; parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG).
Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
Due to the overall low coverage of low-input RRBS replicates, the replicates were combined at the raw count level of methylated and unmethylated CpGs and merged methylation rates were calculated subsequently to increase the coverage.
Only CpGs covered by at least five (single RRBS replicates) or 10 (merged RRBS replicates) and at maximum 150 reads were considered for downstream analyses.
Assembly: mm10 (including mCherry and GFP transgenes)
Supplementary files format and content: Bigwig file containing methylation rates for CpGs covered by at least 5 and at most 150 reads: <chr> <start> <end> <methylation rate>

extract_protocol:
Extraembryonic tissues were removed, and the midgut from the posterior part of 4 embryos were pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained with EPCAM antibody in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 minutes, and then EPCAM+ cells were enriched by magnetic separation (MACS). Finally, the cells were stained with DAPI at 4 ºC for 8 minutes in FACS buffer. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RRBS libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the bisulfite-converted DNA amplification cycle number according to the input. The genomic DNA was digested with both MspI and HaeIII.


title: colorectal cancer tissue sample AUS2_858_T2


title: NCI_control_clone_4_treated with 10 µM Nutlin3a for 16H_replicate_3


title: NCI_control_clone_4_treated with 10 µM Nutlin3a for 16H_replicate_2


title: colorectal cancer tissue sample AUS2_858_T


title: IPAH-Plx-UC007-Full ROI-UC007_a-SMA-003

description: Plexifirm lesion


title: RRBS_E95_exMidgut_EPCAM_mCherry_Rep3


title: NCI_control_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_2


title: IPAH-Intima+Media-UC007-SMA+-UC007_a-SMA-002

description: Intima+Media


title: RRBS_E95_exMidgut_EPCAM_mCherry_Rep2


title: NCI_control_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_2


title: NCI_control_clone_4_treated with 10 µM Nutlin3a for 16H_replicate_1


title: RRBS_E95_exMidgut_EPCAM_mCherry_Rep1


title: NCI_control_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_1


title: NCI_control_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_1


title: RRBS_E95_exHindgut_EPCAM_mCherry_Rep2

extract_protocol:
Extraembryonic tissues were removed, and the most posterior part including the hindgut from 4 embryos were pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained with EPCAM antibody in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 minutes, and then EPCAM+ cells were enriched by magnetic separation (MACS). Finally, the cells were stained with DAPI at 4 ºC for 8 minutes in FACS buffer. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RRBS libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the bisulfite-converted DNA amplification cycle number according to the input. The genomic DNA was digested with both MspI and HaeIII.


title: Control-Intima+Media-AH006-Full ROI-AH006-007

description: Intima+Media

source_name: Control Lung


title: Control-Adventitia-AH006-Full ROI-AH006-008

description: Adventitia


title: RRBS_E95_exHindgut_EPCAM_mCherry_Rep3


title: RRBS_E95_exHindgut_EPCAM_mCherry_Rep4


title: colorectal cancer tissue sample AUS2_855_T2


title: IPAH-Oblit-UC007-SMA+-UC007_a-SMA-001

description: Obliterative Lesion


title: Control-Adventitia-AH006-Full ROI-AH006-004

description: Adventitia


title: Control-Adventitia-AH006-Full ROI-AH006-006

description: Adventitia


title: NCI_KO_clone_3_treated with 10 µM Nutlin3a for 16H_replicate_3

value: A


title: Control-Intima+Media-AH006-Full ROI-AH006-003

description: Intima+Media


title: colorectal cancer tissue sample AUS2_855_T


title: colorectal cancer tissue sample AUS2_854_T3


title: RRBS_E95_exHindgut_EPCAM_mCherry_Rep1


title: NCI_KO_clone_3_treated with 10 µM Nutlin3a for 16H_replicate_2


title: Control-Intima+Media-AH006-Full ROI-AH006-002

description: Intima+Media


title: Control-Intima+Media-AH006-Full ROI-AH006-005

description: Intima+Media


title: colorectal cancer tissue sample AUS2_854_INV


title: colorectal cancer tissue sample AUS2_854_T2


title: colorectal cancer tissue sample AUS2_858_INV


title: RRBS_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep4


title: colorectal cancer tissue sample AUS2_853_T3


title: Control-Adventitia-AH006-Full ROI-AH006-001

description: Adventitia


title: colorectal cancer tissue sample AUS2_853_T


title: NCI_KO_clone_3_untreated_replicate_3


title: NCI_KO_clone_3_treated with 10 µM Nutlin3a for 16H_replicate_1


title: colorectal cancer tissue sample AUS2_854_T


title: NCI_KO_clone_3_untreated_replicate_2


title: RRBS_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep3


title: RRBS_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep4


title: NCI_KO_clone_3_untreated_replicate_1


title: RRBS_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep3


title: Control-Adventitia-UC010-Full ROI-UC010-012

description: Adventitia


title: RRBS_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep2


title: Control-Adventitia-UC010-Full ROI-UC010-014

description: Adventitia


title: Control-Intima+Media-UC010-Full ROI-UC010-010

description: Intima+Media


title: RRBS_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep2


title: Control-Intima+Media-UC010-Full ROI-UC010-009

description: Intima+Media


title: RRBS_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep1


title: NCI_KO_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_3


title: Control-Adventitia-UC010-Full ROI-UC010-008

description: Adventitia


title: NCI_KO_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_2


title: RRBS_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep1


title: NCI_KO_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_1


title: NCI_KO_clone_2_untreated_replicate_3


title: Control-Adventitia-UC010-Full ROI-UC010-011

description: Adventitia


title: colorectal cancer tissue sample AUS2_852_T3


title: NCI_KO_clone_2_untreated_replicate_2


title: RRBS_E95_YsEndo_mCherry_Rep3

extract_protocol:
Yolk sac tissues were separated from 4 embryos, pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained first with EPCAM antibody then with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 and 8 minutes, respectively. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RRBS libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the bisulfite-converted DNA amplification cycle number according to the input. The genomic DNA was digested with both MspI and HaeIII.


title: Control-Intima+Media-UC010-Full ROI-UC010-007

description: Intima+Media


title: colorectal cancer tissue sample AUS2_852_T

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).


title: RRBS_E95_YsEndo_mCherry_Rep2


title: colorectal cancer tissue sample AUS2_851_T2


title: RNA-Seq of Vk12598 growing in vitro

description:
Vk12598_MM_V_V_M_MYC.AIDhet_39248_rna
Vk12598_MM_V_V_M_MYC.AIDhet_39248_rna

value: male

value: in vitro

value: in vitro tumor

value: plasma cell

value: multiple myeloma

value: yes


title: colorectal cancer tissue sample AUS2_851_T3


title: colorectal cancer tissue sample AUS2_852_T2


title: colorectal cancer tissue sample AUS2_853_T2


title: NAN3_KO_clone_3_untreated_replicate_3

value: C

value: untreated


title: colorectal cancer tissue sample AUS2_852_INV

value: colorectal cancer tissue sample


title: RRBS_E95_YsEndo_mCherry_Rep1

value: mCherry+ morula (CD1/G4) aggregated with GFP+ mESCs (G4)

value: WT


title: RRBS_E95_YsEndo_mCherry_Rep4

value: Yolk sac endoderm


title: Control-Intima+Media-UC010-Full ROI-UC010-005

description: Intima+Media


title: Control-Intima+Media-UC010-Full ROI-UC010-006

description: Intima+Media


title: colorectal cancer tissue sample AUS2_851_T

value: no


title: NCI_KO_clone_2_untreated_replicate_1

value: NCI


title: NAN3_control_bulk_untreated_replicate_3

value: bulk


title: RRBS_E135_exSI_EPCAM_mCherry_Trp53KO_Rep3

source_name: Small intestine endoderm

extract_protocol:
Extraembryonic tissues were removed, the intestine was dissected from a single embryo, and split into the small intestine and colon parts with a micro knife. The small intestine was dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained first with EPCAM antibody then with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 and 8 minutes, respectively. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RRBS libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the bisulfite-converted DNA amplification cycle number according to the input. The genomic DNA was digested with both MspI and HaeIII.

value: Small intestine endoderm

value: Trp53 KO


title: NAN3_control_bulk_untreated_replicate_1


title: RRBS_E135_exSI_EPCAM_mCherry_Trp53KO_Rep2


title: Control-Intima+Media-UC010-Full ROI-UC010-004

description: Intima+Media


title: RRBS_E135_exSI_EPCAM_mCherry_Trp53KO_Rep1


title: Control-Intima+Media-UC010-Full ROI-UC010-002

description: Intima+Media


title: Control-Adventitia-UC010-Full ROI-UC010-003

description: Adventitia


title: NAN3_KO_clone_3_untreated_replicate_1


title: NAN3_KO_clone_3_untreated_replicate_2


title: RRBS_E135_exColon_EPCAM_mCherry_Trp53KO_Rep3

source_name: Colon endoderm

extract_protocol:
Extraembryonic tissues were removed, the intestine was dissected from a single embryo, and split into the small intestine and colon parts with a micro knife. The colon was dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained first with EPCAM antibody then with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 and 8 minutes, respectively. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RRBS libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the bisulfite-converted DNA amplification cycle number according to the input. The genomic DNA was digested with both MspI and HaeIII.

value: Colon endoderm


title: Control-Adventitia-UC010-Full ROI-UC010-001

description: Adventitia


title: NAN3_KO_clone_2_untreated_replicate_3


title: RRBS_E135_exColon_EPCAM_mCherry_Trp53KO_Rep2


title: Control-Adventitia-AH015-Full ROI-AH015-002

description: Adventitia


title: colorectal cancer tissue sample AUS2_849_T3


title: Control-Intima+Media-AH015-Full ROI-AH015-001

description: Intima+Media


title: colorectal cancer tissue sample AUS2_849_T2


title: colorectal cancer tissue sample AUS2_850_INV

value: INV


title: colorectal cancer tissue sample AUS2_849_T

value: T


title: Control-Intima+Media-VA008-Full ROI-VA008-010

description: Intima+Media


title: RRBS_E135_emSI_EPCAM_GFP_WT_Rep2


title: NAN3_control_bulk_untreated_replicate_2


title: RRBS_E135_exColon_EPCAM_mCherry_Trp53KO_Rep1


title: NAN3_KO_clone_2_untreated_replicate_2


title: NAN3_KO_clone_1_untreated_replicate_3


title: RRBS_E135_emSI_EPCAM_GFP_WT_Rep3


title: Control-Intima+Media-VA008-Full ROI-VA008-008

description: Intima+Media


title: RRBS_E135_emColon_EPCAM_GFP_WT_Rep3


title: colorectal cancer tissue sample AUS2_850_T2


title: Control-Intima+Media-VA008-Full ROI-VA008-007

description: Intima+Media


title: RRBS_E135_emSI_EPCAM_GFP_WT_Rep1


title: colorectal cancer tissue sample AUS2_850_T


title: JIM3_KO_clone_3_untreated_replicate_3

value: A


title: NAN3_KO_clone_1_untreated_replicate_2


title: RRBS_E135_emColon_EPCAM_GFP_WT_Rep1


title: Control-Intima+Media-VA008-Full ROI-VA008-006

description: Intima+Media


title: colorectal cancer tissue sample AUS2_847_T2


title: colorectal cancer tissue sample AUS2_847_T3


title: JIM3_KO_clone_3_untreated_replicate_2


title: NAN3_KO_clone_1_untreated_replicate_1


title: colorectal cancer tissue sample AUS2_847_T


title: NAN3_KO_clone_2_untreated_replicate_1


title: RRBS_E135_emColon_EPCAM_GFP_WT_Rep2


title: RNAseq_E95_exMidgut_EPCAM_mCherry_Rep4

data_processing:
Raw reads were subjected to adapter and quality trimming with cutadapt (version 4.1; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25 --interleaved --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --interleaved --overlap 20 --minimum-length --adapter "A[100]" --adapter "T[100]").
Reads were aligned to the mouse reference genome (mm10) using STAR (version 2.7.9a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts) and transcripts were quantified using stringtie (version 2.0.6; parameters: -e) with GENCODE annotation (release VM23).
Assembly: mm10 (including mCherry and GFP transgenes)
Supplementary files format and content: Tab-delimited file containing gene abundances: <Gene ID> <Gene Name> <Reference> <Strand> <Start> <End> <Coverage> <FPKM> <TPM>

extract_protocol:
Extraembryonic tissues were removed, and the midgut from the posterior part of 4 embryos were pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained with EPCAM antibody in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 minutes, and then EPCAM+ cells were enriched by magnetic separation (MACS). Finally, the cells were stained with DAPI at 4 ºC for 8 minutes in FACS buffer. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.

value: Midgut endoderm


title: JIM3_KO_clone_3_untreated_replicate_1


title: colorectal cancer tissue sample AUS2_846_T3


title: Control-Intima+Media-VA008-Full ROI-VA008-001

description: Intima+Media


title: colorectal cancer tissue sample AUS2_846_T2


title: Control-Adventitia-VA008-Full ROI-VA008-005

description: Adventitia


title: RNAseq_E95_exMidgut_EPCAM_mCherry_Rep3


title: Control-Intima+Media-AH014-Full ROI-AH014-012

description: Intima+Media


title: JIM3_KO_clone_2_untreated_replicate_2


title: RNAseq_E95_exMidgut_EPCAM_mCherry_Rep2


title: RNAseq_E95_exMidgut_EPCAM_mCherry_Rep1


title: Control-Adventitia-VA008-Full ROI-VA008-004

description: Adventitia


title: Control-Adventitia-VA008-Full ROI-VA008-003

description: Adventitia


title: Control-Adventitia-VA008-Full ROI-VA008-002

description: Adventitia


title: JIM3_KO_clone_2_untreated_replicate_3


title: colorectal cancer tissue sample AUS2_847_INV


title: Control-Intima+Media-AH014-Full ROI-AH014-011

description: Intima+Media


title: RNAseq_E95_exHindgut_EPCAM_mCherry_Rep4

extract_protocol:
Extraembryonic tissues were removed, and the most posterior part including the hindgut from 4 embryos were pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained with EPCAM antibody in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 minutes, and then EPCAM+ cells were enriched by magnetic separation (MACS). Finally, the cells were stained with DAPI at 4 ºC for 8 minutes in FACS buffer. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.

value: Hindgut endoderm


title: JIM3_KO_clone_2_untreated_replicate_1


title: Control-Intima+Media-AH014-Full ROI-AH014-010

description: Intima+Media


title: RNAseq_E95_exHindgut_EPCAM_mCherry_Rep3


title: Control-Adventitia-AH014-Full ROI-AH014-009

description: Adventitia


title: colorectal cancer tissue sample AUS2_842_T2


title: JIM3_KO_clone_1_untreated_replicate_2


title: colorectal cancer tissue sample AUS2_842_INV


title: colorectal cancer tissue sample AUS2_842_T


title: colorectal cancer tissue sample AUS2_840_T2


title: colorectal cancer tissue sample AUS2_846_T


title: colorectal cancer tissue sample AUS2_840_T


title: colorectal cancer tissue sample AUS2_840_T3


title: colorectal cancer tissue sample AUS2_842_T3


title: colorectal cancer tissue sample AUS2_840_INV


title: RNAseq_E95_exHindgut_EPCAM_mCherry_Rep2


title: colorectal cancer tissue sample AUS2_837_T3


title: JIM3_KO_clone_1_untreated_replicate_1


title: Control-Adventitia-AH014-Full ROI-AH014-007

description: Adventitia


title: RNAseq_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep3


title: JIM3_KO_clone_1_untreated_replicate_3


title: JIM3_KO_clone_3_treated with 10 µM Nutlin3a for 16H_replicate_3

value: treated with 10 microM Nutlin3a for 16H


title: RNAseq_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep4


title: JIM3_KO_clone_3_treated with 10 µM Nutlin3a for 16H_replicate_2


title: RNAseq_E95_exHindgut_EPCAM_mCherry_Rep1


title: colorectal cancer tissue sample AUS2_837_T2


title: Control-Intima+Media-AH014-Full ROI-AH014-008

description: Intima+Media


title: Control-Adventitia-AH014-Full ROI-AH014-005

description: Adventitia


title: Control-Adventitia-AH014-Full ROI-AH014-006

description: Adventitia


title: JIM3_KO_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_3


title: Control-Intima+Media-AH014-Full ROI-AH014-004

description: Intima+Media


title: RNAseq_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep1


title: RNAseq_E95_emMidgut_EPCAM_GFP_mCherry_dual_low_Rep2


title: JIM3_KO_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_2


title: JIM3_KO_clone_3_treated with 10 µM Nutlin3a for 16H_replicate_1


title: RNAseq_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep4


title: colorectal cancer tissue sample AUS2_837_T


title: JIM3_KO_clone_2_treated with 10 µM Nutlin3a for 16H_replicate_1


title: colorectal cancer tissue sample AUS2_835_T3


title: Control-Adventitia-AH014-Full ROI-AH014-002

description: Adventitia


title: colorectal cancer tissue sample AUS2_835_T2


title: colorectal cancer tissue sample AUS2_837_INV


title: JIM3_KO_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_3


title: RNAseq_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep2


title: RNAseq_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep3


title: IPAH-Adventitia-BA009-Full ROI-BA009-015

description: Adventitia


title: colorectal cancer tissue sample AUS2_835_T


title: RNAseq_E95_YsEndo_mCherry_Rep4

extract_protocol:
Yolk sac tissues were separated from 4 embryos, pooled and dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained first with EPCAM antibody then with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 and 8 minutes, respectively. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.


title: Control-Adventitia-AH014-Full ROI-AH014-003

description: Adventitia


title: JIM3_KO_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_1

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)


title: colorectal cancer tissue sample AUS2_834_T3


title: Control-Intima+Media-AH014-Full ROI-AH014-001

description: Intima+Media


title: RNAseq_E95_YsEndo_mCherry_Rep3


title: JIM3_control_bulk_untreated_replicate_2

value: untreated


title: IPAH-Adventitia-BA009-Full ROI-BA009-014

description: Adventitia


title: JIM3_control_bulk_untreated_replicate_3


title: IPAH-Adventitia-BA009-Full ROI-BA009-013

description: Adventitia


title: RNAseq_E95_emHindgut_EPCAM_GFP_mCherry_dual_low_Rep1


title: IPAH-Intima+Media-BA009-Full ROI-BA009-012

description: Intima+Media


title: RNAseq_E95_YsEndo_mCherry_Rep2


title: JIM3_control_bulk_treated with 10 µM Nutlin3a for 16H_replicate_3


title: JIM3_control_bulk_untreated_replicate_1


title: RNAseq_E95_YsEndo_mCherry_Rep1


title: JIM3_KO_clone_1_treated with 10 µM Nutlin3a for 16H_replicate_2


title: IPAH-Intima+Media-BA009-Full ROI-BA009-009

description: Intima+Media


title: colorectal cancer tissue sample AUS2_834_T

value: colorectal cancer tissue sample


title: colorectal cancer tissue sample AUS2_828_T3


title: colorectal cancer tissue sample AUS2_830_T2


title: colorectal cancer tissue sample AUS2_834_T2


title: colorectal cancer tissue sample AUS2_830_T


title: JIM3_control_bulk_treated with 10 µM Nutlin3a for 16H_replicate_2


title: IPAH-Oblit-BA009-Full ROI-BA009-007

description: Obliterative Lesion


title: RNAseq_E65_exEndo2_mCherry_Rep3

extract_protocol:
The embryos were bisected at the embryonic-extraembryonic border, incubated for 15 min at 4º C in 0. 5% Trypsin, 2.5% Pancreatin dissolved in PBS. The exEndo 2 tissues from single embryos were manually isolated by drawing the extraembryonic part through a narrow, glass capillary, they were collected into Buffer RLT plus, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.

value: Extraembryonic endoderm (proximal)

value: mCherry+ morula (CD1/G4) aggregated with GFP+ mESCs (G4)


title: JIM3_control_bulk_treated with 10 µM Nutlin3a for 16H_replicate_1


title: IPAH-Intima+Media-BA009-Full ROI-BA009-010

description: Intima+Media


title: IPAH-Oblit-BA009-Full ROI-BA009-005

description: Obliterative Lesion


title: IPAH-Oblit-BA009-Full ROI-BA009-004

description: Obliterative Lesion


title: RNAseq_E65_exEndo2_mCherry_Rep4

value: WT


title: RNAseq_E65_exEndo2_mCherry_Rep1


title: RNAseq_E65_exEndo2_mCherry_Rep2


title: RNAseq_E65_exEndo1_mCherry_Rep4

extract_protocol:
The embryos were bisected at the embryonic-extraembryonic border, incubated for 15 min at 4º C in 0. 5% Trypsin, 2.5% Pancreatin dissolved in PBS. The exEndo 1 tissues from single embryos were manually isolated by drawing the embryonic part through a narrow, glass capillary, they were collected into Buffer RLT plus, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.

value: Extraembryonic endoderm (distal)


title: sPCL_82

source_name: CD138+ sorted cells

value: CD138+ sorted cells

value: sPCL


title: RNAseq_E65_exEndo1_mCherry_Rep3


title: IPAH-Plx-BA009-Full ROI-BA009-003

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_827_T3

value: no


title: IPAH-Plx-BA009-Full ROI-BA009-002

description: Plexifirm lesion


title: colorectal cancer tissue sample AUS2_828_T2


title: RNAseq_E65_exEndo1_mCherry_Rep2


title: sPCL_81


title: IPAH-Plx-BA009-Full ROI-BA009-001

description: Plexifirm lesion


title: IPAH-Adventitia-BA023-Full ROI-BA023-014

description: Adventitia


title: sPCL_80

value: B


title: colorectal cancer tissue sample AUS2_827_T


title: colorectal cancer tissue sample AUS2_825_T2


title: colorectal cancer tissue sample AUS2_827_T2


title: sPCL_83


title: colorectal cancer tissue sample AUS2_825_T


title: RNAseq_E65_exEndo1_mCherry_Rep1


title: colorectal cancer tissue sample AUS2_828_T


title: sPCL_84


title: colorectal cancer tissue sample AUS2_825_INV


title: IPAH-Oblit-BA009-Full ROI-BA009-006

description: Obliterative Lesion


title: sPCL_79


title: RNAseq_E65_Epi_GFP_Rep3

source_name: Epiblast

extract_protocol:
The embryos were bisected at the embryonic-extraembryonic border, incubated for 15 min at 4º C in 0. 5% Trypsin, 2.5% Pancreatin dissolved in PBS. The EmVE tissues from single embryos were manually isolated by drawing the embryonic part through a narrow, glass capillary, they were collected into Buffer RLT plus, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.

value: Epiblast


title: colorectal cancer tissue sample AUS2_823_T2


title: IPAH-Adventitia-BA023-Full ROI-BA023-012

description: Adventitia


title: RNAseq_E65_Epi_GFP_Rep4


title: IPAH-Adventitia-BA023-Full ROI-BA023-011

description: Adventitia


title: RNAseq_E65_Epi_GFP_Rep2


title: sPCL_78


title: colorectal cancer tissue sample AUS2_822_T6

value: sigmoid colon


title: pPCL_77

value: pPCL


title: MM_76_replicate 1

value: MM

value: replicate 1

value: A


title: RNAseq_E65_Epi_GFP_Rep1


title: MM_76_replicate 2

value: replicate 2

value: D


title: RNAseq_E135_exSI_EPCAM_mCherry_Trp53KO_Rep3

extract_protocol:
Extraembryonic tissues were removed, the intestine was dissected from a single embryo, and split into the small intestine and colon parts with a micro knife. The small intestine was dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained first with EPCAM antibody then with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 and 8 minutes, respectively. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.

value: Small intestine endoderm

value: Trp53 KO


title: MM_75


title: colorectal cancer tissue sample AUS2_823_T

value: colorectal cancer tissue sample

value: T


title: MM_74_replicate 2


title: RNAseq_E135_exSI_EPCAM_mCherry_Trp53KO_Rep2

value: mCherry+ morula (CD1/G4) aggregated with GFP+ mESCs (G4)


title: colorectal cancer tissue sample AUS2_822_T4


title: colorectal cancer tissue sample AUS2_822_T5


title: IPAH-Intima+Media-BA023-Full ROI-BA023-007

description: Intima+Media


title: RNAseq_E135_exSI_EPCAM_mCherry_Trp53KO_Rep1


title: IPAH-Plx-BA023-Full ROI-BA023-005

description: Plexifirm lesion


title: IPAH-Plx-BA023-Full ROI-BA023-006

description: Plexifirm lesion


title: IPAH-Intima+Media-BA023-Full ROI-BA023-009

description: Intima+Media


title: MM_74_replicate 1

value: CD138+ sorted cells

value: C


title: colorectal cancer tissue sample AUS2_830_INV

value: no

value: INV


title: RNAseq_E135_exColon_EPCAM_mCherry_Trp53KO_Rep3

extract_protocol:
Extraembryonic tissues were removed, the intestine was dissected from a single embryo, and split into the small intestine and colon parts with a micro knife. The colon was dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, stained first with EPCAM antibody then with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 10 and 8 minutes, respectively. Cells were resuspended in FACS buffer, the indicated populations were sorted into Buffer RLT plus using the BD FACSAria Fusion, and the samples were stored at -80 ºC.
RNA-seq libraries were prepared as part of the Smart-RRBS protocol by Gu, H et al. 2021 Nature Protocols, with the adaptation to low input bulk samples instead of single-cell input by reducing the cDNA amplification cycle number according to the input.

value: Colon endoderm


title: IPAH-Plx-BA023-Full ROI-BA023-004

description: Plexifirm lesion


title: RNAseq_E135_exColon_EPCAM_mCherry_Trp53KO_Rep2


title: MM_72

value: B


title: IPAH-Oblit-BA023-Full ROI-BA023-003

description: Obliterative Lesion


title: RNAseq_E135_exColon_EPCAM_mCherry_Trp53KO_Rep1


title: IPAH-Oblit-BA023-Full ROI-BA023-002

description: Obliterative Lesion


title: colorectal cancer tissue sample AUS2_822_T2

value: hepatic flexure


title: colorectal cancer tissue sample AUS2_822_T3


title: MM_65

value: MM


title: IPAH-Oblit-BA023-Full ROI-BA023-001

description: Obliterative Lesion


title: colorectal cancer tissue sample AUS2_821_T3


title: colorectal cancer tissue sample AUS2_822_INV


title: MM_64


title: RNAseq_E135_emSI_EPCAM_GFP_WT_Rep3

value: WT


title: colorectal cancer tissue sample AUS2_822_T


title: MM_63


title: colorectal cancer tissue sample AUS2_821_T2


title: MM_62


title: RNAseq_E135_emSI_EPCAM_GFP_WT_Rep1


title: IPAH-Intima+Media-UA013-Full ROI-UA013-014

description: Intima+Media


title: IPAH-Intima+Media-UA013-Full ROI-UA013-017

description: Intima+Media


title: IPAH-Intima+Media-UA013-Full ROI-UA013-018

description: Intima+Media


title: RNAseq_E135_emColon_EPCAM_GFP_WT_Rep3


title: MM_58_replicate 1

value: replicate 1


title: colorectal cancer tissue sample AUS2_821_INV


title: RNAseq_E135_emColon_EPCAM_GFP_WT_Rep2


title: colorectal cancer tissue sample AUS2_821_T


title: MM_58_replicate 2

value: replicate 2


title: RNAseq_E135_emColon_EPCAM_GFP_WT_Rep1


title: colorectal cancer tissue sample AUS2_820_T3


title: IPAH-Adventitia-UA013-Full ROI-UA013-013

description: Adventitia


title: RNAseq_E135_emSI_EPCAM_GFP_WT_Rep2


title: colorectal cancer tissue sample AUS2_820_T2


title: MM_56


title: IPAH-Adventitia-UA013-Full ROI-UA013-012

description: Adventitia


title: colorectal cancer tissue sample AUS2_820_T


title: Hippocampus, PBS treatment, Rep3

city: Dresden

first: Tomohisa

last: Toda

address: Tatzberg 41

institute: DZNE

data_processing:
Fragments were demultiplexed using bcl2fastq2 (v2.20.0) and aligned to the mouse reference GRCm39 with the support of Ensembl gene annotation version 104 using the STAR (v2.7.10b) aligner. Fragments per gene and samples were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: Tab separated Excel Table from featureCounts. The rows are genes and the columns provide gene information and list of samples.

source_name: brain region hippocampus

growth_protocol: Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.

extract_protocol:
Total RNA was isolated using miRNeasy Kit with gDNA removal columns. EU-labelled RNA was purified using Biotin-Click reaction and Streptavidin beads. PBS-treated samples underwent the same extraction protocol.
Libraries were prepared using Universal Plus Total RNA-seq kit (TECAN).

treatment_protocol: Mice were injected subcutanuously with EU (50 mg/kg) or PBS (equal volume) at postnatal days P3-P5 (one injection daily). Hippocampus tissue was dissected from the brain on postnatal day P36.

value: brain region hippocampus

value: PBS


title: IPAH-Intima+Media-BA023-Full ROI-BA023-008

description: Intima+Media

extract_protocol: rna kit


title: MM_51


title: MM_73


title: Hippocampus, PBS treatment, Rep2


title: colorectal cancer tissue sample AUS2_820_INV

source_name: Colorectal cancer patient


title: MM_43


title: Hippocampus, PBS treatment, Rep1


title: IPAH-Plx-UA013-Full ROI-UA013-008

description: Plexifirm lesion


title: MM_42_replicate 1


title: MM_42_replicate 2


title: Hippocampus, EU treatment, Rep3

value: EU


title: IPAH-Plx-UA013-Full ROI-UA013-007

description: Plexifirm lesion


title: Hippocampus, EU treatment, Rep2


title: IPAH-Adventitia-UA013-Full ROI-UA013-011

description: Adventitia


title: IPAH-Plx-UA013-Full ROI-UA013-005

description: Plexifirm lesion


title: Hippocampus, EU treatment, Rep1


title: IPAH-Oblit-UA013-Full ROI-UA013-004

description: Obliterative Lesion


title: MM_39


title: MM_38

value: D


title: IPAH-Plx-UA013-Full ROI-UA013-006

description: Plexifirm lesion


title: MM_35


title: NPCs, PBS treatment, Rep3

data_processing:
Fragments were demultiplexed using bcl2fastq2 (v2.20.0). Because the libraries contain UMI information, a separate file was created per library which contains the UMIs per sequenced fragment. Next, the UMI information was added to the files, which contain the sequenced fragments, using UMI-tools (v1.1.2, umi_tools extract). Afterwards, fragments were aligned to the mouse reference GRCm39 with the support of Ensembl gene annotation version 104 using the STAR aligner (v2.7.10b). Deduplication of the aligned fragments based on UMIs and mapping coordinate was done with umi_tools (umi_tools dedup). Fragments per gene and samples were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: Tab separated Excel Table from featureCounts. The rows are genes and the columns provide gene information and list of samples.

source_name: embryonic brain

growth_protocol: Quiescent neural progenitor cells (NPCs) were maintained in DMEM/F12 supplemented with N2, B27, FGF2 (10 ng/ml), Bmp4 (20 ng/ml) at 37°C in a humified incubator.

extract_protocol:
Total RNA was isolated using Trizol and genomic DNA was removed with Dnase I. EU-labelled RNA was purified using Biotin-Click reaction and Streptavidin beads (Life Technologies). PBS-treated samples underwent the same extraction protocol.
Libraries were prepared using Universal Plus Total RNA-seq kit (TECAN).

treatment_protocol: NPCs were treated with EU (250 µM) one day after induction of quiescence and RNA was isolated on day 8 after induction of quiescence.

value: embryonic brain

value: Neural progenitor cells


title: colorectal cancer tissue sample AUS2_818_T2

value: colorectal cancer tissue sample


title: IPAH-Oblit-UA013-Full ROI-UA013-003

description: Obliterative Lesion


title: NPCs, PBS treatment, Rep1


title: IPAH-Oblit-UA013-Full ROI-UA013-002

description: Obliterative Lesion


title: NPCs, EU treatment, Rep3


title: NPCs, PBS treatment, Rep2


title: Control-Adventitia-AH015-Full ROI-AH015_rescan-011

description: Adventitia


title: MM_34

value: CD138+ sorted cells


title: colorectal cancer tissue sample AUS2_817_T2

value: no


title: MM_41

value: C


title: colorectal cancer tissue sample AUS2_818_T3


title: MM_31


title: NPCs, EU treatment, Rep1


title: colorectal cancer tissue sample AUS2_816_T3


title: MM_33


title: MM_18


title: Mouse, kidney, WT, M, H3K4me3

city: Bethesda

first: Jakub

last: Jankowski

state: MD

address: 8 Center DR.

department: NIDDK

institute: NIH

data_processing:
first, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
next, samples were aligned to mm10 genome with bowtie2  (Langmead et al., Nature methods, 2012)
next, MASC2 was used to visualize peaks (Zhang et al., Genome Biology, 2008)
next,  .tdf files were generated using IGV and IGVTools (Robinson et al., Nature Biotechnology 2011)
Assembly: mm10
Supplementary files format and content: .tdf files containing tracks with respective histone modification peak heights and locations, .bedgraph files containing tracks with respective histone modification peak heights and locations

source_name: Kidney

extract_protocol:
Snap-frozen kidneys of 12-14 weeks old mice were ground into powder in liquid nitrogen. After 15 min Chromatin cross-linking in 1% formaldehyde at room temperature the reaction was quenched with 0.125M Glycine. Cells were then lysed using Farnham Lysis Buffer and homogenized on ice. After filtering through a 70um filter, chromatin was sonicated until majority of the fragments were below 1000bp length as assessed by electrophoresis of small aliquots.
Sheared chromatin (>600ug per sample) was incubated with H3K27ac (Active Motif, 39133), H3K4me3 (Millipore, CS200580), and HNF1b (Invitrogen, 720259) antibodies. Libraries for next generation sequencing were prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645) and sequenced on a NovaSeq 6000 or HiSeq 3000 machine (Illumina).

value: Kidney

value: Klotho E1 WT

value: male

tag: antibody

value: Millipore, CS200580


title: NPCs, EU treatment, Rep2


title: colorectal cancer tissue sample AUS2_816_T

value: T


title: Control-Adventitia-AH015-Full ROI-AH015_rescan-009

description: Adventitia

data_processing: Gene expression was normalised with RUVIII (Molania et al. 2019) (v0.9.7.1, k=5). The set of control genes with lowest variation across pseudobiological replicates was identified in a two-step approach, first running RUVIII across log2 transformed counts with all genes as controls, then choosing the 100 genes with the least variation to use for the normalisation.


title: colorectal cancer tissue sample AUS2_817_T


title: colorectal cancer tissue sample AUS2_816_T2


title: MM_17

value: MM


title: MM_15