title: WG_ULB.replicate_42.RNAseq


title: WG_ULB.replicate_41.RNAseq

status: Public on May 11 2023

type: SRA

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

description:
whole.Pig.PCG.TPM.xls
whole.Pig.TUCP.TPM.xls
whole.Pig.lncRNA.TPM.xls
whole.Pig.PCG.counts.xls
whole.Pig.TUCP.counts.xls
whole.Pig.lncRNA.counts.xls

library_source: transcriptomic

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Tpm and counts matrixs were generated using R vresion 3.6.1.
AssemblySusscrofa11.1
Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Sus scrofa

source_name: upper layer of backfat

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 11.97 Gb high-quality data for each library.

tag: tissue

value: upper layer of backfat


title: LLC_CD8_Tumor_PDL1_4

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

data_processing:
Data processing of Bulk TCRseq was performed as described in Aoki et al. (Aoki et al., 2021).
Adapter trimming and quality filtering of sequencing data were performed by using Cutadapt-3.2  (Martin et al., 2011) and PRINSEQ-0.20.4 (Schmieder et al., 2011). Sequencing data were processed by MiXCR-3.0.5 (Bolotin et al., 2015). In MiXCR, filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system: -vParameters.geneFeatureToAlign = VTranscript -vjAlignmentOrder = JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -badQualityThreshold=10, –separateByV=true, --only-productive=true, –region-of-interest=CDR3. The Variable (V) and Joining (J) segment of TCRs were represented in IMGT gene nomenclature.
List of final clones were analyzed by VDJtools-1.2.1 (Shugay et al., 2015). Then, the sequencing reads of sample was normalized to the cell count in each sample by “DownSample” command of VDJtools. T-cell clones were determined as TCR reads with the same TCR V segment, J segment and CDR3 nucleotide sequence.
Assembly: IMGT reference sequences of mouse TRA and TRB
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

organism: Mus musculus

source_name: tumor on day 14 after innoculation of LLC

extract_protocol:
Intravascular leukocytes were stained by i.v. injection of FITC-conjugated anti-CD45.2 mAb (3 mg/mouse, clone 104, BioLegend) three minutes before sacrifice.
dLN cells were prepared by standard method. Tumors were cut into small fragments and digested for 45 minutes at 37°C with 0.1% collagenase (FUJIFILM Wako), then subjected to 40% Percoll PLUS (Cytiva) and Histopaque-1083 (Sigma-Aldrich) gradient, and leukocytes were recovered from the interphase. The cell concentration of the suspensions was determined using Flow-Count fluorospheres (Beckman Coulter) and a Cytoflex flow cytometer (Beckman Coulter).
Cells were stained with a mix of Fc Block (anti-mouse CD16/CD32 mAb; clone 93, BioLegend) and fluorophore-conjugated anti-mouse mAbs. For dLN samples, Lineage+ (CD11b, B220, NK1.1, Ter119) cells were depleted using BD IMag Streptavidin Particles Plus-DM (BD Biosciences). For tumor samples, TCRb+ T cells were enriched magnetically using Anti-APC MicroBeads (Miltenyi) and LS columns (Miltenyi).
CD8+, CD8+ PD1-, CD8+ PD1+ Ly108+ Tim3-, CD8+ PD1+ Ly108+ Tim3+, and CD8+ PD1+ Ly108- Tim3+ T cells from tumor, and CD8+ CD44high T cells from dLN were sorted using FACS Aria II or Aria III (BD Biosciences). Nonviable cells were excluded from the analysis based on forward and side scatter profiles and propidium iodide staining. Intravascular leukocytes were also excluded. Purity of sorted cells was always over 95%.
Bulk TCR sequencing library was prepared according to the previous report (Aoki et al., 2021). In brief, to amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. Beads containing cDNA was resuspended with the 12.5 mL of first PCR mixture comprised 0.5 mL of 10 mM trP1 primer, and 1 mL of TCR primer mix (Trac_ex, and Trbc_ex), 4.75 mL of water, and 6.25 mL of KAPA Hifi Hotstart ReadyMix (KAPA Biosystems). The thermal cycling conditions were programmed as follows: denaturation at 95°C for 3 minutes, 5 cycles of denaturation for 20 seconds at 98°C, annealing for 15 seconds at 65°C and extension for 30 seconds at 72°C, followed by a final extension at 72°C for 2 minutes. Next, 2.5 mL of the first-PCR products were added into the 22.5 mL of second PCR mixture consisted of 1.75 mL of 10 mM primer mix (trP1, Trac_in-Bio, and Trbc_in-Bio), 8.25 mL of water and 12.5 mL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were the same as the first PCR except for the cycle number, which was 25 cycles. Next, 25 mL of the second-PCR products were purified using Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.7:1 ratio (beads to sample) and eluted in 20 mL of 10mM of Tris HCl pH 8.0. Fragmentasion and adaptor ligation were performed using 10-20ng of second-PCR product as a template with NEBNext FS DNA Library Prep Kit (New England Biolabs) with some modifications: NEBNext Adaptor for Illumina in “Adaptor Ligation” step was substituted by 5mM Adaptor P1, and the reaction volume was 1/4 of the recommended in all steps. Adaptor-ligated DNA was purified using Agencort AM Pure XP kit (Beckman Coulter) at a 0.8:1 ratio (beads to sample) and eluted in 20 mL of 10mM of Tris HCl pH 8.0. The third PCR was carried out using barcoded primers to enrich the TCR cDNA flanked with sequencing adapters. The third PCR mixture consisted of 1 mL of 10 mM trP1 primer, 1 mL of 10 mM IonA-BC-Trbc primer, 3 mL of template and 5 mL of NEBNext Ultra II Q5 Master Mix (accessory of NEBNext FS DNA Library Prep Kit). The thermal cycling conditions were programmed as follows: denaturation at 98°C for 30 seconds, 10 cycles of denaturation for 10 seconds at 98°C, annealing and extension for 1minute 15 seconds at 65°C, followed by a final extension at 65°C for 5 minutes. The PCR product was purified and subjected to size selection using Agencort AM Pure XP kit (Beckman Coulter) at a 1.0:1 ratio (beads to sample) and eluted with 20 mL of Tris-HCl (pH 8.0). Amplified TCR libraries were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems) and size distribution was analyzed by Microchip Electrophoresis System MultiNA (Shimadzu, Kyoto, Japan). Primers used for library preparations were summarized in Supplementary Table 1.  Final TCR libraries, whose lengths were 200–300 base pairs, were pooled and sequenced using an Ion 540 Kit Chef, an Ion 540 Chip kit, and an Ion Genestudio S5 Sequencer (Thermo Fisher Scientific) according to the manufacturer’s instructions, except the flow number (500).

treatment_protocol: B16F10 or LLC cells (5 × 105 cells except for sample 103-107: 2 × 105 cells) were inoculated subcutaneously (s.c.) into the right flanks of C57BL/6 mice. Anti-PD-L1 mAb (clone 10F.9G2, BioLegend) or Anti-CD4 mAb (clone GK1.5, BioLegend) was injected intraperitoneally (i.p.) at a dose of 200 μg per mouse on days 5 and 9 after tumor inoculation.

tag: strain

tag: treatment

value: anti-PD-L1 mAb

tag: cell type

value: Intravenous (i.v.) staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRbeta+ and CD4- CD8+ T cells

tag: age

value: 8 weeks

tag: Sex

value: female

tag: tumour cell line

value: B16F10 melanoma

tag: organ

tag: date


title: LLC_CD8_Tumor_PDL1_2


title: LLC_CD8_Tumor_PDL1_3


title: LLC_CD8_Tumor_PDL1_1


title: 20210327_AIID11_8

type: RNA

city: Dublin 4

first: Gabriel

last: Gonzalez

state: Co. Dublin

address: Belfield campus

country: Ireland

institute: University College Dublin

description: NanoString nCounter Immunology panels, NS Immunology v2C2328

hyb_protocol: Nanostring with nCounter Analysis System

data_processing: Raw counts were normalized to 'log2 counts' using a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within that sample lane.

label: Nanostring CodeSet

organism: Homo sapiens

source_name: PBMC

growth_protocol: PBMC frozen in liquid nitrogen after extraction

extract_protocol: RNeasy® Plus Kit

tag: gender

value: F

tag: severity

value: NEG


title: 20210327_AIID11_9

scan_protocol: Nanostring with nCounter Analysis System

value: M


title: WL_GOM.replicate_10.RNAseq

source_name: greater omentum fat

value: greater omentum fat


title: WL_GOM.replicate_1.RNAseq


title: WG_ULB.replicate_40.RNAseq


title: WG_ULB.replicate_44.RNAseq


title: LLC_CD8_Tumor_Control_6

value: Untreated


title: WG_ULB.replicate_36.RNAseq


title: WG_ULB.replicate_38.RNAseq


title: WG_ULB.replicate_34.RNAseq


title: LLC_CD8_Tumor_Control_3


title: LLC_CD8_Tumor_Control_1


title: WG_ULB.replicate_33.RNAseq


title: LLC_CD8_Tumor_CD4PDL1_3

value: combination of anti-CD4 and anti-PD-L1 mAbs


title: WG_ULB.replicate_24.RNAseq


title: WG_ULB.replicate_31.RNAseq


title: LLC_CD8_Tumor_CD4PDL1_1


title: WG_ULB.replicate_23.RNAseq


title: LLC_CD8_Tumor_aCD4_6

value: anti-CD4 mAb


title: LLC_CD8_Tumor_aCD4_5


title: LLC_CD8_Tumor_CD4PDL1_2


title: WG_ULB.replicate_22.RNAseq


title: LLC_CD8_Tumor_aCD4_4


title: WG_ULB.replicate_21.RNAseq


title: WG_ULB.replicate_39.RNAseq


title: LLC_CD8_Tumor_Control_5


title: LLC_CD8_Tumor_aCD4_3


title: LLC_CD8_Tumor_aCD4_1


title: WG_ULB.replicate_37.RNAseq


title: LLC_CD8_Tumor_aCD4_2


title: #6 Inflamed

city: Huddinge

first: Jenny

last: Mjösberg

state: Stockholm

address: Alfred Nobels allé 8

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
Used the 10X Cell Ranger toolkit (v2.1.1) for filtering and aligning reads to human genome hg19 and counting barcodes and unique molecular identifiers (UMI)
Using Seurat (v3.2.3), cells with a percentage of mitochondria genes > 5% were considered as dead cells and were removed. Cells with < 200 genes and > 2500 numbers of detected genes were excluded. Genes detected in < 3 cells were excluded
Using Seurat (v3.2.3), raw unique molecular identifier counts were scaled and normalized through log transformation.
The top 2000 variable genes were selected for principle-component analysis. The top 10 principal components were selected for UMAP (Uniform Manifold Approximation and Projection) and clustering analysis with resolution 0.5 (for combined and non-inflamed) and 0.55 (for inflamed).
Seurat function FindAllMarkers (logFC threshold = 0.25) were used to find cluster- and sample-specific marker genes.
Genome_build: hg19
Supplementary_files_format_and_content: gene count text files generated using 10X Cell Ranger toolkit (v2.1.1)

source_name: Colon

extract_protocol:
Intestinal biopsies were collected in wash buffer medium consisting of HBSS supplemented with antibiotics, FungizoneTM (Life Technologies) and HEPES  (HyClone). Subsequently, enzymatic digestion with DNAse and Collagenase II was performed at 37° C under magnetic stirring. Cell suspension was filtered through a 40 μm cell strainer and rinsed with IMDM 10% FCS.
 Samples were prepared using Chromium Single-Cell v2 3ʹ Reagents Kit (10x Genomics) according to manufacturer’s instructions. Samples were sequenced on a HiSeq4000 (Illumina).

tag: diagnosis

value: IBD-unclassified

tag: endoscopic inflammation status

value: inflamed

tag: sampling location

value: ascendens

tag: age (y)


title: LLC_CD8_Tumor_Control_2


title: LLC_CD8_Tumor_Control_4


title: #6 Non-inflamed

value: non-inflamed

value: rectum


title: WG_ULB.replicate_27.RNAseq

value: upper layer of backfat


title: LLC_CD8_dLN_PDL1_5

source_name: dLN on day 14 after innoculation of LLC

value: anti-PD-L1 mAb

value: Intravenous (i.v.) staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRbeta+, CD4- CD8+ and CD44high T cells


title: 204887840015_R06C01

status: Public on May 12 2023

type: genomic

city: Durham

first: Elizabeth

last: Martin

state: NC

address: 111 TW Alexander Drive

country: USA

institute: NIEHS

description:
genomic DNA from a C3 female mouse
genomic DNA from a B6 female mouse

hyb_protocol: DNA was processed through the Infinum array protocol for hypbridization

scan_protocol: Beachip arrays were scanned on the Illumina iScan ssytem to produce Idat files

data_processing:
Data were processed using ENMix
Processed data file contains: Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: 500ng of DNA were bisulfite convered using the EZ gold DNA methylation kit

growth_protocol: Mice were housed from 8 to 20 weeks

extract_protocol: A 2mm cube of fresh liver tissue was homoginzed immediately following sacrifice into Buffer RLT plus with BME. DNA was then extracted using the Qiagen Allprep kit

value: liver

value: female

tag: subject


title: LLC_CD8_dLN_PDL1_4

value: 8 weeks

value: B16F10 melanoma


title: WG_ULB.replicate_25.RNAseq


title: WG_ULB.replicate_19.RNAseq


title: #5 Inflamed

value: Crohn's disease

value: colon descendens


title: WG_ULB.replicate_18.RNAseq


title: LLC_CD8_dLN_PDL1_2


title: #4 Inflamed

value: caecum


title: WG_ULB.replicate_17.RNAseq


title: LLC_CD8_dLN_Control_5

value: Untreated


title: LLC_CD8_dLN_Control_6


title: LLC_CD8_dLN_Control_4


title: WG_ULB.replicate_16.RNAseq


title: #3 Inflamed


title: LLC_CD8_dLN_Control_3


title: LLC_CD8_dLN_Control_2


title: #3 Non-inflamed

value: colon ascendens


title: #2 Inflamed

value: colon


title: LLC_CD8_dLN_Control_1


title: WG_ULB.replicate_15.RNAseq


title: LLC_CD8_dLN_CD4PDL1_2

value: combination of anti-CD4 and anti-PD-L1 mAbs


title: WG_ULB.replicate_20.RNAseq


title: LLC_CD8_dLN_CD4PDL1_3


title: LLC_CD8_dLN_CD4PDL1_1


title: WG_ULB.replicate_13.RNAseq


title: LLC_CD8_dLN_aCD4_6

value: anti-CD4 mAb


title: LLC_CD8_dLN_PDL1_3


title: WG_ULB.replicate_14.RNAseq


title: WG_ULB.replicate_12.RNAseq


title: LLC_CD8_dLN_PDL1_1


title: #1 Inflamed

value: inflamed


title: LLC_CD8_dLN_aCD4_5


title: LLC_CD8_dLN_aCD4_4


title: #4 Non-Inflamed

value: non-inflamed

value: colon transversum


title: WG_ULB.replicate_11.RNAseq

value: upper layer of backfat


title: #1 Non-inflamed


title: LLC_CD8_dLN_aCD4_2

value: Intravenous (i.v.) staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRbeta+, CD4- CD8+ and CD44high T cells


title: LLC_CD8_dLN_aCD4_3


title: LLC_CD8_dLN_aCD4_1


title: B16_CD8_Tumor_PDL1_7

source_name: tumor on day 14 after innoculation of B16

value: anti-PD-L1 mAb

value: Intravenous (i.v.) staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRbeta+ and CD4- CD8+ T cells


title: WG_ULB.replicate_9.RNAseq


title: #2 Non-inflamed

value: rectum


title: WG_ULB.replicate_8.RNAseq


title: WG_ULB.replicate_7.RNAseq


title: WG_ULB.replicate_10.RNAseq


title: B16_CD8_Tumor_PDL1_6

value: 8 weeks

value: female

value: B16F10 melanoma


title: B16_CD8_Tumor_PDL1_4


title: WG_ULB.replicate_6.RNAseq


title: B16_CD8_Tumor_PDL1_3


title: B16_CD8_Tumor_PDL1_5


title: B16_CD8_Tumor_PDL1_1


title: B16_CD8_Tumor_PDL1_2


title: WG_ULB.replicate_5.RNAseq


title: B16_CD8_Tumor_Control_4


title: WG_ULB.replicate_3.RNAseq


title: B16_CD8_Tumor_Control_5


title: B16_CD8_Tumor_Control_3


title: WG_ULB.replicate_2.RNAseq


title: B16_CD8_Tumor_Control_1


title: B16_CD8_Tumor_Control_2


title: B16_CD8_Tumor_CD4PDL1_9


title: B16_CD8_Tumor_CD4PDL1_8


title: B16_CD8_Tumor_Control_6


title: WG_ULB.replicate_1.RNAseq


title: B16_CD8_Tumor_CD4PDL1_7


title: WG_MAD.replicate_46.RNAseq

source_name: mesenteric adipose

value: mesenteric adipose


title: B16_CD8_Tumor_CD4PDL1_6


title: B16_CD8_Tumor_CD4PDL1_5


title: B16_CD8_Tumor_CD4PDL1_4


title: B16_CD8_Tumor_CD4PDL1_3


title: WG_MAD.replicate_43.RNAseq


title: B16_CD8_Tumor_CD4PDL1_10


title: B16_CD8_Tumor_CD4PDL1_2


title: WG_MAD.replicate_42.RNAseq


title: Phase-II D1-3

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

description: m6A of mouse PBMC

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 4 out of 8 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.  Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: Mouse blood was collected by abdominal aorta bleed or by cardiac puncture. Mouse peripheral blood mononucleated cells (PBMCs) were isolated from mouse blood samples by density gradient centrifugation using the PBMC isolation kit (TBD sciences, China) according to the manufacturer's instructions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Total RNAs were directly extracted from PBMC without treatment.

value: 6-8 weeks


title: Phase-II D1-2

description: m6A of mouse PBMC


title: B16_CD8_Tumor_CD4PDL1_1


title: Phase-II D14-2

description: m6A of mouse PBMC


title: Phase-II D14-1

description: m6A of mouse PBMC


title: B16_CD8_Tumor_aCD4_8


title: Phase-II D1-1

description: m6A of mouse PBMC


title: Phase-II D14-3

description: m6A of mouse PBMC


title: B16_CD8_Tumor_aCD4_6


title: B16_CD8_Tumor_aCD4_7


title: Phase-I D30-2

description: m6A of mouse PBMC


title: Phase-II D0-1

description: m6A of mouse PBMC


title: WG_MAD.replicate_41.RNAseq


title: WG_MAD.replicate_44.RNAseq


title: WG_MAD.replicate_39.RNAseq


title: B16_CD8_Tumor_aCD4_4


title: B16_CD8_Tumor_aCD4_5


title: Phase-II D0-3

description: m6A of mouse PBMC


title: Phase-II D0-2

description: m6A of mouse PBMC


title: B16_CD8_Tumor_aCD4_3


title: B16_CD8_Tumor_aCD4_2


title: WG_MAD.replicate_38.RNAseq


title: B16_CD8_Tumor_aCD4_1


title: B16_CD8_dLN_PDL1_7

source_name: dLN on day 14 after innoculation of B16


title: Phase-I D30-3

description: m6A of mouse PBMC


title: Phase-I D30-1

description: m6A of mouse PBMC


title: Phase-I D14-3

description: m6A of mouse PBMC


title: Phase-I D14-2

description: m6A of mouse PBMC


title: WG_MAD.replicate_34.RNAseq


title: Phase-I D14-1

description: m6A of mouse PBMC


title: B16_CD8_dLN_PDL1_6


title: B16_CD8_dLN_PDL1_5


title: B16_CD8_dLN_PDL1_4


title: Phase-I D7-3

description: m6A of mouse PBMC


title: WG_MAD.replicate_33.RNAseq


title: WG_MAD.replicate_31.RNAseq


title: B16_CD8_dLN_PDL1_3


title: WG_MAD.replicate_30.RNAseq


title: WG_MAD.replicate_37.RNAseq


title: WG_MAD.replicate_29.RNAseq


title: B16_CD8_dLN_PDL1_2


title: B16_CD8_dLN_PDL1_1


title: B16_CD8_dLN_Control_6

value: Untreated


title: B16_CD8_dLN_Control_3


title: B16_CD8_dLN_Control_2


title: B16_CD8_dLN_Control_4


title: B16_CD8_dLN_Control_5


title: WG_MAD.replicate_28.RNAseq


title: B16_CD8_dLN_Control_1


title: B16_CD8_dLN_CD4PDL1_10


title: B16_CD8_dLN_CD4PDL1_9


title: WG_MAD.replicate_27.RNAseq


title: WG_MAD.replicate_26.RNAseq


title: B16_CD8_dLN_CD4PDL1_8


title: WG_MAD.replicate_24.RNAseq


title: B16_CD8_dLN_CD4PDL1_6


title: B16_CD8_dLN_CD4PDL1_5


title: B16_CD8_dLN_CD4PDL1_4


title: B16_CD8_dLN_CD4PDL1_7


title: WG_MAD.replicate_23.RNAseq


title: Phase-I D1-3

description: m6A of mouse PBMC


title: Phase-I D7-1

description: m6A of mouse PBMC


title: B16_CD8_dLN_CD4PDL1_2


title: Phase-I D7-2

description: m6A of mouse PBMC


title: Phase-I D3-2

description: m6A of mouse PBMC


title: Phase-I D3-1

description: m6A of mouse PBMC


title: Phase-I D3-3

description: m6A of mouse PBMC


title: WG_MAD.replicate_20.RNAseq


title: Phase-I D1-2

description: m6A of mouse PBMC


title: Phase-I D1-1

description: m6A of mouse PBMC


title: Phase-I D0-3

description: m6A of mouse PBMC


title: B16_CD8_dLN_CD4PDL1_1


title: B16_CD8_dLN_CD4PDL1_3


title: WG_MAD.replicate_19.RNAseq


title: WG_MAD.replicate_16.RNAseq


title: B16_CD8_dLN_aCD4_8


title: B16_CD8_dLN_aCD4_7


title: WG_MAD.replicate_15.RNAseq


title: WG_MAD.replicate_17.RNAseq


title: B16_CD8_dLN_aCD4_6


title: B16_CD8_dLN_aCD4_5


title: B16_CD8_dLN_aCD4_4


title: B16_CD8_dLN_aCD4_2


title: B16_CD8_dLN_aCD4_1


title: Phase-I D0-2

description: m6A of mouse PBMC


title: WG_MAD.replicate_14.RNAseq


title: B16_CD8_dLN_aCD4_3


title: ATACseq-T-E145-Col2a1GFP-GFPn-R1

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
NextSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q30 -m15). Reads were then mapped to GRCm39/mm39 using Bowtie2 v2.3.5.1 (--very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000). Reads with mapping quality below 30, mapping to mitochondria, or not properly paired were removed from the analysis with Samtools view v1.10. PCR duplicates were filtered using Picard v2.21.1. BAM file was converted to BED with Bedtools v2.28.0. Coverage was done using MACS2 v2.2.7.1 (callpeak --nomodel --call-summits --extsize 200 --shift -100 --keep-dup all). Coverage was normalized by the number of millions of reads falling into MACS2 summits +/- 500bp using Bedtools v2.28.0. When indicated, coverage profiles represent an average of the normalized coverage of all replicates.
Assembly: mm39
Supplementary files format and content: bigWig

source_name: Embryonic Trunk

growth_protocol: Limbs and trunks from E14.5 mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status.

extract_protocol:
After sorting, cells were centrifuged for 5′ at 400 × g at 4 °C and supernatant was discarded. Two biological replicates of 7.5 × 104 cells for each condition were then isolated for direct processing with Nextera Tn5 enzyme (Illumina, FC-131-1096). Samples were treated as previously described (67) with the exception that elution of the Tn5 treated DNA was performed using the Monarch PCR and DNA clean-up kit (NEB T1030S) following a 5:1 ratio of Binding Buffer:Sample.
We then build libraries using customized NextSeq primers and Kapa HiFi HotStart ReadyMix (Roche, 07958927001). Libraries were sequenced on an Illumina HiSeq 4000 with paired-end reads of 50 bases.

tag: background

value: Embryonic Trunk

tag: embryonic stage

tag: genotype

tag: gfp status

value: GFP-

tag: biological replicate


title: ATACseq-T-E145-Col2a1GFP-GFPn-R2

tag: tissue


title: WG_MAD.replicate_13.RNAseq


title: 20210327_AIID11_7

label_protocol: Nanostring with nCounter Analysis System

value: M

tag: age


title: 20210327_AIID11_5

value: F

value: MILD


title: ATACseq-T-E145-Col2a1GFP-GFPp-R1

value: GFP+


title: WG_MAD.replicate_11.RNAseq


title: 20210327_AIID11_4


title: 20210327_AIID11_6


title: 20210327_AIID11_3


title: 20210327_AIID11_2


title: 20210327_AIID11_1


title: ATACseq-L-E145-Col2a1GFP-GFPn-R2

source_name: Embryonic Limb Bud

value: Embryonic Limb Bud


title: WG_MAD.replicate_10.RNAseq


title: ATACseq-L-E145-Col2a1GFP-GFPn-R1


title: 20210327_AIID11_12

value: NEG


title: Phase-I D0-1

description: m6A of mouse PBMC


title: ATACseq-L-E145-Col2a1GFP-GFPp-R2


title: 20210227_AIID09_12


title: 20210227_AIID09_10


title: 20210227_AIID09_11


title: WG_MAD.replicate_7.RNAseq


title: ATACseq-T-E145-Col2a1GFP-GFPp-R2


title: WG_MAD.replicate_12.RNAseq


title: WG_MAD.replicate_6.RNAseq


title: 20210227_AIID09_9


title: 20210227_AIID09_8


title: RNAseq-T-E145-Col2a1GFP-GFPn-R2

data_processing:
NextSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q30 -m15). Unstranded reads were then mapped to GRCm39/mm39. We used STAR v2.7.2b with a filtered GTF (see Genomic data section in Darbellay et al.) allowing to get a gene quantification simultaneously (--outSAMstrandField intronMotif --sjdbOverhang '99' --sjdbGTFfile $gtfFile --quantMode GeneCounts --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1). Coverage was computed with Bedtools v2.28.0 using uniquely mapped reads (NH:i:1 tag). When indicated, coverage profiles represent an average of the replicates, this was done by dividing each replicate by the number of millions of uniquely mapped reads (for normalization) and calculating the average coverage.
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
After sorting, cells were centrifuged for 5′ at 400 × g at 4 °C, supernatant was discarded, and cells frozen at −80 °C. Two biological replicates of 1.5 × 105 cells each were used to extract total RNA using RNeasy Micro Kit (Qiagen,169030531).
SMART-Seq v4 kit (Clontech, 634893) was used for the reverse transcription and cDNA amplification according to the manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using Nextera XT (Illumina, FC-131-1096). Libraries were sequenced on an Illumina HiSeq 4000 with single-end reads of 50 bases.


title: WG_MAD.replicate_5.RNAseq


title: RNAseq-T-E145-Col2a1GFP-GFPn-R1


title: 20210227_AIID09_7


title: WG_MAD.replicate_4.RNAseq


title: 20210327_AIID11_11


title: 20210227_AIID09_6


title: 20210227_AIID09_5


title: 20210227_AIID09_4


title: WG_MAD.replicate_9.RNAseq


title: RNAseq-T-E145-Col2a1GFP-GFPp-R1


title: WG_MAD.replicate_3.RNAseq


title: 20210227_AIID09_3


title: RNAseq-T-E145-Col2a1GFP-GFPp-R2


title: 20210327_AIID11_10


title: 20210227_AIID09_1


title: 20210226_AIID10_12


title: 20210226_AIID10_11


title: ATACseq-L-E145-Col2a1GFP-GFPp-R1


title: 20210226_AIID10_10


title: RNAseq-L-E145-Col2a1GFP-GFPn-R2


title: WG_MAD.replicate_2.RNAseq


title: WG_MAD.replicate_1.RNAseq


title: RNAseq-L-E145-Col2a1GFP-GFPn-R1


title: WG_RAD.replicate_46.RNAseq

source_name: retroperitoneal adipose

value: retroperitoneal adipose


title: RNAseq-L-E145-Col2a1GFP-GFPp-R2


title: 20210226_AIID10_7


title: 20210226_AIID10_8


title: 20210227_AIID09_2


title: WG_RAD.replicate_45.RNAseq


title: 20210226_AIID10_6


title: RNAseq-L-E145-Col2a1GFP-GFPp-R1


title: 20210226_AIID10_5


title: WG_RAD.replicate_43.RNAseq


title: WG_RAD.replicate_44.RNAseq


title: 20210226_AIID10_3


title: scRNAseq-L-E145-Col2a1GFP

library_source: transcriptomic single cell

data_processing: used for validation

growth_protocol: Limbs and trunks from E14.5 mouse embryos were microdissected in PBS and a single cell suspention was produced.

extract_protocol: Cells from a single-cell suspension of dissociated Col2a1EGFP/EGFP E14.5 limbs were counted and processed on a Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 following the manufacture’s protocol (10X Genomics, PN-1000075). Library was then sequenced on an Illumina HiSeq 4000 with paired-end reads of 28/90 bases.

value: Full limb (bulk)


title: 20210226_AIID10_2


title: 20210226_AIID10_1


title: Uninfected, Knockout, Replicate3

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: GRCm38
Supplementary files format and content: Tab delimited file (txt) for raw hit counts

molecule: polyA RNA

source_name: cervicovaginal tissues

extract_protocol:
Trizol
polyA capture mRNA-seq

value: cervicovaginal tissues

tag: strain

value: IFNe KD

tag: treatment

value: Depo-Provera


title: Uninfected, Knockout, Replicate2


title: 20210219_AIID06_12


title: WG_RAD.replicate_41.RNAseq


title: Uninfected, Knockout, Replicate1


title: WG_RAD.replicate_42.RNAseq


title: 20210219_AIID06_11


title: 20210219_AIID06_9


title: 20210219_AIID06_10


title: 20210226_AIID10_9


title: WG_RAD.replicate_40.RNAseq


title: Uninfected, WildType, Replicate3

value: WT


title: 20210219_AIID06_8


title: 20210219_AIID06_6


title: WG_RAD.replicate_39.RNAseq


title: 20210226_AIID10_4


title: Uninfected, WildType, Replicate2


title: WG_RAD.replicate_38.RNAseq


title: Uninfected, WildType, Replicate1


title: WG_RAD.replicate_37.RNAseq


title: E13.5 Osr1 GCE/+ scRNAseq

city: Berlin

first: Pedro

last: Vallecillo García

state: Berlin

address: Augustenburger Platz 1

department: Hematology and Oncology

country: Germany

institute: Charité Berlin

data_processing:
The ~58 M sequencing reads generated were mapped against the primary assembly of the mouse genome mm10, for which we included an additional synthetic sequence encompassing the eGFPCreERt2 and PGK‐Neo cassettes corresponding to the Osr1GCE allele, using the STARsolo algorithm from STAR v2.7.5c (parameters: ‐‐solotype CB_UMI_Simple; ‐‐sjdbOverhang 97; ‐‐soloCBstart 1; ‐ ‐soloCBlen 16; ‐‐soloUMIstart 17; ‐‐soloUMIlen 12; ‐‐soloStrand Forward; ‐‐outSAMtype BAM SortedByCoordinate; ‐‐outMultimapperOrder Random; ‐‐outSAMattributes NH HI NM MD AS nM CR CB CY UR UB UY GX GN). The primary comprehensive gene model from the GENCODE vM25, excluding pseudogenes and small non‐coding RNA genes but including the additional Osr1GCE allele, was used as reference annotation (‐‐sjdbGTFfile) and the 10X Chromium barcode whitelist v3 (3M February 2018) was provided for error correction and demultiplexing of cell barcodes (‐‐soloCBwhitelist), while allowing multiple matches in whitelist with no more than one mismatched base (‐‐soloCBmatchWLtype 1MM_multi).
Following mapping, multi‐mapped reads were extracted from the alignment map according to the NH tag using SAMtools v1.10 and intersected against the gene annotation model using BEDtools bamtobed (parameters: ‐tag HI; ‐split) and intersect (parameters: ‐s; ‐wa; ‐wb; ‐loj) v2.29.2. Multi‐mapped reads that were found to overlap with a single gene were retrieved and merged with the uniquely‐mapped reads, resulting in a total of ~48M aligned reads (83.1% of initial sequencing reads).
Next, reads mapped on genes were counted using featureCounts v2.0.1 (parameters: ‐M; ‐s 1) according to first exon features (‐t exon) and then transcript features (‐t transcript) to include reads that originated from introns (pre‐mRNAs) as well.
Gene counting at the UMI level per cell was performed using STARsolo error‐corrected barcodes and UMI‐tools count v1.0.0, while using the directional method to group reads per UMI with a maximum hamming distance of 1 (parameters: ‐‐ extract‐umi‐method=tag; ‐‐umi‐tag=UR; ‐‐cell‐tag=CB; ‐‐method=directional; ‐‐per‐gene; ‐‐per‐cell).
The resulting count matrix was then parsed to exclude low‐quality cells (< 600 counts, < 500 genes and >= 10% mitochondrial counts) and sparse genes (expressed in < 0.05% cells, i.e. < 4 cells). The 6849 cells that remained after filtering, with a median number of counts per cell of 3473 and covering 21,412 genes for a median number of genes per cell of 1844, were further analyzed using Pegasus v1.0.0.
Assembly: mm10
Supplementary files format and content: Processed data files correspond to the raw counts of the 6849 cells used for downstream analysis, including (i) the list of cell barcodes; (ii) the list of gene features; and (iii) the sparse matrix in MatrixMarket format in which the first column contains the gene ID (ordered according to the rows of the barcodes file), the second column contains the cell ID (ordered according to the rows of the features file), and the third column contains the UMI count.

source_name: Mesenchymal cells

extract_protocol:
Axillary, cervical and inguinal regions of a E13.5 Osr1 GCE/+  embryo were extracted, minced and digested using a collagenase A solution in growth medium. Cell suspensions were stained with propidium iodine prior FACS. GFP-expressing live cells were isolated using a FACS Aria II device and collected directly into Dulbecco´s Modified Eagle Medium containing 4.5 g/l glucose and 10% fetal calf serum.
10,000 collected cells were run using the 10x Chromium (10x Genomics) system with the Chromium Single Cell 3’ chemistry V3 Kit according to the manufacturer's recommendations. Libraries were sequenced on an Illumina HiSeq 4000 device using the following read specifications: 8‐bp index, 28‐bp read 1 (16‐bp barcode and 12‐bp UMI), and 98‐bp strand‐specific read 2.

value: Axillary, cervical and inguinal regions

tag: developmental stage

value: Heterozygous


title: 20210219_AIID06_4

tag: gender


title: 20210219_AIID06_2

tag: severity


title: 20210219_AIID06_1


title: WG_RAD.replicate_36.RNAseq


title: WG_RAD.replicate_35.RNAseq


title: 20210218_AIID08_12


title: WG_RAD.replicate_34.RNAseq


title: 20210219_AIID06_7


title: 20210218_AIID08_11


title: 20210218_AIID08_10


title: U2OS pQ CFZ-1

city: Solna

first: Xuexin

last: Li

address: Tomtebodavägen 23A

department: Department of Medical Biochemistry and Biophysics

description:
DH_34
CFZ_Raw_Counts.txt
CFZ_Metadata.txt

data_processing:
Sequence alignment was performed using STAR
Gene quantification was performed using featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw gene counts for each sample

extract_protocol:
RNA was extracted using Agilent Absolutely RNA Miniprep Kit following the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
The sequencing library was constructed with the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen), and approximately 10 million reads were obtained per sample by Illumina sequencing.

tag: cell line

tag: cell type

value: osteosarcoma cells

value: PolyQ rexpressing

value: CFZ

tag: time

value: Day 8


title: U2OS pQ CFZ-2

description:
DH_35
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: 20210218_AIID08_9

value: M


title: 20210218_AIID08_6

value: MILD


title: 20210218_AIID08_8


title: U2OS WT CFZ-3

description:
DH_33
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: 20210218_AIID08_7


title: WG_RAD.replicate_33.RNAseq


title: WG_RAD.replicate_31.RNAseq


title: 20210219_AIID06_3


title: 20210218_AIID08_5

value: F


title: 20210218_AIID08_2


title: 20210218_AIID08_3


title: 20210218_AIID08_4


title: 20210219_AIID06_5


title: WG_RAD.replicate_30.RNAseq


title: U2OS pQ CFZ-3

description:
DH_36
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: U2OS WT CFZ-2

description:
DH_32
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: U2OS WT CFZ-1

description:
DH_31
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: 20210218_AIID08_1


title: WG_RAD.replicate_28.RNAseq


title: U2OS pQ D8-3

description:
DH_30
CFZ_Raw_Counts.txt
CFZ_Metadata.txt

value: NT


title: 20210217_AIID07_12

value: NEG


title: 20210217_AIID07_11


title: WG_RAD.replicate_27.RNAseq

value: retroperitoneal adipose


title: 20210217_AIID07_9


title: WG_RAD.replicate_26.RNAseq


title: 20210217_AIID07_10


title: WG_RAD.replicate_25.RNAseq


title: 20210217_AIID07_8


title: U2OS pQ D1-3

description:
DH_27
CFZ_Raw_Counts.txt
CFZ_Metadata.txt

value: Day 1


title: 20210217_AIID07_7


title: 20210217_AIID07_6


title: WG_RAD.replicate_21.RNAseq


title: 20210217_AIID07_4


title: 20210217_AIID07_3


title: 20210217_AIID07_2


title: U2OS pQ D1-2

description:
DH_26
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: WG_RAD.replicate_20.RNAseq


title: WG_RAD.replicate_19.RNAseq


title: U2OS pQ D1-1

description:
DH_25
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: 20210217_AIID07_1


title: 20210205_AIID04_12


title: U2OS pQ NT-3

description:
DH_24
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: 20210205_AIID04_10


title: WG_RAD.replicate_16.RNAseq


title: U2OS pQ D8-2

description:
DH_29
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: 20210205_AIID04_8


title: 20210205_AIID04_9


title: U2OS pQ D8-1

description:
DH_28
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: 20210205_AIID04_6


title: 20210217_AIID07_5


title: U2OS pQ NT-1

description:
DH_22
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: WG_RAD.replicate_14.RNAseq

description:
whole.Pig.PCG.TPM.xls
whole.Pig.TUCP.TPM.xls
whole.Pig.lncRNA.TPM.xls
whole.Pig.PCG.counts.xls
whole.Pig.TUCP.counts.xls
whole.Pig.lncRNA.counts.xls


title: 20210205_AIID04_5

description: NanoString nCounter Immunology panels, NS Immunology v2C2328


title: 20210205_AIID04_3


title: 20210205_AIID04_4


title: 20210205_AIID04_2


title: WG_RAD.replicate_13.RNAseq


title: WL_ULB.replicate_10.hic

description: whole.samples.ABindex.results.txt.gz

data_processing:
Contacts matrix were generated by using juicer tools.
TADs were identified using deDoc.
Compartment A/B were defined by ABindex.
Susscrofa11.1
TAD files
ABindex files

extract_protocol:
1 g adipose tissue were pulverized, and 37% formaldehyde was added to obtain a final concentration of 4% for chromatin cross-linking. Mixture were incubated at room temperature (20–25℃) for 30 minutes, then glycine was added to obtain a final concentration of 0.25 mol/L to quench the formaldehyde. The mixture was then centrifuge at 1,500×g for 10 min at room temperature, and sediment was added the lysis buffer and homogenized. Homogenate was centrifuge at 5,000×g for adipocytes sediment. Nuclei of formaldehyde fixed adipose tissue were permeabilized and DNA was digested with 200 units of MboI (a 4-cutter restriction enzyme) for one hour at 37℃. The restriction fragment overhangs were filled and labbled by biotinylated nucleotides, then ligated in a small volume.
After crosslink. reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina NovaSeq 6000 sequencing.

value: upper layer of backfat


title: WL_ULB.replicate_9.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_18.RNAseq


title: 20210205_AIID04_11


title: WG_RAD.replicate_11.RNAseq


title: U2OS pQ NT-2

description:
DH_23
CFZ_Raw_Counts.txt
CFZ_Metadata.txt


title: WL_ULB.replicate_7.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210128_AIID03_12


title: 20210128_AIID03_11


title: 20210205_AIID04_7


title: 20210128_AIID03_10


title: 20210128_AIID03_9


title: WL_ULB.replicate_6.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_10.RNAseq


title: WG_RAD.replicate_15.RNAseq


title: 20210128_AIID03_8


title: 20210128_AIID03_7


title: WG_RAD.replicate_8.RNAseq


title: 20210128_AIID03_5


title: 20210128_AIID03_6


title: WL_ULB.replicate_4.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210205_AIID04_1


title: WL_ULB.replicate_5.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210128_AIID03_4


title: WL_ULB.replicate_8.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_7.RNAseq


title: WL_ULB.replicate_3.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_6.RNAseq


title: WL_ULB.replicate_2.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210121_AIID02_12


title: 20210128_AIID03_2


title: WG_RAD.replicate_9.RNAseq


title: WG_RAD.replicate_5.RNAseq


title: 20210121_AIID02_11


title: WG_RAD.replicate_4.RNAseq


title: 20210121_AIID02_8


title: 20210121_AIID02_6


title: WL_MAD.replicate_10.hic

description: whole.samples.ABindex.results.txt.gz

value: mesenteric adipose


title: WG_RAD.replicate_2.RNAseq


title: WG_RAD.replicate_3.RNAseq


title: 20210128_AIID03_3


title: WG_GOM.replicate_46.RNAseq

value: greater omentum fat


title: WG_RAD.replicate_1.RNAseq


title: WL_MAD.replicate_7.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210121_AIID02_1


title: 20210121_AIID02_3


title: 20210121_AIID02_4


title: WL_MAD.replicate_6.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_MAD.replicate_8.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210128_AIID03_1


title: 20210121_AIID02_5


title: WL_ULB.replicate_1.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_45.RNAseq


title: WL_MAD.replicate_5.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210121_AIID02_10


title: WG_GOM.replicate_44.RNAseq


title: 20210113_AIID01_11


title: 20210113_AIID01_12


title: 20210113_AIID01_9


title: 20210113_AIID01_10


title: WL_MAD.replicate_4.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_43.RNAseq


title: 20210113_AIID01_7


title: 20210121_AIID02_9


title: 20210113_AIID01_6


title: 20210121_AIID02_7


title: 20210113_AIID01_4


title: WG_GOM.replicate_42.RNAseq


title: WL_RAD.replicate_10.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_MAD.replicate_2.hic

description: whole.samples.ABindex.results.txt.gz


title: 20210113_AIID01_5


title: 20210113_AIID01_3


title: WL_MAD.replicate_1.hic

description: whole.samples.ABindex.results.txt.gz


title: 3’-RNA_R2_DNA

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

data_processing:
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to reference RNA with botie2 as default parameters
calulate reverse transcript stop sites as icshape-pipe
calculate icSHAPE score as icshape-pipe
Assembly: retrotransposons
Supplementary files format and content: tab-delimited text files for icshape file
Supplementary files format and content: smartshape score
Library strategy: icSHAPE

organism: Bombyx mori

source_name: Bombyx mori

growth_protocol: RNA was prepared as in the cryo-EM studies in three conditions: apo RNA, RNA-protein complex, and RNA-DNA-protein ternary complex.

extract_protocol:
35 μl of buffer RLT was added to stop the reaction on ice. The RNA was purified with an RNeasy mini column and eluted with 50 μl of pure water twice.
The modified RNA was incubated with DIBO-biotin at 37°C for 2 hr and then purified with the Zymo RNA kit. Reverse transcription was performed for each sample with its specific primers. Then, all the samples were merged after RNA-cDNA hybrid purification. It was then subjected to RNase I treatment and biotin enrichment for the modified RNA-cDNA hybrid. After RNA degradation, linker ligation, and the second DNA chain synthesis, libraries were amplified using qPCR with about 14-16 cycles.

treatment_protocol: In each condition, the RNA sequence has three types: 5’ORF, 3UTR, and 5’ORF-linker-3’UTR chimeric. We design reverse transcription primers for the nine RNA samples with specific barcodes. RNA modification reagent NAI-N3 was added to the nine samples to a final concentration 100 mM independently, mixed gently, and incubated at 37°C for 10 min.

value: Bombyx mori

tag: group

value: RNA-DNA-protein ternary complex


title: WG_GOM.replicate_41.RNAseq


title: 5’-RNA_R2_DNA


title: 5’-RNA_R2

value: RNA-protein complex


title: WG_GOM.replicate_40.RNAseq


title: 3’-RNA_R2


title: WG_GOM.replicate_38.RNAseq


title: 3’-RNA

value: Apo-RNA


title: WG_GOM.replicate_39.RNAseq


title: 20210113_AIID01_1


title: 20210113_AIID01_2


title: WL_RAD.replicate_9.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_MAD.replicate_3.hic

description: whole.samples.ABindex.results.txt.gz


title: 5’-RNA


title: L-RNA_R2


title: L-RNA_R2_DNA


title: WL_RAD.replicate_8.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_37.RNAseq


title: WL_RAD.replicate_7.hic

description: whole.samples.ABindex.results.txt.gz


title: L-RNA


title: 333: P33, rectum, tumor, untreated, scRNA-seq

city: Guangzhou

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software vcellranger-5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: CRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: rectum

extract_protocol:
Tumor biopsy samples were first stored in liquid nitrogen with the SenotechTM Tissue Storage Buffer(#JZ-SC-5802，Senotech Genomics, Shanghai, China)or proceed directly to tissue disassociation. Heat the frozen tissue in a 37 ° C water bath,then transfer the tissue samples together with the freezed-storage solution to a new 15mL centrifuge tube, add 5mL preheated RPMI-1640 medium (Gibco).Centrifuge at room temperature at 300×g for 5min to remove the supernatant without disturbing the tissue sample at the bottom of the centrifuge tube.The tissue samples enzymatically digested with Neuronal Isolation Enzyme(Thermo Scientific) for 20-30 min at 37 C according to the manufacturer’s protocol.The dissociated cells were next passed through a 40-mm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. The recommended cell washing and resuspension solution is 1X PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 µg/ml).
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Kit v2 or v3 from 10x Genomics, following the manufacturer’s instructions. In brief, single cells were  resuspended in PBS containing 0.04% BSA to a final concentration of 500~1,200 cells/ml as determined by Countess 3 Automated Cell Counters(Invitrogen). ~10,000 cells were captured in droplets to generate nanoliter-scale Gel bead in EMulsion (GEMs). GEMs were then reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad) programmed at 53C for 45 min, 85C for 5 min, and held at 4C. After reverse transcription and cell barcoding, emulsions were broken and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Fisher Scientific), followed by PCR amplification. Amplified cDNA was fragmented and end-repaired, double-sided size-selected, PCR-amplified with sample indexing primers, and double-sided size-selected or RNA-seq library construction. Libraries prepared according to the manufacturer’s user guide were then purified and profiled for quality assessment. Single-cell RNA libraries were sequenced by an Illumina NovaSeq 6000 or BGISEQ DNBSEQ-T7 sequencer with 150 bp paired-end reads.

tag: subject

value: Goblet cells

value: rectum

value: tumor

value: untreated


title: WG_GOM.replicate_36.RNAseq


title: 323: P32, colon, tumor, untreated, scRNA-seq

description: 10x Genomics

source_name: colon

value: colon


title: 313: P31, colon, tumor, untreated, scRNA-seq

description: 10x Genomics


title: WL_RAD.replicate_6.hic

description: whole.samples.ABindex.results.txt.gz


title: 321: P32, colon, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_34.RNAseq


title: WG_GOM.replicate_35.RNAseq


title: 322: P32, colon, normal, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics

value: normal


title: WL_RAD.replicate_5.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_33.RNAseq


title: 312: P31, colon, normal, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WL_RAD.replicate_4.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_RAD.replicate_3.hic

description: whole.samples.ABindex.results.txt.gz


title: 311: P31, colon, tumor, anti-PD-1, scRNA-seq

description: 10x Genomics


title: 303: P30, colon, tumor, untreated, scRNA-seq

description: 10x Genomics


title: 302: P30, colon, normal, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_31.RNAseq


title: WG_GOM.replicate_30.RNAseq


title: WL_RAD.replicate_2.hic

description: whole.samples.ABindex.results.txt.gz


title: 292: P29, colon, normal, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WL_RAD.replicate_1.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_29.RNAseq


title: 301: P30, colon, tumor, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WL_GOM.replicate_10.hic

description: whole.samples.ABindex.results.txt.gz


title: 282: P28, colon, normal, anti-PD-1, scRNA-seq

description: 10x Genomics


title: 291: P29, colon, tumor, anti-PD-1, scRNA-seq

description: 10x Genomics


title: 283: P28, colon, tumor, untreated, scRNA-seq

description: 10x Genomics


title: 281: P28, colon, tumor, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_28.RNAseq


title: 273: P27, colon, tumor, untreated, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_27.RNAseq


title: WL_GOM.replicate_8.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_GOM.replicate_9.hic

description: whole.samples.ABindex.results.txt.gz


title: 271: P27, colon, tumor, anti-PD-1, scRNA-seq

description: 10x Genomics


title: 272: P27, colon, normal, anti-PD-1, scRNA-seq

description: 10x Genomics


title: 261: P26, colon, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WL_GOM.replicate_7.hic

description: whole.samples.ABindex.results.txt.gz


title: 253: P25, colon, tumor, untreated, scRNA-seq

description: 10x Genomics


title: 252: P25, colon, normal, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: 251: P25, colon, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WL_GOM.replicate_6.hic

description: whole.samples.ABindex.results.txt.gz


title: 243: P24, colon, tumor, untreated, scRNA-seq

description: 10x Genomics


title: 241: P24, colon, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WL_GOM.replicate_5.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_GOM.replicate_4.hic

description: whole.samples.ABindex.results.txt.gz


title: 213: P21, rectum, tumor, untreated, scRNA-seq

description: 10x Genomics


title: 233: P23, colon, tumor, untreated, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_23.RNAseq


title: WG_GOM.replicate_25.RNAseq


title: WG_GOM.replicate_26.RNAseq


title: WG_GOM.replicate_24.RNAseq


title: WG_GOM.replicate_22.RNAseq


title: 211: P21, rectum, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_21.RNAseq


title: WL_GOM.replicate_3.hic

description: whole.samples.ABindex.results.txt.gz


title: 192: P19, colon, normal, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: 191: P19, colon, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WL_GOM.replicate_2.hic

description: whole.samples.ABindex.results.txt.gz


title: 152: P15, colon, normal, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WL_MAD.replicate_9.hic

description: whole.samples.ABindex.results.txt.gz


title: 151: P15, colon, tumor, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_20.RNAseq


title: WL_GOM.replicate_1.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_19.RNAseq


title: 122: P12, colon, normal, anti-PD-1, scRNA-seq

description: 10x Genomics


title: 121: P12, colon, tumor, anti-PD-1, scRNA-seq

description: 10x Genomics


title: WG_ULB.replicate_46.hic

description: whole.samples.ABindex.results.txt.gz

source_name: upper layer of backfat


title: WG_GOM.replicate_18.RNAseq


title: 111: P11, colon, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WG_GOM.replicate_17.RNAseq


title: 112: P11, colon, normal, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics


title: WG_ULB.replicate_45.hic

description: whole.samples.ABindex.results.txt.gz


title: C1568

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

country: United Kingdom

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

data_processing:
Aligned to GRCh38.91 using HiSat2
Feature counting was carried out using htseq-count
Assembly: GRCh38.91

source_name: Peripheral Blood

extract_protocol:
RNeasy Blood & Tissue Kits (Qiagen)
RNA libraries were prepared using DNBseq sequencing technology

value: Peripheral Blood

tag: patientid

tag: disease state

value: poor risk AML patient


title: WG_ULB.replicate_44.hic

description: whole.samples.ABindex.results.txt.gz


title: C1706

source_name: Unknown

value: Unknown


title: WG_ULB.replicate_42.hic

description: whole.samples.ABindex.results.txt.gz


title: C1099


title: C1520

source_name: Bone Marrow

value: Bone Marrow


title: WG_GOM.replicate_15.RNAseq

source_name: greater omentum fat


title: WG_GOM.replicate_16.RNAseq


title: C0982


title: C0210


title: 141: P14, colon, tumor, Anti-PD-1+celecoxib, scRNA-seq

description: 10x Genomics

tag: genotype


title: T8769


title: T8546


title: WG_ULB.replicate_41.hic

description: whole.samples.ABindex.results.txt.gz

value: upper layer of backfat


title: WG_GOM.replicate_13.RNAseq


title: WG_ULB.replicate_39.hic

description: whole.samples.ABindex.results.txt.gz


title: T8725


title: T8169


title: WG_GOM.replicate_12.RNAseq


title: WG_ULB.replicate_38.hic

description: whole.samples.ABindex.results.txt.gz


title: T7880


title: WG_ULB.replicate_37.hic

description: whole.samples.ABindex.results.txt.gz


title: T7714


title: WG_GOM.replicate_11.RNAseq


title: WG_GOM.replicate_10.RNAseq


title: WG_GOM.replicate_14.RNAseq


title: T6733


title: WG_ULB.replicate_36.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_9.RNAseq


title: T5876


title: T6391


title: T6083


title: WG_GOM.replicate_8.RNAseq


title: WG_ULB.replicate_34.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_ULB.replicate_40.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_GOM.replicate_7.RNAseq


title: WG_ULB.replicate_32.hic

description: whole.samples.ABindex.results.txt.gz


title: T5306


title: T5656


title: T8401


title: T5896


title: WG_GOM.replicate_6.RNAseq


title: T1553


title: WG_GOM.replicate_5.RNAseq


title: T1929


title: WG_ULB.replicate_31.hic

description: whole.samples.ABindex.results.txt.gz


title: T2410

source_name: Leucopheresis

value: Leucopheresis


title: T6810


title: WG_ULB.replicate_27.hic

description: whole.samples.ABindex.results.txt.gz


title: T1809


title: T2353


title: WG_GOM.replicate_4.RNAseq

value: greater omentum fat


title: WG_ULB.replicate_25.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_ULB.replicate_33.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_ULB.replicate_24.hic

description: whole.samples.ABindex.results.txt.gz


title: T5062


title: WG_GOM.replicate_2.RNAseq


title: WG_GOM.replicate_3.RNAseq


title: R9605


title: T0990


title: R9527


title: 20210121_AIID02_2

source_name: PBMC

value: M


title: WG_ULB.replicate_23.hic

description: whole.samples.ABindex.results.txt.gz


title: R9150


title: NC_ULB.replicate_12.RNAseq


title: R9090


title: WG_ULB.replicate_22.hic

description: whole.samples.ABindex.results.txt.gz


title: R9089


title: WG_ULB.replicate_21.hic

description: whole.samples.ABindex.results.txt.gz


title: R7773


title: WG_ULB.replicate_20.hic

description: whole.samples.ABindex.results.txt.gz


title: R6357


title: R7026


title: R6275


title: T1663


title: NC_ULB.replicate_5.RNAseq


title: WG_ULB.replicate_19.hic

description: whole.samples.ABindex.results.txt.gz


title: T1225


title: NC_ULB.replicate_7.RNAseq


title: R6171


title: WG_ULB.replicate_18.hic

description: whole.samples.ABindex.results.txt.gz


title: R6679


title: R6490


title: WG_GOM.replicate_1.RNAseq


title: NC_ULB.replicate_2.RNAseq


title: R5150


title: R5278


title: R3455


title: NC_MAD.replicate_12.RNAseq

source_name: mesenteric adipose

value: mesenteric adipose


title: WG_ULB.replicate_16.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_ULB.replicate_9.RNAseq


title: R3730


title: NC_MAD.replicate_11.RNAseq


title: WG_ULB.replicate_15.hic

description: whole.samples.ABindex.results.txt.gz


title: F9788


title: R3054


title: F9681


title: F9056


title: WG_ULB.replicate_14.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_MAD.replicate_9.RNAseq


title: NC_MAD.replicate_10.RNAseq


title: F9141


title: WG_ULB.replicate_13.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_MAD.replicate_8.RNAseq


title: F8903


title: x7892


title: NC_MAD.replicate_7.RNAseq


title: WG_ULB.replicate_17.hic

description: whole.samples.ABindex.results.txt.gz


title: F8757


title: WG_ULB.replicate_12.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_ULB.replicate_11.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_MAD.replicate_6.RNAseq


title: NC_MAD.replicate_5.RNAseq


title: WG_ULB.replicate_9.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_MAD.replicate_4.RNAseq


title: WG_ULB.replicate_8.hic

description: whole.samples.ABindex.results.txt.gz


title: mouse melanoma - WT31 subline after 5 passages - biological repilcate 1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Gene expression data from in vitro cultured WT31_Passage mouse melanoma cells, subline replicate 1.
WT31_Passage_5/1_31

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: GRCm38.p6
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

source_name: malignant melanoma cells

growth_protocol: Parental WT31 ("WT31_Urspungszellen") and its subline WT31_P5 ("WT31_Passage_5") were maintained in RPMI 1640 media (Thermo Fisher Scientific, MA, USA) with 10% (v/v) fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin at 37° C, 5% CO2.  After thawing the cells were not passaged more than three times and maximum culture time prior to RNA extraction was one week.  The cells were seeded at 4.5 e-10 cells. The next day cells were detached with enzyme free cell dissociation buffer and RNA was extracted.

extract_protocol:
Total RNA from sub-confluent (50%), cultured melanoma cells was extracted with innuPREP RNA Mini Kit (845-KS-2080250, Analytik Jena, Germany) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Cultured melanoma cells were not treated by any drugs.


title: mouse melanoma - WT31 subline after 5 passages - biological repilcate 5

description:
Gene expression data from in vitro cultured WT31_Passage mouse melanoma cells, subline replicate 5.
WT31_Passage_5/5_35


title: mouse melanoma - WT31 subline after 5 passages - biological repilcate 3

description:
Gene expression data from in vitro cultured WT31_Passage mouse melanoma cells, subline replicate 3.
WT31_Passage_5/3_33


title: mouse melanoma - WT31 - parental biological repilcate 4

description:
Gene expression data from in vitro cultured WT31 mouse melanoma cells, parental replicate 4.
WT31_Ursprungszellen_5_29


title: mouse melanoma - WT31 subline after 5 passages - biological repilcate 4

description:
Gene expression data from in vitro cultured WT31_Passage mouse melanoma cells, subline replicate 4.
WT31_Passage_5/4_34


title: mouse melanoma - WT31 - parental biological repilcate 5

description:
Gene expression data from in vitro cultured WT31 mouse melanoma cells, parental replicate 5.
WT31_Ursprungszellen_6_30


title: mouse melanoma - WT31 subline after 5 passages - biological repilcate 2

description:
Gene expression data from in vitro cultured WT31_Passage mouse melanoma cells, subline replicate 2.
WT31_Passage_5/2_32


title: mouse melanoma - WT31 - parental biological repilcate 3

description:
Gene expression data from in vitro cultured WT31 mouse melanoma cells, parental replicate 3.
WT31_Ursprungszellen_4_28


title: NC_MAD.replicate_3.RNAseq

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Tpm and counts matrixs were generated using R vresion 3.6.1.
AssemblySusscrofa11.1
Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 11.97 Gb high-quality data for each library.


title: mouse melanoma - WT31 - parental biological repilcate 1

description:
Gene expression data from in vitro cultured WT31 mouse melanoma cells, parental replicate 1.
WT31_Urpsrungszellen_1_26


title: MEF_rep3

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description:
replicates were merged for processing
EP_and_PP.MEF.network.xls

data_processing:
Library strategy: RIC-seq
Illumina bcl2fastq (v2.16) conversion software used for basecalling.
After sequencing, RIC-seq reads were aligned to the human genome using the RICpipe program with minor revisions. Briefly, RIC-seq reads were first mapped to the reference genome (assembly version: hg19 for human and mm9 for mouse) using the STAR software (v2.5.2b). The parameters were set as: --runMode alignReads --genomeDir index --readFilesIn read.fq --outFileNamePrefix prefix --outReadsUnmapped Fastx --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --limitOutSJcollapsed 10000000 --limitIObufferSize 1500000000 --runThreadN 16 --alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterMatchNminOverLread 0.5 --outFilterScoreMinOverLread 0.5. Next, unmapped reads reported by STAR were aligned again to the reference genome by the bwa program (v0.7.17) with the following parameters: bwa mem -k 12 -T 15. Alignments from STAR and bwa were combined and sent to RICpipe for the subsequent analysis to extract chimeric reads.
Enhancer and promoter intervals for each cell are defined as previously described (Cai et al. Nature, 2020, 582(7812): 432-437.), using ChIP-seq data of H3K4me3, H3K4me1 and H3K27ac downloaded from the ENCODE or GEO database.
Using these defined promoter and enhancer regions, we adopted a Monte Carlo simulation strategy to detect significant enhancer-promoter interactions (P < 0.05, unique chimeric reads ≥ 2) as previously described.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: enhancer-promoter and promoter-promoter interaction networks in Excel format

source_name: mouse MEF cells

growth_protocol: GM12878 and K562 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Life Technologies; 15140). IMR-90 cells were grown in DMEM/F12 + Glutamax (Life Technologies; 10565) supplemented with 5 ng/ml fibroblast growth factor-basic (R&D), 1 μg/ml hydrocortisone hemisuccinate, 50 μg/ml ascorbic acid, 5 μg/ml rhInsulin, 2% fetal bovine serum and 100 U/ml penicillin/streptomycin. Human embryonic stem cells (WA01, Line H1) were obtained from Dr. Hongjie Yao laboratory and cultured according to the protocol from WiCell Research Institute. The hESCs were maintained in mTeSR1 medium (Stem Cell Technologies) in feeder-free conditions on hESC qualified Matrigel (BD Biosciences). mTeSR1 media was changed daily and cells were passaged every 6-8 days with 1 ml of ReLeSR (Stem Cell Technologies). hNPC cells were grown in DMEM/F12 + Glutamax (Life Technologies; 10565) supplemented with 20 ng/ml fibroblast growth factor-basic (R&D), 0.5× N-2, 0.5× B-27,  and 100 U/ml penicillin/streptomycin. MEF and HepG2 cells were grown in DMEM containing 10% fetal bovine serum plus 100 U/ml penicillin/streptomycin.

extract_protocol:
Cells were treated with micrococcal nuclease and proteinase K. Total RNA was extracted with TRIzol LS.
Total RNA was extracted, and rRNA was depleted with specific probes. After fragmentation, the biotin-marked RNA fragments were enriched with streptavidin magnetic beads, and converted into Illumina HiSeq X10 compatible libraries.

treatment_protocol: Cells were fixed with  PBS containing 1% formaldehyde, and then treated with 1/20 volume of 2.5 M glycine.

value: MEF


title: WG_ULB.replicate_7.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_MAD.replicate_2.RNAseq


title: NC_RAD.replicate_12.RNAseq

value: retroperitoneal adipose


title: WG_ULB.replicate_3.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_ULB.replicate_10.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_ULB.replicate_5.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF_rep1


title: IgG, replicate 1, scRNAseq [K3_IgG_Skin]

city: Chicago

first: Kyle

last: Amber

state: Illinois

address: 1735 W Harrison St. Lab 741

institute: Rush University Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control of all data sets was performed using Seurat (Version 3.0.0), Scrublet (Version 0.2.1).
Processed files were analyzed with Seurat V3.1.0,  Monocle (Version 2.101.), scEpath (Version 1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ear skin

growth_protocol: N/A. Primary cells were used in this study.

extract_protocol:
Blood was collected following anesthesia by retroorbital bleeding, immediately followed by RBC lysis (Biolegend). Skin from lesional skin harvested by punch biopsies and was enzymatically digested using the whole skin digestion kit (Miltenyi) per manufacturer instructions with modifications as below. Following addition of enzymes, samples were incubated in water bath at 37°C for two hours and shaken every 15 minutes. Mechanical dissociation by pipetting was only performed at the end of the incubation. Cells were then filtered using a 70 μM filter, centrifuged at 300g for 10 minutes at 4°C, washed and resuspended in 0.04% BSA/HBSS (ThermoFisher). Cell viability was immediately assessed by trypan blue (ThermoFisher) using the Countess 3 FL automated cell counter (ThermoFisher). Single cell suspensions were then processed for scRNA-seq (10X Genomics).
Library was performed according to the manufacture’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Sequencing was performed using a NovaSeq6000 (Illumina).

treatment_protocol: Mice were housed under specific pathogen-free conditions and were provided standard mouse chow and acidified drinking water ad libitum. Mice were conditioned at last 2 weeks prior to experiments, and were under 12h:12h light/dark cycles.

value: Skin cells

value: Ear skin

value: 6-8 weeks old

value: control rabbit IgG


title: EBA, replicate 1, scRNAseq [K4_EBA_Skin]

description: 10x Genomics

value: antigen affinity purified vWFA2-COL7 IgG


title: MEF_rep2


title: NC_RAD.replicate_11.RNAseq

source_name: retroperitoneal adipose


title: WG_ULB.replicate_2.hic

description: whole.samples.ABindex.results.txt.gz


title: IgG, replicate 1, scRNAseq [K1_IgG_WBC]

description: 10x Genomics

source_name: Peripheral blood

value: Whole blood cells

value: Peripheral blood


title: mouse melanoma - WT31 - parental biological repilcate 2

description:
Gene expression data from in vitro cultured WT31 mouse melanoma cells, parental replicate 2.
WT31_Ursprungszellen_2_27


title: WG_ULB.replicate_6.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_RAD.replicate_10.RNAseq


title: WG_ULB.replicate_1.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_36_wt_day-4_VC

city: Rochester

first: Francesco

last: Morandini

state: NY

address: 402 Hutchison Hall

institute: University of Rochester

data_processing:
Raw FASTQ files were evaluated for quality, adapter content and duplication rates with FastQC.
Reads were trimmed using TrimGalore!
Trimmed reads were aligned to the GRCm39 mouse genome assembly using Hisat2
The number of reads per gene was measured using the featureCounts function in the subread package
Assembly: GRCm39
Supplementary files format and content: Tab-delimited counts for samples in the TGFB experiment
Supplementary files format and content: Tab-delimited counts for samples in the timeline of reprogramming (TOR) experiment

source_name: Fibroblasts (Tail tip)

growth_protocol: Tail tip fibroblasts (TTF) were extracted from mice using Collagenase I (Sigma, C0130) and Dispase II (Sigma, D4693) and cultured in DMEM (Gibco, 11960085) containing 1% non-essential amino acids (Gibco, 11140035), 1% GlutaMax (Gibco, 35050061), 1% Sodium Pyruvate (Gibco, 11360039) and 10% fetal bovine serum (FBS, Hyclone, SH30088.03) at 37°C in hypoxic conditions (3% O2). Subsequently, fibroblasts were cultured and passaged (3 or less) according to standard protocols

extract_protocol:
Total RNA was extracted from cells using the Qiagen AllPrep DNA/RNA Micro Kit (New England Biolab) and protocols were followed.
The RNA-Seq library preparation and sequencing was done by Novogene (UK) Company Limited on an Illumina NovaSeq 6000 in 150 bp paired-end mode.

treatment_protocol:
Experiments for TGFb inhibitors used Ercc1(d/-) cells (4 week old female) and Ercc1(+/+) TTF cells (14 week old female)
Induction of the OSKM reprogramming factors in vitro followed treatment with doxycycline 2ug/ml in culture media for the specified time points. Enhanced reprogramming followed the same protocols but added fresh ascorbic acid (50ug/ml) and CHIR-99201 (3uM) as previously reported(Bar-Nur et al., 2014).

value: Fibroblasts (Tail tip)

tag: Sex

value: F

value: 22 weeks

value: D4 reprogramming+VC


title: WG_MAD.replicate_44.hic

first: jin

last: long

address: Hui ming

description: whole.samples.ABindex.results.txt.gz


title: NC_MAD.replicate_1.RNAseq


title: TOR_31_wt_day-2_VC

value: D2 reprogramming+VC


title: EBA, replicate 1, scRNAseq [K2_EBA_WBC]

description: 10x Genomics


title: NC_RAD.replicate_7.RNAseq


title: WG_MAD.replicate_46.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_34_wt_day-4_VC


title: NC_RAD.replicate_8.RNAseq


title: WG_MAD.replicate_43.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_RAD.replicate_6.RNAseq


title: TOR_28_wt_control_VC

value: D0 reprogramming+VC


title: TOR_27_wt_day-4

value: D4 reprogramming


title: WG_MAD.replicate_42.hic

description: whole.samples.ABindex.results.txt.gz

value: mesenteric adipose


title: TOR_35_wt_day-4_VC


title: TOR_32_wt_day-2_VC


title: NC_RAD.replicate_5.RNAseq


title: NC_RAD.replicate_9.RNAseq


title: TOR_33_wt_day-2_VC


title: NC_RAD.replicate_4.RNAseq


title: TOR_29_wt_control_VC


title: TOR_23_wt_day-2

value: D2 reprogramming


title: WG_MAD.replicate_41.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_24_wt_day-2


title: WG_MAD.replicate_39.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_30_wt_control_VC


title: TOR_21_wt_control

value: D0 reprogramming


title: TOR_20_wt_control


title: TOR_22_wt_day-2


title: TOR_19_wt_control


title: NC_RAD.replicate_2.RNAseq

value: retroperitoneal adipose


title: TOR_18_ercc1_day-4_VC

value: M

value: 8 weeks


title: NC_RAD.replicate_1.RNAseq


title: NC_RAD.replicate_3.RNAseq


title: TOR_26_wt_day-4


title: TOR_15_ercc1_day-2_VC


title: TOR_16_ercc1_day-4_VC


title: NC_GOM.replicate_10.RNAseq

value: greater omentum fat


title: TOR_25_wt_day-4


title: WG_MAD.replicate_34.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_14_ercc1_day-2_VC


title: WG_MAD.replicate_33.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_MAD.replicate_32.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_GOM.replicate_9.RNAseq


title: TOR_11_ercc1_control_VC


title: TOR_12_ercc1_control_VC


title: WG_MAD.replicate_37.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_MAD.replicate_38.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_13_ercc1_day-2_VC


title: WG_MAD.replicate_31.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_10_ercc1_control_VC


title: WG_MAD.replicate_30.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_MAD.replicate_29.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_7_ercc1_day-4


title: TOR_5_ercc1_day-2


title: NC_GOM.replicate_6.RNAseq


title: TOR_9_ercc1_day-4


title: TOR_8_ercc1_day-4


title: TOR_17_ercc1_day-4_VC


title: TOR_6_ercc1_day-2


title: NC_GOM.replicate_5.RNAseq


title: WG_MAD.replicate_28.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_3_ercc1_control


title: WG_MAD.replicate_27.hic

description: whole.samples.ABindex.results.txt.gz


title: TOR_1_ercc1_control


title: NC_GOM.replicate_2.RNAseq


title: TOR_2_ercc1_control


title: TOR_4_ercc1_day-2


title: TGFB_21_ercc1_A83-01

value: 4 weeks


title: TGFB_22_wt_TGFB

value: TGFB


title: WG_MAD.replicate_26.hic

description: whole.samples.ABindex.results.txt.gz


title: NC_GOM.replicate_3.RNAseq


title: NC_GOM.replicate_7.RNAseq


title: TGFB_17_ercc1_DMH-1


title: TGFB_24_wt_TGFB


title: NC_GOM.replicate_1.RNAseq


title: WG_MAD.replicate_23.hic

description: whole.samples.ABindex.results.txt.gz


title: TGFB_18_ercc1_DMH-1


title: WL_ULB.replicate_5.H3K27ac

data_processing:
H3K27ac ChIP-seq reads were mapped to the pig reference genome (Sscrofa 11.1) using BWA (version 0.7.15)
PCR duplicates were removed using Samtools (version 1.3.1).
Peaks were called using the SICER tool
Enhancers and super-enhancers were identified by ROSE algorithm
AssemblySusscrofa11.1
RE and SE files

extract_protocol:
Adipose tissue samples were fixed with 1% formaldehyde. Then samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin with average DNA length of 200–500 bp.
Half of the soluble chromatin was stored at -20°C for sequencing as input DNA, while the remaining was used for immunoprecipitation reacted with H3K27ac (ab4729, Abcam) antibodies. For both input DNA and immunoprecipitated DNA, each ChIP-seq library was sequenced on Illumina HiSeq X Ten platform to generate 150 bp paired-end reads.

value: upper layer of backfat

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: WL_ULB.replicate_7.H3K27ac

tag: tissue


title: TGFB_23_wt_TGFB

value: Fibroblasts (Tail tip)

value: F

tag: age


title: WG_MAD.replicate_19.hic

description: whole.samples.ABindex.results.txt.gz


title: TGFB_16_ercc1_DMH-1


title: WL_RAD.replicate_5.H3K27ac


title: NC_GOM.replicate_8.RNAseq


title: WG_MAD.replicate_24.hic

description: whole.samples.ABindex.results.txt.gz


title: TGFB_14_ercc1_vactoserib

value: Vacto


title: WG_MAD.replicate_20.hic

description: whole.samples.ABindex.results.txt.gz


title: TGFB_20_ercc1_A83-01


title: WL_RAD.replicate_7.H3K27ac


title: TGFB_15_ercc1_vactoserib


title: WG_MAD.replicate_17.hic

description: whole.samples.ABindex.results.txt.gz


title: TGFB_13_ercc1_vactoserib


title: TGFB_12_ercc1_repsox

value: Repsox


title: WL_RAD.replicate_4.H3K27ac


title: WL_RAD.replicate_1.H3K27ac


title: WG_MAD.replicate_15.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_MAD.replicate_16.hic

description: whole.samples.ABindex.results.txt.gz


title: TGFB_11_ercc1_repsox


title: TGFB_10_ercc1_repsox


title: TGFB_19_ercc1_A83-01


title: TGFB_8_ercc1_control

value: control


title: TGFB_9_ercc1_control


title: TGFB_7_ercc1_control


title: TGFB_6_wt-2_control

source_name: Fibroblasts (Skin)

value: Fibroblasts (Skin)

value: 14 weeks


title: WG_MAD.replicate_12.hic

description: whole.samples.ABindex.results.txt.gz

value: mesenteric adipose


title: WL_MAD.replicate_7.H3K27ac


title: WG_MAD.replicate_14.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_MAD.replicate_13.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_MAD.replicate_5.H3K27ac


title: TGFB_5_wt-2_control


title: TGFB_4_wt-2_control


title: WG_MAD.replicate_11.hic

description: whole.samples.ABindex.results.txt.gz


title: WL_MAD.replicate_4.H3K27ac


title: TGFB_2_wt_control


title: WL_GOM.replicate_5.H3K27ac


title: WL_GOM.replicate_7.H3K27ac


title: WG_MAD.replicate_10.hic

description: whole.samples.ABindex.results.txt.gz


title: TGFB_1_wt_control


title: TGFB_3_wt_control


title: WL_GOM.replicate_4.H3K27ac


title: Striatum, batch 4, single-cell multi-omics [scATAC-seq]

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
10x Genomics
tmp.repl1_atac.all.v2.all_peaks.npz
tmp.repl1_atac.all.v2_peaks.all.ygi
tmp.repl1_atac.all.v2.xgi
Batch 4 [scATAC-seq]

data_processing:
Illumina base call files for all libraries were demultiplexed and converted to FASTQ files using bcl2fastq 2.20.0.422 (Illumina). A filtered joint digital gene expression and chromatin accessibility matrix was generated against the 10x Genomics mm10-2020-A reference build (version 2020-A, Assembly: GRCm38, ENSEMBL release 98; Annotations: Gencode vM23) using a modified 10x Genomics CellRanger-ARC count pipeline (v2.0.0), which had the 20,000 cell limit of cell calling removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files; more in the 'processed_data_file_descriptions.txt'

source_name: Striatum

extract_protocol:
For single nuclei preparation, frozen striatum were placed into 500 µl Miltenyi Nuclei Extraction Buffer (Miltenyi 130-128-024) plus 0.8 U/µl RiboLock RNase Inhibitor (ThermoFisher EO0382) in a gentleMACS C tube (Miltenyi 130-093-237) on ice, and then nuclei were immediately extracted in batches of 4 through the “4C_nuclei_1” program on the MACS Dissociator. Nuclei were placed on ice and filtered through a 70 µm pluriStrainer Mini into a pre-chilled 2 ml tube, and the C tube was washed with an additional 500 µl cold Miltenyi Nuclei Extraction Buffer and filtered. Nuclei were spun down at 350 rcf at 4 °C for 5 minutes and resuspended in 80 µl cold PBS with 2% BSA and 1 U/µl RiboLock. Nuclei were counted (~4,000 nuclei/µl) and 60,000 nuclei from each of the 8 samples were mixed in a chilled 1.5 ml Eppendorf tube. The pooled nuclei were spun at 300 rcf at 4 °C for 3 minutes and resuspended in 30 µl 10x Genomics Nuclei Buffer with 1 U/µl RNase inhibitor. The pooled nuclei were counted once more to confirm counts (~10,000 nuclei/ul), single-cell suspension, and lack of debris.
Nuclei viability was assessed on a LUNA-FX7 automated cell counter (Logos Biosystems), and up to 40,000 nuclei (~5,000 from each sample) were loaded onto each of 4 lanes of a 10X Chromium microfluidic chip. Single nuclei capture and library preparation were performed using the 10X Chromium platform and according to the manufacturer’s protocol (#CG000388 Chromium Next GEM Single Cell Multiome ATAC + Gene Expression). Because the 10X chip was superloaded, to reduce duplicate reads arising from multiple PCR steps, the number of cycles was adjusted from the 10X protocol. After GEM generation, barcoded cDNA and transposed DNA fragments were pre-amplified using 6 cycles. The pre-amplified sample was divided and used for two separate steps. An additional 6 cycles were used for adding a sample index for ATAC library construction and 12 PCR cycles for the gene expression library construction. cDNA and ATAC libraries were checked for quality on Agilent 4200 Tapestation and ThermoFisher Qubit Fluorometer, and quantified by KAPA qPCR, before sequencing; each gene expression library was sequenced using NovaSeq 6000 S4 v1.5 200 cycle flow cell lane, dual index scRNAseq asymmetric read configuration 28-10-10-90, targeting 20,000 nuclei with an average sequencing depth of 50,000 read pairs per nucleus. Each ATAC library was sequenced using Illumina NovaSeq 6000 S2 v1.5 100 cycle flow cell lane, with a 50-8-24-49 read configuration, also targeting 20,000 nuclei with an average sequencing depth of 50,000 reads per cell.

value: Primary cells

value: Striatum

tag: strain

value: A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/H1LtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ

value: 12 weeks old

tag: molecule subtype

value: Nuclei


title: WG_MAD.replicate_7.hic

city: Chengdu

institute: Sichuan Agricultural University

description: whole.samples.ABindex.results.txt.gz


title: Striatum, batch 4, single-cell multi-omics [scRNA-seq]

description:
10x Genomics
metadata.csv
Batch 4 [scRNA-seq]


title: Striatum, batch 3, single-cell multi-omics [scATAC-seq]

description:
10x Genomics
tmp.repl1_atac.all.v2.all_peaks.npz
tmp.repl1_atac.all.v2_peaks.all.ygi
tmp.repl1_atac.all.v2.xgi
Batch 3 [scATAC-seq]


title: WL_GOM.replicate_1.H3K27ac

value: greater omentum fat


title: WG_MAD.replicate_9.hic

description: whole.samples.ABindex.results.txt.gz


title: Striatum, batch 3, single-cell multi-omics [scRNA-seq]

description:
10x Genomics
metadata.csv
Batch 3 [scRNA-seq]


title: Striatum, batch 2, single-cell multi-omics [scATAC-seq]

description:
10x Genomics
tmp.repl1_atac.all.v2.all_peaks.npz
tmp.repl1_atac.all.v2_peaks.all.ygi
tmp.repl1_atac.all.v2.xgi
Batch 2 [scATAC-seq]


title: WG_ULB.replicate_45.H3K27ac

description: WG_group6_ULB_merge_AllEnhancers.table.txt


title: Striatum, batch 1, single-cell multi-omics [scATAC-seq]

description:
10x Genomics
tmp.repl1_atac.all.v2.all_peaks.npz
tmp.repl1_atac.all.v2_peaks.all.ygi
tmp.repl1_atac.all.v2.xgi
Batch 1 [scATAC-seq]


title: WG_MAD.replicate_5.hic

description: whole.samples.ABindex.results.txt.gz


title: Striatum, batch 1, single-cell multi-omics [scRNA-seq]

description:
10x Genomics
metadata.csv
Batch 1 [scRNA-seq]


title: Striatum, batch 2, single-cell multi-omics [scRNA-seq]

description:
10x Genomics
metadata.csv
Batch 2 [scRNA-seq]


title: WG_ULB.replicate_44.H3K27ac


title: WG_ULB.replicate_43.H3K27ac

description: WG_group5_ULB_merge_AllEnhancers.table.txt


title: High-fat diet fed WT mice, shYap, Tumor, scRNAseq

city: Los Angeles

first: Ekihiro

last: Seki

state: CA

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

data_processing:
The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) (Dobin et al., 2013) with default parameters, using mouse mm10 transcriptome reference from Ensembl version 84 annotation, containing all protein coding and long non-coding RNA genes.
Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 4.0.0 (10X Genomics).
The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Assembly: mm10 transcriptome reference from Ensembl version 84 annotation
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver Tumor

extract_protocol:
Tumor-infiltrating immune cells were isolated by dissociation of MC38 liver metastatic tumors separated from non-tumor liver tissues,
followed by positive selection using anti-CD45 antibodies conjugated to magnetic beads for single-cell analysis
Single-cell RNA-Seq libraries were prepared per the 10x Genomics Single Cell 3′ v3.1 Reagent Kits User Guide using the Chromium Controller, X, or Connect (10x Genomics, Pleasanton, California).

value: Liver Tumor

value: Liver Tumor-infiltrating immune cells

tag: treatment

value: High-fat diet, shYap, liver metastasis


title: WG_ULB.replicate_41.H3K27ac

source_name: upper layer of backfat

value: upper layer of backfat

value: H3K27ac (Abcam, #ab4729)


title: WG_ULB.replicate_38.H3K27ac


title: Low-fat diet fed WT mice, Tumor, scRNAseq

value: Low-fat diet, WT, liver metastasis


title: Low-fat diet fed WT mice, shYap, Tumor, scRNAseq


title: WG_MAD.replicate_3.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_MAD.replicate_2.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF, KO, A485+IL1β, rep1

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
vari-bbc/rnaseq_workflow (https://github.com/vari-bbc/rnaseq_workflow)
Sequence reads were trimmed using Trim Galore 0.6.0 (-q 20)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR version 2.7.8a (parameters- --twopassMode Basic, --outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts)
Indexing was done using samtools version 1.9 (parameters- --twopassMode Basic, --outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts)
Read count extraction was done using salmon version 1.5.2 (parameters - -l A, --validateMappings)
Read count normalization was performed DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene counts values for each Sample

source_name: mouse embryonic fibroblast

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mouse embryonic fibroblast

value: LKB1 knockout


title: WG_MAD.replicate_4.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF, KO, A485+IL1β, rep3


title: WG_MAD.replicate_6.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF, KO, IL1β, rep3


title: High-fat diet fed WT mice, Tumor, scRNAseq

value: High-fat diet, WT, liver metastasis


title: MEF, KO, IL1β, rep2


title: MEF, KO, IL1β, rep1


title: WG_MAD.replicate_1.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_ULB.replicate_21.H3K27ac


title: WG_ULB.replicate_30.H3K27ac


title: WG_RAD.replicate_46.hic

description: whole.samples.ABindex.results.txt.gz

value: retroperitoneal adipose


title: WG_RAD.replicate_45.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF, WT, A485+IL1β, rep3

value: WT


title: WG_ULB.replicate_25.H3K27ac


title: WG_ULB.replicate_20.H3K27ac


title: MEF, WT, IL1β, rep2


title: MEF, WT, A485+IL1β, rep1


title: MEF, WT, A485+IL1β, rep2


title: MEF, WT, IL1β, rep3


title: WG_ULB.replicate_15.H3K27ac


title: MEF, WT, IL1β, rep1


title: WG_RAD.replicate_44.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_43.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_46.H3K27ac

description: WG_group5_RAD_merge_AllEnhancers.table.txt


title: MEF, KO, A485, rep2


title: WG_RAD.replicate_42.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF, KO, A485, rep1


title: WG_RAD.replicate_45.H3K27ac


title: MEF, KO, ctrl, rep3

value: control


title: MEF, KO, ctrl, rep2


title: WG_RAD.replicate_44.H3K27ac


title: WG_RAD.replicate_41.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF, KO, ctrl, rep1


title: WG_RAD.replicate_40.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_43.H3K27ac


title: MEF, WT, A485, rep3


title: WG_RAD.replicate_38.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_42.H3K27ac

description: WG_group6_RAD_merge_AllEnhancers.table.txt


title: WG_RAD.replicate_39.hic

description: whole.samples.ABindex.results.txt.gz


title: MEF, WT, ctrl, rep3


title: MEF, WT, A485, rep1


title: MEF, WT, A485, rep2


title: MEF, KO, A485, rep3


title: MEF, WT, ctrl, rep1


title: WG_RAD.replicate_38.H3K27ac


title: WG_RAD.replicate_30.H3K27ac


title: WG_RAD.replicate_36.hic

description: whole.samples.ABindex.results.txt.gz


title: WG_RAD.replicate_28.H3K27ac


title: WG_RAD.replicate_35.hic

description: whole.samples.ABindex.results.txt.gz