title: HPAP048_pLN

city: Gainesville

first: Miguel

middle: A

last: Medina-Serpas

state: FL

address: 1275 Center Dr

institute: University of Florida

description:
Library name: MM029_HPAP048_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing

data_processing:
Raw .bcl files were processed using the 10x Genomics mkfastq wrapper to generated demultiplexed FASTQ files.
Sequences were aligned to the GRCh38 Homo Sapiens referene genome and quantification of gene expression counts was performed using 10x Genomics Space Ranger pipeline using default parameters.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: List of spatial barcodes
Supplementary files format and content: features.tsv.gz: List of gene IDs
Supplementary files format and content: matrix.mtx.gz: Gene expression count data
Supplementary files format and content: aligned fiducials.jpg: Fiducial frame alignment for H&E stained tissue sections
Supplementary files format and content: detected_tissue_image.jpg: Image depicting tissue area coverage over capture spots
Supplementary files format and content: scalefactors_json.json: Scaling factors for pixel coordinate conversion of image data to 55µm capture spot size
Supplementary files format and content: tissue_hires_image.png: High resolution H&E stained tissue image
Supplementary files format and content: tissue_lowres_image.png: Low resolution H&E stained tissue image
Supplementary files format and content: tissue_positions_list.csv: List of unique spatial barcodes and the corresponding coordinates of each 55µm capture spot
Library strategy: Spatial Transcriptomics

source_name: Pancreatic Lymph Node

extract_protocol:
Formalin-fixed parrafin-embedded pancreas and associated pancreatic lymph nodes were sectioned to a thickness of 5µm and mounted to a standard positively-charged tissue slide. Tissues were permeabilizied and probe hybridized with a whole transcriptome cocktail on-slide. In situ hybridized probes were released and transferred onto a Visium CytAssist Gene Expression slide using the Visium CytAssist Instrument for 30 min at 37˚C.
Spatial transcriptomic libraries were prepared in accordance with the 10x Genomics Visium CytAssist Spatial Gene Expression User Guide (Rev D)

treatment_protocol: Prior to in situ probe hybridization and final library construction, each section was incubated at 60˚C for 2 hours to melt parrafin wax. Post incubation, sections per deparaffanized, heamaztoxylin and eosin stained, and decrosslinked according the 10x Genomics Visium Tissue Preparation guide.

value: Pancreatic Lymph Node

value: Type 1 Diabetes


title: HPAP102_pLN

status: Public on Jun 23 2025

type: SRA

country: USA

description:
Library name: MM029_HPAP102_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: disease state

tag: batch


title: HPAP123_pLN

description:
Library name: MM029_HPAP123_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP020_pLN

description:
Library name: MM029_HPAP020_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: Lymph node metastasis_2, MDA-MB-231 xenograft model, Mouse 43978

city: Darlinghurst

first: Shabarni

last: Gupta

state: NSW

address: Precinct Loading Dock,, West Street (off Burton Street)

country: Australia

institute: Garvan Institute of Medical Researc

description:
Library name: S9
10X Genomics

library_source: transcriptomic single cell

data_processing:
The cellranger count pipeline (version 3.0.2) was used for alignment, filtering, barcode counting, and UMI counting from FASTQ files
Assembly: hg19 + mm10
Supplementary files format and content: h5ad file with normalized cell counts and relevant cell and sample-level metadata

source_name: Lymph node metastasis

extract_protocol:
Post-euthanasia, organs were harvested, washed in cold 1× PBS to remove blood, and either processed immediately or minced into small fragments and cryopreserved in 5% DMSO-FBS in liquid nitrogen. For immediate processing, tissues were finely minced using stacked blades in 100–200 µL FV media until a homogenous paste was obtained, then transferred to 15 mL Falcon tubes containing 4.5 mL FV media (5% FBS added fresh) and kept on ice.  Enzymatic dissociation was initiated with 500 µL Collagenase-Hyaluronidase (C-H) per tube, incubated at 37°C on a rotating wheel for 40 minutes. At 15–20 minutes, tissues were mechanically disrupted using 5 mL serological pipettes. Dissociation efficiency was assessed using a 96-well plate, and tubes were returned to the wheel for another 15–20 minutes. After final pipetting, reactions were stopped by placing tubes on ice and adding cold FACS buffer (2% FBS in PBS), followed by centrifugation at 1300 rpm for 6 minutes.  Red blood cell lysis was performed using 1.5 mL freshly prepared RBL buffer (1:10 in Buxter water), incubated for 2 minutes, then stopped with FACS buffer and centrifuged. Pellets were resuspended in 10 mL FACS buffer with 50 µL DNase and filtered through pre-wetted 40 µm strainers to collect single-cell suspension 1 (SCS1).  Filters were inverted and flushed with 12 mL FACS media to recover retained tissue, centrifuged, resuspended in 100 µL DNase, and treated with 1–2 mL TEG trypsin at 37°C for up to 2 minutes using a cut P1000 tip. Trypsin was neutralized with FACS buffer, and cells were centrifuged and resuspended in 10 mL FACS buffer + 100 µL DNase, then filtered through activated 40 µm strainers to yield SCS2.  Both SCS1 and SCS2 were centrifuged (1300 rpm, 6 minutes), combined in 2 mL FACS buffer, and a 50–100 µL aliquot was reserved as an unstained control. Remaining cells were pelleted and stained with 1 mL of pre-titrated antibody solution, incubated at 4°C for 40 minutes with gentle shaking, washed twice, and resuspended in 500 µL FACS buffer for sorting. GFP-expressing MDA-MB-231 cells were sorted and processed for scRNA-seq following 10x Genomics protocols.
Single-cell suspensions were processed using the Chromium Controller (10x Genomics) and the Single Cell 3′ Reagent Kits v2 (PN-120237), following the manufacturer’s instructions (10x Genomics, CG00052, Rev F). Cells were encapsulated into nanoliter-scale Gel Bead-in-Emulsions (GEMs), where cell lysis and reverse transcription occurred, barcoding each cDNA molecule with a unique 10x barcode and UMI. Following GEM-RT incubation, emulsions were broken and cDNA was purified using Silane Dynabeads. Amplified cDNA was enzymatically fragmented and processed through end repair, A-tailing, adaptor ligation, and indexing PCR using sample-specific barcodes (Chromium i7 Sample Index Plate, PN-220103). Libraries were quality controlled using Bioanalyzer or TapeStation, quantified, and sequenced on an Illumina platform using a paired-end 2×150 bp configuration, with Read 1 containing 26 bp (barcode + UMI), i7 index of 8 bp, and Read 2 of 98 bp.

value: Lymph node metastasis

tag: cell line


title: HPAP043_pLN

description:
Library name: MM030_HPAP043_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing

value: Non-Diabetic Multiple Autoantibody Positive


title: HPAP149_pLN

description:
Library name: MM030_HPAP149_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP148_pLN

description:
Library name: MM030_HPAP148_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP114_pLN

description:
Library name: MM029_HPAP114_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing

value: Non-Diabetic Single Autoantibody Positive


title: HPAP019_pLN

description:
Library name: MM029_HPAP019_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP095_pLN

description:
Library name: MM029_HPAP095_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing

value: Non-Diabetic


title: HPAP012_pLN

description:
Library name: MM029_HPAP012_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP048_Pancreas

description:
Library name: MM029_HPAP048_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing

source_name: Pancreas

value: Pancreas


title: HPAP034_pLN

description:
Library name: MM029_HPAP034_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP123_Pancreas

description:
Library name: MM029_HPAP123_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP087_Pancreas

description:
Library name: MM029_HPAP087_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP032_Pancreas

description:
Library name: MM029_HPAP032_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP020_Pancreas

description:
Library name: MM029_HPAP020_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP107_Pancreas

description:
Library name: MM029_HPAP107_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP032_pLN

description:
Library name: MM029_HPAP032_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP016_Pancreas

description:
Library name: MM029_HPAP016_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP149_Pancreas

description:
Library name: MM030_HPAP149_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP148_Pancreas

description:
Library name: MM030_HPAP148_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP043_Pancreas

description:
Library name: MM030_HPAP043_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP072_Pancreas

description:
Library name: MM029_HPAP072_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP114_Pancreas

description:
Library name: MM029_HPAP114_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP110_Pancreas

description:
Library name: MM029_HPAP110_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP019_Pancreas

description:
Library name: MM029_HPAP019_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP036_Pancreas

description:
Library name: MM029_HPAP036_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: Tumor_017_S99

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

description: Library name: Tumor_017_S99

data_processing:
The raw sequence reads were mapped to GRCh38 using STAR (V2.5.3a).
The alignmented bam file were performed using markduplicated.
The FPRM value extract were performed using cufflinks.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.

value: Tumor


title: HPAP102_Pancreas

description:
Library name: MM029_HPAP102_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP071_Pancreas

description:
Library name: MM030_HPAP071_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP110_pLN

description:
Library name: MM029_HPAP110_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP095_Pancreas

description:
Library name: MM029_HPAP095_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP036_pLN

description:
Library name: MM029_HPAP036_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: HPAP072_pLN

description:
Library name: MM029_HPAP072_pLN
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: Late passage iPSC WT WGBS

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
Library name: Sample 5
WGBS

library_source: genomic

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20.
Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for autsomes and coverage (10-150 reads).
Assembly: T2T (CHM13v2.0)
Supplementary files format and content: bigWig file of coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

molecule: genomic DNA

source_name: cell line

growth_protocol: ZIP8K8 or ZIP34K14 iPSCs (Tandon et al., 2018, Rosebrock et al., 2022) were maintained in mTeSR Plus (Stemcell Technologies, #100-0276) supplemented with 100U/ml Penicillin and 100µg/ml Streptomycin (Thermo Fisher Scientific, #15140122) on pre-coated culture ware (1:100 diluted Matrigel (Corning, #354234) in KnockOut DMEM (Thermo Fisher Scientific, #10829–018)) at 20-80% confluency by splitting every two to three days. Clump-based cell splitting was performed by incubating the cells in EDTA pH 8.0 (Thermo Fisher Scientific, #15575–038) and DPBS (Thermo Fisher Scientific, #14190-250) in a final concentration of 5 mM for 3 minutes at 37°C and 5% CO2. Single-cell splitting was performed by incubating the cells with Accutase (Sigma-Aldrich, A6964) supplemented with 10µM Y-27632 (Tocris, #1254) for 15 min at 37°C and 5% CO2. All centrifugation steps were performed at 300 x g for 5 minutes at room temperature (RT) unless otherwise specified. Cell counting was performed using an automated cell-counter (Thermo Fisher Scientific) on a single-cell suspension diluted 1:1 in 0,4% Trypan Blue staining-solution (Thermo Fisher Scientific, #15250-061). Definitive endoderm differentiation was performed using the STEMdiff Trilineage Differentiation media (Stemcell Technologies, #05230). Single-cell suspensions of mTeSR Plus-maintained ZIP8K8 iPSCs were seeded into 6-well plates at the cell-number recommended by the manufacturer’s instructions. Fresh STEMdiff Trilineage Endoderm Differentiation media was given to the cells every 24h during the duration of the differentiation protocol. On day 5 cells were collected using a single-cell split prepared for FACS analysis. For the cell cycle arrest cells were treated with 2 µg/ml nocodazole (Sigma-Aldrich, #M1404-10MG) for 16 hours.

extract_protocol:
Proliferating and G2-arrested iPSCs were harvested using a single-cell suspension (see growth protocol) and snap-frozen for further use. A subset of G2-arrested cells was taken for cell cycle analysis to verify the arrest. Fort the cell cycle analysis cells were collected using a single-cell split and quenched with DPBS. 1M cells were transferred into a protein lo-bind Eppendorf tube (#) and centrifuged. The supernatant was discarded and the cell pellet resuspended in 100ul PBS-T (0.2% Tween 20, Thermo Fisher Scientific, #J20605.AP) To permeabilize and fix the cells 1ml of 70% EtOH was added dropwise for a final concentration 1ml/1M cells and incubated at 4°C for two hours or overnight. For one wash the cell suspension was then centrifuged and resuspended in 1ml PBS-T. After centrifuging the cell pellet was in 1ml Dapi solution of 0.1% Triton-PBS (Triton-X-100. Thermo Fisher Scientific, #85111) and 1ug/ml Dapi (Invitrogen, #D1306) and incubated at RT for 30 minutes in the dark. The cells were washed with 1ml PBS-T. Finally, the cells were resuspended in 200ul DPBS-10% FBS and filtered for FACS analysis. Endoderm differentiated cells were harvested using a single-cell suspension (see growth protocol) and prepared for FACS analysis. ZIP8K8 single-cell suspensions were quenched DPBS-10% Fetal bovine serum (FBS, PAN Biotech, #P30-2602)). Next, cells were centrifuged at 4°C. Cells were then resuspended in DPBS-10% FBS containing the surface marker anti-CXCR4 antibody (Biologend, #306506) in a 1:200 dilution and incubated for 15 min at 4 °C in the dark. Next, cells were washed once again with DPBS-10% FBS and centrifuged at 4°C before FACS. Finally, cells were resuspended in DPBS-10% FBS and passed through a 70µm cell strainer (Corning, #431751). NCAM positive cells were sorted and snap-frozen for further use. FACS analysis was performed on the FACSCelesta Flow Cytometer (Beckton Dickinson).
BiSulfite-seq

value: cell line

tag: cell type

value: iPSC

tag: genotype


title: HPAP034_Pancreas

description:
Library name: MM029_HPAP034_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: Late passage iPSC DNMT3A DNMT3B DKO WGBS

description:
Library name: Sample 4
WGBS

value: DNMT3A + DNMT3B DKO (p35)


title: Late passage iPSC DNMT3B KO WGBS

description:
Library name: Sample 3
WGBS

value: DNMT3B KO (p35)


title: iPSC HELLS KO #G2 WGBS

description:
Library name: Sample 2
WGBS

value: HELLS KO #G2 (p5)


title: B16F10 cells, ppif knockout-1, Normoxia for 24 hours

city: ulsan

first: Hye Kyung

last: Park

state: Ulsan

address: 50, UNIST-gil, Eonyang-eup, Ulju-gu, unist-gil 50,  EB110, room402-12

country: South Korea

institute: UNIST ( 울산과학기술원)

description: Library name: N_KO_1

data_processing:
Sequencing : High throughoutput sequencing was performed as paired-end 150 sequencing runs using NovaSeq 6000 (Illumina).
Read alignment : Raw reads were assembled and low-quality reads were filtered using Cutadapt (version 3.4). Filtered reads were aligned on a reference genome downloaded from Ensembl GRCm39 (Mus musculus) using STAR (version 2.7.8a) and gene level expression per each sample was calculated using RSEM (version 1.3.1)
Read count normalization : Read counts were normalized for effective library size using DESeq2 package (version 1.26.0)
Assembly: GRCm39
Supplementary files format and content: tab-delimted text file
Supplementary files format and content: TPM values for each sample

organism: Mus musculus

growth_protocol: wild-type B16F10 cells and ppif knockout cells incubated for 24 hours under normoxic condtion (21% O2) Control and PPIF overexpressing stable cell lines incubated for 24 hours under hypoxic condtion (1% O2)

extract_protocol:
RNA isolation method : QIAamp RNA Mini kit (Qiagen) according to the manufacturer’s instruction RNA quality assessment : RNA quality was assessed with an 4200 TapeStaion System using an RNA Screen Tape (Agilent Technologies), and RNA was quantified using an Qubit. (Thermo Fisher Scientific)
Library preparation : Library with total RNAs were constructed using the KAPA RNA HyperPrep Kit with RiboErase (Roche) according to the manufacturer’s instructions.

value: melanoma

value: ppif knockout

tag: treatment

value: 21% O2, normoxic condition


title: iPSC HELLS KO #F11 WGBS

description:
Library name: Sample 1
WGBS

value: HELLS KO #F11 (p5)


title: B16F10 cells, ppif knockout, Normoxia for 24 hours

institute: UNIST ( 울산과학기술원)

description: Library name: N_KO


title: iPSC HELLS KO rep3 RNA

description:
Library name: Sample 6
Element Aviti

data_processing:
Raw reads were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25 --interleaved --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --interleaved --overlap 20 --minimum-length --adapter "A[100]" --adapter "T[100]").
Reads were aligned to the mouse reference genome (T2T) using STAR (version 2.7.5a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts) and transcripts were quantified using stringtie (version 2.0.6; parameters: -e) with GENCODE annotation (release VM19).
Assembly: T2T (CHM13mm10v2.0)
Supplementary files format and content: Supplementary files format and content: Tab-delimited file containing gene abundances: <Gene ID> <Gene Name> <Reference> <Strand> <Start> <End> <Coverage> <FPKM> <TPM>

growth_protocol: ZIP8K8 iPSCs (Tandon et al., 2018) were maintained in mTeSR Plus (Stemcell Technologies, #100-0276) supplemented with 100U/ml Penicillin and 100µg/ml Streptomycin (Thermo Fisher Scientific, #15140122) on pre-coated culture ware (1:100 diluted Matrigel (Corning, #354234) in KnockOut DMEM (Thermo Fisher Scientific, #10829–018)) at 20-80% confluency by splitting every two to three days. Clump-based cell splitting was performed by incubating the cells in EDTA pH 8.0 (Thermo Fisher Scientific, #15575–038) and DPBS (Thermo Fisher Scientific, #14190-250) in a final concentration of 5 mM for 3 minutes at 37°C and 5% CO2. Single-cell splitting was performed by incubating the cells with Accutase (Sigma-Aldrich, A6964) supplemented with 10µM Y-27632 (Tocris, #1254) for 15 min at 37°C and 5% CO2. All centrifugation steps were performed at 300 x g for 5 minutes at room temperature (RT) unless otherwise specified. Cell counting was performed using an automated cell-counter (Thermo Fisher Scientific) on a single-cell suspension diluted 1:1 in 0,4% Trypan Blue staining-solution (Thermo Fisher Scientific, #15250-061). Definitive endoderm differentiation was performed using the STEMdiff Trilineage Differentiation media (Stemcell Technologies, #05230). Single-cell suspensions of mTeSR Plus-maintained ZIP8K8 iPSCs were seeded into 6-well plates at the cell-number recommended by the manufacturer’s instructions. Fresh STEMdiff Trilineage Endoderm Differentiation media was given to the cells every 24h during the duration of the differentiation protocol. On day 5 cells were collected using a single-cell split prepared for FACS analysis.

extract_protocol:
iPSCs were harvested using a single-cell suspension (see growth protocol) and snap-frozen for further use.
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034). Three biological replicates were collected per condition. Each sample was resuspend-ed in 350µl of RLT buffer containing 10% β-mercaptoethanol (Thermo, #21985023), followed by the addition of 350µl of 70% ethanol. RNA was then purified according to the manufacturer’s in-structions. RNA quality and concentration were assessed prior to library preparation. For RNA sequencing, the KAPA RNA HyperPrep Kit (Roche, # KK8560) was used to generate libraries from 500ng RNA per sample. The final libraries were purified using Agencourt AMPure XP beads, and diluted to 4nM for 100 bp paired-end sequencing on Element Biosciences’ AVITI system.

value: HELLS KO


title: iPSC HELLS KO rep2 RNA

description:
Library name: Sample 5
Element Aviti


title: B16F10 cells, wild type-1, Normoxia for 24 hours

institute: UNIST ( 울산과학기술원)

description: Library name: N_Con_1

value: WT


title: B16F10 cells, wild type, Normoxia for 24 hours

institute: UNIST ( 울산과학기술원)

description: Library name: N_Con


title: B16F10 cells, ppif overexpressing stable cell-1, Hypoxia for 24 hours

institute: UNIST ( 울산과학기술원)

description: Library name: H_OE_1

value: PPIF overexpressing stable cell

value: 1% O2, hypoxic condition, 24 hours


title: iPSC WT rep 2 RNA

description:
Library name: Sample 2
Element Aviti


title: B16F10 cells, ppif overexpressing stable cell, Hypoxia for 24 hours

institute: UNIST ( 울산과학기술원)

description: Library name: H_OE


title: iPSC HELLS KO rep1 RNA

description:
Library name: Sample 4
Element Aviti


title: HPAP012_Pancreas

description:
Library name: MM029_HPAP012_Pancreas
Fromalin fixed parrafin embedded spatial transcriptome sequencing


title: iPSC WT rep 3 RNA

description:
Library name: Sample 3
Element Aviti


title: B16F10 cells, control stable cell-1, Hypoxia for 24 hours

institute: UNIST ( 울산과학기술원)

description: Library name: H_Con_1

value: pcDNA stable cell


title: Late passage iPSC HELLS KO #B3 WGBS

description:
Library name: Sample 6
WGBS

value: HELLS KO #B3 (p33)


title: Medalist trial patient Responderj1422_sampE1

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

description: Library name: j1422_sampE1

data_processing:
RNA seq read mapping, differential expression analysis, and splicing analysis:  We used HISAT2 2.0.0-beta to align readings with GRCh38. The htseq-count tool was used to find the total number of read pairs that were uniquely mapped. We have made the data accessible through the NCBI's Gene Expression Omnibus (GEO) repository. To identify transcripts undergoing alternative splicing (AS) events between conditions, we utilized the rMATS (Robust Multi-array Average Transcript Splicing) tool. This tool was employed to detect various AS events, such as skipped exons, alternative 5' or 3' splice sites, and retained introns. The inclusion level (percent spliced-in, PSI) for each splicing event across samples was calculated. Using rMATS, a statistical model was applied to pinpoint AS events showing significant changes in PSI between conditions. Differentially spliced events were identified based on a user-defined fold-change threshold for PSI alteration and an adjusted p-value threshold for statistical significance.
Reads were aligned to the reference with tophat2 using the “-g 1” parameter setting.
Gene expression was enumerated with htseq2 using gencode.v24.primary_assembly
Assembly: GRCh38_no_alt_analysis (hg38)
Supplementary files format and content: tab delimited txt file with Ensembl identifier and count columns

source_name: Medalist trial patient Responder

growth_protocol: Cells were cultured in IMDM, 15% FBS, 15% human serum, 1% penicillin/steptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA library preparation:  The RNA quality was analyzed using a bioanalyzer. RNA samples with RQN scores above an 8 were considered suitable for RNA library preparation. The library preparation process followed the manufacturer's protocol (QIAseq Stranded RNA Lib Kit UDI-B, Cat# 180452). Initially, RNA molecules were fragmented into smaller fragments, and then reverse transcriptase was used to convert the fragmented RNA into double-stranded cDNA. Adaptor ligation was performed, followed by library amplification to ensure sufficient cDNA fragments for sequencing. Prior to sequencing, the library underwent quality control and quantification. Sequencing was conducted using an Illumina sequencer (Nextseq500) with 150 paired-end sequencing, resulting in the generation of approximately 30 million reads per sample.
RNA was harvested using Rneasy mini plus kit (Qiagen). RNA was eluted in RNAse free water. At least 0.5 ug of total RNA was used to prepare libraries.
QIAseq Stranded RNA Lib Kit UDI (24) Cat no. / ID.  180450

treatment_protocol: Cells were either treated with GDF11 (100 ng/mL) or TGFb1 (20 ng/mL)

value: BMMNCs

value: Luspatercept


title: Medalist trial patient Non-responderj1422_sampD1

description: Library name: j1422_sampD1

source_name: Medalist trial patient Non-responder


title: NT

city: Paris

first: Alexandre

last: Boissonnas

address: 91 bd de l'hopital

country: France

institute: Inserm

description:
Library name: NT
10x Genomics

data_processing:
Sequencing data for mouse samples were processed using the Cell Ranger 6.1 pipeline. Utilizing the cellranger count function, we transformed FASTQ files and conducted alignment, filtering, barcoding, and unique molecular identifier (UMI) counting. The reads were aligned with count against the mm10 mouse genome for mouse samples. This process harnesses chromium cellular barcodes to generate feature barcode matrices, ascertain clusters, and conduct gene expression analysis. Cellranger count was performed using default parameters.
Assembly: mm10 mouse
Supplementary files format and content: barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files obtained from CellRanger alignment.

source_name: Lung tumor

extract_protocol:
For cell sorting, the lungs from three mice per condition were harvested, pooleand enzymatically digested with 0.1 mg/mL DNase I (Sigma-Aldrich), 1.5 U/mL Dispase II (Gibco), and 200 U/mL Collagenase Type IV (Gibco) in RPMI+ GlutaMAX (Gibco) for 30 min at 37°C under agitation. Samples were filtered using 70 µm cell strainer and washed with RPMI+ GlutaMAX (Gibco) with 10% FBS. After digestion, red blood cells were lysed with ACK lysis buffer (Gibco) for 5 min at room temperature and washed with PBS.27,000 monocytes and tumor associated macrophages (defined as CD45+ CD11b+ ECFP+ EGFP+ CD4- CD8- Ly6G- SiglecF-), 3,000 alveolar macrophages (defined as CD45+ SiglecF+ CD11b- ECFP+ CD4- CD8- Ly6G-), 10,000 CD8+ T cells (defined as CD45+ CD8+ CD4- CD11b- Ly6G- SiglecF-), and 20,000 CD4+ T cells (defined as CD45+ CD4+ CD8- CD11b- Ly6G- SiglecF-) were sorted in PBS 0.5% BSA from a pool of three tumor-bearing mice per condition. After sorting, all cell preparations were resuspended at 106cells/mL in PBS containing 0.5% BSA and loaded onto a Chromium Controller (10X Genomics).
Samples were processed for single-cell encapsulation and cDNA library generation according to the manufacturer’s instructions using the 10x Genomics Single Cell 3′v2 Reagent Kit (for mouse). The library was  sequenced using a NovaSeq 6000 (Illumina).

treatment_protocol: TC1 cells expressing luciferase (TC1-Luc) were obtained from T.-C. Wu (Johns Hopkins University, Baltimore, MD). Cell line authentication was previously performed(20) TC1-luc cells were cultured in RPMI-1640 with 10% fetal bovine serum (FBS), Na-pyruvate, antibiotics, and anti-mycotics (GIBCO BRL Invitrogen) and incubated at 37°C in 5% CO2. TC1-luc cells were initially tested for Mycoplasma contamination using Lonza’s MycoAlert™ Mycoplasma Detection Assay (Ozyme, #LT07-318) prior cryopreservation. After thawing, cells were cultured for a maximum of 10 days (2-3 passages). 3x105 cells were injected intravenously into the tail vein to generate lung tumors, as described previously (19).Chemotherapy treatment was performed by a single intraperitoneal injection of cyclophosphamide (Sigma-Aldrich) diluted in PBS at 175 mg/kg 10 days after tumor inoculation.The anti-TNFR2 (CD120b) antibody (clone TR75-54.7, BioXcell, RRID:AB_2687728) was administered intraperitoneally (300 µg in 100µL PBS / injection) 5 and 6 days after chemotherapy.The mice are irradiated with 7.5 Gy under lead shielding, using a personalized protective device that allows for targeted irradiation specifically to the thoracic (lung) area. Lungs were harvested 17 days after tumor inoculation.

value: Lung tumor

value: non treated


title: IR

description:
Library name: IR
10x Genomics

value: irradiation 7.5 Gy


title: CP

description:
Library name: CP
10x Genomics

value: cyclophosphamide


title: iPSC WT rep 1 RNA

description:
Library name: Sample 1
Element Aviti

value: cell line

value: iPSC


title: Medalist trial patient Non-responderj1422_sampA1

description: Library name: j1422_sampA1


title: CP_aTNFRII

description:
Library name: CP_aTNFRII
10x Genomics

value: cyclohosphamide + anti-TNFRII


title: CD34+ d6 erythroid progenitors treated with vehiclej1469_rna_7_S7

description: Library name: j1469_rna_7_S7

value: In vitro HSC cultures

value: Vehicle


title: Medalist trial patient Non-responderj1422_sampC1

description: Library name: j1422_sampC1


title: CD34+ d6 erythroid progenitors treated with GDF11j1469_rna_8_S8

description: Library name: j1469_rna_8_S8


title: HCC, miR-885-5p_2

city: Pathumwan

first: Archittapon

last: Nokkeaw

state: Bangkok

address: Padtayapatana Building, 1873, Henri Dunant Road

department: Biochemistry

country: Thailand

institute: Chulalongkorn university, faculty of medicine

description: Library name: Sample 5

data_processing:
The acquisition of clean data was achieved by filtering and removing raw data that had adapters, low-quality data, and readings with a Q-score below 30. Subsequently, the transcriptome was assembled using StringTie (V2.2.1), and the clean reads were mapped to the human-specific genome GRCH38 using HISAT2 software (V2.0.4). The DESeq2 R software (V1.38.3) was utilized to conduct differential expression analysis between two groups. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized to identify gene biological function and investigate signaling networks.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

growth_protocol: The JHH-4 cell line was obtained from the Japanese Collection of Research Bioresources (JCRB) Cell Bank and grown in Eagle's Minimum Essential Medium (EMEM) (Gibco™, Thermo Fisher Scientific, Massachusetts, USA), supplemented with 10% FBS, 1% L-glutamine, and 1% antibiotic-antimycotic.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepare using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: Epithelial-like

value: hsa-miR-885-5p overexpress


title: HCC, miR-885-5p_1

description: Library name: Sample 4


title: Myccap Tumor Vehicle - 3

city: Ann Arbor

first: Arul

middle: M

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description: Library name: SI_40588

data_processing:
FASTQs were trimmed using BBDuk. Transcripts were quantified by kallisto with mouse reference genome (GRCm38/mm10) and then summarized to obtain gene level counts and TPM.
Assembly: GRCm38
Supplementary files format and content: counts_tumor_tissue.csv - gene level counts for the six in vivo samples
Supplementary files format and content: tpm_tumor_tissue.tsv - gene level TPM values for the six in vivo samples.

source_name: Myc-Cap tumor tissue

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and quantified by NanoDrop 2000 Spectrophotometers (Thermo Scientific).
RNA-seq libraries were prepared using KAPA RNA Hyper+RiboErase HMR (Roche Cat#: 08098140702). Ribosomal RNA was removed by enzymatic digestion from 800 ng total RNA, following with cDNA and double strand cDNA synthesis, end repair, A-tailing, and ligation with NEB adapters. cDNA fragments with sizes between 250-300 bp were separated using double AMPure beads and PCR amplified using 2x KAPA HiFi HotStart mix and NEB dual indexes (Roche Cat#: E6440L). Library quality was measured on an Agilent 2100 Bioanalyzer for concentration and product size. Paired-end libraries were sequenced with the Illumina NovaSeq 6000 (2 × 150 nucleotide read length) with sequence coverage to 20-30 million paired reads.

value: Myc-Cap tumor tissue


title: Myccap Tumor Vehicle - 2

description: Library name: SI_40587


title: HCC, Control 2

description: Library name: Sample 2

value: WT


title: HCC, Control 1

description: Library name: Sample 1


title: TREM2-KO2

city: Zhuhai

first: Guanmin

last: Jiang

address: No.52 Meihua East Road, Xiangzhou District, Zhuhai, Guangdong Province, China

department: Department of Clinical Laboratory

country: China

institute: the Fifth Affiliated Hospital of Sun Yat-sen University

description: Library name: TREM2-KO2

data_processing:
fastp (https://github.com/OpenGene/fastp); HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml); StringTie (https://ccb.jhu.edu/software/stringtie/)
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/edgeR/Limma/NOIseq, DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 (DESeq2/edgeR/Limma) / P-adjust ≤ 0.001 (DEGseq) / Prob > 0.8 (NOIseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO (Gene Ontology, http://www.geneontology.org) and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at P-adjust ≤ 0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do).
Assembly: Mus musculus GRCm39 release-109
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Mouse bone marrow

growth_protocol: Mouse bone marrow-derived macrophages were cultured in DMEM supplemented with 30% v/v L929 conditioned media and 10% FBS and 1% P/S medium.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
The transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).

treatment_protocol: C57BL/6J wildtype or TREM2 knockout (TREM2 KO) mouse bone marrow-derived macrophages were treated with 10 μM ASC-J9 or DMSO for 48 h.

value: Mouse bone marrow

value: bone marrow-derived macrophages

value: TREM2 knockout

value: DMSO


title: TREM2-KO3

description: Library name: TREM2-KO3


title: S30, DLBCL, HIV+/ART-naïve, Male

city: Chapel Hill

first: Yuri

last: Fedoriw

state: NC

address: 160 Medical Drive

institute: University of North Carolina

description: Library name: S30

data_processing:
BWA-MEM
Biombambam2
Picard, Multiplemetrics, FASTQC
coverageBed
Strelka2, Cadabra, Mutect2
variant filtering (tumor and germline read depth >15, germline alt allele count <1, tumor alt allele count >5,  variant allele frequency >0.05)
Assembly: hg38
Supplementary files format and content: tab-delimited text file of filtered variants by sample, based on tumor-only variant calling pipeline, considering genes included in 334 gene panel published by Chapman et al. 2021
Supplementary files format and content: tab-delimited text file of filtered variants by sample with paired germline

source_name: FFPE tumor

extract_protocol:
GeneRead DNA FFPE Kit, QIAmp Blood Mini Kit
Agilent SureSelect Human All Exon V6 r2

value: FFPE tumor

tag: Sex

value: Male

value: HIV+/ART-naïve

tag: diagnosis

value: DLBCL


title: TREM2-KO1

description: Library name: TREM2-KO1


title: S29, DLBCL, HIV+/ART-exp, Female

description: Library name: S29

value: Female

value: HIV+/ART-exp


title: B16F10 cells, control stable cell, Hypoxia for 24 hours

institute: UNIST ( 울산과학기술원)

description: Library name: H_Con

value: melanoma

value: pcDNA stable cell

value: 1% O2, hypoxic condition, 24 hours


title: Myccap Tumor YJ1206 - 2

description: Library name: SI_40590


title: S27, DLBCL, HIV+/ART-naïve, Female

description: Library name: S27


title: S26, DLBCL, HIV+/ART-exp, Female

description: Library name: S26


title: Myccap Tumor YJ1206 - 3

description: Library name: SI_40591


title: S28, DLBCL, HIV+/ART-exp, Male

description: Library name: S28


title: WT-CTL2

description: Library name: WT-CTL2


title: WTASC-J9-3

description: Library name: WTASC-J9-3


title: WT-CTL3

description: Library name: WT-CTL3


title: Myccap Tumor YJ1206 - 1

description: Library name: SI_40589


title: WTASC-J9-2

description: Library name: WTASC-J9-2


title: S24, DLBCL, HIVneg, Female

description: Library name: S24

value: HIVneg


title: S25, DLBCL, HIVneg, Female

description: Library name: S25


title: WTASC-J9-1

description: Library name: WTASC-J9-1


title: Normal_186_S31

description: Library name: Normal_186_S31

source_name: Tumor (adjacent normal)

value: Tumor (adjacent normal)


title: S22, DLBCL, HIV+/ART-exp, Male

description: Library name: S22


title: Myccap Tumor Vehicle - 1

description: Library name: SI_40586

value: Myc-Cap tumor tissue

value: Vehicle


title: HTS_S065_08_RCTKO_2

city: Philadelphia

first: Craig

last: Bassing

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Library name: HTS_S065_08_RCTKO_2

data_processing:
To analyze the Micro-Capture C data, we employed the pipeline provided by Arima Genomics https://github.com/ArimaGenomics/CHiC, which combines the HiCUP (https://pubmed.ncbi.nlm.nih.gov/26835000/) for the raw data processing and CHiCAGO (https://pubmed.ncbi.nlm.nih.gov/27306882/) for loop calling. We then used the hicup2juicer conversion tool (part of the HiCUP package) to generate files that could be further processed to .hic files for visualization and loop calling with MUSTACHE. The figures show the resulting heatmaps with vanilla coverage (VC) normalization.
Assembly: mm10
Supplementary files format and content: Combined and down sampled .hic files (use VC normalization, coverage in juicebox)
Supplementary files format and content: Bait file in txt format

source_name: Rag1-/- DN thymocytes

extract_protocol:
(B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes were sorted from Rag1-/- mice.
MicroCapture C was performed using a custom kit from Arima per manufacture instructions. The bait file report details the probe sequences.

value: Rag1-/- DN thymocytes


title: HTS_S065_07_V1TxS_2

description: Library name: HTS_S065_07_V1TxS_2


title: S21, DLBCL, HIVneg, Female

description: Library name: S21


title: S20, DLBCL, HIV+/ART-exp, Female

description: Library name: S20


title: HTS_S065_06_V1PKO_2

description: Library name: HTS_S065_06_V1PKO_2


title: S19, DLBCL, HIV+/ART-exp, Male

description: Library name: S19


title: HTS_S065_04_RCTKO_1

description: Library name: HTS_S065_04_RCTKO_1


title: HTS_S065_03_V1TxS_1

description: Library name: HTS_S065_03_V1TxS_1


title: S18, DLBCL, HIV+/ART-exp, Female

description: Library name: S18


title: S17, DLBCL, HIV+/ART-exp, Male

description: Library name: S17


title: S15, DLBCL, HIV+/ART-exp, Male

description: Library name: S15


title: HTS_S065_02_V1PKO_1

description: Library name: HTS_S065_02_V1PKO_1


title: HTS_S065_01_R1KO_1

description: Library name: HTS_S065_01_R1KO_1


title: S14, DLBCL, HIVneg, Male

description: Library name: S14


title: S16, EBV+ DLBCL, HIV+/ART-exp, Male

description: Library name: S16

value: EBV+ DLBCL


title: S13, FL/DLBCL, HIV+/ART-naïve, Female

description: Library name: S13

value: FL/DLBCL


title: EBKO DNs ConventionalHic 2

description: Library name: EBKO_rep2_conventional

data_processing:
For HiC, paired end raw reads were mapped with bwa version (https://pubmed.ncbi.nlm.nih.gov/19451168/), treating forward and reverse reads separately, as described and implemented with the HiCExplorer command tool version 3.6 (https://pubmed.ncbi.nlm.nih.gov/29335486/). For Figure 1, we combined experimental data from conventional and Arima HiC because they had sufficient pairwise spearman correlations. For Figures 3 and 4, we down-sampled data from the genotype with the most reads to be equivalent to the number of reads from the genotype with the least reads. Visualization was done via UCSC genome browser (https://pubmed.ncbi.nlm.nih.gov/12045153/), using the interact format, and juicebox (https://pubmed.ncbi.nlm.nih.gov/29428417/). MUSTACHE version 1.2.0 (https://pubmed.ncbi.nlm.nih.gov/32998764/) was used to identify significant looping at resolutions 10K, 5K and 3K.
Assembly: mm10
Supplementary files format and content: Combined and down sampled .hic files

extract_protocol:
DN thymocytes were isolated from Rag1-/- mice.
The final conventional HiC library was generated with 5 PCR cycles using the NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB) for Illumina sequencing. For the Arima HiC the KAPA Hyper Prep Kit was used.


title: EBKO DNs ConventionalHic 1

description: Library name: EBKO_rep1_conventional


title: EBKO DNs ArimaHic 1

description: Library name: EBKO_rep3_arima


title: R1KO_CTCF0905CR_DN_2

description: Library name: R1KO_CTCF0905CR_DN_2

data_processing:
For C&R and paired-end reads were aligned to the mm10 genome using bowtie2 (version 2.4.5) (https://pubmed.ncbi.nlm.nih.gov/22388286/). Peak calling was done using the macs2 algorithm (version 2.2.7.1) (https://pubmed.ncbi.nlm.nih.gov/18798982/). Bigwig files for the visualization in the UCSC genome browser were yielded by the bamCoverage tool inside the deeptools package (version 3.5.1) (https://pubmed.ncbi.nlm.nih.gov/27079975/) applying the RPGC normalization. Finally, the bioconducter package chipqc (version 1.30.0) (https://pubmed.ncbi.nlm.nih.gov/24782889/) helped determine our samples had a RiP (Reads in Peaks) score of at least 4.
Assembly: mm10
Supplementary files format and content: bigwig files produced by bamCoverage and normalized by RPGC.
Library strategy: CUT&Run

extract_protocol:
(B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes were sorted from Rag1-/- mice. CUT&RUN was performed using the CUTANA CUT&RUN Kit from Epicypher (SKU:14-1048) per manufacture instructions (version 4). Nuclei extraction was performed per the Appendix in manufacture protocol.
Library was prepared using the CUTANA CUT&RUN Library Prep Kit (SKU: 14-1001) per manufacturer instruction.

tag: chip antibody

value: CTCF


title: S12, DLBCL, HIVneg, Male

description: Library name: S12

value: FFPE tumor


title: S23, DLBCL, HIV+/ART-naïve, Female

description: Library name: S23


title: S10, DLBCL, HIVneg, Female

description: Library name: S10


title: R1KO_CTCF0821CR_DN_1

description: Library name: R1KO_CTCF0821CR_DN_1


title: S09, DLBCL, HIVneg, Male

description: Library name: S09

value: Male


title: HTS_SO85_22_EbKO_CTCF1212CR_DN_2_S22

description: Library name: HTS_SO85_22_EbKO_CTCF1212CR_DN_2_S22


title: HTS_SO85_12_EbKO_CTCF1206CR_DN_1_S12

description: Library name: HTS_SO85_12_EbKO_CTCF1206CR_DN_1_S12


title: S08, DLBCL, HIV+/ART-exp, Male

description: Library name: S08


title: S07, DLBCL, HIV+/ART-exp, Male

description: Library name: S07


title: WT-CTL1

description: Library name: WT-CTL1

value: Mouse bone marrow

value: bone marrow-derived macrophages

value: WT

value: DMSO


title: HTS_SO85_09_RCTKO_CTCF1206CR_DN_2_S9

description: Library name: HTS_SO85_09_RCTKO_CTCF1206CR_DN_2_S9


title: S05, DLBCL, HIV+/ART-exp, Male

description: Library name: S05

value: HIV+/ART-exp

value: DLBCL


title: S06, EBV+ DLBCL, HIV+/ART-exp, Male

description: Library name: S06


title: HTS_SO85_01_RCTKO_CTCF1030CR_DN_1_S1

description: Library name: HTS_SO85_01_RCTKO_CTCF1030CR_DN_1_S1


title: S04, DLBCL, HIV+/ART-naïve, Female

description: Library name: S04

value: Female

value: HIV+/ART-naïve


title: V1PKO_Rad21712CR_DN_1

description: Library name: V1PKO_Rad21712CR_DN_1


title: S03, DLBCL, HIV+/ART-naïve, Male

description: Library name: S03


title: S11, DLBCL, HIVneg, Male

description: Library name: S11

value: HIVneg


title: SW480-PCAT2-KI - WGS (D01)

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
OneWGSlibrary was sequenced on 3 PacBio Sequel II SMRTCells with whole genome libraries using SMRTbell prep kit 3.0.
Sample yields 2.5 to 2.7 million ccs reads, with mean read length 15.06 kb and mean read quality QV33.6. The HiFi reads from all the SMRTCells were mapped to a hg38 reference genome andpbsvwas used for structural variant calling.
Assembly: hg38
Supplementary files format and content: The big-wig files were created by using genomeCoverage of the Deeptools utility program with the option -bs 10 on the PCAT2-KI sequence.
Library strategy: Whole genome sequencing

source_name: Colon origin

growth_protocol: Both cell lines are grown in RPMI with 10% FBS and 5% CO2 at 37C.

extract_protocol:
PacBio® Nanobind® HMW DNA extraction kits following suppliers protocols.
HiFi libraries using the SMRTbell Express Template Prep Kit 2.0 following the supplier guide (PN 101-853-100 Version 05, PacBio).

treatment_protocol: No treatments were given to the cells included for sequenceing analysis.

value: Colon origin

value: SW480 Colorectal cancer

value: Epithelial

value: myc+; myb+; ras+; fos+; sis+; p53+; abl-; ros-; src-


title: V1CScr_Rad210712CR_DN_1

description: Library name: V1CScr_Rad210712CR_DN_1

value: Rag1-/- DN thymocytes


title: S02, EBV+ DLBCL, HIVneg, Male

description: Library name: S02

value: EBV+ DLBCL


title: SW480-PCAT2-KI - WGS (A01)


title: SW480-PCAT2-KI - WGS (C01)


title: S01, DLBCL, HIV+/ART-exp, Male

description: Library name: S01

value: FFPE tumor


title: R1KO_Rad210712CR_DN_2

description: Library name: R1KO_Rad210712CR_DN_2


title: R1KO_Rad210712CR_DN_1

description: Library name: R1KO_Rad210712CR_DN_1


title: TIL431

city: Milano

first: Serena

last: Pellegatta

state: Italy/Milano/Lombardia

address: via Giovanni Celoria, 11

country: Italy

institute: Fondazione IRCCS istituto Neurologico Carlo Besta

description: Library name: Sample 9

data_processing:
TCRSeq data in FASTQ format were pre-processed with MiXCR Immune Repertoire Analyzer software (v4.7.0) for read alignment and clonotype assembly.
Assembly: GRCh38
Supplementary files format and content: text files includes read counts for each sample
Library strategy: TCR-Seq

source_name: Tumor infiltrating lymphocytes

extract_protocol:
RNA was harvested using Rneasy mini kit (Quiagen).
10ng of input RNA was used for the construction of  TCR libraries. NGS libraries were prepared using AmpliSeq for Illumina TCR beta-SR Panel. The quality of TCR libraries was assessed using Bioanalyzer2100-High Sensitivity DNA kit (Agilent) and Qubit Fluorometric – Qubit dsDNA HS Assay kit (ThermoFisher Scientific).

value: Tumor infiltrating lymphocytes


title: TIL429

description: Library name: Sample 8


title: CDK12 WT, metastatic prostate adenocarcinoma - 2

description: Library name: SI_38469

data_processing:
library strategy: spatial transcriptomics
For analyzing the spatial transcriptomics data, FASTQ files were generated from the raw base call files using 10x Genomics Space Ranger v3.1.0 mkfastq. The gene count matrices at an 8µm bin size were generated from the FASTQ files using the count command and the 10x supplied human probe-set reference. The data were processed using Seurat v5.1.0 [52]. The 8 µm bin size spots were clustered using sketch-based clustering and integrated across conditions for downstream analyses according to the Seurat Visium HD workflow.
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image for each sample
Supplementary files format and content: aligned_tissue_image.jpg: aligned CytAssist and tissue images for each sample
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes for each sample
Supplementary files format and content: cytassist_image.tiff: CytAssist image for each sample
Supplementary files format and content: detected_tissue_image.jpg: detected tissue areas in image for each sample
Supplementary files format and content: features.tsv.gz: list of gene IDs for each sample
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format for each sample
Supplementary files format and content: scalefactors_json.json: image scaling factors for each sample
Supplementary files format and content: tissue_hires_image.png: high resolution tissue image for each sample
Supplementary files format and content: tissue_lowres_image.png: low resolution tissue image for each sample
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and their respective positions in the tissue image for each sample

source_name: Lymph node

extract_protocol:
Spatial transcriptomics was performed using the Visium HD, Human Transcriptome (10x Genomics; #1000673) and Visium CytAssist (10x Genomics; #1000441) following the instructions from the manufacturer. Briefly, 5 µm FFPE tissue on tissue slide was applied to HE staining, imaging, destaining, and decrosslinking. Tissue was nexted permeabilized and hybridized with human transcriptomic probes overnight. Hybridized probes were then transferred to the Visium slide, which contains millions of barcodes, through the CytAssist instrument.
cDNAs were synthesized and amplified with sample indexes for the final libraries. Quality of the libraries was evaluated by Agilent Bioanalyzer.

value: Lymph node

value: CDK12 WT


title: TIL412

description: Library name: Sample 7


title: TIL435

description: Library name: Sample 10


title: V1PKO_Rad21712CR_DN_2

description: Library name: V1PKO_Rad21712CR_DN_2


title: TIL391

description: Library name: Sample 4


title: HCC, miR-885-5p_3

description: Library name: Sample 6

value: Epithelial-like

value: hsa-miR-885-5p overexpress


title: CDK12 WT, metastatic prostate adenocarcinoma - 1

description: Library name: SI_38364


title: TIL393

description: Library name: Sample 5


title: HTS_SO85_10_EbKO_Rad211206CR_DN_3_S10

description: Library name: HTS_SO85_10_EbKO_Rad211206CR_DN_3_S10


title: TIL343

description: Library name: Sample 2


title: HTS_SO85_06_RCTKO_Rad211206CR_DN_2_S6

description: Library name: HTS_SO85_06_RCTKO_Rad211206CR_DN_2_S6


title: TIL390

description: Library name: Sample 3


title: CDK12 mutated, metastatic prostate adenocarcinoma - 2

description: Library name: SI_38363

value: CDK12 mutated


title: TIL326

description: Library name: Sample 1


title: HTS_SO85_02_RCTKO_Rad211030CR_DN_1_S2

description: Library name: HTS_SO85_02_RCTKO_Rad211030CR_DN_1_S2


title: HEK293T cells, disome fraction

city: Heidelberg

first: Günter

last: Kramer

address: Im Neuenheimer Feld 329

institute: Center for Molecular Biology of Heidelberg University (ZMBH)

description:
Library name: HEK293T_Dis
Footprints (approx. 30nt) from Disome fraction

data_processing:
The 3' adaptor sequences were trimmed form demultiplexed raw read sequencing files with Cutadapt (v1.13) with the following command for NextSeq550 files: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a ATCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz. For samples sequenced on HiSeq2000 the following command was used: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz
Unique molecular identifiers (UMIs) were extracted from each read for the downstream analysis using a custom Julia script (available as supplement information in Bertolini et al., 2021) with the following command: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 2. Only samples 5-8 did not contain UMI sequences in the adaptors, therefore this step was not included for U2OS samples.
For removal of human rRNA contaminants, sequenced libraries were aligned to rRNA sequences including: RNA45SN1 - RNA45SN5 (human 28S, 18S, 5.8S), RNA5S1 (human 5S), MTRNR2L10 (Mito 16S), MT-RNR1 (Mito 12S), MT-RNR2U1 (Mito 16S), 22 mito tRNAs, 631 nuclear human tRNAs. All rRNA contaminations were removed by Bowtie2 (v.2.3.5.1) with the following command: bowtie2 -p4 -t -x <path_to_folder_with_Bowtie-indexed_rRNA_contamination> -q <path_to_input_file>.fastq.gz' --un <path_to_output_file>.fastq -S /dev/null
Reads that did not align to rRNA were aligned to the human genome (GRCh38p10) using STAR (v2.7.1a) with the following command: STAR --runThreadN 24 --genomeDir <path_to_indexed_genome> --readFilesIn <path_to_input>.fastq --outFilterMultimapNmax 1 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix <path_to_output> --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
All reads aligning to the coding sequence (CDS) were assigned (a-, p-, e-site) via a custom Julia script (available as supplement information in Bertolini et al., 2021). p-site assigned reads were used for all downstream analysis. This script accounts for soft-clipping via the '-c 1' option: the integer indicates the bases at the 5' end that often arise from untemplated addition by the reverse transcriptase during library preparation by using the following command: julia <path_to_script>/Script2.jl -c 1 -g <path_to_genome_annotation>.gff' -u -o <path_to_output> <path_to_input>.bam
Assembly: Human genome (GRCh38p10)
Supplementary files format and content: HDF5 files containing raw reads assigned to ribosomal P-sites, organised by coding sequence (CDS). Depending on the library preparation method PCR duplicates are removed based on the unique molecular identifier (UMI).
Library strategy: Ribo-Seq

source_name: Embryonic kidney

growth_protocol: Human cells were cultivated in DMEM with GlutaMAX, pyruvate, 10% FCS, pen/strep, 37°C, 5% CO2, humidified. Cells were passaged regularly through trypsinization. For all experiments cells were seeded 18-24 hours before lysis in 15 cm2 dishes (3.5 million U2OS and 6 million HEK293-T cells) to reach 70-90% confluency at the time of harvesting.

extract_protocol:
RNA from frozen ribosome fractions was extracted using the hot acid phenol method as described in Galmozzi and Merker et al. 2019
Libraries from isolated ribosome footprints were prepared following the previously published protocol (Galmozzi and Merker et al. 2019)

value: Embryonic kidney

tag: fraction

value: disome fraction

value: wild type

value: 150 mM KCl-containing lysis buffer


title: V1TxS DNs GRO-Seq 2

description: Library name: HTS_SO100_04_V1TxS_2_S4

library_source: other

data_processing:
GRO-Seq reads were trimmed using bbduk as part of bbmap (version 38.92) (https://sourceforge.net/projects/bbmap/). Reads were then aligned to mm10 using STAR (version 2.7.9a) (https://pubmed.ncbi.nlm.nih.gov/23104886/). bamCoverage from the deeptools package (version 3.5.1) (https://pubmed.ncbi.nlm.nih.gov/27079975/) yielded the bigwig coverage files and was run using flags to separate the coverage tracks by stranded-ness and to normalize to counts per million (cpm). Normalized bigwig coverage files were uploaded to the UCSC genome browser (https://pubmed.ncbi.nlm.nih.gov/12045153/). Gene expression levels were quantified using TPMcalculator (version 0.0.3) (https://pubmed.ncbi.nlm.nih.gov/30379987/) with the GENCODE annotation for the mm10 genome (version M23_GRCm38.p6). For normalization and identification of significantly differentially expressed genes, the raw read counts were analyzed with the limma-voom package from Bioconductor (version 3.54.2)(Law et al., 2014).
Assembly: mm10
Supplementary files format and content: bigwig coverage files as produced by bamCoverage. The coverage is seperated into reads originating from the forward (fwd) or reverse (rev) strand.
Library strategy: GRO-Seq

molecule: other

extract_protocol:
(B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes were sorted from Rag1-/- mice.
Following the isolation of nascent RNA, the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Kit (20040525) with the IDT for Illumina RNA UD Indexes Set A (20040529) were used for library prep minus the ribosomal RNA depletion steps.


title: CDK12 mutated, metastatic prostate adenocarcinoma - 1

description: Library name: SI_38361

source_name: Bladder

value: Bladder


title: HTSSO57_V1TxS_Rad210712CR_DN_1

description: Library name: HTSSO57_V1TxS_Rad210712CR_DN_1


title: V1TxS DNs GRO-Seq 1

description: Library name: HTS_SO100_03_V1TxS_1_S3


title: HEK293T cells, monosome fraction

description:
Library name: HEK293T_Mono
Footprints (approx. 30nt) from monosome fraction

value: monosome fraction


title: TIL404

description: Library name: Sample 6


title: WT DNs GRO-Seq 2

description: Library name: HTS_SO100_02_R1KO_2_S2


title: CN210 Control ATAC

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

description: 10x genomics (scMultiome-SEQ)

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ARC software v7.0  (https://www.10xgenomics.com/support/software/cell-ranger-arc/latest)
CellRanger count and aggr functions to aggregate reads across sequencing lanes into a single set of  barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (CellRanger ARC output files:  barcodes.tsv.gz, features.tsv.gz,matrix.mtx.gz)

source_name: Blood

extract_protocol:
Human peripheral blood mononuclear cells were isolated by Ficoll-Paque density gradient centrifugation and cryopreserved 2x10e6 cells per sample. Cell viability was 95% or greater for all samples. PBMCs were quickly thawed at 37°C in a water bath and washed with culture medium RPMI 1640 supplemented with 10% FBS. DNase treatment was done before the nuclei isolation. The nuclei isolation was conducted with an RNase inhibitor. Nuclei suspension was filtered with a 40μm cell strainer and counted in a Countess 3 FL Automated Cell Counter (Invitrogen); all samples had <5% live cells. High-quality nuclei were checked by 60x brightfield microscopy. The targeted number of nuclei was 5000 nuclei per sample. Finally, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) was used to generate single-cell multiome data.
CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevF (Using a microfluidic chip, the nuclei of different patients are partitioned into nanoliterscale Gel Beads-in-emulsion (GEMs) with thousands of Barcodes to separately and uniquely index the transposed DNA and cDNA of each individual nucleus. ATAC and gene expression (GEX) libraries are generated from the same pool of pre-amplified transposed DNA/cDNA and sequenced)

value: Blood

value: PBMCs

value: control


title: WT DNs GRO-Seq 1

description: Library name: HTS_SO100_01_R1KO_1_S1

value: Rag1-/- DN thymocytes


title: CN209 Control ATAC

description: 10x genomics (scMultiome-SEQ)


title: V1TxS_Nipbl0816CR_DN_2

description: Library name: V1TxS_Nipbl0816CR_DN_2

value: Nipbl


title: HTSSO52_V1TxS_Rad210712CR_DN_2

description: Library name: HTSSO52_V1TxS_Rad210712CR_DN_2


title: HTS_SO85_20_EbKO_Rad211212CR_DN_4_S20

description: Library name: HTS_SO85_20_EbKO_Rad211212CR_DN_4_S20


title: RPTEC-TERT1 cell KO2, biol rep 4

city: London

first: Maria

last: Caluianu

address: Gower Street

country: United Kingdom

institute: University College London

description: Library name: Sample12

data_processing:
nf-core/rnaseq pipeline v3.12.0
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: RPTEC-TERT1 cells (ATCC, #CRL-4031™) were cultured in DMEM:F12 Medium (ATCC® 30-2006™), supplemented with hTERT RPTEC Growth Kit (ATCC® ACS-4007™) (1% Supplement A and 1.6% Supplement B), 2% FBS, and 0.1 mg/mL Geneticin™ Selective Antibiotic (G418 Sulfate) (Thermo Fisher, #10131035). Cells were cultured at 37 °C with 5% CO2.

extract_protocol:
RPTEC-TERT1 Control, KO1, and KO2 clones were cultured to 70-80% confluency before RNA extraction with the RNeasy Plus Mini kit (QIAGEN, #74136). 1.0 µg of total RNA was used for the construction of the libraries
RNA for RNA-seq libraries was prepared with with the Watchmaker RNA Library Prep Kit with Polaris™ Depletion following manufacturer's protocol

value: Proximal tubule

value: VPS33B KO


title: RPTEC-TERT1 cell KO2, biol rep 3

description: Library name: Sample11


title: RPTEC-TERT1 cell KO2, biol rep 1

description: Library name: Sample9


title: RPTEC-TERT1 cell KO2, biol rep 2

description: Library name: Sample10


title: CN205 Control ATAC

description: 10x genomics (scMultiome-SEQ)


title: CN206 Control ATAC

description: 10x genomics (scMultiome-SEQ)


title: V1PKO_Nipbl0816CR_DN_2

description: Library name: V1PKO_Nipbl0816CR_DN_2


title: RPTEC-TERT1 cell KO1, biol rep 3

description: Library name: Sample7


title: RPTEC-TERT1 cell KO1, biol rep 4

description: Library name: Sample8


title: RPTEC-TERT1 cell KO1, biol rep 2

description: Library name: Sample6


title: AA043 Patient ATAC

description: 10x genomics (scMultiome-SEQ)

value: alopecia areata


title: V1PKO_Nipbl0816CR_DN_1

description: Library name: V1PKO_Nipbl0816CR_DN_1


title: RPTEC-TERT1 cell KO1, biol rep 1

description: Library name: Sample5


title: AA041 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: RPTEC-TERT1 cell control, biol rep 3

description: Library name: Sample3

value: WT


title: V1CScr_Nipbl0816CR_DN_1

description: Library name: V1CScr_Nipbl0816CR_DN_1


title: AA035 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: R1KO_Nipbl0816CR_DN_2

description: Library name: R1KO_Nipbl0816CR_DN_2


title: RPTEC-TERT1 cell control, biol rep 2

description: Library name: Sample2


title: AA034 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: Naïve CD8 T cells, WT, rep 4

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description: Library name: WT5

data_processing:
Quantification of gene abundance for each sample was performed by Salmon v1.4.068 and genes were kept for subsequent analysis if they contained more than 10 reads in at least one sample.  Normalization and differential gene expression was performed using the DESeq269 1.42.0 Bioconductor (Axten et al., 2013) package in R.  Gene set enrichment analysis70 was performed using the fgsea 1.28.0 Bioconductor package. Gene sets were obtained from the mouse Hallmark Pathways 71, and human C7 ImmuneSigDB  MSigDB13 (v2023.1).
Additional GSEA was performed on two datasets derived from Miller et al. (2019)44.  Signatures for TEXprog CD8+ T cells and TEXterm CD8+ T cells were identified by selecting all genes with an adjusted p-value less than or equal to 0.05 and a log2 fold change greater than 1.5 (TEXprog) or less than -1.5 (TEXterm)
Assembly: GRCm38_p6_vM25
Supplementary files format and content: tab delimited file contains raw counts for all samples

molecule: polyA RNA

source_name: Spleen

growth_protocol: CD8+ T Cells were purified from spleens of naïve mice using the EasySep Mouse CD8+ T Cell Isolation Kit (STEMCELL Technologies) according to the manufacturer’s instructions.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer’s instructions.
Libraries were constructed with the TruSeq Standard mRNA kit (Illumina) according to the manufacturer’s instructions. Dual-indexed libraries were sequenced on an IlluminaNextSeq2000 P2 flow cell with 2x50 bp paired end reads to a depth of approximately 50 million clusters.

value: Spleen

value: Naive CD8 T Cells


title: R1KO_Nipbl0816CR_DN_1

description: Library name: R1KO_Nipbl0816CR_DN_1


title: Naïve CD8 T cells, WT, rep 3

description: Library name: WT4


title: Naïve CD8 T cells, WT, rep 1

description: Library name: WT1


title: V1TxS_Nipbl0816CR_DN_1

description: Library name: V1TxS_Nipbl0816CR_DN_1


title: Naïve CD8 T cells, ATF4 overexpression, rep 4

description: Library name: ATF4OE5

value: ATF4 Tg/Tg


title: HTS_SO85_21_EbKO_Nipbl1212CR_DN_4_S21

description: Library name: HTS_SO85_21_EbKO_Nipbl1212CR_DN_4_S21


title: AA033 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: Naïve CD8 T cells, ATF4 overexpression, rep 3

description: Library name: ATF4OE4


title: HTS_SO85_11_EbKO_Nipbl1206CR_DN_3_S11

description: Library name: HTS_SO85_11_EbKO_Nipbl1206CR_DN_3_S11


title: Naïve CD8 T cells, ATF4 overexpression, rep 1

description: Library name: ATF4OE1


title: V1CScr_Nipbl0821CR_DN_2

description: Library name: V1CScr_Nipbl0821CR_DN_2


title: AA042 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: RPTEC-TERT1 cell control, biol rep 1

description: Library name: Sample1


title: Japanese quail, Nucleus Taeniae, Long Photoperiod, Sample 6

city: Glasgow

first: Tyler

last: Stevenson

address: Jarret Building

department: School of Biodiversity, One Health, and Comparative Medicine

institute: University of Glasgow

description: Library name: Quail Tn 33

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25bp reads)
Minimap2 used to align reads to either Mus musculus (GRCm39) or Coturnix japonica (2.0) genome
Transcript expression levels generated using Salmon
Assembly: GCF_000001635.27 (Mus musculus) or GCF_001577835.1 (Coturnix japonica)
Supplementary files format and content: Comma Separated Values Files with expressed gene transcripts for each sample

organism: Coturnix japonica

source_name: Nucleus Taeniae

extract_protocol:
RNA was extracted using TRIzol reagent according to manufacturer instructions and cleaned using a Qiagen RNEasy MinElute Cleanup Kit
RNA was processed into cDNA libraries using the SQK PCB 111.24 cDNA Barcoding Kit (Oxford Nanopore Technologies) according to manufacturer instructions

value: Nucleus Taeniae

value: Long 18L Photoperiod


title: Naïve CD8 T cells, ATF4 overexpression, rep 2

description: Library name: ATF4OE2


title: V1CScr_Rad210712CR_DN_2

description: Library name: V1CScr_Rad210712CR_DN_2


title: AA049 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: HTS_SO85_07_RCTKO_Nipbl1206CR_DN_2_S7

description: Library name: HTS_SO85_07_RCTKO_Nipbl1206CR_DN_2_S7


title: AA040 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: AA038 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: Japanese quail, Nucleus Taeniae, Long Photoperiod, Sample 5

description: Library name: Quail Tn 31


title: HTS_SO85_03_RCTKO_Nipbl1030CR_DN_1_S3

description: Library name: HTS_SO85_03_RCTKO_Nipbl1030CR_DN_1_S3


title: Japanese quail, Nucleus Taeniae, Long Photoperiod, Sample 3

description: Library name: Quail Tn 10


title: AA037 Patient ATAC

description: 10x genomics (scMultiome-SEQ)


title: Japanese quail, Nucleus Taeniae, Long Photoperiod, Sample 4

description: Library name: Quail Tn 30


title: Japanese quail, Nucleus Taeniae, Long Photoperiod, Sample 2

description: Library name: Quail Tn 9


title: Naïve CD8 T cells, WT, rep 2

description: Library name: WT2


title: Japanese quail, Nucleus Taeniae, Long Photoperiod, Sample 1

description: Library name: Quail Tn 7


title: V1TxS_H3K27ac0727CR_DN_2

description: Library name: V1TxS_H3K27ac0727CR_DN_2


title: V1TxS_H3K27ac0724CR_DN_1

description: Library name: V1TxS_H3K27ac0724CR_DN_1


title: Japanese quail, Nucleus Taeniae, Short Photoperiod, Sample 4

description: Library name: Quail Tn 40

value: Short 6L Photoperiod


title: Japanese quail, Nucleus Taeniae, Short Photoperiod, Sample 5

description: Library name: Quail Tn 41


title: Japanese quail, Nucleus Taeniae, Short Photoperiod, Sample 6

description: Library name: Quail Tn 47


title: R1KO_H3K27ac0727CR_DN_2

description: Library name: R1KO_H3K27ac0727CR_DN_2


title: Japanese quail, Nucleus Taeniae, Short Photoperiod, Sample 3

description: Library name: Quail Tn 23


title: Japanese quail, Nucleus Taeniae, Short Photoperiod, Sample 2

description: Library name: Quail Tn 18


title: R1KO_H3K27ac0727CR_DN_1

description: Library name: R1KO_H3K27ac0727CR_DN_1


title: CN209 Control GEX

description: 10x genomics (scMultiome-SEQ)


title: Japanese quail, Hippocampus, Long Photoperiod, Sample 6

description: Library name: Quail Hp 33

source_name: Hippocampus

value: Hippocampus


title: Japanese quail, Nucleus Taeniae, Short Photoperiod, Sample 1

description: Library name: Quail Tn 11


title: Day3_QA-92-TQ17_replicate3

city: San Diego

first: Bin

last: Fang

state: CA

address: 10675 John Jay Hopkins Dr

department: Discovery Science

institute: Novartis

description: 10x Genomics

data_processing:
Raw reads were mapped to the mm10 mouse reference genome and a per-cell count matrix was generated using CellRanger pipeline (10X Genomics, version 5.0.1).The processed count matrix was used to filter out low quality cells with <700 detected genes or >10% mitochondrial reads. Doublets were identified using DoubletFinder with default parameters and excluded from downstream analysis.
Assembly: mm10
Supplementary files format and content: tab delimited text files with cell barcodes, gene ids, and raw counts.

source_name: lung organoids

growth_protocol: Adult Hopx-GFP+ mice were sacrificed with isoflurane, perfused with PBS through the right ventricle, and the lungs were extracted. Trachea, connective tissue, and upper bronchiole was removed under dissection, microscope. Lungs were cut into small pieces (>2 mm2) and incubated in protease solution for 30 minutes at 37°C in a shaking incubator. Protease solution contained: 450 U/mL Collagenase Type I (Gibco; 17100–017), 4 U/mL Elastase (Worthington Biochemical Company; LS002279), Dispase 5 U/mL (BD Biosciences;354235), and 0.33 U/mL DNaseI (Roche; 10104159001) dissolved in DMEM/F12 (Gibco; 11320033). Digestion enzymes were inactivated with DMEM/F12 + 10% FBS, cells were centrifuged at 500g and resuspended in Trypsin/DNAse solution and incubated for 30 minutes at 37°C in a shaking incubator. Trypsin/DNase solution contained: 0.1% Trypsin-EDTA (Gibco, 25200056) + 0.13 U/mL DNaseI (Roche; 10104159001) in DMEM/F12. Trypsin/DNase solution was inactivated with DMEM/F12 + 10% FBS, cells were filtered through a 70 μM cell strainer, centrifuged at 300g (2x), resuspended in RBC cell lysis buffer (Sigma; R7757), and digestion enzymes inactivated with DMEM/F12 + 10% FBS. Cells were centrifuged at 500g, resuspended in DMEM/F12 + 2% FBS, counted on a hemacytometer, and diluted to 1 x 10^6 cells per mL. Cells were filtered through a 40 μM cell strainer, resuspended 1:1 in Matrigel Growth Factor Reduced (Corning; 354230), and 4-7 drops of 50 μL cells-medium/Matrigel mixture in each well of a 6-well plate. Once solidified 2 mL of ITS media was added per well and plates were incubated in a standard cell culture incubator. ITS media contained: DMEM/F12 + 5% FBS, 1/100 ITS-G (Gibco; 41400045), 1/100 Antibiotic-Antimycotic (Gibco; 15240096), 0.5 ng/mL TGFβ1 (R&D Systems; 240-B-002). Fresh ITS media was added on top after 4-5 days in culture.

extract_protocol:
At designated times (day 0, day 1, day 3, day 11) cells were removed from Matrigel. Briefly, media was removed and washed with ice cold PBS. TrypLE Express (Gibco; 12604013) was added to wells and incubated at 37°C, followed by scraping of Matrigel bubbles to collect in a 15 mL conical tube. Cells were mechanically disrupted by pipetting ~10 times and incubated at 37°C for an additional 10 minutes. Cells were mechanically disrupted again and enzyme was inactivated with DMEM/F12 + 10% FBS + 1/100 Penicillin-Streptomycin (Gibco; 15140122). Cells were centrifuged at 300g at 4°C, resuspended to 1000 cells/ μL in DMEM/F12 + 10% FBS, and filtered through a Flowmi 40 μM cell strainer (Sigma; BAH136800040).
The Chromium Next GEM Single Cell 3’ reagent kit v3.1 from 10X Genomics (protocol CG000204 Rev C) was used in scRNA-seq library preparation. Single-cells were partitioned into nanoliter-scale Gel Beads-inemulsion (GEMs) using Chromium Controller. Upon cell lysis, the poly-A tails of mRNA are captured on the beads containing an Illumina read 1 sequencing primer, 16nt 10X barcode, 12nt UMI and 30nt poly (dT) sequence. Reverse transcription occurs followed by amplification of full-length cDNA from polyA mRNA. Enzymatic fragmentation and size-selection was used to optimize cDNA amplicon size. End repair, Atailing, Adaptor ligation and PCR create the final sequencing libraries that contain the P5 and P7 primers used in Illumina bridge amplification.
The libraries were sequenced using NextSeq 550 High Output Kit v2.5 (150 cycles).

treatment_protocol: Compounds (DMSO, DB-11-BE87, or QA-92-TQ17) were added at time of plating (10 μM final concentration). Day 0 samples have no treatment.

value: lung organoids

value: lung cells

value: TGFB1 + QA-92-TQ17


title: Japanese quail, Hippocampus, Long Photoperiod, Sample 5

description: Library name: Quail Hp 31


title: CN206 Control GEX

description: 10x genomics (scMultiome-SEQ)

value: Blood

value: PBMCs

value: control


title: HTS_S065_05_R1KO_2

description: Library name: HTS_S065_05_R1KO_2

value: Rag1-/- DN thymocytes


title: EbKO_H3K27ac10727CR_DN_1

description: Library name: EbKO_H3K27ac10727CR_DN_1


title: CN205 Control GEX

description: 10x genomics (scMultiome-SEQ)


title: Day3_QA-92-TQ17_replicate2

description: 10x Genomics


title: Japanese quail, Hippocampus, Long Photoperiod, Sample 4

description: Library name: Quail Hp 30


title: Misc_IgGcntrl0905CR_DN

description: Library name: Misc_IgGcntrl0905CR_DN

value: IgG


title: AA032 Patient ATAC

description: 10x genomics (scMultiome-SEQ)

value: alopecia areata


title: Japanese quail, Hippocampus, Long Photoperiod, Sample 3

description: Library name: Quail Hp 10


title: AA043 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: Day3_QA-92-TQ17_replicate1

description: 10x Genomics


title: Day3_DMSO_replicate3

description: 10x Genomics

value: TGFB1 + DMSO


title: AA041 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: Day3_DMSO_replicate2

description: 10x Genomics


title: V1TxS_RNAPol2Ser20905CR_DN_2

description: Library name: V1TxS_RNAPol2Ser20905CR_DN_2


title: CN210 Control GEX

description: 10x genomics (scMultiome-SEQ)


title: AA038 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: EbKO_H3K27ac10727CR_DN_2

description: Library name: EbKO_H3K27ac10727CR_DN_2


title: Japanese quail, Hippocampus, Long Photoperiod, Sample 1

description: Library name: Quail Hp 7


title: V1TxS_RNAPol2Ser20821CR_DN_1

description: Library name: V1TxS_RNAPol2Ser20821CR_DN_1


title: Japanese quail, Hippocampus, Short Photoperiod, Sample 6

description: Library name: Quail Hp 47


title: R1KO_RNAPol2Ser20905CR_DN_2

description: Library name: R1KO_RNAPol2Ser20905CR_DN_2


title: AA035 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: HCC, Control 3

description: Library name: Sample 3

data_processing:
The acquisition of clean data was achieved by filtering and removing raw data that had adapters, low-quality data, and readings with a Q-score below 30. Subsequently, the transcriptome was assembled using StringTie (V2.2.1), and the clean reads were mapped to the human-specific genome GRCH38 using HISAT2 software (V2.0.4). The DESeq2 R software (V1.38.3) was utilized to conduct differential expression analysis between two groups. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized to identify gene biological function and investigate signaling networks.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepare using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: Epithelial-like

value: WT


title: Japanese quail, Hippocampus, Short Photoperiod, Sample 5

description: Library name: Quail Hp 41


title: R1KO_RNAPol2Ser20821CR_DN_1

description: Library name: R1KO_RNAPol2Ser20821CR_DN_1


title: Day3_DMSO_replicate1

description: 10x Genomics


title: Misc_IgGcntrl0821CR_DN

description: Library name: Misc_IgGcntrl0821CR_DN


title: Japanese quail, Hippocampus, Short Photoperiod, Sample 4

description: Library name: Quail Hp 40


title: V1 TxS DNs ChIP H3K4me3 2

description: Library name: HTS056_02_V1TxS_K4me31P_031223_S2

data_processing:
For ChiP-Seq, paired-end reads were aligned to the mm10 genome using bowtie2 (version 2.4.5) (https://pubmed.ncbi.nlm.nih.gov/22388286/). Peak calling was done using the macs2 algorithm (version 2.2.7.1) (https://pubmed.ncbi.nlm.nih.gov/18798982/). Bigwig files for the visualization in the UCSC genome browser were yielded by the bamCoverage tool inside the deeptools package (version 3.5.1) (https://pubmed.ncbi.nlm.nih.gov/27079975/) applying the RPGC normalization. Finally, the bioconducter package chipqc (version 1.30.0) (https://pubmed.ncbi.nlm.nih.gov/24782889/) helped determine our samples had a RiP (Reads in Peaks) score of at least 4.
Assembly: mm10
Supplementary files format and content: bigwig files produced by bamCoverage and normalized by RPGC.

extract_protocol:
ChIP Seq was performed in DN thymocytes from ~5 Rag1-/- mice per experiment with either a WT Tcrb locus or with the indicated mutations with the indicated antibodies.
Library was generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S)


title: AA049 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: Day3_DB-11-BE87_replicate1

description: 10x Genomics

value: TGFB1 + DB-11-BE87


title: AA033 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: Japanese quail, Hippocampus, Short Photoperiod, Sample 3

description: Library name: Quail Hp 23


title: V1 TxS DNs input

description: Library name: HTS038_20_20_V1TxS_1p_input_0310_1_S20

value: input


title: Day3_DB-11-BE87_replicate2

description: 10x Genomics


title: Japanese quail, Hippocampus, Long Photoperiod, Sample 2

description: Library name: Quail Hp 9

value: Long 18L Photoperiod


title: Japanese quail, Hippocampus, Short Photoperiod, Sample 2

description: Library name: Quail Hp 18

value: Short 6L Photoperiod


title: V1 TxS DNs ChIP H3K4me3 1

description: Library name: HTS038_19_19_V1TxS_K4me3_0310_1_S3


title: AA042 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: Day11_QA-92-TQ17_replicate2

description: 10x Genomics


title: AA040 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: Japanese quail, Hippocampus, Short Photoperiod, Sample 1

description: Library name: Quail Hp 11

value: Hippocampus


title: Day3_DB-11-BE87_replicate3

description: 10x Genomics

value: lung organoids


title: WT DNs input

description: Library name: HTS038_05_5_R1KO_1p_input_1228_S5


title: Day11_QA-92-TQ17_replicate1

description: 10x Genomics

value: lung cells


title: AA037 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: AA034 Patient GEX

description: 10x genomics (scMultiome-SEQ)


title: Day11_DMSO_replicate4

description: 10x Genomics


title: GD+β-OHB

city: Hefei

first: Rui

last: Li

state: Anhui

address: Yuhuangshan Road, Thirty Head Street

department: cell biology

institute: Anhui Medical University

description: Library name: sample4

data_processing:
The sequencing library adopts various second-generation sequencing platforms such as NovaSeq, etc
Perform sequencing. The library will be converted into the initial output file basecall files using advanced optical equipment in the sequencing instrument; Then utilize
The bcl2fastq software converts these output files basecall files into FASTQ files corresponding to each library on each lane in FlowCell
At this point, the FASTQ file is raw sequencing data that has not undergone quality control
Assembly: hg38
Supplementary files format and content: bigWIG
Library strategy: CUT&Tag

extract_protocol:
Collect cells at room temperature and count them. The collected cells were resuspended in 900 μ l PBS. If transcription factors are detected instead of histones, the cross-linking reaction can be terminated by first crosslinking with 37% formaldehyde (2.7 μ l) for 10 minutes, then adding 1.25M 10 × glycine at room temperature for 5 minutes. Take the required number of cells for the experiment and place them in a 1.5 ml EP tube. Centrifuge at low speed of 2500 rpm (600 × g) for 5 minutes at room temperature, and discard the supernatant. (During centrifugation, the EP tube is oriented in the same direction for easy confirmation of the sedimentation position) Add 500 μ l of Wash Buffer to resuspend cells at room temperature, centrifuge at low speed of 2500 rpm (600 × g) for 5 minutes, and discard the supernatant. Add 100 μ l of Wash Buffer to resuspend cells for each sample.
Mix VAHTS DNA Clean Beads (Vazyme # N411) with vortex oscillation and aspirate 100 μ l into the PCR reaction product mentioned above. Vortex or pipette 10 times to ensure uniformity of the entire system, and incubate at room temperature for 5 minutes. Beads need to be incubated at room temperature for 15 minutes in advance ▲ Magnetic beads are quite viscous, use a pipette to ensure sufficient volume is taken and slowly ejected. 2. The reaction tube is briefly centrifuged and placed on a magnetic rack to separate the magnetic beads and liquid. After the solution is clarified (about 5 minutes), carefully remove the supernatant and be careful not to disturb the magnetic beads. 3. Keep the PCR tube always on the magnetic rack, add 200 μ l of freshly prepared 80% ethanol to rinse the magnetic beads, incubate at room temperature for 30 seconds, and carefully remove the supernatant. 4. Repeat step 3 and rinse twice in total. 5. Keep the PCR tube on the magnetic rack at all times, open the lid and air dry for 3-5 minutes. 6. After drying the magnetic beads, remove the PCR tube from the magnetic rack and add 22 μ l ddH2O for elution. Vortex or use a pipette to blow the beads 10 times and mix thoroughly. Incubate at room temperature for 5 minutes. 7. Centrifuge the PCR tube briefly and place it on a magnetic rack to separate the magnetic beads and liquid. After the solution becomes clear (about 5 minutes), carefully transfer 20 μ l of supernatant to a new EP tube and store at -30~-15 ℃. Measure DNA concentration, usually between 10-100 ng/ul.

value: GD+β-OHB


title: WT DNs ChIP H3K4me3 2

description: Library name: HTS038_04_4_R1KO_K4me3_1228_Neb_S4


title: AA032 Patient GEX

description: 10x genomics (scMultiome-SEQ)

value: Blood


title: V1P KO/KO DNs input

description: Library name: 28_CB02-V1PKO-DN_ChIP_input_0616_COLib25


title: Day11_DMSO_replicate3

description: 10x Genomics


title: V1P KO/KO DNs ChIP H3K4me3 1

description: Library name: 27_CB02-V1PKO-DN_ChIP_H3K4me3_0616_COLib25


title: MIX treatment, biological replicate 1

city: New York

first: Anna

last: Podlesny-Drabiniok

state: NY

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v2.1.1
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files

growth_protocol: THP-1 monocytic leukemia line was differentiated to THP-1 macrophages for 72h in 25ng/ml 12-phorbol 13-myristate acetate (PMA).

extract_protocol:
Control or cytokine treated THP-1 macrophages were first washed with PBS, then trypsinized for 10 min at 37°C (Gibco, cat. 25200). Trypsinization was halted by the addition of an equal volume of warm RPMI medium with 10mM HEPES and 10% FBS, cells were spun at 400×g for 5 min and resuspended in 1.0% PBS/bovine serum albumin (BSA). Cells were filtered through 40μm cell strainer to exclude cell clumps.
Gel bead-in-emulsion (GEM) encapsulation and single cell indexing reactions were performed using a Chromium X™ Controller instrument (10× Genomics, Inc., Cat. No. 1000202). Single-cell 3’ RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit (version 3.1 chemistry, 10× Genomics, Inc., Cat. No. 1000121), according to the manufacturer’s instructions.

treatment_protocol: THP-1 macrophages were treated with 20ng/ml IL-4, 25ng/ml M-CSF, 50ng/ml TGF-β and 100ng/ml IL-34 for 2 days and cells were collected.

value: THP-1 macrophages

value: MIX


title: MIX treatment, biological replicate 2


title: no cytokines, biological replicate 2

value: non-treated


title: GD

description: Library name: sample2

value: GD


title: Day11_QA-92-TQ17_replicate3

description: 10x Genomics

value: TGFB1 + QA-92-TQ17


title: Ctrl

description: Library name: sample1

value: Ctrl


title: WT DNs ChIP H3K4me3 1

description: Library name: 23_CB02-WT-DN_ChIP_H3K4me3_0616_COLib25

value: Rag1-/- DN thymocytes


title: Day11_DMSO_replicate2

description: 10x Genomics

value: TGFB1 + DMSO


title: Day11_DMSO_replicate1

description: 10x Genomics


title: Adult_BMMC_AML_sample1_DNA

city: Miami

first: Katarina

last: Micin

state: Florida

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
Illumina NovaSeq S4 200 V1.5
Demultiplexing, adaptor trimming, reference genome alignment, barcode processing, and DNA variant calling was performed using the Tapestri MRD-AML DNA + Protein v1.0.2 pipeline.
Assembly: hg19
Supplementary files format and content: Mission Bio output files: POSTPROCESS_per_sample.h5 - contains per-sample DNA variants, clone assignments, and DNA + protein read count data.

source_name: bone marrow

extract_protocol:
Prospective patient bone marrow sample collection; CD34 and CD117- enriched single cells were oil encapsulated and barcoded to prepare the DNA and protein libraries according to the Tapestri® Single-Cell DNA + Protein Sequencing v3 User Guide (https://support.missionbio.com/hc/en-us/article_attachments/18345161765655).
Two cryopreserved bone marrow mononuclear cell (BMMC) samples were prepared for scMRD DNA and AOC library generation and sequencing as outlined by Mission Bio in the BMMC Preparation for Tapestri® Single-Cell MRD User Guide (https://support.missionbio.com/hc/en-us/article_attachments/17880236165527).
Single-Cell (Mission Bio)

value: bone marrow

value: bone marrow mononuclear cells

tag: library type

value: DNA


title: no cytokines, biological replicate 1

value: WT


title: Day11_DB-11-BE87_replicate3

description: 10x Genomics

value: TGFB1 + DB-11-BE87


title: Adult_BMMC_AML_sample1_Protein

molecule: protein

value: AOC

tag: aoc

value: TotalSeq™- D Heme Oncology Cocktail


title: DNMT3A knockout, endometriosis model, replicate 3

city: Houston

first: Nuri

last: Sung

state: Texas

address: One Baylor plaza, Houston, Rm807

department: Molecular and Cellular biology

institute: Baylor college of Medicine

description: Library name: BO_72140

data_processing:
Galaxy server version24.2.4.dev0
Adapter trimming was performed using Trimmomatic in Galaxy.
Reads were aligned to the Mus musculus genome (GRCm39).
Gene-level quantification was performed using featureCounts.
Differential expression analysis was performed with DESeq2.
Assembly: GRCm39
Supplementary files format and content: Gene-level count matrix (rows: genes, columns: samples) generated by featureCounts. Differential expression results includeGeneID,Gene name,Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj,-log10.

source_name: mouse endometriosis

growth_protocol: Uterine horns from female mice (either wild-type or DNMT3A knock-out) were dissected and then cut into 20 small fragments. These tissue fragments were pipetted into 1 ml of 1X PBS to create a suspension. The suspension was then loaded into a 1 ml syringe and intraperitoneally injected into wild-type recipient mice that had received estrogen pellets one week earlier.

extract_protocol:
RNA was extracted using the RNeasy Mini Plus kit (Qiagen). For constructing sequencing libraries, 1.3 µg of RNA was used.
The Sample Quality was checked by using the NanoDrop spectrophotometer, Invitrogen Qubit 2.0 quantitation assay and Agilent Bioanalyzer. Library was prepared by using Illumina TruSeq Stranded mRNA library preparation protocol.

value: mouse endometriosis

value: DNMT3A knock-out

tag: time

value: 4 weeks


title: Day11_DB-11-BE87_replicate2

description: 10x Genomics

value: lung organoids

value: lung cells


title: Testis, adult, 1 day old, ATAC, rep4

first: Ingrid

last: Lohmann

address: Im Neuenheimer Feld 230

institute: Centre for Organismal Studies Heidelberg

data_processing:
The 10x genomics Cell Ranger ARC v2.0.2 pipeline was used in Cluster mode on a slurm-enabled system.
Assembly: BDGP6.32, Ensemble release 107
Supplementary files format and content: All processed files are direct outputs from the Cell Ranger ARC pipeline.

organism: Drosophila melanogaster

source_name: Testis

extract_protocol:
Flash-frozen nuclei were pooled per replicate. Tissue was dounced in 1x lysis buffer (10x Genomics protocol CG000366, RevD), followed by 3x centrigugation and filtering at 700g for 7 min.
Libraries were constructed according to 10x Genomics Single Cell Multiome ATAC + Gene Expression v1 chemistry, protocol CG000338 Revision E.

value: Testis


title: DNMT3A knockout, endometriosis model, replicate 2

description: Library name: BO_72139


title: Day11_DB-11-BE87_replicate1

description: 10x Genomics


title: β-OHB

description: Library name: sample3

value: β-OHB


title: DE HELLS KO rep1 ATAC

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

institute: Max Planck Institute for Molecular Genetics

data_processing:
The sequencing reads were aligned to the human hg19 and T2T reference genome using BWA mem using the default parameter.
Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Narrow peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Assembly: hg19 and T2T (CHM13v2.0)
Supplementary files format and content: bigWig coverage files and MACS2 narrow peak call files

source_name: cell line

extract_protocol:
Two replicates each of undifferentiated iPSCs and endoderm differentiated cells were harvested using a single-cell suspension (see growth protocol) and prepared for FACS analysis. ZIP8K8 single-cell suspensions were quenched DPBS-10% Fetal bovine serum (FBS, PAN Biotech, #P30-2602)). Next, cells were centrifuged at 4°C. Cells were then resuspended in DPBS-10% FBS containing the surface marker anti-CXCR4 antibody (Biologend, #306506) in a 1:200 dilution and incubated for 15 min at 4 °C in the dark. Next, cells were washed once again with DPBS-10% FBS and centrifuged at 4°C before FACS. Finally, cells were resuspended in DPBS-10% FBS and passed through a 70µm cell strainer (Corning, #431751). FACS analysis was performed on the FACSCelesta Flow Cytometer (Beckton Dickinson). For each replicate 50,000 cells were collected by sorting either NCAM negative iPSCs or positive Endoderm differentiated cells.
ATAC-seq libraries were prepared as described previously (Corces et al., 2017) with minor adjustments. In brief, 50,000 cells were centrifuged at 4°C for 5 minutes at 500 x g. The cell pellet was resuspended in 50ul of a water-based buffer containing 10mM TRIS-HCL pH 7.4 (Thermo Fisher Scientific, #J67501-AK), 10mM NaCl (Thermo Fisher Scientific, #AM9759), 3mM MgCl2 (#AM9530G), 0.1% Igepal (Sigma-Aldrich, #I8896) and 0.1% Tween-20.The lyse the cells the solution was incubated on ice for 3 minutes after which the reaction was quenched with 1ml of the resuspension buffer without lysing reagent (10mM TRIS-HCL pH7.4, 10mM NaCl, 3mM MgCl2, and 0.1% Tween-20). Nuclei were collected by centrifuging the solution for at 4°C for 10 minutes at 500 x g. The supernatant was carefully removed and the nuclei resuspended in 50ul of the DPBS-based transposition mixture consisting of a 2X water-based buffer with 20mM TRIS-HCL pH 7.4, 10mM MgCl2, 20% Dimethyl Formamide (Sigma-Aldrich, #PHR1553), and 0.1% Tween-20, 1% H2O, and 100mM Transposase (EpiCypher, #15-1017). The transposition reaction was incubated in a thermomixer at 37°C for 30 minutes at 1,000 RPM. The reaction was purified using the Zymo Clean & Concentrator 5 Kit following the manufacturer’s instructions for fragmented DNA and eluted in 20ul. The sequencing library was prepared by amplifying the 20ul purified DNA with a total of 50uM Nextera indexing primers using the NEB Q5 Hot Start High Fidelity 2X Master Mix (#M0494L) for 5 minutes at 72°C, 30 seconds of 98°C, and 9 cycles of 30 seconds 98°C, 30 seconds of 63°C, and 1 minutes of 72°C, followed by cooling down to 4°C. The final libraries were purified using Agencourt AMPure XP beads, and diluted to 4nM for sequencing.

value: cell line

value: Definitive Endoderm

value: HELLS KO


title: Testis, adult, 1 day old, GEX, rep4

molecule: nuclear RNA


title: Day1_QA-92-TQ17_replicate3

description: 10x Genomics

value: TGFB1 + QA-92-TQ17


title: DE WT rep 2 ATAC