title: configuration7_short_release_clone8


title: configuration5_short_release_clone8

status: Public on Dec 21 2024

type: SRA

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

country: China

institute: Shenzhen Bay Lab

description: mitosis: condensin(-);extrusive-cohesin(-);cohesive-cohesin(-)

library_source: genomic

data_processing:
Conventional ChIP-seq processing pipeline were adopted. Briefly, paired-end reads were aligned to mouse reference genome mm9 through the Bowtie2 (v2.3.5.1) software with default parameters and soft clipping allowed ("--local"). All unmapped reads and low quality alignments with MAPQ score lower than 30 was removed using SAMtools (v1.9). PCR duplicates were removed using Picard (v2.23.3) with default parameters. Reads aligned to mitochondria, random contigs and ENCODE blacklisted regions were also removed using BEDtools (v2.27.1)(2). Counts per million mapped reads (CPM) normalization was performed using the bamCoverage function of Deeptools (v3.1.3).
In-situ Hi-C data from each individual clone or biological replicates were aligned to mouse reference genome mm9 using bowite2 (global parameters: --very-sensitive -L 30 --score-min L, -0.6,-0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder). Reads were paired up and PCR duplicates were removed through the Hi-C Pro software (v3.0.0) to generate a valid interaction pair file. The output pair files were then converted to “.hic” files using the hicpro2juicebox utility. HiC files were also converted to “.cool” files using the Hicexplorer (v3.7). For replicate or clone-merged samples, similar steps were taken on reads merged from each clone or biological replicates.
Assembly: mm9
Supplementary files format and content: cool, hic and bigwig files of each individual biological replicate are provided.

molecule: genomic DNA

organism: Mus musculus

source_name: erythroid

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultured in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
For Hi-C, FACS purified cells (0.1 million) were lysed in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 10min on ice. Nuclei were pelleted at 4℃ and washed once with cold 1.4 × NEB buffer 3.1 (NEB Cat#B7203S). Nuclei were then re-suspended in 25ul of 1.4 × NEB buffer 3.1 and treated with 0.1% SDS for 10min at 65℃. Nuclei were then treated with 1% Triton X-100 to quench SDS for 1h at 37℃. Chromatin was digested with 25U DpnII restriction enzyme (NEB, Cat#R0543M) at 37℃ overnight with shaking (950rpm on a thermal mixer). After overnight digestion, an additional stroke of 25U DpnII was added into the system to further digest the genome for 4 hours at 37℃. After the 2nd stroke of digestion, nuclei were incubated at 65℃ for 20min to inactivate DpnII. Digested chromatin fragments were then cooled down to room temperature and blunted with dCTP, dGTP, dTTP (Diamond Cat#B110049, B110050, B110051) and Biotin-14-dATP (active motif, Catalog No: 14138) using 6.6U DNA Polymerase I, Large (Klenow) fragment (NEB, Cat#M0210). Chromatin was then ligated in-situ with 2000U T4 DNA ligase (NEB, Cat#M0202M) for 4 hours at 16℃ followed by further incubation for 2 hours at room temperature. Chromatin was then reverse-crosslinked overnight at 65℃ in the presence of 1% SDS and proteinase K (G-clone Cat#EZ0970). After reverse-crosslinking, DNase-free RNase A (Vazyme Cat#DE111-01) was added to the system for 30min at 37℃ to remove RNA. DNA was then extracted by phenol-chloroform extraction, precipitated, and dissolved in 130ul of nuclease free water. For ChIP-seq, FACS purified cells were re-suspended in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl and 0.2% NP-40) supplemented with 1:500 protease inhibitor and 1:100 PMSF for 20min on ice. Notably, for Rad21 ChIP-seq experiments in the WapldTag/SororinmAID and WapldTag/SMC2mAID/SororinmAID cells, roughly 30% of crosslinked 293T cells were added into the cell mixture. Nuclei were then pelleted and re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS, fresh supplemented with PI and PMSF) for 20min on ice. Chromatin was then fragmented by sonication (Qsonica Q800R3, 80% amplitude, 20s ON, 40s OFF) for 17min. Cell debris were removed by centrifugation at 15000g for 10min at 4℃. The supernatant was collected and diluted with 4 volumes of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) supplemented with protease inhibitor, PMSF and 50ul of A/G agarose beads (Santa Cruz Cat#sc-2003). Preclear of chromatin was performed at 4℃ for 4-8h with rotation. Precleared chromatin was then incubated with 35μl A/G agarose beads (A:G = 1:1) pre-bound with antibody and incubated on a rotator at 4℃ overnight. Beads were washed once with IP wash buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing steps were performed on ice. Beads were moved to room temperature and DNA was eluted in 200μl fresh Elution Buffer (100mM NaHCO3, 1%SDS). ChIP and input chromatin were reverse crosslinked at 65℃ overnight in the presence of proteinase K. IP and input samples were supplemented with 10ul of 3M sodium acetate (pH 5.2), and DNA was purified with PCR purification kit (QIAGEN Cat#28106).
For Hi-C, DNA was sonicated to 200-300bp fragments with a QSonica Q800R3 sonicator (40% amplitude, 15s ON and 15s OFF, 13min sonication) and purified with VAHTS DNA Clean Beads (Vazyme Cat#N411). Biotin-labeled DNA fragments was enriched by incubation with 100μl Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, Cat#65002) at room temperature for 15min. Streptavidin C1 beads were then washed twice with 1 × B&W buffer (5mM Tris-HCl, pH 7.5; 0.5mM EDTA; 1M NaCl). Beads were re-suspended in 30ul of 1 × NEB Buffer2 (NEB Cat#7002S) containing 9U of T4 DNA polymerase (NEB, Cat#M0203S) and 40uM dATG/dGTP and incubated at 20℃ for 4 hours to remove unligated fragments. Beads were then washed twice with 1 × B&W buffer and subject to library construction. DNA end repair, dA-tailing and adaptor ligation were constructed on beads, using the AHTS Universal DNA Library Prep Kit for Illumina or MGI (Vazyme, Cat# ND627-01, NDM607-02) based on the manufacturer's protocol. To elute DNA from streptavidin beads, the library mixture was treated with 0.1% SDS and incubated at 98℃ for 10min. Released DNA was collected from the supernatant and purified with VAHTS DNA Clean Beads. Finally, the library was amplified for 9 cycles on a thermal cycler, using the VAHTS® HiFi Amplification Mix. PCR products were then purified with VAHTS DNA Clean Beads and sequenced on an Illumina NextSeq500 or MGI DNBSEQ-T7 sequencing platform. For ChIP, libraries were constructed using the VAHTS Universal DNA Library Prep Kit for MGI (Vazyme, Cat#NDM607-02) according to the manufacturer's protocol. ChIP libraries were sequenced on the MGI DNBSEQ-T7 sequencing platform.
HiC and ChIP-seq libraries were constructed using the VATHS DNA library preparation kit from Vazyme (N607) according to the manufacturer's protocol.

treatment_protocol: The G1E-ER4 derivative cell lines: Wapl-dTag/SMC2-AID; Wapl-dTag/Sororin-AID (with or without Sororin-9A) and Wapl-dTag/SMC2-AID/Sororin-AID (with or without Sororin-9A mutant) were arrested by RO3306 at G2/M transition with combinations of dTag13 and 5-Ph-IAA treatment. Samples were then released from RO-3306 for either 4h or 30min for mitotic enrichment before FACS purification.

tag: tissue

value: erythroid

tag: cell line

value: G1E-ER4 cells

tag: cell type

value: erythroblasts

tag: genotype

tag: treatment

value: RO-3306 short_arrest (8h) and short_release (30min); 5_ph_IAA (8.5h); dTag13(-)


title: configuration5_short_release_clone7


title: configuration5_clone7

value: RO-3306 arrest (20h) and release (4h); 5_ph_IAA (24h); dTag13(-)


title: configuration7_short_release_clone7

description: mitosis: condensin(-);extrusive-cohesin(-);cohesive-cohesin(+)

value: Wapl-dtag/SMC2-aid/Sororin-aid + Sororin-9A mutant


title: configuration5_clone5


title: configuration5_clone8


title: configuration5_short_release_clone5


title: configuration8_clone7_9aa

description: mitosis: condensin(-);extrusive-cohesin(+);cohesive-cohesin(+)

value: RO-3306 arrest (20h) and release (4h); 5_ph_IAA (24h); dTag13(8h)


title: configuration7_short_release_clone5


title: configuration8_light_load_clone7_9aa

value: RO-3306 arrest (20h) and release (4h); 5_ph_IAA (24h); dTag13(4.75h)


title: human_sg12_2

status: Public on Dec 18 2024

city: New Orleans

first: Kuan-Jui

last: Su

state: LA

address: 1440 Canal St,suite 1619G

department: Center for Biomedical Informatics and Genomics

country: USA

institute: Tulane University

description:
Library name: Sg12_2
Frozen fresh spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
Raw sequencing data were preprocessed using the 10X Genomics Space Ranger (v2.1.1) pipeline with the reference human genome GRCh38 to generate FASTQ files.
Pre-processed and aligned was used as initial input for spatial transcriptomics analysis with Seurat (v4.3.0).
For data quality control, spots with less than 100 UMIs were filtered out. Individual count matrices were normalized with SCTransform.
Assembly: Human genome GRCh38
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: hi-res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: list of counts of each gene with the barcode information
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: filtered_feature_bc_matrix.h5: filtered gene counts of genes in HDF5 binary data format
Supplementary files format and content: matrix.mtx.gz: raw gene counts in matrix format
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Human femoral head

extract_protocol:
During the hip replacement surgery, the human femoral head samples were collected and temporarily stored at 4 °C before being transferred to the wet laboratory at Tulane School of Medicine. Samples, measuring approximately 1 cm × 1 cm × 0.5 cm, were excised from a location close to the central area of the femoral head and immediately fixed in 10% formalin and placed on the shaker at 4 °C for 48 hours, during which the reagent was changed every 12 hours. Subsequently, the samples were rinsed with sterile PBS and decalcified in 14% EDTA for 3 weeks on a shaker, with a fresh reagent change every 3 days. The decalcified samples were dehydrated by immersion in increasing concentrations of ethanol. The dehydrated samples were then cleared by Xylene. The samples were embedded in paraffin and stored for future use.
Spatial transcriptome sequencing libraries were prepared using the 10x Genomics Visium Spatial Gene Expression Slides & Reagent Kit according to the manufacturer’s instructions.

value: Human femoral head

tag: Sex

value: Male


title: configuration9_clone9


title: 7298-JF-7

status: Public on Dec 14 2024

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

library_source: transcriptomic single cell

data_processing:
Cellranger for alignment and seurat for data processing
Assembly: hg38
Supplementary files format and content: cellranger output format

source_name: skin

extract_protocol:
Half of a 6 mm biopsy was cryopreserved in CryoStor CS10 media (BioLife Solutions). Samples were thawed on ice, washed briefly in cold Hank’s Balanced Saline Solution (Gibco, Thermo Fisher Scientific) to remove residual CryoStor CS10 media, and bisected before being enzymatically digested in either 0.25% Trypsin-EDTA (Gibco, Thermo Fisher Scientific) with 10U/mL DNase I (Thermo Fisher Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), or 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) with 10U/ml DNase I in plain medium for 1.5 hours at 37°C with rotation. The resulting cell suspensions were filtered through 70-μm cell strainers twice and re-suspended in PBS containing 0.04% BSA. Dermal and epidermal cells were combined in a 2:1 ratio.
libraries were constructed by the University of Michigan Advanced Genomics Core on the 10X Genomics Chromium system with chemistry v2 and v3

value: skin

tag: disease

value: LP

value: treatment

tag: time

value: day 0


title: 8272-JF-2

source_name: pbmcs

value: pbmcs

value: Control

value: control


title: 7298-JF-9

value: week 2


title: 7298-JF-8


title: configuration6_light_load_clone8

description: mitosis: condensin(-);extrusive-cohesin(+);cohesive-cohesin(-)

value: erythroid

value: G1E-ER4 cells


title: 7298-JF-6


title: 7298-JF-5


title: 8687-JF-5


title: 8272-JF-4


title: 7298-JF-3


title: 7298-JF-2


title: 7298-JF-4


title: 7298-JF-1


title: 6939-JF-6


title: 7298-JF-10


title: 6939-JF-4


title: 6939-JF-5


title: 6939-JF-3


title: 6654-JF-6


title: 6939-JF-1


title: 6654-JF-4


title: 6654-JF-2


title: 6654-JF-1


title: 6515-JF-6


title: 6515-JF-4


title: 6515-JF-3


title: 6515-JF-5


title: 6515-JF-1


title: 6494-JF-3


title: 6494-JF-1


title: 6494-JF-2


title: 6411-JF-1


title: 18_M00063628

status: Public on Dec 02 2024

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39)
Supplementary files format and content: Raw count data in tab-delimited salmon file

source_name: PDAC tumors

extract_protocol:
Samples were snap frozen in liquid nitrogen. Tissues were homogenised using metal beads and collected in 1 mL of TRIzol Reagent. The RNA was extracted the same day using the the PureLink RNA mini kit (12183018A; Invitrogen)
Illumina mRNA library

value: PDAC tumors

value: T6 LOH

value: KPC-derived organoid

value: KPC

value: ROSA

tag: strain source

tag: strain sex

value: male


title: 11_M00063620

value: KO


title: 12_M00063621


title: 6939-JF-2


title: 6494-JF-4

value: skin


title: 1_M00063609


title: 6411-JF-2

value: LP


title: 6654-JF-3

value: treatment


title: 6494-JF-5


title: 3_M00063611


title: 4_M00063612


title: 34_T93LOH_264KO_mono_org

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39_release-102_kmer23
Supplementary files format and content: Raw count data in tab-delimited salmon file

source_name: KO

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent and stored at -80C. The RNA was extracted using the the PureLink RNA mini kit (12183018A; Invitrogen)
Illumina mRNA library. mRNA library preparations were performed using 55 uL of 10 ng/mL per sample

value: Organoid

value: Monoculture


title: 6654-JF-5


title: 33_T93LOH_263KO_mono_org


title: 35_T93LOH_265WT_mono_org

source_name: WT

value: WT


title: 32_T95LOH_265WT_mono_org


title: 31_T95LOH_263KO_mono_org


title: 30_T93LOH_265WT_cocx_fibro

value: Fibroblast

value: Coculture


title: 29_T93LOH_265WT_cocx_org


title: 6515-JF-2

value: pbmcs

value: day 0


title: 27_T93LOH_264KO_cocx_org


title: 28_T93LOH_264KO_cocx_fibro


title: 26_T93LOH_263KO_cocx_fibro


title: 25_T93LOH_263KO_cocx_org


title: 24_T95LOH_265WT_cocx_fibro


title: 8_M00063616

value: PDAC tumors


title: 23_T95LOH_265WT_cocx_org


title: 21_T95LOH_264KO_cocx_org


title: 6_M00063614

value: T6 LOH


title: 22_T95LOH_264KO_cocx_fibro


title: 6_T93LOH_265WT_mono_org


title: 15_T93LOH_264KO_cocx_org


title: 7_T95LOH_263KO_cocx_org


title: 20_T95LOH_263KO_cocx_fibro


title: 13_T93LOH_263KO_cocx_org


title: 14_T93LOH_263KO_cocx_fibro


title: 16_T93LOH_264KO_cocx_fibro


title: 4_T93LOH_263KO_mono_org


title: 19_T95LOH_263KO_cocx_org


title: 1_T95LOH_263KO_mono_org


title: 18_T93LOH_265WT_cocx_fibro


title: 17_T93LOH_265WT_cocx_org


title: 2_T95LOH_264KO_mono_org


title: 3_T95LOH_265WT_mono_org


title: 9_T95LOH_264KO_cocx_org


title: 40_T6LOH_RosaSmad4KO_PSC4

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm38_release-102_kmer23
Supplementary files format and content: Raw count data in tab-delimited salmon file


title: 43_T6LOH_S1Smad4KO_PSC4


title: 12_T95LOH_265WT_cocx_fibro


title: 34_T69A_S1Smad4KO_PSC4


title: 37_T69A_S2Smad4KO_PSC4


title: 31_T69A_RosaSmad4KO_PSC4


title: 28_T69A_S2Smad4KO_PSC5


title: 25_T69A_S1Smad4KO_PSC5


title: 22_T69A_RosaSmad4KO_PSC5


title: 8_T95LOH_263KO_cocx_fibro


title: 10_T95LOH_264KO_cocx_fibro


title: 18_T6LOH_S2Smad4KO_PSC21


title: 5_T93LOH_264KO_mono_org


title: 11_T95LOH_265WT_cocx_org


title: 12_T6LOH_RosaSmad4KO_PSC21


title: 44_T6LOH_S2Smad4KO_Monoculture


title: 45_T6LOH_S2Smad4KO_PSC4


title: 09_T6LOH_S2Smad4KO_PSC5


title: 03_T6LOH_RosaSmad4KO_PSC5


title: 41_T6LOH_S1Smad4KO_Monoculture


title: 15_T6LOH_S1Smad4KO_PSC21


title: 39_T6LOH_RosaSmad4KO_PSC4


title: 46_T6LOH_S2Smad4KO_PSC4


title: 35_T69A_S2Smad4KO_Monoculture


title: 38_T6LOH_RosaSmad4KO_Monoculture


title: 06_T6LOH_S1Smad4KO_PSC5


title: 42_T6LOH_S1Smad4KO_PSC4


title: 36_T69A_S2Smad4KO_PSC4


title: 29_T69A_RosaSmad4KO_Monoculture


title: 33_T69A_S1Smad4KO_PSC4


title: 32_T69A_S1Smad4KO_Monoculture


title: 30_T69A_RosaSmad4KO_PSC4


title: 26_T69A_S2Smad4KO_Monoculture


title: 21_T69A_RosaSmad4KO_PSC5


title: 17_T6LOH_S2Smad4KO_PSC21


title: 23_T69A_S1Smad4KO_Monoculture


title: 27_T69A_S2Smad4KO_PSC5


title: 24_T69A_S1Smad4KO_PSC5


title: 16_T6LOH_S2Smad4KO_Monoculture


title: 14_T6LOH_S1Smad4KO_PSC21


title: 10_T6LOH_RosaSmad4KO_Monoculture


title: 13_T6LOH_S1Smad4KO_Monoculture


title: 08_T6LOH_S2Smad4KO_PSC5


title: 07_T6LOH_S2Smad4KO_Monoculture


title: 05_T6LOH_S1Smad4KO_PSC5


title: 04_T6LOH_S1Smad4KO_Monoculture


title: 86_mMSC-448c_mMSC-Ago

status: Public on Nov 29 2024

city: Montpellier

first: Claudia

last: Terraza Aguirre

address: 80, Avenue Augustin Fliche

country: France

institute: Inserm U1183

description:
Library name: 86_mMSC-448c_mMSC-Ago
Colum name in raw_counts_mMSC448_samples.txt: 86_mMSC-448c_mMSC-Ago
raw_counts_mMSC448_samples.txt

data_processing:
Bioinformatics steps were performed using a Snakemake pipeline. Sample sequences were demultiplexed using a python script, and raw paired-end fastq files were transformed into a single-end fastq file for each sample and aligned on the Ensembl transcriptome hg38 using bwa.
Aligned reads were parsed, and UMIs were counted for each gene in each sample to create an expression matrix containing the absolute abundance of mRNAs across all samples. Reads aligned on multiple genes or containing more than three mismatches with the reference were excluded. Prior to differential expression analysis, genes with low counts (total UMIs per gene ≤ 10) were filtered out to ensure robust results. Differential expressed analysis was then conducted using the DeSeq2 package in RStudio, following the standard workflow.
Assembly: hg19, mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone marrow

growth_protocol: Cells were grown in a complete medium, consisting of DMEM high glucose supplemented with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, and 1%P/S  at 37ºC in a humidified 5% CO2 atmosphere

extract_protocol:
The library was sequenced on a NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (#20,027,464, Illumina) with 17*-8–105* cycle reads (* addition of one cycle according to Illumina’s recommendation).
The library was prepared from 10 ng of total RNA in 4 µL. The mRNA poly-A tails were tagged with universal adapters, well-specific barcodes, and unique molecular identifiers (UMIs) during template-switching reverse transcriptase (Thermo Scientific™, EP0751, Maxima H Minus Reverse Transcriptase). Barcoded cDNAs from 96 samples were then pooled and purified using a Zymo kit. cDNAs were treated with exonuclease I (NEB, M0293S) before being amplified (12 cycles) and fragmented using a transposon-fragmentation approach that enriched for 3′ ends of cDNA. The library was sequenced on a NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (#20,027,464, Illumina) with 17*-8–105* cycle reads (* addition of one cycle according to Illumina’s recommendation).

treatment_protocol: MSC were treated  with 1 µM of a selective PPARβ/δ agonist (GW501516) for 24 hours at 37ºC in a humidified 5% CO2 atmosphere.

value: Bone marrow

value: Primary cell

value: Mesechymal stromal cell

value: Wild type

value: PPARb/d agonist 1uM


title: 74_mMSC-448a_mMSC-Ago

description:
Library name: 74_mMSC-448a_mMSC-Ago
Colum name in raw_counts_mMSC448_samples.txt: 74_mMSC-448a_mMSC-Ago
raw_counts_mMSC448_samples.txt


title: 73_mMSC-448a_mMSC-CT

description:
Library name: 73_mMSC-448a_mMSC-CT
Colum name in raw_counts_mMSC448_samples.txt: 73_mMSC-448a_mMSC-CT
raw_counts_mMSC448_samples.txt

value: Control


title: 80_mMSC-448b_mMSC-Ago

description:
Library name: 80_mMSC-448b_mMSC-Ago
Colum name in raw_counts_mMSC448_samples.txt: 80_mMSC-448b_mMSC-Ago
raw_counts_mMSC448_samples.txt


title: 55_COR-86_COR-CT

description:
Library name: 55_COR-86_COR-CT
Colum name in raw_counts_UC-MSC_samples.txt: 55_COR-86_COR-CT
raw_counts_UC-MSC_samples.txt

source_name: Umbilical cord

value: Umbilical cord


title: 79_mMSC-448b_mMSC-CT

description:
Library name: 79_mMSC-448b_mMSC-CT
Colum name in raw_counts_mMSC448_samples.txt: 79_mMSC-448b_mMSC-CT
raw_counts_mMSC448_samples.txt


title: 02_T6LOH_RosaSmad4KO_PSC5


title: 01_T6LOH_RosaSmad4KO_Monoculture


title: 50_COR-83F_COR-Ago

description:
Library name: 50_COR-83F_COR-Ago
Colum name in raw_counts_UC-MSC_samples.txt: 50_COR-83F_COR-Ago
raw_counts_UC-MSC_samples.txt


title: 49_COR-83F_COR-CT

description:
Library name: 49_COR-83F_COR-CT
Colum name in raw_counts_UC-MSC_samples.txt: 49_COR-83F_COR-CT
raw_counts_UC-MSC_samples.txt


title: 44_MA-27_MA-Ago

description:
Library name: 44_MA-27_MA-Ago
Colum name in raw_counts_BM-MSC_samples.txt: 44_MA-27_MA-Ago
raw_counts_BM-MSC_samples.txt


title: 67_COR-91_COR-CT

description:
Library name: 67_COR-91_COR-CT
Colum name in raw_counts_UC-MSC_samples.txt: 67_COR-91_COR-CT
raw_counts_UC-MSC_samples.txt


title: 62_COR-87_COR-Ago

description:
Library name: 62_COR-87_COR-Ago
Colum name in raw_counts_UC-MSC_samples.txt: 62_COR-87_COR-Ago
raw_counts_UC-MSC_samples.txt


title: 38_MA-25_MA-Ago

description:
Library name: 38_MA-25_MA-Ago
Colum name in raw_counts_BM-MSC_samples.txt: 38_MA-25_MA-Ago
raw_counts_BM-MSC_samples.txt


title: 56_COR-86_COR-Ago

description:
Library name: 56_COR-86_COR-Ago
Colum name in raw_counts_UC-MSC_samples.txt: 56_COR-86_COR-Ago
raw_counts_UC-MSC_samples.txt


title: 37_MA-25_MA-CT

description:
Library name: 37_MA-25_MA-CT
Colum name in raw_counts_BM-MSC_samples.txt: 37_MA-25_MA-CT
raw_counts_BM-MSC_samples.txt


title: 31_MA-24_MA-CT

description:
Library name: 31_MA-24_MA-CT
Colum name in raw_counts_BM-MSC_samples.txt: 31_MA-24_MA-CT
raw_counts_BM-MSC_samples.txt


title: 68_COR-91_COR-Ago

description:
Library name: 68_COR-91_COR-Ago
Colum name in raw_counts_UC-MSC_samples.txt: 68_COR-91_COR-Ago
raw_counts_UC-MSC_samples.txt


title: 26_MA-16b_MA-Ago

description:
Library name: 26_MA-16b_MA-Ago
Colum name in raw_counts_BM-MSC_samples.txt: 26_MA-16b_MA-Ago
raw_counts_BM-MSC_samples.txt


title: 11_T6LOH_RosaSmad4KO_PSC21


title: 32_MA-24_MA-Ago

description:
Library name: 32_MA-24_MA-Ago
Colum name in raw_counts_BM-MSC_samples.txt: 32_MA-24_MA-Ago
raw_counts_BM-MSC_samples.txt


title: 85_mMSC-448c_mMSC-CT

description:
Library name: 85_mMSC-448c_mMSC-CT
Colum name in raw_counts_mMSC448_samples.txt: 85_mMSC-448c_mMSC-CT
raw_counts_mMSC448_samples.txt


title: 61_COR-87_COR-CT

description:
Library name: 61_COR-87_COR-CT
Colum name in raw_counts_UC-MSC_samples.txt: 61_COR-87_COR-CT
raw_counts_UC-MSC_samples.txt


title: 25_MA-16b_MA-CT

description:
Library name: 25_MA-16b_MA-CT
Colum name in raw_counts_BM-MSC_samples.txt: 25_MA-16b_MA-CT
raw_counts_BM-MSC_samples.txt


title: 20_LIPO-47_Lipo-Ago

description:
Library name: 20_LIPO-47_Lipo-Ago
Colum name in raw_counts_hASC_samples.txt: 20_Lipo-47-Ago
raw_counts_hASC_samples.txt

source_name: Adipose tissue

value: Adipose tissue


title: 19_LIPO-47_Lipo-CT

description:
Library name: 19_LIPO-47_Lipo-CT
Colum name in raw_counts_hASC_samples.txt: 19_Lipo-47-CT
raw_counts_hASC_samples.txt


title: 13_LIPO-43_Lipo-CT

description:
Library name: 13_LIPO-43_Lipo-CT
Colum name in raw_counts_hASC_samples.txt: 13_Lipo-43-CT
raw_counts_hASC_samples.txt


title: 1_LIPO-41b_Lipo-CT

description:
Library name: 1_LIPO-41b_Lipo-CT
Colum name in raw_counts_hASC_samples.txt: 1_Lipo-41b-CT
raw_counts_hASC_samples.txt


title: D425 cells, DMSO, 24 hours, replicate 3, RNAseq

status: Public on Nov 14 2024

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: processed_file: PLX227988_assay_data.csv: S_5T3

data_processing:
FASTQ files were processed using a pipeline to perform bulk rapid quantification of RNA-seq data.
Adapter sequences were removed with Trim Galore (v0.6.6).
Reads were aligned to GRCh38 and quantified to gene counts using kallisto (v0.46.1).
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: Myc-amplified medulloblastoma

growth_protocol: D425 and D458 cell lines were cultured in DMEM supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (GIBCO), 1 × penicillin/streptomycin solution (Cellgro), and with 1 × L-glutamine (Cellgro).

extract_protocol:
Cells were collected in Qiazol and RNA extraction was performed using Rneasy Plus Mini Kit (Qiagen)
RNA purity, quantity and integrity was determined with NanoDrop (ThermoFisher Scientific) and TapeStation 4200 (Agilent) analysis prior to RNA-seq library preparation.  The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries.  Paired-end sequencing reads of 150bp was generated on NovaSeq 6000 (Illumina) sequencer at a target depth of 80 million paired-end reads per sample.  Raw sequencing reads were de-multiplexed using bcl2fastq.

treatment_protocol: Cells were treated with either 200 nM TG02, established IC50 value of atuveciclib, or DMSO control. TG02-treated cells were collected at 24 hours, while atuveciclib-treated cells were collected at 72 hours.

value: Myc-amplified medulloblastoma

tag: timepoint

value: 24 hours

value: DMSO


title: 43_MA-27_MA-CT

description:
Library name: 43_MA-27_MA-CT
Colum name in raw_counts_BM-MSC_samples.txt: 43_MA-27_MA-CT
raw_counts_BM-MSC_samples.txt


title: 7_LIPO-42_Lipo-CT

description:
Library name: 7_LIPO-42_Lipo-CT
Colum name in raw_counts_hASC_samples.txt: 7_Lipo-42-CT
raw_counts_hASC_samples.txt


title: D425 cells, TG02, 24 hours, replicate 2, RNAseq

description: processed_file: PLX227988_assay_data.csv: S_5D2

tag: dosage


title: D425 cells, DMSO, 24 hours, replicate 1, RNAseq

description: processed_file: PLX227988_assay_data.csv: S_5T1


title: D425 cells, TG02, 24 hours, replicate 1, RNAseq

description: processed_file: PLX227988_assay_data.csv: S_5D1


title: D458 cells, DMSO, 24 hours, replicate 1, RNAseq

description: processed_file: PLX229783_kallisto_counts_geneName_level.csv: S_8T1


title: D458 cells, DMSO, 24 hours, replicate 2, RNAseq

description: processed_file: PLX229783_kallisto_counts_geneName_level.csv: S_8T2


title: D458 cells, TG02, 24 hours, replicate 3, RNAseq

description: processed_file: PLX229783_kallisto_counts_geneName_level.csv: S_8D3


title: D458 cells, DMSO, 24 hours, replicate 3, RNAseq

description: processed_file: PLX229783_kallisto_counts_geneName_level.csv: S_8T3


title: 26012021_LTRI-2231_S448_R3C2_3H_S448_R1_001

status: Public on Nov 08 2024

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
homo sapiens and SARS-CoV-2
sparseq_sample_data_GEOver_v5.txt

data_processing:
Library strategy: RNAseq with limited amplicons.
Samples sequenced using Illumina NextSeq, MiSeq, and MiniSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were developed to track and quantify key mutations within samples and to aggregate data.
Final anaylsis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1)

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: human nasopharyngeal swab

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)

value: human nasopharyngeal swab

tag: sample type

value: positive sample

value: preclinical


title: D458 cells, TG02, 24 hours, replicate 2, RNAseq

description: processed_file: PLX229783_kallisto_counts_geneName_level.csv: S_8D2


title: D458 cells, TG02, 24 hours, replicate 1, RNAseq

description: processed_file: PLX229783_kallisto_counts_geneName_level.csv: S_8D1


title: 26012021_LTRI-2199_S394_R3C2_19D_S394_R1_001


title: 26012021_LTRI-2056_S156_R2C2_2H_S156_R1_001


title: 26012021_LTRI-2051_S146_R2C2_14G_S146_R1_001


title: 26012021_LTRI-2020_S84_R2C2_18D_S84_R1_001


title: 26012021_LTRI-2040_S124_R2C2_14F_S124_R1_001


title: 26012021_LTRI-2023_S90_R2C2_2E_S90_R1_001


title: 26012021_LTRI-2054_S152_R2C2_20G_S152_R1_001


title: 26012021_LTRI-1983_S10_R2C2_10A_S10_R1_001


title: 14_LIPO-43_Lipo-Ago

description:
Library name: 14_LIPO-43_Lipo-Ago
Colum name in raw_counts_hASC_samples.txt: 14_Lipo-43-Ago
raw_counts_hASC_samples.txt


title: 26012021_LTRI-1976_S173_R2C2_19H_S173_R1_001


title: Negative-BCE364

status: Public on Oct 28 2024

first: Junluan

last: MO

address: Buxin Road, Luohu District

institute: Shenzhen Center for Chronic Disease Control

data_processing:
The following sequence is used for adapter trimming: "AACTGTAGGCACCATCAAT". Adapter trimming was performed using Trimmomatic sorftware.The remained reads were aligned to miRBase, piRBase and tRFdb using BWA sorftware.
Assembly: hg38
Supplementary files format and content: read counts table and TPM  table

source_name: plasma exosomes

extract_protocol:
Exosomes were captured using QIAGEN exoRNeasy Midi Kit (QIAGEN,1116083).The exosomal RNA was isolated using  TRIzol™ Reagent(Thermo Fisher Scientific,15596018).
The libraries were constructed using QIAseq® miRNA Library Kit(QIAGEN, 331502).
sncRNA-seq, small non-coding RNA sequencing

value: plasma exosomes


title: 2_LIPO-41b_Lipo-Ago

description:
Library name: 2_LIPO-41b_Lipo-Ago
Colum name in raw_counts_hASC_samples.txt: 2_Lipo-41b-Ago
raw_counts_hASC_samples.txt


title: D425 cells, DMSO, 24 hours, replicate 2, RNAseq

description: processed_file: PLX227988_assay_data.csv: S_5T2


title: 8_LIPO-42_Lipo-Ago

description:
Library name: 8_LIPO-42_Lipo-Ago
Colum name in raw_counts_hASC_samples.txt: 8_Lipo-42-Ago
raw_counts_hASC_samples.txt


title: D425 cells, TG02, 24 hours, replicate 3, RNAseq

description: processed_file: PLX227988_assay_data.csv: S_5D3


title: Negative-BCE363


title: Negative-BCE362


title: Negative-BCE361


title: Negative-BCE358


title: Negative-BCE359


title: Negative-BCE357


title: donor_3313_visceral fat

status: Public on Nov 11 2024

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

data_processing:
Per sample, reads were transformed into a raw counts matrix with 10x Genomics CellRanger software1 6.0.1
raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_feature_keys:gene symbol; raw_matrix_background_barcodes_included:False
Assembly: raw_matrix_assembly:GRCh38; raw_matrix_genome_annotation:GENCODE 32
Supplementary files format and content: raw_matrix_file_format:hdf5; raw_matrix_value_units:UMI

source_name: visceral fat

extract_protocol:
Adipose tissue biopsies with at least 1g  were obtained from adult patients without severe morbid states or obesity complications who had signed in advance a written informed consent before undergoing elective abdominal surgeries. Five patients donated subcutaneous adipose tissue and visceral adipose tissue samples (paired). Tissues were immediately delivered from the operating room to the lab, where they were snap frozen in liquid nitrogen and stored at −80°C.
13,000-16,500 nuclei/sample were  loaded onto 10X Chromium Controller (10X GENOMICS, CA, USA) according to the manufacturer’s protocol (Chromium Next GEM Chip C. Chromium Next GEM Single Cell 3’ Kits v3.1).

value: visceral fat

tag: raw matrix_cellranger_assay_chemistry

tag: assay

value: female

tag: ethnicity

value: unknown

tag: age

value: adult

value: TRUE

tag: donor id


title: Negative-BCE355

tag: tissue

tag: cell line


title: Negative-BCE353

tag: cell type

tag: genotype


title: Negative-BCE352


title: Negative-BCE350


title: Negative-BCE348


title: Negative-BCE346


title: Negative-BCE354


title: Negative-BCE345


title: Negative-BCE344


title: Negative-BCE342


title: Negative-BCE341


title: Negative-BCE343


title: Negative-BCE340


title: Negative-BCE337


title: Negative-BCE336


title: Negative-BCE338


title: Negative-BCE333


title: Negative-BCE360


title: Negative-BCE356


title: Negative-BCE332


title: Negative-BCE331


title: Negative-BCE330


title: Negative-BCE329


title: Negative-BCE328


title: Negative-BCE327


title: Negative-BCE326


title: Negative-BCE325


title: Negative-BCE349


title: Negative-BCE347


title: Negative-BCE324


title: Negative-BCE351


title: Negative-BCE323


title: Negative-BCE321


title: Negative-BCE319


title: Negative-BCE320


title: Negative-BCE318


title: Negative-BCE316


title: Negative-BCE322


title: Negative-BCE314


title: Negative-BCE315


title: Negative-BCE311


title: Negative-BCE313


title: Negative-BCE312


title: Negative-BCE310


title: Negative-BCE309


title: Negative-BCE308


title: Negative-BCE339


title: Negative-BCE307


title: Negative-BCE306


title: Negative-BCE302


title: Negative-BCE303


title: Positive-BCE263


title: Negative-BCE305


title: Positive-BCE264


title: Positive-BCE265


title: Negative-BCE317


title: Positive-BCE261


title: Positive-BCE257


title: Positive-BCE254


title: Positive-BCE253


title: Positive-BCE262


title: Positive-BCE260


title: Positive-BCE256


title: Positive-BCE258


title: Positive-BCE247


title: Positive-BCE259


title: Positive-BCE250


title: Positive-BCE249


title: Positive-BCE245


title: Positive-BCE244


title: Positive-BCE246


title: Positive-BCE243


title: Positive-BCE242


title: Positive-BCE248


title: Positive-BCE241


title: Positive-BCE240


title: Positive-BCE235


title: Positive-BCE234


title: Positive-BCE236


title: Positive-BCE233


title: Positive-BCE237


title: Positive-BCE232


title: Positive-BCE231


title: Positive-BCE229


title: Positive-BCE230


title: Positive-BCE228


title: Positive-BCE251


title: Positive-BCE222


title: Positive-BCE225


title: Positive-BCE224


title: Positive-BCE227


title: Positive-BCE221


title: Positive-BCE218


title: Positive-BCE217


title: Positive-BCE219


title: Positive-BCE215


title: Positive-BCE216


title: Positive-BCE213


title: Positive-BCE214


title: Positive-BCE238


title: Positive-BCE210


title: Positive-BCE211


title: Positive-BCE208


title: Positive-BCE212


title: Positive-BCE207


title: Positive-BCE205


title: Positive-BCE206


title: Positive-BCE226


title: Positive-BCE201


title: Positive-BCE202


title: Positive-BCE203


title: Positive-BCE165


title: Positive-BCE239


title: Positive-BCE164


title: Positive-BCE162


title: Positive-BCE160


title: Positive-BCE161


title: Positive-BCE159


title: Positive-BCE158


title: Positive-BCE163


title: Positive-BCE155


title: Positive-BCE157


title: Positive-BCE151


title: Positive-BCE148


title: Positive-BCE150


title: Positive-BCE149


title: Positive-BCE145


title: Positive-BCE146


title: Positive-BCE147


title: Positive-BCE204


title: Positive-BCE144


title: Positive-BCE143


title: Positive-BCE142


title: Positive-BCE141


title: Positive-BCE140


title: Positive-BCE139


title: Positive-BCE138


title: Positive-BCE137


title: Positive-BCE136


title: Positive-BCE135


title: Positive-BCE134


title: Positive-BCE132


title: Positive-BCE131


title: Positive-BCE129


title: Positive-BCE126


title: Positive-BCE133


title: Positive-BCE154


title: Positive-BCE128


title: Positive-BCE125


title: Positive-BCE124


title: Positive-BCE152


title: Positive-BCE123


title: Positive-BCE120


title: Positive-BCE122


title: Positive-BCE118


title: Positive-BCE119


title: Positive-BCE116


title: Positive-BCE117


title: Positive-BCE113


title: Positive-BCE115


title: Positive-BCE112


title: Positive-BCE110


title: Positive-BCE111


title: Positive-BCE114


title: Positive-BCE108


title: Positive-BCE102


title: Positive-BCE107


title: scn_glauc_154

status: Public on Oct 23 2024

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

country: Germany

institute: University of Lübeck

data_processing:
The sequencing reads were demultiplexed using the BRB-seq Tools suite and aligned against mouse genome (mm10) using STAR and count matrices were generated using HTSeq.
All the downstream analyses were based on the clean data with high quality. FeatureCounts was used to count the reads numbers mapped to each gene. Normalized DESEq2 data in log values were used for all subsequent analyzes
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Suprachiasmatic nucleus (SCN)

extract_protocol:
The RNA from SCN was extracted using Trizol according to the manufacturer's recommendation. High-quality RNA with 260/280 and 260/230 ratios higher than 1.8 were used. RNA integrity was assessed by gel electrophoresis or bioanalyzer
At least 100 ng of RNA was used to generate cDNA libraries using the MERCURIUS kit (Alithea Genomics). Transcriptome analysis was performed by Alithea Genomic using the Bulk RNA Barcoding and sequencing (BRB-seq). Libraries were sequenced on Illumina NovaSeq 6000 platform at a depth of 8 million raw reads per sample.

value: Suprachiasmatic nucleus (SCN)

tag: group

value: advanced glaucoma

value: WT


title: Positive-BCE103


title: Positive-BCE101


title: scn_cont_570

value: control


title: scn_cont_565


title: Positive-BCE105


title: scn_glauc_152


title: SC222AC

city: Pittsburgh

first: Kathryn

last: Torok

state: PA

address: 4401 Penn Ave

department: Pediatric Rheuamatology

institute: University of Pittsburgh

data_processing:
Cell Ranger 3.0
Seurat
Harmony
Assembly: GRCh38
Supplementary files format and content: Matrix  table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
Miltenyi Biotec Whole Skin Dissociation Kit Human
10X Genomics Single Cell RNA Seq 3 Prime V2 Libraries

value: Skin

tag: disease state

value: Localized Scleroderma (LS)

tag: onset

value: Adult


title: SC272


title: HSK054

value: Healthy

value: Pediatric


title: PHC003


title: HSK053


title: SC297


title: SC296


title: Positive-BCE109


title: SC300


title: SC259


title: SC246


title: SC144


title: Positive-BCE106


title: SC198


title: SC126


title: HJ867


title: Positive-BCE104


title: scn_glauc_153


title: scn_cont_567


title: scn_cont_568


title: SC260


title: SC266


title: HJ809


title: CHLA9

status: Public on Oct 02 2024

first: Philipp

last: Maass

address: 686 Bay St

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

description:
signature_cis_50KB_merged_zscoresall.txt
signature_cis_50KB_merged_pvalueAll.txt
signature_trans1vsAll_1MB_merged_zscoresall.txt
signature_trans1vsAll_1MB_merged_pvalueAll.txt
signature_trans1vsAll_1MB_merged_qvalueAll.txt

data_processing:
4D Nucleome pipeline was used. More details on OmniC analysis are described in the paper.
Signature pipeline was used to analyze the OmniC data. More details on Signature are described in the paper.
Assembly: hg38
Supplementary files format and content: txt data including z-scores and p-values of cis interactions (50KB resolution) for all data in this submission and other datasets in the paper.
Supplementary files format and content: txt data including z-scores, p-values, and q-values of trans interactions (1MB resolution) for all data in this submission and other datasets in the paper.
Library strategy: OmniC

extract_protocol:
Mapping OmniC protocol is described in the manuscript.
Details on library preparation are described in the manuscript.

value: Ewing sarcoma


title: Chondrocyte, 21d

value: Hypertrophic chondrocyte


title: teloHAEC

source_name: teloHAEC

value: teloHAEC

value: Arterial endothelial cells


title: ME13_50um_3_RNA

status: Public on Oct 22 2024

city: Philadelphia

first: Liran

last: Mao

address: 422 Curie Boulevard

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
library strategy: spatial-RNA-seq
For ATAC and CUT&Tag data, linkers 1 and 2 are used for targeted filtering of read 2, aligning utilizing BWA followed by sorting and indexing via Samtools to facilitate efficient data handling and retrieval. This reformatting process assigned genome sequences to the first read and incorporated barcodes A and B into the second read. We aligned these fastq files against mouse (GRCm38) reference genomes. The conversion produced tsv-like fragments files, enriched with spatial and genomic information through the integration of barcode pairs, facilitating comprehensive downstream analysis.   For RNA sequencing data, we refined read 2 to extract barcode A, barcode B, and the Unique Molecular Identifier (UMI). Using the Spatial Transcriptomics (ST) pipeline version 1.7.2, this processed data was mapped against the appropriate mouse (GRCm38) genome references. This step produced a gene matrix that captures both gene expression and spatial positioning data, encoded through the combination of barcodes A and B, enabling detailed spatial transcriptomic analysis.
Assembly: GRCm38
Supplementary files format and content: TSV files for downstream analysis. For CUT&Tag and ATAC-seq, the tsv file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Supplementary files format and content: For RNA-seq, Tab-delimited text files include counts for each pixels for each Sample.
Supplementary files format and content: The *spatial.tar.gz file is a compressed folder that stores spatial-related files including quality control (QC) images. These QC images are useful to confirm accurate fiducial alignment and tissue detection. Inside the folder, it contains tissue_lowres_image.png, scalefactors_json.json, and tissue_positions_list.csv. tissue_lowres_image.png is a downsampled version of the original, full-resolution light microscope image. scalefactors_json.json contains basic information about the pixel positions and sizes. tissue_positions_list.csv is a table with rows that correspond to pixels.

source_name: Embryo

extract_protocol:
The workflow of simultaneous profiling of chromatin accessibility or a panel of cell surface proteins with two histone modifications and gene expression on the same tissue cryosections is shown schematically in Fig. 1a and Extended Data Fig. 1a-b. For joint analysis of chromatin accessibility, two histone modifications, and transcriptome (Extended Data Fig. 1a, Methods), a frozen tissue section was first fixed with formaldehyde and in situ Tn5 transposition was performed to insert a unique barcoded ligation linker to the accessible DNA loci. The same tissue section was then incubated with two primary antibodies targeting different histone modifications simultaneously, such as the combination of H3K27me3 with H3K27ac or H3K4me3. Afterwards, species specific nanobody-Tn5 fusion proteins loaded with unique barcoded ligation linkers were added to enable the demultiplexing of different histone modification loci. Next, the tissue section was incubated with a biotinylated DNA adaptor containing a universal ligation linker and poly-T sequence that binds to the messenger RNA (mRNA) to perform in situ reverse transcription (RT). Next, barcodes A (A1-A50) and barcodes B (B1-B50) were sequentially flowed over the tissue using microchannels and were conjugated to the universal ligation liker via templated ligation, which formed a two-dimensional grid of spatially barcoded tissue pixels (n =2,500), allowing all of modalities from the same pixel share the same spatial barcodes. Finally, barcoded complementary DNA (cDNA) and genomic DNA (gDNA) fragments were released by reverse crosslinking. cDNAs were separated from gDNA by streptavidin beads. Sequencing libraries for cDNAs and gDNA were separately constructed. For co-profiling of protein, gene expression, and histone modifications (Extended Data Fig. 1b, Methods), the fixed frozen tissue section was first incubated with two primary antibodies targeting different histone modifications, followed by nanobody-Tn5 in situ transposition. The same tissue section was then labeled with a panel of barcoded poly-A-tailed oligo-conjugated antibodies, which recognize surface antigens. Next, in situ reverse transcript was performed using the Biotinylated poly-T RT primer to capture complimentary DNA of both poly-A-tailed oligo-conjugated antibodies and mRNA. The subsequent steps for spatial barcoding and library construction were similar to above discussed methods. The protein library and RNA library can be separated by SPRI bead purification.
Frozen tissue slides were thawed for 1 min at 37 °C. Tissue was fixed with formaldehyde (0.2%, with 0.05 U μl–1 RNase Inhibitor) for 5 min and quenched with 1.25 M glycine for a further 5 min. After fixation, tissue was washed twice with 1 ml of 0.5× DPBS-RI and cleaned with ddH2O. The sequential order for spatial multiple profiling is as follows: 1. ATAC-seq; 2. Nanobody-based CUT&Tag; 3. In situ reverse transcription; 4. Ligation of barcode A; 5. Ligation of barcode B; 6. Reverse crosslink; 7. gDNA and cDNA separation; 8. Library construction; 9. Library QC and sequencing.

value: Embryo


title: Chondrocyte, 01d

value: Mesenchymal condensate


title: Chondrocyte, 07d

value: Chondrogenic precursor


title: Chondrocyte, 14d

value: Proliferating chondrocyte


title: TasteOrganoids_CQVsLPM_CQ_Sample2

status: Public on Sep 30 2024

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Pre-processed (post adapter and low-quality sequence removal) paired-end raw fastq sequences received from Nonogene Inc. were analyzed using FastQC 0.11.9 for quality assurance, and aligned against Sus scrofa 11.1 genome using the STAR aligner 2.7.10b in “GeneCounts” mode. Alignment quality for each sample was checked using MultiQC 1.14. Post-quality assurance, the resulting BAM files from STAR aligner were run through featureCounts in “countReadPairs” mode to obtain gene-wise transcript counts for each sample. A gene-wise count matrix was compiled for samples pertaining to each analysis (e.g Organoids Vs Foliate etc.) and subjected to subsequent differential gene expression analysis using DESeq2 available in Bioconductor version 3.17
Assembly: Assembly: Sus scrofa 11.1
Supplementary files format and content: All processed data files are the default output of featureCounts software in txt format

organism: Sus scrofa

source_name: Foliate cell line

extract_protocol:
Organoid harvesting from 6-well/12-well plates was done using the Cultrex™ Organoid Harvesting Solution (Cat 3700-100-01). Briefly; working on ice the cell culture media was gently aspirated and each well was washed with PBS (2ml/1ml). 1ml of the organoid harvesting solution was added to each well, the domes gently dislodged using a cell scraper/lifter and incubated for 1hr at 4C0 on a rocking shaker (Reliable Scientific Inc.) at a speed of 50, for BME digestion. Post incubation, the organoids were spun down and washed three times with 1ml PBS. Each spin down was done at 400g for 4mins at 4C0. The palleted organoids from each well were lysed in 600µl of RLT Plus lysis buffer (Qiagen) with 6µl of ß-mercaptoethanol (Sigma Life Science Cat# 63689-100ML-F) and homogenized using ~200µl of 1.0mm Zirconia (BioSpec Cat# 11079110ZX) beads with a single 30 second, 6,000 rpm cycle on a Precellys24 homogenizer (Bertin Corp). Homogenized solution was spun down for 20mins at 8000rpm prior to RNA isolation using RNEasy Plus Mini Kit (Qiagen Cat# 74134/74136) according to manufacturer’s protocol. FP were homogenized in the Extraction Buffer provided in the Arcturus™ PicoPure™ RNA Isolation Kit (Applied Biosystems Cat# 12204-01) using the same bead based method described above. RNA extraction followed the recommended Arcturus™ PicoPure™ RNA Isolation Kit protocol without performing the DNAse step since TaqMan probes are at the junctions of gene exons
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Porcine foliate organoids grown in LPM against porcine foliate organoids grown in LPM (day 0 to day 10) and then transfered to CQ (day 10 to day 16/17), total RNA was extracted (using Qiagen RNEasy MiniKit) from comparable organoid cultures grown only LPM, and cultures that were finished off with CQ

value: Foliate cell line

value: Stem cells/mature taste cells

tag: treatment

value: CQ


title: TasteOrganoids_CQVsLPM_CQ_Sample1


title: TasteOrganoids_CQVsLPM_LPM_Sample2

value: LPM


title: HeLa 24hpi sample 4

status: Public on Sep 11 2024

city: Moscow

first: Scott

middle: Stephen

last: Grieshaber

state: ID

address: 875 Perimeter Drive MS 3051

department: Biological Sciences

institute: University of Idaho

data_processing:
Aligned with Bowtie2
Counts generated using Htseq
Differentail gene expression calcualted using Deseq2
Assembly: Alinged to C. trachomatis L2 434/Bu using Bowtie2
Supplementary files format and content: Tab delinated text file of counts

organism: Chlamydia trachomatis

source_name: HeLa

growth_protocol: HeLa cells (CRL-1651) were grown in RPMI-1640, supplemented with 10% FBS and 10 μg/mL gentamicin (Cellgro).

extract_protocol:
Total RNA was isolated from cells infected with the indicated strains. Expression of each protein was induced at 15 hpi with either 0.5 mM theophylline and 30ng/ml anhydrotetracycline (HctB) or 0.5 mM theophylline (Clover, HctA, CtcB and Euo) and the Ctr isolated at 18 and 24 hpi on ice. Briefly, the infected monolayer was scraped into ice cold PBS, lysed using a Dounce homogenizer. Total RNA was isolated using TRIzol reagent (Life Technologies) following the protocol provided and genomic DNA removed (TURBO DNA-free Kit, Invitrogen). The enriched RNA samples were quantified and the libraries built and barcoded by the IBEST Genomics Resources Core at the University of Idaho.
Kapa RNA Hyper Prep

treatment_protocol: HeLa Cells were infected with either C. trachomatis L2 434/Bu-clover, L2 434/Bu-euo, L2 434/Bu-hctA, L2 434/Bu-hctB, L2 434/Bu-ctcB

value: HeLa

value: CTR 434 L2 infected isolated at 24 hpi


title: HeLa 24hpi sample 3


title: TasteOrganoids_CQVsLPM_LPM_Sample1


title: TasteOrganoids_CQVsLPM_LPM_Sample3


title: HeLa 24hpi sample 2


title: SC267

value: Skin

value: Localized Scleroderma (LS)

value: Adult


title: HeLa 24hpi sample 1


title: SC275


title: HeLa 18hpi sample 4

value: CTR 434 L2 infected isolated at 18 hpi


title: TC32

value: Ewing sarcoma


title: HeLa 18hpi sample 2


title: PQN85_HW04_1hr_auxin_L3_rep1

status: Public on Sep 09 2024

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

data_processing:
Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 with default parameters. Bam sorting and indexing was performed using samtools version 1.11. BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage with a bin size of 10 bp and 200 bp read extension. Only reads with a minimum mapping quality of 20 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed. The average coverage data was generated by averaging ChIP-Input enrichment scores per 10 bp bins across the genome.  ChIP-seq peaks are identified using MACS2 version 2.1.1 (https://github.com/macs3-project/MACS). Peaks are called using both the individual replicates and combined bam files with minimum false discovery rate of 0.05. The peaks shown below average ChIP-seq tracks are peaks called using the combined bam files, whereas the peaks shown below individual replicates are peaks called using the corresponding replicate.
Assembly: WS220
Supplementary files format and content: bw file contains signal track, input subtracted enrichment at each binned genomic loci
Supplementary files format and content: bed file contains binarized chip enrichment across the genome

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. L3 worms were kept on plates with or without auxin prior to collection.

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

treatment_protocol: collected worms were treated with auxin using NGM media containing 1 mM auxin. The worms were left on NGM plate to crawl around for an hour.

value: whole worms

tag: development stage

tag: chip antibody


title: Mouse 6-9 somites, SAG treated, replicate 3

status: Public on Aug 26 2024

city: Raleigh

first: Eric

last: Brooks

state: North Carolina

address: 1051 William Moore Dr

department: Molecular Biomedical Sciences

institute: NORTH CAROLINA STATE UNIVERSITY RALEIGH

data_processing:
FASTQ files were preprocessed using the using the Sequence Quality Control (SEQC) bioinformatics pipeline (Azizi et al., 2018) aligning reads to the mm38 mouse reference genome with default parameters for the 10x single-cell 3-prime library. The SEQC pipeline performs read alignment, multi-mapping read resolution, as well as cell barcode and UMI correction to generate a cells x genes count matrix.
Assembly: mm38
Supplementary files format and content: CSV, count matrix, h5ad file (containing all WT FVB cells meeting quality control cutoffs, with annotations including replicate, stage, cell type, and clustering)

source_name: Mouse embryo, cranial region

extract_protocol:
FVB embryos were dissected from the uterine horn on ice in pre-chilled DMEM/F-12 with Glutamax (ThermoFisher), hereafter referred to as DMEM, including resection of the yolk sac and amnion. Embryo stages were assigned as follows:  0 somites (E7.5), 1-2 somites (E7.75), 3 somites (E8.0), 4-6 somites (E8.25), 7-9 somites (E8.5), 10+ somites (E8.75-E-9.0). Cranial tissues from E8.25-E9.0 embryos were collected by dissecting embryos just posterior to the otic sulcus. Cranial tissues from E7.5-E8.0 embryos were collected by dissecting at the posterior limit of the cranial neural plate. Due to differences in embryo size, a larger region of the hindbrain was dissected at earlier stages, which may account for some transcripts that were present in early but not late hindbrain samples. Visible cardiac structures, including the early heart tube, were manually resected. Cranial tissues from 3-5 embryos were pooled per replicate. Individual cells were dissociated by transferring pooled cranial tissues into 2 mL of pre-chilled phosphate buffered saline (PBS) containing 2.5% pancreatin (Sigma) and 0.5% trypsin (Sigma) and incubated 5 min on ice. Tissues were then washed 1 min in cold DMEM with 10% calf serum (Gibco), followed by a 1 min wash in cold DMEM alone. Pooled tissues were then transferred to a clean watch glass containing 200 µL of a 1:2 mixture of accutase (Sigma) and 0.25% trypsin in PBS and incubated 15 min at 37ºC, gently swirled, and incubated for an additional 15 min. After incubation, tissues were returned to ice and 600 µL of DMEM with 20% calf serum in DMEM was added to each watch glass. Tissues were manually triturated on ice using tungsten needles for 5-10 min, then passed over a 40 µm FlowMi cell strainer (Sigma) and concentrated by 450 g centrifugation at 4ºC. After centrifugation, the supernatant was removed and the cells were resuspended in 50 µL PBS with 0.4% bovine serum albumin (BSA). 10 µL of cells were combined with 10 µL of Trypan blue and placed in a hemocytometer to analyze the proportion of single cells and dead cells. Pools with less than 85% singlets or 85% viable cells were discarded. Isolated cells were then encapsulated and barcoded using standard protocols on the Chromium V3 chemistry platform from 10X Genomics.
3’ RNA-seq libraries were subsequently generated following standard 10X Genomics protocols.
For replicates 3-23 and 40-43, cell suspensions were loaded on a Chromium instrument (10X Genomics) following the user guide manual for 3′ v3. In brief, cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells/μL. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification following the manual instructions. For replicates 44-47 and 49-55, single cell suspensions were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following quality control, the single cell suspension was loaded onto Chromium Next GEM Chip G (10X Genomics PN 1000120) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of up to 5,000 cells proceeded using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics PN 1000268) according to the manufacturer’s protocol. cDNA amplification included 11 cycles and 17-265 ng of the material was used to prepare sequencing libraries with 8-14 cycles of PCR. After PicoGreen quantification and quality control by Agilent TapeStation, indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 or PE28/90 run, using the NovaSeq 6000 SP, S1, S2, or S4 Reagent Kit (100 or 200 cycles) (Illumina).

treatment_protocol: For treatment with Smoothened Agonist (SAG) (Sigma 912545-86-9), FVB embryos were dissected at E8.0 for culture following standard protocols in a 50:50 mixture of pre-warmed and gassed (37ºC, 5% CO2) DMEM and whole embryo culture rat serum (Inotiv). After dissection, embryos were randomly assigned to treatment with 2 µM SAG in DMSO or an equivalent volume (0.02% v/v) of DMSO alone as a control and cultured 12 h in pre-warmed and gassed (37ºC, 5% CO2) DMEM in 24-well Lumox plates (Sarstedt). After the culture period, rare embryos with signs of excessive cell death or developmental failure were discarded; the frequency of these embryos did not differ between control and SAG-treated conditions. After final resection of the yolk sac and amnion, embryo dissection, cell dissociation, and library preparation were performed as described.

value: Mouse embryo, cranial region

tag: developmental stage

value: 6-9 somites

value: WT FVB

value: Smoothened agonist, 2 uM


title: HeLa 18hpi sample 3


title: Mouse 6-9 somites, SAG treated, replicate 2


title: Mouse 6-9 somites, control DMSO treated, replicate 2

value: DMSO control


title: Mouse 6-9 somites, SAG treated, replicate 1


title: Mouse 10+ somites WT replicate 3

value: 10+ somites


title: Mouse 10+ somites WT replicate 5


title: TasteOrganoids_CQVsLPM_CQ_Sample3

value: Foliate cell line

value: Stem cells/mature taste cells


title: Mouse 10+ somites WT replicate 4


title: Mouse 10+ somites WT replicate 2


title: Mouse 10+ somites WT replicate 1


title: Mouse 7-9 somites WT replicate 6

value: 7-9 somites


title: Chondrocyte, 03d

value: Chondrogenic precursor


title: Mouse 7-9 somites WT replicate 5


title: Mouse 7-9 somites WT replicate 3


title: Mouse 7-9 somites WT replicate 4


title: Mouse 7-9 somites WT replicate 2


title: Mouse 7-9 somites WT replicate 1


title: Mouse 4-6 somites WT replicate 6

value: 4-6 somites


title: HeLa 18hpi sample 1

value: HeLa


title: Mouse 4-6 somites WT replicate 5


title: Mouse 4-6 somites WT replicate 4


title: Mouse 4-6 somites WT replicate 2


title: Mouse 4-6 somites WT replicate 1


title: Mouse 3 somites WT replicate 2

value: 3 somites


title: Mouse 4-6 somites WT replicate 3


title: Mouse 6-9 somites, control DMSO treated, replicate 1


title: Mouse 1-2 somites WT replicate 5

value: 1-2 somites


title: Mouse 1-2 somites WT replicate 4


title: Mouse 3 somites WT replicate 1


title: Mouse 3 somites WT replicate 4


title: Mouse E7.5 WT replicate 4


title: Mouse 3 somites WT replicate 3


title: Mouse 1-2 somites WT replicate 3


title: Mouse E7.5 WT replicate 3


title: Mouse E7.5 WT replicate 2


title: Mouse E7.5 WT replicate 1


title: Female, never-smoker, ATAC, subject4

status: Public on Aug 14 2024

city: Rockville

first: Jiyeon

last: Choi

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

description:
10X Genomics
FN4_raw_feature_bc_matrix.h5
FN4_ATAC

data_processing:
The demultiplexing, barcode processing, and alignment to human genome reference sequences (GRCh38) were performed using Cell Range ARC software (10x Genomics, v.2.0.1 or 2.0.0)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: ATAC-seq fragments and index files

source_name: Tumor-distant normal lung

extract_protocol:
The tissues were collected at a ~2 cm3 size and put in MACS Tissue Storage Solution (Miltenyl biotec cat.130-100-008) within 30 mins of surgical dissection. Samples were kept at 4°C and processed within 3 hours of dissection. Tissues were chopped into 2 mm diameter pieces within a dissociation tube to reduce the cell loss. Multi Tissue Dissociation Kit 1 and gentleMACS Octo Dissociator (Miltenyi Biotec) were used for dissociation of the tissue into single-cell suspension with a reduced amount of enzyme R (25% of the regular amount). Red blood cells were removed using Red Blood Cell Lysis Solution (Miltenyl biotec cat.130-094-183). Single-cell suspension of samples was frozen using 90% FBS and 10% DMSO and stored in liquid nitrogen until further processing except for the time of transfer in dry ice. The dissociated single-cell suspensions were thawed and filtered using a 70 μm cell strainer (Miltenyi Biotec) to remove debris. The filtered cells were labelled with cell viability marker (DAPI) and antibody markers of EPCAM, CD31, and CD45. Live single-cells (DAPI-negative) were sorted into lysis plates based on three gates: EPCAM+CD45- (designated “epithelial”), EPCAM-CD45+ (designated “immune”), and EPCAM-CD45- (designed “endothelial or stromal”). To enrich epithelial cells, which are considered to have key roles in lung cancer etiology, we collected all “epithelial” cells from EPCAM+CD45- gates and balanced the ratios to 6:3:1 (“epithelial”: “immune”: “endothelial or stromal”). Nuclei isolation was performed based on “Low Cell Input Nuclei Isolation” protocol (CG000365-Rev C, 10X Genomics) with a modification of the 1X lysis buffer treatmenet time (3-second duration).
Isolated nuclei were used for single-cell capture and sequencing library preparation using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits following the manufacturer’s guidelines (CG000338- Rev E, 10X Genomics, USA).

value: Tumor-distant normal lung

tag: Sex

value: Female

tag: subject status

value: never-smoker

tag: subject id


title: Mouse 1-2 somites WT replicate 2

value: Mouse embryo, cranial region


title: Mouse 1-2 somites WT replicate 1


title: Female, never-smoker, ATAC, subject2

description:
10X Genomics
FN2_raw_feature_bc_matrix.h5
FN2_ATAC


title: Female, never-smoker, ATAC, subject3

description:
10X Genomics
FN3_raw_feature_bc_matrix.h5
FN3_ATAC


title: Female, never-smoker, ATAC, subject1

description:
10X Genomics
FN1_raw_feature_bc_matrix.h5
FN1_ATAC


title: Female, smoker, ATAC, subject4

description:
10X Genomics
FS4_raw_feature_bc_matrix.h5
FS4_ATAC

value: smoker


title: Female, smoker, ATAC, subject3

description:
10X Genomics
FS3_raw_feature_bc_matrix.h5
FS3_ATAC


title: Male, never-smoker, ATAC, subject1

description:
10X Genomics
MN1_raw_feature_bc_matrix.h5
MN1_ATAC

value: Male


title: Male, never-smoker, ATAC, subject4

description:
10X Genomics
MN4_raw_feature_bc_matrix.h5
MN4_ATAC


title: Male, never-smoker, ATAC, subject3

description:
10X Genomics
MN3_raw_feature_bc_matrix.h5
MN3_ATAC


title: Male, smoker, ATAC, subject4

description:
10X Genomics
MS4_raw_feature_bc_matrix.h5
MS4_ATAC


title: Male, never-smoker, ATAC, subject2

description:
10X Genomics
MN2_raw_feature_bc_matrix.h5
MN2_ATAC


title: Male, smoker, ATAC, subject3

description:
10X Genomics
MS3_raw_feature_bc_matrix.h5
MS3_ATAC


title: KO_ZT22b

status: Public on Aug 13 2024

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Reference genome (GRCm38/mm10) and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
All the downstream analyses were based on the clean data with high quality. FeatureCounts was used to count the reads numbers mapped to each gene. Normalized DESEq2 data in log values were used for all subsequent analyzes
Assembly: mm10
Supplementary files format and content: raw counts

source_name: liver

extract_protocol:
Total RNA was extracted from livers using Trizol reagent (Thermofisher, Germany) according to the manufactory’s instructions.
Truseq RNAseq comprising 40 million reads per sample (12GB) was performed at Novogene (Germany). Samples underwent quality control and only those with RNA integrity number (RIN) higher than 6.5 were used. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: liver

tag: diet

value: chow

value: KO

tag: time


title: KO_ZT18c


title: KO_ZT22c


title: Male, smoker, ATAC, subject2

description:
10X Genomics
MS2_raw_feature_bc_matrix.h5
MS2_ATAC


title: Male, smoker, ATAC, subject1

description:
10X Genomics
MS1_raw_feature_bc_matrix.h5
MS1_ATAC


title: KO_ZT18a


title: KO_ZT22a


title: KO_ZT14c


title: KO_ZT18b


title: KO_ZT14b


title: KO_ZT10c


title: KO_ZT14a


title: KO_ZT10b


title: KO_ZT10a


title: KO_ZT6b


title: Female, smoker, ATAC, subject2

description:
10X Genomics
FS2_raw_feature_bc_matrix.h5
FS2_ATAC


title: KO_ZT2c


title: KO_ZT2a


title: Female, smoker, ATAC, subject1

description:
10X Genomics
FS1_raw_feature_bc_matrix.h5
FS1_ATAC


title: KO_ZT6a


title: WT_ZT22c

value: WT


title: WT_ZT22b


title: WT_ZT22a


title: WT_ZT14c


title: WT_ZT18a


title: WT_ZT18c


title: WT_ZT14a


title: WT_ZT10b


title: WT_ZT6c


title: WT_ZT10a


title: WT_ZT6b


title: WT_ZT2b


title: WT_ZT6a


title: WT_ZT10c


title: EpiLC, primed pluripotency, QKO, CUT&RUN, rep3

status: Public on Aug 09 2024

city: San Francisco

first: Harold

last: Marin

address: 555 Mission Bay Boulevard South

department: Smith Cardiovascular Institute

institute: University of California San Francisco

data_processing:
Raw sequencing reads were mapped to the "soft masked" mm39 mouse genome using Bowtie2 version 2.3.5.1: -X 2000 -N 1 --local --dovetail.
SAMtools version 1.10 was used to keep properly paired, primary alignments and filter out unassembled contigs, read duplicates, and reads mapped to mitochondria.
RPKM signal coverage in 1kb and 10kb bins were calculated using the deepTools2 (version 3.4.3) function bamCoverage using the GENCODE M30 primary annotation file and the output was saved as bigwig files. Blacklist regions in the mm39 genome were obtained from a published dataset (PMID: 37067481) and excluded from the RPKM calculation.
Scale factors were calculated from the S. cerevisiae spike-in control to quantitatively compare RPKM signal between samples. Raw sequencing reads were mapped to the sacCer3 genome assembly. As was done for mm39, Bowtie2 and SAMtools were used for alignment and post-alignment processing, respectively. The SAMtools function flagstat was used to find the number of properly paired reads in sacCer3 alignments. These were used to calculate a scale factor that was defined by dividing an arbitrary constant number (3,000 for H3K9me2 CUT&RUN) by the number of properly paired reads (Zheng Y et al (2020). Protocol.io). Using with the deepTools2 function bamCoverage, the scale factors for each library were used to generate 1kb- and 10kb-binned bigWig files containing spike-in normalized RPKM signal coverage tracks.
For transposable elements, spike-in controlled LAP2B RPKM signal coverage in 10kb bins were calculated with the deepTools2 function bamCoverage using a custom annotation file from the Hammell lab and including Blacklist regions where many transposable elements reside. For calculating modified z-scores of RPKM signal, RPKM values for each transposable element were first averaged across replicates of wildtype naive mESCs. Then, the median RPKM and median absolute deviation were calculated for all transposable elements. A modified z-score for each transposable element was calculated using the following formula: 0.6745 * (individual TE RPKM - median RPKM score) / (median absolute deviation RPKM).
Assembly: mm39
Supplementary files format and content: bigWig, RPKM values per 10kb bins.
Supplementary files format and content: bigWig, spike-in normalized RPKM values per 1kb bins.
Supplementary files format and content: bigWig, spike-in normalized RPKM values per 10kb bins.
Supplementary files format and content: csv file includes spike-in normalized signal from H3K9me2 CUT&RUN in gene bodies
Supplementary files format and content: csv file includes spike-in normalized signal from H3K9me2 CUT&RUN in transposable elements
Supplementary files format and content: csv file includes modified z-scores for H3K9me2 CUT&RUN signal in transposable elements in wildtype naive mESCs
Library strategy: CUT&RUN

source_name: EpiLC

growth_protocol: Cells were cultured at 5% CO2 and 37°C. mESCs were grown in serum- and feeder-free 2i + LIF medium: N2B27 basal medium supplemented with the following compounds at a final concentration of 3 μM CHIR-99021 (Selleckchem S1263), 1 μM PD0325901 (Selleckchem S1036), 103 U/mL LIF (MilliporeSigma™ ESG1107), 55 μM β-mercaptoethanol (Gibco™ 21985023), and 1X PenStrep (GenClone 25-512). N2B27 medium was made by mixing equal parts of DMEM:F12 (GenClone 25-503) and Neurobasal medium (Gibco™ 21103049) then adding 1X N-2 (Gibco™ 17502001), 1X B-27 (Gibco™ 17504001) and 2 mM Glutamax (Gibco™ 35050061). mESCs were seeded at 2.11 x 104 cells/cm2 on dishes pre-coated with either Geltrex (Gibco™ A1413202) or Cultrex (Bio-Techne 3445-005-01). mESCs were replenished with fresh 2i + LIF medium after 24 hours then collected at 48 hours for CUT&RUN. EpiLCs were differentiated by seeding 2.11 x 104 cells/cm2 mESCs into either Geltrex or Cultrex coated dishes containing N2B27 media supplemented with 20 ng/mL FGF (Peprotech 100-18B) and 12 ng/mL Activin A (Peprotech 120-14E). EpiLCs were replenished with fresh differentiation medium after 24 hours then collected at 48 hours for CUT&RUN.

extract_protocol:
CUT&RUN was performed as described in Skene et al. 2018 (Nature Protocols). Live cells were harvested with accutase and washed once with PBS prior to starting the procedure. Three replicates containing 200,000 mESCs or EpiLCs each were used per condition plus 2,000 HEK293T cells as a spike-in control. H3K9me2 antibody (abcam 1220) was used at 1:100 dilution in antibody buffer. Primary antibody incubation was performed at 4°C overnight. Rabbit anti-mouse secondary antibody (abcam ab6709) was used at 1:100 dilution and incubated for 4°C for 1 hour. pA-MNase (batch #6 143µg/mL) gifted from the Hennikoff lab was used for the cleavage reaction. DNA was isolated by phenol-chloroform extraction. Purified DNA was resuspended with 40µL of 1mM Trish-HCl pH 8.0 and 0.1mM EDTA.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep with Sample Purification Beads (NEB E7103S) following the manufacturer’s protocol with 5ng of starting DNA input. Libraries were amplified using 8 cycles on the thermocycler. Each library was uniquely indexed with NEBNext Multiplex Oligos for Illumina (NEB E6440S), then pooled together in equimolar amounts. Library size was analyzed with the Agilent Bioanalyzer 2100 using the High sensitivity DNA kit.

value: EpiLC


title: WT_ZT2a


title: mESC, naive pluripotency, TKO, CUT&RUN, rep3

source_name: mESC

value: mESC


title: KO_ZT2b


title: KO_ZT6c


title: mESC, naive pluripotency, QKO, CUT&RUN, rep3


title: EpiLC, primed pluripotency, WT, CUT&RUN, rep3

value: wildtype


title: mESC, naive pluripotency, QKO, CUT&RUN, rep2


title: mESC, naive pluripotency, LBRKO, CUT&RUN, rep3


title: mESC, naive pluripotency, TKO, CUT&RUN, rep2


title: EpiLC, primed pluripotency, LBRKO, CUT&RUN, rep2


title: WT_ZT14b


title: EpiLC, primed pluripotency, QKO, CUT&RUN, rep2


title: EpiLC, primed pluripotency, TKO, CUT&RUN, rep3


title: WT_ZT2c


title: EpiLC, primed pluripotency, WT, CUT&RUN, rep2


title: mESC, naive pluripotency, WT, CUT&RUN, rep2


title: EpiLC, primed pluripotency, LBRKO, CUT&RUN, rep3


title: WT_ZT18b


title: EpiLC, primed pluripotency, QKO, CUT&RUN, rep1


title: mESC, naive pluripotency, LBRKO, CUT&RUN, rep2


title: mESC, naive pluripotency, TKO, CUT&RUN, rep1


title: mESC, naive pluripotency, WT, CUT&RUN, rep1


title: mESC, naive pluripotency, LBRKO, CUT&RUN, rep1


title: EpiLC, primed pluripotency, WT, CUT&RUN, rep1


title: EpiLC, primed pluripotency, TKO, CUT&RUN, rep1


title: flox_3

status: Public on Aug 04 2024

city: Saint Louis

first: Fumihiko

last: Urano

state: Missouri

address: 660 South Euclid Ave

institute: Washington University School of Medicine

data_processing:
an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software
Assembly: Ensembl release 101
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Pancreatic islet

extract_protocol:
Total RNA was isolated using RNeasy Kits (Qiagen, 74106)
Samples were prepared according to library kit manufacturer’s protocol on an Illumina NovaSeq 6000

value: Pancreatic islet

value: flox


title: EpiLC, primed pluripotency, LBRKO, CUT&RUN, rep1


title: flox_2


title: flox_Cre_4


title: mESC, naive pluripotency, WT, CUT&RUN, rep3


title: flox_Cre_2


title: flox_Cre_3


title: EpiLC, primed pluripotency, TKO, CUT&RUN, rep2


title: C4

status: Public on Jul 19 2024

city: Buffalo

first: Henry

middle: G.

last: Withers

state: New York

address: Elm and Carlton Streets

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

description:
C4
raw_counts_NKG2D_and_CD28_treatments.tsv

data_processing:
Quality of sequencing reads in fastq files were assessed by FastQC (version 0.11.8) and alignment quality was assessed by RSeQC (version 4.0.0).
Paired-end reads were aligned to GRCh38 using STAR (version 2.7.9a) and transcripts were gene-level quantified by FeatureCounts from the Subread package (version 2.0.1).
The differential gene expression was analyzed by R/Bioconductor package DESeq2.
Assembly: GRCh38
Supplementary files format and content: Processed data in supplementary tab-delimited file contains a matrix of raw read counts consolidated from FeatureCounts output for gene level counts for each gene_accession number (rows) and sample (columns).

source_name: C8+ T cells

extract_protocol:
RNeasy Mini kit and RNase-Free Dnase Set.
The sequencing libraries are prepared with the mRNA HyperPrep kit (Roche), from 100ng total RNA.  Following manufacturer’s instructions, the first step selects for PolyA RNA using the mRNA Capture Beads (Roche).  After PolyA selection, the remaining RNA is purified, fragmented and primed for cDNA synthesis.  Fragmented RNA is then reverse transcribed into first strand cDNA using random primers.  The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA.  Pure Beads (Roche) are used to separate the ds cDNA from the second strand reaction mix resulting in blunt-ended cDNA.  A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments.  Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, are ligated to the ends of the ds cDNA, preparing them for hybridization onto a flow cell.   Adapter ligated libraries are amplified by PCR, purified using Pure Beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.).   The DNA libraries are quantitated using KAPA Biosystems qPCR kit, and are pooled together in an equimolar fashion, following experimental design criteria.  Each pool is denatured and diluted to 200pM with 1% PhiX control library added.  The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge, as determined by the desired sequencing depth and number of samples.  100-cycle paired-end sequencing is then performed on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: Dynabead-induced CTLs from 3 human donors were stimulated by anti-human CD3 (OKT3) with or without anti-human DNAM-1 (OKT3 + anti-DNAM1), anti-human NKG2D (OKT3 + anti-NKG2D), or anti-human CD28 (OKT3 + anti-CD28) for 4 hours.

value: C8+ T cells

value: OKT3 + anti-CD28


title: flox_Cre_1


title: B2

description:
B2
raw_counts_NKG2D_and_CD28_treatments.tsv

value: OKT3 + anti-NKG2D


title: flox_1


title: B4

description:
B4
raw_counts_NKG2D_and_CD28_treatments.tsv


title: A2

description:
A2
raw_counts_NKG2D_and_CD28_treatments.tsv


title: A4

description:
A4
raw_counts_NKG2D_and_CD28_treatments.tsv


title: B3

extract_protocol:
RNeasy Mini kit and RNase-Free Dnase Set.
Illumina TruSeq Stranded Total RNA with RiboZero Gold: The sequencing libraries are prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA.  Following manufacturer’s instructions, the first step depletes rRNA from total RNA.  After ribosomal depletion, the remaining RNA is purified, fragmented and primed for cDNA synthesis.  Fragmented RNA is then reverse transcribed into first strand cDNA using random primers.  The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA.  AMPure XP beads (Beckman Coulter) are used to separate the ds cDNA from the second strand reaction mix resulting in blunt-ended cDNA.  A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments.  Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, are ligated to the ends of the ds cDNA, preparing them for hybridization onto a flow cell.   Adapter ligated libraries are amplified by PCR, purified using Ampure XP beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.).   The DNA libraries are quantitated using KAPA Biosystems qPCR kit, and are pooled together in an equimolar fashion, following experimental design criteria.

treatment_protocol: Dynabead-induced CTLs from 3 human donors were stimulated by anti-human CD3 (OKT3) with or without anti-human DNAM-1 (OKT3 + anti-DNAM1), anti-human NKG2D (OKT3 + anti-NKG2D or anti-human CD28 (OKT3 + anti-CD28) for 4 hours.

value: OKT3 + anti-DNAM1


title: mESC, naive pluripotency, QKO, CUT&RUN, rep1


title: B1


title: A3


title: C1


title: A1


title: flox_4


title: SPG, CTRL, APOE60

status: Public on Jun 04 2024

city: Boston

first: Neta

last: Rosenzweig

state: Massachusetts

address: 60 Fenwood Road, 10002K, Brigham and Women’s Hospital

institute: Brigham and Women's Hospital, Harvard Medical School

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were perfomed using CellRanger (version 7.0.0).
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Brain

extract_protocol:
Fresh frozen brain tissue (10 sections of 1cm2 with a thickness of 40µm) were cut and collected and lysed in a sucrose lysis buffer (10 mM Tris-HCL (pH 8.0); 320 mM sucrose; 5 mM CaCl2; 3 μM Mg(Ac)2; 0.1 mM EDTA; 1 mM dithiothreitol (DTT) and 0.1% Triton X-100). Lysates were then filtered through a 70 µm cell strainer. Nuclei were purified by ultracentrifugation (107,000× g for 1.5 h at 4 °C) through a dense sucrose buffer (10 mM Tris–HCL (pH 8.0); 1.8 M sucrose; 3 μM Mg(Ac)2; 0.1 mM EDTA and 1 mM DTT). The supernatants were removed and pellets were re-suspended in 2% BSA/PBS containing RNase inhibitor (0.35 U/μL). The nuclei were incubated with fluorescently-conjugated antibodies directed against the neuronal marker NEUN (RBFOX3/NEUN (1B7) AF647 mouse mAB, Novus Biologicals, NBP1-92693AF647) and the transcription factor OLIG2 for the oligodendrocyte lineage (Anti-OLIG2 clone 211F1.1 AF488 mouse mAb, Merck Millipore, MABN50A4). After washing, the DNA dye DAPI was added and nuclei were sorted on a MoFlo Astrios. For each sample, we collected DAPIposNEUNnegOLIG2neg nuclei for snRNAseq
Library construction was performed to the manufacturer's instuctions (single cell 3' v3.1 single index, 10X Genomics). Briefly, nuclei were resuspended in the master mix and loaded together with partioning oil and gel beads to form gel bead-in-emulsion (GEM). tThe poly-A RNA from the nucleus lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, unique molecular identifier (UMI) na dht e 10X barcode. The pooled barcoded cDNA was then cleaned with Silane Dynabeads, amplified by PCR and apropriated size fragments were selected using AMPure XP beads for subsequent library contruction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Brain

value: male

tag: apoe genotype

value: CTRL

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: O

tag: braaklb

tag: pmd

tag: ph

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: CONTR

tag: dcode

tag: dcodewk

value: A0B1C0; infarction cerebellar

tag: wcode

value: G-PAR-SUP

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: 1. CVA (2011) 2. Prostate carcinoma (2007) 3. Polymyalgia rheumatica (1997) 4. Diabetes mellitus type II (1995) 5. Depression

value: Unknown.

value: 1. Brain with a recent cerebellar infarction of 3 cm and an infarction of 2 mm is found in the caudate nucleus. 2. Furthermore signs of hypertension and an old infarction is found in the left hemisphere. 3. Next to this signs of senescence (A0B1C0). 4. No substrate of the depression.

tag: diabetes

value: Diabetes Mellitus Type II.

tag: education

tag: profession


title: SPG, CTRL, APOE50

description: 10X Genomics

tag: tissue

tag: Sex

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: B

tag: braaklb

tag: pmd

tag: ph

value: ad(1,B); infarct; lacune

value: 1. Cardiac decompensation 2. Myocardial infarct 3. Diabetes Mellitus type II

value: Cardiac decompensation.

value:
1. Slight senile involutive cortical changes.
2. Small infarction in the left medio-occipital cortex and white matter; lacunar infarction left putamen; a small infarction in right parietal white matter:all three are old; elective neuronal losses in CA1 left side, more recently.

value: Hairdresser.


title: SPG, AD, APOE46

description: 10X Genomics

value: Brain

value: male

value: AD

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

tag: wcode

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

tag: diabetes

tag: education


title: SPG, CTRL, APOE47

description: 10X Genomics

tag: tissue

tag: Sex

value: female

tag: apoe genotype

tag: disease state

value: CTRL

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

value: CONTR

value: 1. Extensive metastasized non-small cell lung carcinoma (mediastinum, liver, retroperitoneal glands, right adrenal gland, right hip) 2. Unclear complaints of pain and tingling since 1988.

value: Euthanasia.

value: 1. Slight senile involutive cortical changes, possibly rather a lot in view of the patient's age. 2. Adenocarcinoma (lung) metastases in cerebro (2x) and cerebello (1x).

value: Elementary school. School of fashion design, although she did not finish it.

tag: profession

value: She stopped working in 1980.


title: SPG, CTRL, APOE49

description: 10X Genomics

value: O

tag: ph

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: COPSY

tag: dcode

tag: dcodewk

value: Thal 0; A0B1C0; slight tauopathy in white matter and periventriculair; subpial moderate glial tauopathy; signs of terminal hypoxia and some gliosis

tag: wcode

value: G-PAR-SUP

tag: region

value: superior parietal gyrus

tag: specific

value: left

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: 1. Arthrosis 2. Myocard infarct (1991) 3. Total hip replacement (L+R) (1999) Diabetes mellitus (2003) 4. Renal insufficiency (2012) Decompensatio cordis (2012) Cataract (2014) 5. Gout (2014)

value: Heart failure.

value: 1. Brain with slight age-related tauopathy 2. Slight age-related tauopathy in the periventricular white matter and moderate subpial glial tauopathy. 3. In addition, signs of terminal hypoxia and some gliosis are found.

tag: diabetes

value: Nurse.


title: SPG, AD, APOE44

description: 10X Genomics

tag: tissue

value: Brain

tag: Sex

value: male

tag: apoe genotype

tag: disease state

value: AD

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: C

tag: braaklb

tag: pmd

value: PID!

value: AD!

value: AD(5,C); atherosclerose; infarct

value: 1. Pick's disease 2. Dsfunctional frontal cortex.

value: Cardiac arrest following dehydration.

value: 1. Compatible with Alzheimer's disease. The Alzheimer changes are frontally severe, and probably (this is difficult to evaluate due to the infarction) parietally much less. 2. Severe atherosclerosis with a large posterior infarction with fresh and old components, infarction in the right striatum, right thalamus, right pons, with loss of the corticospinal tract; signs of severe agonal hypoxia.

tag: education

value: Highschool

value: Manager.


title: C2

description:
C2
raw_counts_NKG2D_and_CD28_treatments.tsv

tag: cell type

value: C8+ T cells

tag: treatment

value: OKT3 + anti-NKG2D


title: SPG, CTRL, APOE57

description: 10X Genomics

tag: tissue

value: female

value: CTRL

value: B

tag: ph

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: CONTR

tag: dcode

tag: dcodewk

tag: wcode

value: G-PAR-SUP

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: 1. Carditis and rheumatism 2. Cataract both sides

value: Aspiration pneumonia.

tag: diabetes

tag: profession


title: SPG, CTRL, APOE40

description: 10X Genomics

tag: tissue

value: Brain

tag: Sex

value: male

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: O

tag: braaklb

tag: pmd

value: ad(1,O); infarct;

value: Suffered multiple TIA's.

value: Heart failure.

tag: education

value: Universitary education.

value: Biologist and as geologist.


title: SPG, CTRL, APOE38

description: 10X Genomics

tag: ph

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

value: ad(3,B); ca; arg grain

tag: wcode

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

value: 1. Cholelithiasis, cholecystectomy (1984) 2. Chronic Asthmatic bronchitis with hyperreactive bronchial mucosa (1991) Glaucoma OS (1986) 3. Percutaneous Transluminal Coronary Angioplasty 4. Dilation of the lateral a. anterior descendens (1991) 5. Diverticulosis sigmoid (1995) 6. Relapsing bronchitis/pneumonia (1999-2000) 7. Benign cyst in left kidney (1996) 8. Enteritis (2005) 9. Heart rhythm disturbance (trifascicular) (2007) 10. Prostate carcinoma (2008) 11. Rectum carcinoma (2009)

value: Cachexia and dehydration by rectum carcinoma and prostate carcinoma.

value: 1. Brain with senile-involutive cortical changes and some congophilic angiopathy. 2. Furthermore a slight, clinically irrelevant, kind of argyrophilic grains disease.

tag: diabetes

value: Instrument maker.


title: SPG, AD, APOE45

description: 10X Genomics

tag: tissue

tag: Sex

value: female

tag: apoe genotype

tag: disease state

value: AD

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: C

tag: braaklb

tag: pmd

value: AD!

value: G-PAR-SUP

value: superior parietal gyrus

value: Dementia, probably of the Alzheimer type.

value: Cachexia.

value: Compatible with the clinical diagnosis of senile dementia of the Alzheimer type.

value: Finished elementary school.

tag: profession

value: Tailor.


title: SPG, AD, APOE36

description: 10X Genomics

value: Brain

value: male

tag: ph

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

tag: wcode

tag: region

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

tag: education


title: C3

tag: cell type

value: C8+ T cells

tag: treatment

value: OKT3 + anti-DNAM1


title: SPG, AD, APOE34

description: 10X Genomics

tag: tissue

tag: Sex

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

value: ADVD

value: AD (5,B/C); lacuna; ischemia; atherosclerose.

value: Alzheimer's disease, possibly in combination with multi infarct dementia.

value: Sudden death, suspected heart-failure.

value:
1. The neuropathological diagnosis is compatible with the clinical diagnosis of senile dementia of the Alzheimer type.
2. Moderate vascular pathology; lacunary infarction in the left caudate nucleus, slight cortical occipitla infarction on the right, slight cortical necrosis of the cerebellum right, with severe atherosclerosis.

tag: diabetes

value: Graphical vocational education.

tag: profession

value: Printer and instructor in the printing profession.


title: SPG, CTRL, APOE39

description: 10X Genomics

tag: tissue

value: female

value: CTRL

value: A

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: CONTR

tag: dcode

tag: dcodewk

value: Thal phase 1 / 5; A1B1C0; ARTAG in white matter, perivascular, subpial and in cortex (specially in amygdala)

tag: wcode

value: G-PAR-SUP

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

tag: freezer

value: 1. Polio (1951) 2. Burnout (1965) 3. Post-polio syndrome (1983, 2007) 4. Frozen shoulder (2000, 2007) 5. Mitral valve prolapse (2008) 5. Arthrosis (2009) 6. Hypercholesterolemia (2013) 7. Polymyalgia rheumatic (2013) 8. Urinary infection (2013, 2014) 9. Renal insufficiency (2014) 10. Osteoporosis (2015) 11. Ovarian cancer (2015) 12. Ileus (2015) 13. Sterilization

value: Euthanasia, metastatic ovarian cancer, and ileus.

value: Brain with at most slight signs of senescenceand slight age-related tauopathy of astroglia. According to medical chart after poliomyelitis with post-polio syndrome. Morphological abnormalities were not found in the motor cortex (or known with post-polio syndrome). The left motor cortex (leg area) has not been dissected for diagnostic purposes, but has been frozen.

tag: education

value: Academy of arts.

value: Artist.


title: SPG, CTRL, APOE29

description: 10X Genomics

value: Brain

tag: Sex

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: O

tag: braaklb

tag: pmd

tag: ph

value: plastic bag -80°C

value: Metastasized lung carcinoma.

value: Septic shock caused by peritonitis.

value: Shows no cerebral abnormalities.

tag: diabetes

value: Worked as shop assistant.


title: SPG, AD, APOE35

description: 10X Genomics

tag: tissue

value: female

value: AD

value: C

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: NAD

tag: dcode

value: AD!

tag: dcodewk

tag: wcode

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

value: 1. Multi infarct dementia 2. Urosepsis 3. Macular degeneration

value: Dehydration, cachexia.

value: Compatible with the clinical diagnosis of senile dementia of the Alzheimer type.

tag: profession


title: SPG, CTRL, APOE28

description: 10X Genomics

tag: Sex

value: male

tag: apoe genotype

tag: disease state

value: CTRL

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

value: PSYCH

value: CONTR

value: A1B1C0; signs of terminal hypoxia

value:
SOMATIC 1. Appendectomy (1953) 2. Inguinal herniation surgery (2000) 3. Prostate carcinoma stadium IV with bone metastases (2008) 4. Paroxysmal atrial fibrillation (2008) 5. Dyspnea d'Ã©ffort and decreased exercise tolerance (2009) 6. Severe mitral valve insufficiency (2010) 7. Chronic thromboembolic pulmonary hypertension (2010) 8. Traumatic frontal subarachnoid bleeding and cerebral contusions with edema after fall (2015) 9. Mitral valve endocarditis (2017) 10. Anemia (2017)
11. Cardiac mitral valve surgery (2017) 12. Slow progressive renal insufficiency pneumothorax 2x PSYCHIATRIC 1. Bipolar disorder (1979)

value: Combined cardiogenic and distributive shock after cardial mitral valve surgery due to endocarditis..

value: 1. Brain with on both sides of the frontal pole remnants of a cerebral contusion (maximally 3 cm). Furthermore, slight age related changes fitting the age (Braak stage 2 of 6 for tau and Thal phase 2 of 5 for amyloid beta; there are no neuritic plaques according to the CERAD score; therefor, ABC criteria according to Montine et al. (2012):ABC:A1 B1 C0). In addition, there are signs of terminal hypoxia. There is no substrate of the bipolar psychiatric disorder. No CAA or Lewy bodies.

tag: education


title: SPG, AD, APOE25

description: 10X Genomics

tag: tissue

value: Brain

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

tag: wcode

value: G-PAR-SUP

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: Alzheimer's disease

value: Myocardial infarction.

tag: diabetes

value: Finished elementary school.

value: Housewife.